Query 041990
Match_columns 225
No_of_seqs 180 out of 1541
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 12:52:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041990hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13639 zf-RING_2: Ring finge 99.6 3.1E-16 6.6E-21 101.9 2.4 43 180-222 2-44 (44)
2 KOG4628 Predicted E3 ubiquitin 99.6 1.2E-15 2.5E-20 138.1 3.6 74 152-225 203-277 (348)
3 PF12678 zf-rbx1: RING-H2 zinc 99.3 6.8E-13 1.5E-17 95.5 2.7 43 180-222 21-73 (73)
4 PHA02929 N1R/p28-like protein; 99.3 1.2E-12 2.7E-17 113.6 4.7 73 153-225 147-226 (238)
5 COG5540 RING-finger-containing 99.3 1.1E-12 2.4E-17 116.0 3.5 48 178-225 323-371 (374)
6 COG5243 HRD1 HRD ubiquitin lig 99.2 1E-11 2.3E-16 112.4 3.1 51 175-225 284-344 (491)
7 PF13923 zf-C3HC4_2: Zinc fing 99.1 8.7E-11 1.9E-15 74.3 3.1 39 181-221 1-39 (39)
8 cd00162 RING RING-finger (Real 99.1 1.2E-10 2.5E-15 73.8 3.6 44 180-225 1-45 (45)
9 PF13920 zf-C3HC4_3: Zinc fing 99.0 2.1E-10 4.6E-15 76.3 3.3 43 180-225 4-47 (50)
10 KOG0317 Predicted E3 ubiquitin 99.0 1.2E-10 2.7E-15 102.4 2.6 47 176-225 237-283 (293)
11 PLN03208 E3 ubiquitin-protein 99.0 2.5E-10 5.4E-15 96.0 3.8 45 178-225 18-78 (193)
12 KOG0823 Predicted E3 ubiquitin 99.0 1.8E-10 4E-15 98.6 2.8 46 177-225 46-94 (230)
13 KOG0802 E3 ubiquitin ligase [P 98.9 2.2E-10 4.7E-15 110.4 1.6 48 177-224 290-339 (543)
14 PF12861 zf-Apc11: Anaphase-pr 98.9 9.3E-10 2E-14 81.0 3.0 45 180-224 23-80 (85)
15 PF15227 zf-C3HC4_4: zinc fing 98.9 1.2E-09 2.6E-14 70.4 3.1 38 181-221 1-42 (42)
16 PHA02926 zinc finger-like prot 98.9 7.5E-10 1.6E-14 94.6 2.5 47 179-225 171-229 (242)
17 PF14634 zf-RING_5: zinc-RING 98.9 1.7E-09 3.8E-14 70.1 3.1 44 180-223 1-44 (44)
18 smart00504 Ubox Modified RING 98.9 2.7E-09 5.8E-14 73.5 4.1 43 180-225 3-45 (63)
19 PF00097 zf-C3HC4: Zinc finger 98.8 1.6E-09 3.5E-14 68.8 2.6 39 181-221 1-41 (41)
20 smart00184 RING Ring finger. E 98.8 3.4E-09 7.4E-14 64.7 3.1 38 181-221 1-39 (39)
21 KOG0320 Predicted E3 ubiquitin 98.8 1.7E-09 3.7E-14 89.4 2.3 48 177-225 130-177 (187)
22 COG5194 APC11 Component of SCF 98.7 1.5E-08 3.2E-13 73.5 2.9 27 198-224 53-79 (88)
23 COG5219 Uncharacterized conser 98.7 4.2E-09 9.1E-14 104.5 -0.2 66 160-225 1451-1522(1525)
24 TIGR00599 rad18 DNA repair pro 98.6 1.9E-08 4E-13 93.4 3.0 44 179-225 27-70 (397)
25 KOG1493 Anaphase-promoting com 98.5 3.2E-08 6.9E-13 71.1 0.4 45 180-224 22-79 (84)
26 smart00744 RINGv The RING-vari 98.5 1.2E-07 2.7E-12 63.0 2.8 42 180-222 1-49 (49)
27 COG5574 PEX10 RING-finger-cont 98.5 7.2E-08 1.6E-12 84.2 2.1 46 176-224 213-260 (271)
28 PF13445 zf-RING_UBOX: RING-ty 98.4 1.4E-07 3.1E-12 61.1 2.9 38 181-219 1-43 (43)
29 KOG2164 Predicted E3 ubiquitin 98.4 8.5E-08 1.8E-12 90.3 2.4 44 179-225 187-235 (513)
30 PF04564 U-box: U-box domain; 98.3 4.2E-07 9.2E-12 65.1 3.0 43 180-225 6-49 (73)
31 KOG1734 Predicted RING-contain 98.3 1.4E-07 3E-12 82.8 0.5 48 177-224 223-279 (328)
32 KOG0287 Postreplication repair 98.3 2.6E-07 5.7E-12 83.3 1.6 43 180-225 25-67 (442)
33 KOG0828 Predicted E3 ubiquitin 98.3 2.7E-07 5.9E-12 86.6 1.5 50 176-225 569-633 (636)
34 COG5432 RAD18 RING-finger-cont 98.2 5.2E-07 1.1E-11 80.0 2.5 42 180-224 27-68 (391)
35 KOG0804 Cytoplasmic Zn-finger 98.2 3.9E-07 8.4E-12 84.7 1.6 43 179-223 176-219 (493)
36 PF11793 FANCL_C: FANCL C-term 98.2 2.4E-07 5.1E-12 66.1 -0.5 46 180-225 4-65 (70)
37 KOG2930 SCF ubiquitin ligase, 98.0 4.9E-06 1.1E-10 63.2 2.6 27 198-224 80-106 (114)
38 KOG0311 Predicted E3 ubiquitin 97.7 3.8E-06 8.2E-11 76.2 -1.8 45 179-225 44-89 (381)
39 PF14835 zf-RING_6: zf-RING of 97.6 1.4E-05 3.1E-10 55.9 0.3 41 180-224 9-49 (65)
40 KOG0825 PHD Zn-finger protein 97.6 1.3E-05 2.8E-10 79.0 -0.1 46 180-225 125-170 (1134)
41 KOG4265 Predicted E3 ubiquitin 97.5 6.1E-05 1.3E-09 68.5 2.8 45 178-225 290-335 (349)
42 KOG1039 Predicted E3 ubiquitin 97.5 3.9E-05 8.5E-10 70.2 1.5 47 178-224 161-219 (344)
43 KOG4445 Uncharacterized conser 97.4 3.5E-05 7.5E-10 68.8 0.3 39 173-213 112-150 (368)
44 KOG4159 Predicted E3 ubiquitin 97.2 0.00019 4.1E-09 67.0 2.2 46 177-225 83-128 (398)
45 KOG1941 Acetylcholine receptor 97.2 0.00011 2.4E-09 67.7 0.5 44 180-223 367-413 (518)
46 KOG1785 Tyrosine kinase negati 97.2 0.00012 2.6E-09 67.7 0.6 43 180-225 371-415 (563)
47 KOG0297 TNF receptor-associate 97.2 0.00019 4.1E-09 66.9 1.9 47 177-225 20-66 (391)
48 PF11789 zf-Nse: Zinc-finger o 97.1 0.00032 6.9E-09 48.1 2.4 40 179-220 12-53 (57)
49 KOG4172 Predicted E3 ubiquitin 97.1 7.7E-05 1.7E-09 50.6 -0.8 44 179-225 8-53 (62)
50 KOG0978 E3 ubiquitin ligase in 96.9 0.00028 6E-09 69.6 0.5 46 177-225 642-688 (698)
51 KOG0801 Predicted E3 ubiquitin 96.9 0.00031 6.8E-09 57.7 0.7 40 166-205 165-204 (205)
52 PF12906 RINGv: RING-variant d 96.6 0.0014 3.1E-08 43.0 1.9 40 181-221 1-47 (47)
53 KOG2660 Locus-specific chromos 96.4 0.00065 1.4E-08 61.4 -0.5 44 179-224 16-59 (331)
54 KOG1428 Inhibitor of type V ad 96.2 0.003 6.6E-08 66.3 3.0 73 153-225 3460-3543(3738)
55 PF10367 Vps39_2: Vacuolar sor 96.2 0.0019 4.2E-08 48.4 1.2 30 179-209 79-108 (109)
56 KOG2879 Predicted E3 ubiquitin 96.2 0.0044 9.6E-08 54.9 3.6 47 176-224 237-285 (298)
57 KOG3039 Uncharacterized conser 96.2 0.0048 1E-07 54.0 3.6 49 177-225 220-269 (303)
58 PF14570 zf-RING_4: RING/Ubox 96.1 0.0036 7.7E-08 41.5 2.0 44 181-224 1-46 (48)
59 PF05883 Baculo_RING: Baculovi 96.1 0.003 6.4E-08 50.5 1.8 35 179-213 27-67 (134)
60 COG5152 Uncharacterized conser 96.1 0.0018 3.9E-08 55.0 0.6 42 180-224 198-239 (259)
61 KOG3970 Predicted E3 ubiquitin 95.9 0.0052 1.1E-07 53.2 2.5 45 180-225 52-104 (299)
62 PHA03096 p28-like protein; Pro 95.9 0.0039 8.4E-08 55.9 1.6 45 179-223 179-231 (284)
63 KOG1814 Predicted E3 ubiquitin 95.8 0.0052 1.1E-07 57.2 2.1 44 179-222 185-236 (445)
64 KOG4692 Predicted E3 ubiquitin 95.7 0.0071 1.5E-07 55.4 2.6 46 176-224 420-465 (489)
65 PF08746 zf-RING-like: RING-li 95.7 0.0072 1.6E-07 39.0 1.8 41 181-221 1-43 (43)
66 KOG1813 Predicted E3 ubiquitin 95.7 0.004 8.7E-08 55.7 0.8 42 180-224 243-284 (313)
67 PF04641 Rtf2: Rtf2 RING-finge 95.5 0.016 3.5E-07 51.1 3.9 48 176-224 111-159 (260)
68 KOG1952 Transcription factor N 95.4 0.0064 1.4E-07 61.0 1.4 49 175-223 188-244 (950)
69 KOG1571 Predicted E3 ubiquitin 95.2 0.0089 1.9E-07 54.7 1.5 40 180-225 307-346 (355)
70 KOG4275 Predicted E3 ubiquitin 95.1 0.0035 7.6E-08 56.0 -1.3 41 178-225 300-341 (350)
71 KOG0826 Predicted E3 ubiquitin 95.1 0.016 3.5E-07 52.6 2.9 47 175-223 297-343 (357)
72 KOG1002 Nucleotide excision re 94.8 0.0097 2.1E-07 57.1 0.6 43 179-224 537-584 (791)
73 KOG0827 Predicted E3 ubiquitin 94.5 0.0024 5.3E-08 59.0 -4.1 46 180-225 198-244 (465)
74 KOG1940 Zn-finger protein [Gen 94.3 0.022 4.8E-07 50.8 1.6 44 180-223 160-204 (276)
75 KOG3268 Predicted E3 ubiquitin 94.1 0.029 6.3E-07 47.0 1.9 46 180-225 167-227 (234)
76 PHA02825 LAP/PHD finger-like p 94.0 0.041 8.8E-07 45.2 2.5 48 177-224 7-57 (162)
77 KOG1001 Helicase-like transcri 93.7 0.024 5.3E-07 56.4 0.8 42 179-224 455-498 (674)
78 KOG3002 Zn finger protein [Gen 93.5 0.049 1.1E-06 49.2 2.3 39 180-225 50-90 (299)
79 PF10272 Tmpp129: Putative tra 93.1 0.06 1.3E-06 49.8 2.4 27 199-225 311-350 (358)
80 PF14447 Prok-RING_4: Prokaryo 92.9 0.052 1.1E-06 36.9 1.1 33 191-225 17-49 (55)
81 KOG2932 E3 ubiquitin ligase in 92.7 0.047 1E-06 49.3 1.1 40 180-223 92-131 (389)
82 COG5236 Uncharacterized conser 92.5 0.11 2.5E-06 47.6 3.3 43 179-224 62-106 (493)
83 KOG2114 Vacuolar assembly/sort 91.8 0.084 1.8E-06 53.3 1.7 40 179-223 841-880 (933)
84 COG5222 Uncharacterized conser 91.6 0.1 2.2E-06 47.1 1.8 42 179-223 275-318 (427)
85 KOG0298 DEAD box-containing he 89.7 0.093 2E-06 55.1 -0.2 42 180-223 1155-1196(1394)
86 KOG3899 Uncharacterized conser 88.3 0.25 5.3E-06 44.5 1.5 27 199-225 325-364 (381)
87 KOG2034 Vacuolar sorting prote 87.5 0.26 5.7E-06 50.0 1.3 34 179-213 818-851 (911)
88 KOG1609 Protein involved in mR 87.0 0.25 5.3E-06 43.8 0.7 47 178-224 78-132 (323)
89 KOG0309 Conserved WD40 repeat- 86.9 0.39 8.6E-06 48.2 2.1 28 193-220 1042-1069(1081)
90 PF14446 Prok-RING_1: Prokaryo 86.5 0.54 1.2E-05 31.9 2.0 30 179-208 6-36 (54)
91 KOG3053 Uncharacterized conser 86.1 0.25 5.5E-06 43.6 0.3 45 180-224 22-80 (293)
92 KOG2817 Predicted E3 ubiquitin 83.9 0.95 2.1E-05 42.2 3.0 44 180-223 336-382 (394)
93 PF03854 zf-P11: P-11 zinc fin 83.3 0.51 1.1E-05 31.2 0.7 29 197-225 16-45 (50)
94 KOG1812 Predicted E3 ubiquitin 82.3 0.49 1.1E-05 44.2 0.5 37 178-214 146-183 (384)
95 COG5175 MOT2 Transcriptional r 81.7 0.78 1.7E-05 42.2 1.5 45 180-224 16-62 (480)
96 KOG0802 E3 ubiquitin ligase [P 80.7 0.62 1.4E-05 45.3 0.6 38 180-224 481-518 (543)
97 KOG1100 Predicted E3 ubiquitin 79.7 1 2.2E-05 38.6 1.5 37 181-224 161-198 (207)
98 KOG4718 Non-SMC (structural ma 74.4 1.6 3.5E-05 37.6 1.3 41 179-221 182-222 (235)
99 KOG0825 PHD Zn-finger protein 73.3 1.6 3.5E-05 44.2 1.1 45 179-223 97-151 (1134)
100 KOG0269 WD40 repeat-containing 73.0 3 6.4E-05 42.1 2.8 40 180-220 781-820 (839)
101 KOG4362 Transcriptional regula 72.4 0.98 2.1E-05 45.0 -0.6 42 180-224 23-67 (684)
102 PF07975 C1_4: TFIIH C1-like d 71.9 2.8 6.2E-05 28.0 1.7 42 181-222 2-50 (51)
103 PF06906 DUF1272: Protein of u 71.6 6 0.00013 27.0 3.2 44 180-225 7-51 (57)
104 PF02891 zf-MIZ: MIZ/SP-RING z 69.1 6.4 0.00014 25.9 3.0 42 180-224 4-50 (50)
105 KOG2068 MOT2 transcription fac 67.9 3.8 8.1E-05 37.5 2.2 46 179-224 250-296 (327)
106 PF13901 DUF4206: Domain of un 67.3 3.7 7.9E-05 34.9 1.9 39 180-223 154-197 (202)
107 KOG1815 Predicted E3 ubiquitin 67.2 2.6 5.7E-05 39.9 1.1 34 179-214 71-104 (444)
108 smart00249 PHD PHD zinc finger 67.1 3.3 7.1E-05 25.3 1.2 31 181-211 2-32 (47)
109 PF05290 Baculo_IE-1: Baculovi 66.2 3.9 8.4E-05 32.8 1.7 43 179-224 81-130 (140)
110 KOG1829 Uncharacterized conser 65.0 2.1 4.6E-05 42.0 0.0 25 195-222 533-557 (580)
111 PF00628 PHD: PHD-finger; Int 64.8 3.6 7.8E-05 26.5 1.1 43 181-223 2-50 (51)
112 KOG1812 Predicted E3 ubiquitin 63.9 4.1 8.9E-05 38.1 1.7 41 180-221 308-351 (384)
113 KOG2807 RNA polymerase II tran 63.4 4.6 9.9E-05 37.1 1.8 29 195-223 347-375 (378)
114 KOG3005 GIY-YIG type nuclease 61.9 4.1 8.9E-05 36.3 1.2 44 180-223 184-240 (276)
115 PF04710 Pellino: Pellino; In 59.4 3.1 6.6E-05 39.1 0.0 41 180-223 279-336 (416)
116 smart00132 LIM Zinc-binding do 59.2 8.5 0.00018 22.6 2.0 36 181-225 2-37 (39)
117 KOG2066 Vacuolar assembly/sort 52.3 5.8 0.00013 40.2 0.6 41 180-221 786-830 (846)
118 KOG3113 Uncharacterized conser 51.7 16 0.00034 32.5 3.2 44 179-224 112-156 (293)
119 PF06844 DUF1244: Protein of u 51.6 8.7 0.00019 27.1 1.2 12 202-213 11-22 (68)
120 PF04423 Rad50_zn_hook: Rad50 50.3 4.6 0.0001 26.8 -0.3 9 217-225 22-30 (54)
121 PF13832 zf-HC5HC2H_2: PHD-zin 49.0 17 0.00037 27.2 2.7 30 180-211 57-88 (110)
122 KOG1729 FYVE finger containing 48.3 3.3 7.2E-05 37.3 -1.6 35 180-214 216-250 (288)
123 KOG3039 Uncharacterized conser 46.1 14 0.00031 32.7 2.0 30 181-213 46-75 (303)
124 TIGR00622 ssl1 transcription f 43.7 20 0.00042 27.9 2.2 44 180-223 57-111 (112)
125 PF04216 FdhE: Protein involve 42.4 5.1 0.00011 35.7 -1.3 45 179-223 173-219 (290)
126 PF14169 YdjO: Cold-inducible 42.1 13 0.00029 25.6 1.0 16 210-225 28-49 (59)
127 PF13240 zinc_ribbon_2: zinc-r 40.7 5.2 0.00011 22.2 -1.0 12 214-225 12-23 (23)
128 PF13717 zinc_ribbon_4: zinc-r 40.6 20 0.00042 22.0 1.5 25 180-204 4-36 (36)
129 COG5109 Uncharacterized conser 39.1 22 0.00049 32.6 2.2 44 179-222 337-383 (396)
130 PF07191 zinc-ribbons_6: zinc- 37.2 4.7 0.0001 28.8 -1.9 38 180-225 3-40 (70)
131 KOG3842 Adaptor protein Pellin 37.0 28 0.00062 32.0 2.5 28 197-224 376-412 (429)
132 cd00350 rubredoxin_like Rubred 36.6 22 0.00047 21.2 1.2 20 198-223 6-25 (33)
133 PF13771 zf-HC5HC2H: PHD-like 36.2 17 0.00036 26.1 0.8 29 180-210 38-68 (90)
134 PF01363 FYVE: FYVE zinc finge 35.4 22 0.00048 24.3 1.3 35 178-212 9-44 (69)
135 PF07649 C1_3: C1-like domain; 32.5 33 0.00071 19.8 1.5 29 180-208 2-30 (30)
136 PF10572 UPF0556: Uncharacteri 31.9 55 0.0012 26.9 3.2 26 7-40 75-100 (158)
137 KOG4185 Predicted E3 ubiquitin 31.7 7.8 0.00017 34.3 -1.9 44 180-223 209-264 (296)
138 COG4847 Uncharacterized protei 30.9 52 0.0011 24.9 2.7 34 180-214 8-41 (103)
139 PF10571 UPF0547: Uncharacteri 29.9 14 0.00031 21.1 -0.3 22 180-203 2-24 (26)
140 PF00412 LIM: LIM domain; Int 29.4 25 0.00054 22.8 0.7 12 180-191 28-39 (58)
141 PF14311 DUF4379: Domain of un 29.4 38 0.00082 22.3 1.6 23 198-221 33-55 (55)
142 PF13719 zinc_ribbon_5: zinc-r 29.1 39 0.00085 20.6 1.5 25 180-204 4-36 (37)
143 COG3813 Uncharacterized protei 27.4 60 0.0013 23.4 2.4 42 181-224 8-50 (84)
144 KOG1815 Predicted E3 ubiquitin 26.9 19 0.00042 34.1 -0.3 35 180-214 228-267 (444)
145 PF10497 zf-4CXXC_R1: Zinc-fin 26.7 48 0.001 25.2 2.0 24 200-223 37-69 (105)
146 KOG4443 Putative transcription 26.0 32 0.00068 34.5 1.0 26 198-223 40-70 (694)
147 cd00065 FYVE FYVE domain; Zinc 25.7 42 0.00091 21.8 1.3 34 180-213 4-38 (57)
148 COG3492 Uncharacterized protei 24.6 35 0.00077 25.7 0.8 12 202-213 42-53 (104)
149 PF14569 zf-UDP: Zinc-binding 24.3 64 0.0014 23.6 2.1 45 180-224 11-60 (80)
150 KOG4218 Nuclear hormone recept 24.1 21 0.00046 33.2 -0.5 44 180-224 17-76 (475)
151 KOG1245 Chromatin remodeling c 24.0 24 0.00053 38.5 -0.2 45 180-224 1110-1158(1404)
152 KOG4021 Mitochondrial ribosoma 23.8 41 0.00089 28.8 1.2 20 205-224 97-117 (239)
153 COG5183 SSM4 Protein involved 23.6 44 0.00095 34.6 1.5 24 201-224 39-64 (1175)
154 KOG3579 Predicted E3 ubiquitin 23.4 38 0.00083 30.7 0.9 35 180-215 270-306 (352)
155 PF09723 Zn-ribbon_8: Zinc rib 22.1 30 0.00064 21.8 0.0 26 197-223 9-34 (42)
156 smart00734 ZnF_Rad18 Rad18-lik 22.1 44 0.00096 18.9 0.7 7 217-223 3-9 (26)
157 PF10146 zf-C4H2: Zinc finger- 21.8 61 0.0013 28.2 1.9 21 204-224 197-217 (230)
158 KOG3799 Rab3 effector RIM1 and 21.5 21 0.00046 28.8 -0.9 48 176-223 63-115 (169)
159 PF06937 EURL: EURL protein; 20.2 77 0.0017 28.4 2.2 41 180-220 32-75 (285)
160 smart00647 IBR In Between Ring 20.1 33 0.00071 22.6 -0.1 18 194-211 40-58 (64)
161 PF10235 Cript: Microtubule-as 20.0 59 0.0013 24.3 1.2 35 179-225 45-79 (90)
No 1
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.60 E-value=3.1e-16 Score=101.89 Aligned_cols=43 Identities=51% Similarity=1.300 Sum_probs=40.3
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCR 222 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR 222 (225)
+|+||++.+..++.+..++|+|+||.+||.+|++++.+||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 5799999999999999999999999999999999999999998
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.57 E-value=1.2e-15 Score=138.14 Aligned_cols=74 Identities=28% Similarity=0.679 Sum_probs=60.6
Q ss_pred CCCCCCHHHHHhcccccccccccccccccccccccccccCceeEEeCcCCeecHHHHHHHhhcC-CCCCCcCCCC
Q 041990 152 VAEGASREAIERLERVQIDEDRLRRQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS-KSCPLCRSEL 225 (225)
Q Consensus 152 ~~~~as~~~i~~L~~~~~~~~~~~~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~-~sCPlCR~~l 225 (225)
+...+.+..++++|..++.........-.|+||||+|..|++++.|||+|.||..||++||.+. +.||+||+.+
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 3356678888888888886554433224689999999999999999999999999999999886 5699999863
No 3
>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=99.32 E-value=6.8e-13 Score=95.49 Aligned_cols=43 Identities=42% Similarity=1.004 Sum_probs=35.2
Q ss_pred cccccccccccC----------ceeEEeCcCCeecHHHHHHHhhcCCCCCCcC
Q 041990 180 LCAICLQEFVVG----------LQVTRLPCSHIFHGDCVLNWLTKSKSCPLCR 222 (225)
Q Consensus 180 ~C~ICLee~~~g----------~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR 222 (225)
.|+||++.|... ..+...+|+|.||..||.+||+.+.+||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 479999999432 2345568999999999999999999999998
No 4
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.32 E-value=1.2e-12 Score=113.57 Aligned_cols=73 Identities=22% Similarity=0.545 Sum_probs=54.0
Q ss_pred CCCCCHHHHHhccccccccccc--ccccccccccccccccCce-----eEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 153 AEGASREAIERLERVQIDEDRL--RRQQCLCAICLQEFVVGLQ-----VTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 153 ~~~as~~~i~~L~~~~~~~~~~--~~~~c~C~ICLee~~~g~~-----~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
..+.++..++.+|.+..+.... .....+|+||++.+..+.. ...++|+|.||..||.+|++.+.+||+||.++
T Consensus 147 k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred hcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 3455888888888876433221 2234578999998775431 23447999999999999999999999999864
No 5
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.30 E-value=1.1e-12 Score=115.96 Aligned_cols=48 Identities=42% Similarity=1.002 Sum_probs=44.2
Q ss_pred cccccccccccccCceeEEeCcCCeecHHHHHHHhhc-CCCCCCcCCCC
Q 041990 178 QCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSEL 225 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~l 225 (225)
.++|+|||+.|-.+++++.|||.|.||..|+.+|+.. ++.||+||.++
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 3789999999998899999999999999999999984 78899999875
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.18 E-value=1e-11 Score=112.42 Aligned_cols=51 Identities=39% Similarity=0.997 Sum_probs=43.1
Q ss_pred ccccccccccccc-cccCc---------eeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 175 RRQQCLCAICLQE-FVVGL---------QVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 175 ~~~~c~C~ICLee-~~~g~---------~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.+++-.|.||+++ |..+. +.+++||||.+|.+|++.|++++.+||+||.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence 3455578999999 65552 458899999999999999999999999999873
No 7
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=99.08 E-value=8.7e-11 Score=74.29 Aligned_cols=39 Identities=41% Similarity=1.028 Sum_probs=33.5
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlC 221 (225)
|+||++.+.. .++.++|||+||..||.+|++++..||+|
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 7999998874 55778999999999999999999999998
No 8
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.07 E-value=1.2e-10 Score=73.85 Aligned_cols=44 Identities=45% Similarity=1.136 Sum_probs=36.5
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc-CCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~l 225 (225)
.|+||++.+. .....++|+|.||..|+..|++. +..||+||..+
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 4899999882 34445569999999999999998 77899999864
No 9
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=99.02 E-value=2.1e-10 Score=76.27 Aligned_cols=43 Identities=37% Similarity=0.964 Sum_probs=37.0
Q ss_pred cccccccccccCceeEEeCcCCe-ecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHI-FHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|.||++... .+..+||+|. ||..|+.+|++++..||+||+++
T Consensus 4 ~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-
T ss_pred CCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhh
Confidence 5899999754 4677899999 99999999999999999999875
No 10
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=1.2e-10 Score=102.43 Aligned_cols=47 Identities=34% Similarity=0.923 Sum_probs=40.2
Q ss_pred cccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 176 RQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
...-.|.+||+....+ ..+||||+||+.||..|......||+||.+.
T Consensus 237 ~a~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~ 283 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP---SATPCGHIFCWSCILEWCSEKAECPLCREKF 283 (293)
T ss_pred CCCCceEEEecCCCCC---CcCcCcchHHHHHHHHHHccccCCCcccccC
Confidence 3444689999987655 6799999999999999999999999999853
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.00 E-value=2.5e-10 Score=95.99 Aligned_cols=45 Identities=29% Similarity=0.777 Sum_probs=36.9
Q ss_pred cccccccccccccCceeEEeCcCCeecHHHHHHHhhc----------------CCCCCCcCCCC
Q 041990 178 QCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK----------------SKSCPLCRSEL 225 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~----------------~~sCPlCR~~l 225 (225)
..+|+||++.+..+ +.++|+|+||..||.+|+.. ...||+||.++
T Consensus 18 ~~~CpICld~~~dP---VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 18 DFDCNICLDQVRDP---VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred ccCCccCCCcCCCc---EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 34789999988654 66899999999999999852 34799999864
No 12
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.99 E-value=1.8e-10 Score=98.62 Aligned_cols=46 Identities=35% Similarity=0.777 Sum_probs=37.7
Q ss_pred ccccccccccccccCceeEEeCcCCeecHHHHHHHhhc---CCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK---SKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~---~~sCPlCR~~l 225 (225)
..-+|.|||+.-+. .+++.|||.||+.||.+||+. ++.||+||..+
T Consensus 46 ~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~V 94 (230)
T KOG0823|consen 46 GFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEV 94 (230)
T ss_pred CceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCcccccc
Confidence 33478999987544 478899999999999999986 45699999864
No 13
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.95 E-value=2.2e-10 Score=110.41 Aligned_cols=48 Identities=44% Similarity=1.108 Sum_probs=42.9
Q ss_pred ccccccccccccccCce--eEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 177 QQCLCAICLQEFVVGLQ--VTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~--~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
....|+||++++..+.+ ..++||+|+||..|+.+|++.+++||+||..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~ 339 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTV 339 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhh
Confidence 34468999999998765 7889999999999999999999999999973
No 14
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.89 E-value=9.3e-10 Score=81.05 Aligned_cols=45 Identities=38% Similarity=0.877 Sum_probs=34.9
Q ss_pred cccccccccccC--------c--eeEEeCcCCeecHHHHHHHhhc---CCCCCCcCCC
Q 041990 180 LCAICLQEFVVG--------L--QVTRLPCSHIFHGDCVLNWLTK---SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g--------~--~~~~lpC~H~FH~~CI~~WL~~---~~sCPlCR~~ 224 (225)
.|.||...|... + .++.-.|+|.||.+||.+||++ +..||+||++
T Consensus 23 ~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 23 VCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQP 80 (85)
T ss_pred ceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCe
Confidence 578888888742 1 2233369999999999999986 4689999985
No 15
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.89 E-value=1.2e-09 Score=70.41 Aligned_cols=38 Identities=39% Similarity=0.883 Sum_probs=29.4
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhhcC----CCCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS----KSCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~----~sCPlC 221 (225)
|+||++.|..+ +.|+|||+|+..||.+|.+.. ..||.|
T Consensus 1 CpiC~~~~~~P---v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDP---VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSE---EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCc---cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 79999999755 779999999999999999863 369998
No 16
>PHA02926 zinc finger-like protein; Provisional
Probab=98.88 E-value=7.5e-10 Score=94.58 Aligned_cols=47 Identities=30% Similarity=0.735 Sum_probs=35.5
Q ss_pred ccccccccccccC-----ceeEEe-CcCCeecHHHHHHHhhcC------CCCCCcCCCC
Q 041990 179 CLCAICLQEFVVG-----LQVTRL-PCSHIFHGDCVLNWLTKS------KSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g-----~~~~~l-pC~H~FH~~CI~~WL~~~------~sCPlCR~~l 225 (225)
.+|+|||+..-.. ..-+.| +|+|.||..||.+|.+.+ .+||+||..+
T Consensus 171 ~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f 229 (242)
T PHA02926 171 KECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRF 229 (242)
T ss_pred CCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCccee
Confidence 4689999976332 123445 799999999999999753 4699999853
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.86 E-value=1.7e-09 Score=70.14 Aligned_cols=44 Identities=32% Similarity=0.778 Sum_probs=38.4
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.|+||++.+........++|+|+||..|+.++......||+||+
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 48999999955566788899999999999999866789999985
No 18
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.86 E-value=2.7e-09 Score=73.52 Aligned_cols=43 Identities=23% Similarity=0.472 Sum_probs=38.5
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|+||++.+..+ +.+||||+|+..||.+|++.+.+||+|+.++
T Consensus 3 ~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~ 45 (63)
T smart00504 3 LCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHGTDPVTGQPL 45 (63)
T ss_pred CCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence 489999998765 6679999999999999999999999999764
No 19
>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=98.85 E-value=1.6e-09 Score=68.79 Aligned_cols=39 Identities=51% Similarity=1.152 Sum_probs=33.5
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhh--cCCCCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT--KSKSCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~--~~~sCPlC 221 (225)
|+||++.+..+ ...++|+|.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 79999998754 35789999999999999999 46689998
No 20
>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=98.81 E-value=3.4e-09 Score=64.72 Aligned_cols=38 Identities=42% Similarity=1.180 Sum_probs=32.8
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhh-cCCCCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT-KSKSCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~-~~~sCPlC 221 (225)
|+||++.. .....++|+|.||..|+..|++ .+..||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 79999883 4567789999999999999998 56789998
No 21
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.81 E-value=1.7e-09 Score=89.36 Aligned_cols=48 Identities=27% Similarity=0.756 Sum_probs=39.9
Q ss_pred ccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
+...|+|||+.+..... ..+.|||+||..||..-+++.+.||+||.+|
T Consensus 130 ~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkI 177 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKI 177 (187)
T ss_pred cccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence 33578999999874322 4478999999999999999999999999764
No 22
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.66 E-value=1.5e-08 Score=73.46 Aligned_cols=27 Identities=41% Similarity=1.051 Sum_probs=25.9
Q ss_pred CcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 198 PCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 198 pC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
-|.|.||.+||.+||.+++.||++|++
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~ 79 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLDRQT 79 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCCCce
Confidence 699999999999999999999999986
No 23
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.65 E-value=4.2e-09 Score=104.48 Aligned_cols=66 Identities=27% Similarity=0.563 Sum_probs=44.3
Q ss_pred HHHhcccccccccccccccccccccccccccCce----eEEeCcCCeecHHHHHHHhhc--CCCCCCcCCCC
Q 041990 160 AIERLERVQIDEDRLRRQQCLCAICLQEFVVGLQ----VTRLPCSHIFHGDCVLNWLTK--SKSCPLCRSEL 225 (225)
Q Consensus 160 ~i~~L~~~~~~~~~~~~~~c~C~ICLee~~~g~~----~~~lpC~H~FH~~CI~~WL~~--~~sCPlCR~~l 225 (225)
..+.|...+........+..+||||+..+..-++ .++-.|.|.||..|+.+|++. +++||+||.++
T Consensus 1451 ~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1451 FMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred HHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 3344433333333333555678999988763221 133359999999999999987 56899999875
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.62 E-value=1.9e-08 Score=93.37 Aligned_cols=44 Identities=39% Similarity=0.751 Sum_probs=38.6
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
..|+||++.|..+ +.+||+|.||..||..|+.....||+||..+
T Consensus 27 l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~ 70 (397)
T TIGR00599 27 LRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQPKCPLCRAED 70 (397)
T ss_pred cCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence 4789999998654 4689999999999999999988999999853
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=3.2e-08 Score=71.12 Aligned_cols=45 Identities=36% Similarity=0.848 Sum_probs=34.1
Q ss_pred cccccccccccCceeE---------Ee-CcCCeecHHHHHHHhhc---CCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVT---------RL-PCSHIFHGDCVLNWLTK---SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~---------~l-pC~H~FH~~CI~~WL~~---~~sCPlCR~~ 224 (225)
.|.||...|...-..- .+ -|.|.||.+||.+|+.. +..||+||++
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence 6799988887532111 12 49999999999999976 4579999985
No 26
>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=98.45 E-value=1.2e-07 Score=63.03 Aligned_cols=42 Identities=31% Similarity=0.834 Sum_probs=32.8
Q ss_pred cccccccccccCceeEEeCcC-----CeecHHHHHHHhhcC--CCCCCcC
Q 041990 180 LCAICLQEFVVGLQVTRLPCS-----HIFHGDCVLNWLTKS--KSCPLCR 222 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~-----H~FH~~CI~~WL~~~--~sCPlCR 222 (225)
.|.||++. ..+.....+||. |.+|..|+.+|+..+ .+||+|+
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 37999983 334455678985 899999999999764 4899995
No 27
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=7.2e-08 Score=84.21 Aligned_cols=46 Identities=39% Similarity=0.871 Sum_probs=37.7
Q ss_pred cccccccccccccccCceeEEeCcCCeecHHHHHH-HhhcCC-CCCCcCCC
Q 041990 176 RQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLN-WLTKSK-SCPLCRSE 224 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~-WL~~~~-sCPlCR~~ 224 (225)
..+..|+||++.... ...+||||+||..||.. |-.++. .||+||+.
T Consensus 213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak 260 (271)
T COG5574 213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAK 260 (271)
T ss_pred ccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhh
Confidence 345578999988654 47789999999999999 977765 49999985
No 28
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.45 E-value=1.4e-07 Score=61.12 Aligned_cols=38 Identities=39% Similarity=0.888 Sum_probs=22.9
Q ss_pred ccccccccccC-ceeEEeCcCCeecHHHHHHHhhcCC----CCC
Q 041990 181 CAICLQEFVVG-LQVTRLPCSHIFHGDCVLNWLTKSK----SCP 219 (225)
Q Consensus 181 C~ICLee~~~g-~~~~~lpC~H~FH~~CI~~WL~~~~----sCP 219 (225)
|+||.+ |... .....|||||+|+.+||.+|++++. .||
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 799999 7554 4567899999999999999998642 577
No 29
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.44 E-value=8.5e-08 Score=90.32 Aligned_cols=44 Identities=45% Similarity=0.974 Sum_probs=35.6
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcC-----CCCCCcCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS-----KSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~-----~sCPlCR~~l 225 (225)
-.|||||+..... .+|.|||+||..||.+++... ..||+||..|
T Consensus 187 ~~CPICL~~~~~p---~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I 235 (513)
T KOG2164|consen 187 MQCPICLEPPSVP---VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTI 235 (513)
T ss_pred CcCCcccCCCCcc---cccccCceeeHHHHHHHHhhhcccCCccCCchhhhc
Confidence 3689999886544 566799999999999998753 5799999754
No 30
>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=98.31 E-value=4.2e-07 Score=65.13 Aligned_cols=43 Identities=26% Similarity=0.503 Sum_probs=34.4
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc-CCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~l 225 (225)
.|+|+.+.+..+ +++|+||+|.+.||.+||++ +.+||+||.++
T Consensus 6 ~CpIt~~lM~dP---Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l 49 (73)
T PF04564_consen 6 LCPITGELMRDP---VILPSGHTYERSAIERWLEQNGGTDPFTRQPL 49 (73)
T ss_dssp B-TTTSSB-SSE---EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-
T ss_pred CCcCcCcHhhCc---eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcC
Confidence 589999999765 77899999999999999999 88999998764
No 31
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=1.4e-07 Score=82.76 Aligned_cols=48 Identities=33% Similarity=0.942 Sum_probs=39.2
Q ss_pred ccccccccccccccCc-------eeEEeCcCCeecHHHHHHHh--hcCCCCCCcCCC
Q 041990 177 QQCLCAICLQEFVVGL-------QVTRLPCSHIFHGDCVLNWL--TKSKSCPLCRSE 224 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~-------~~~~lpC~H~FH~~CI~~WL--~~~~sCPlCR~~ 224 (225)
++..|+||=..+.... +.-+|.|+|+||..||+.|. .++.+||.|+.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKek 279 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEK 279 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHH
Confidence 3457899988776543 56788999999999999996 468899999865
No 32
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.28 E-value=2.6e-07 Score=83.30 Aligned_cols=43 Identities=33% Similarity=0.812 Sum_probs=39.2
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|.||.+-|..+ ..+||+|.||.-||.+.|..+..||.|+.++
T Consensus 25 RC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~ 67 (442)
T KOG0287|consen 25 RCGICFEYFNIP---MITPCSHTFCSLCIRKFLSYKPQCPTCCVTV 67 (442)
T ss_pred HHhHHHHHhcCc---eeccccchHHHHHHHHHhccCCCCCceeccc
Confidence 689999999766 7789999999999999999999999999763
No 33
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=2.7e-07 Score=86.60 Aligned_cols=50 Identities=38% Similarity=0.929 Sum_probs=38.0
Q ss_pred cccccccccccccccCc---e-----------eEEeCcCCeecHHHHHHHhhcCC-CCCCcCCCC
Q 041990 176 RQQCLCAICLQEFVVGL---Q-----------VTRLPCSHIFHGDCVLNWLTKSK-SCPLCRSEL 225 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~---~-----------~~~lpC~H~FH~~CI~~WL~~~~-sCPlCR~~l 225 (225)
.....|+|||..+.--. . -..+||.|+||..|+.+|..+-+ .||+||.++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pL 633 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPL 633 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCC
Confidence 34447899999775321 1 12359999999999999999644 899999875
No 34
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.24 E-value=5.2e-07 Score=79.99 Aligned_cols=42 Identities=29% Similarity=0.710 Sum_probs=38.2
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.|-||-+-|..+ ..++|||.||.-||...|..+..||+||.+
T Consensus 27 rC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~ 68 (391)
T COG5432 27 RCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQPFCPVCRED 68 (391)
T ss_pred Hhhhhhheeecc---eecccccchhHHHHHHHhcCCCCCcccccc
Confidence 689999888765 667999999999999999999999999975
No 35
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.23 E-value=3.9e-07 Score=84.68 Aligned_cols=43 Identities=33% Similarity=0.935 Sum_probs=36.1
Q ss_pred ccccccccccccCce-eEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 179 CLCAICLQEFVVGLQ-VTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~~-~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.+||||||-+..... +..+.|.|.||..|+.+| ...+||+||+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~ 219 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRY 219 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhh
Confidence 479999998876543 345589999999999999 7789999997
No 36
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.20 E-value=2.4e-07 Score=66.14 Aligned_cols=46 Identities=28% Similarity=0.632 Sum_probs=22.1
Q ss_pred cccccccccc-cCcee--EEe--CcCCeecHHHHHHHhhc-----------CCCCCCcCCCC
Q 041990 180 LCAICLQEFV-VGLQV--TRL--PCSHIFHGDCVLNWLTK-----------SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~-~g~~~--~~l--pC~H~FH~~CI~~WL~~-----------~~sCPlCR~~l 225 (225)
+|+||++.+. .+... ..- .|++.||..|+.+||.. .+.||.|+.+|
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 6899999866 33322 222 59999999999999973 12599999864
No 37
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=4.9e-06 Score=63.23 Aligned_cols=27 Identities=41% Similarity=0.971 Sum_probs=25.2
Q ss_pred CcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 198 PCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 198 pC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
-|.|.||.+||.+||++++.||+|-++
T Consensus 80 ~CNHaFH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred ecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence 699999999999999999999999764
No 38
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=3.8e-06 Score=76.23 Aligned_cols=45 Identities=36% Similarity=0.775 Sum_probs=36.0
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc-CCCCCCcCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~l 225 (225)
-.|+|||+.++.. .....|.|.||.+||.+-++. +++||.||+.+
T Consensus 44 v~c~icl~llk~t--mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l 89 (381)
T KOG0311|consen 44 VICPICLSLLKKT--MTTKECLHRFCFDCIWKALRSGNNECPTCRKKL 89 (381)
T ss_pred hccHHHHHHHHhh--cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhc
Confidence 4689999988632 333469999999999888875 78999999853
No 39
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.62 E-value=1.4e-05 Score=55.88 Aligned_cols=41 Identities=29% Similarity=0.776 Sum_probs=21.7
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.|++|.+.+..+ +....|.|+||..||..-+.. -||+|+.+
T Consensus 9 rCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~~--~CPvC~~P 49 (65)
T PF14835_consen 9 RCSICFDILKEP--VCLGGCEHIFCSSCIRDCIGS--ECPVCHTP 49 (65)
T ss_dssp S-SSS-S--SS---B---SSS--B-TTTGGGGTTT--B-SSS--B
T ss_pred CCcHHHHHhcCC--ceeccCccHHHHHHhHHhcCC--CCCCcCCh
Confidence 689999988744 334479999999999886554 49999875
No 40
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.60 E-value=1.3e-05 Score=79.01 Aligned_cols=46 Identities=28% Similarity=0.629 Sum_probs=41.5
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|++|+..+..+......+|+|.||.+||..|-+.-.+||+||.++
T Consensus 125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF 170 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF 170 (1134)
T ss_pred hhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence 5799999998887777789999999999999999999999999753
No 41
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=6.1e-05 Score=68.55 Aligned_cols=45 Identities=31% Similarity=0.785 Sum_probs=36.5
Q ss_pred cccccccccccccCceeEEeCcCCe-ecHHHHHHHhhcCCCCCCcCCCC
Q 041990 178 QCLCAICLQEFVVGLQVTRLPCSHI-FHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
..+|.|||.+. ..+..|||.|. -|..|.+..--+.+.||+||+++
T Consensus 290 gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi 335 (349)
T KOG4265|consen 290 GKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPI 335 (349)
T ss_pred CCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccch
Confidence 45799999875 45688999997 68889877665788899999874
No 42
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=3.9e-05 Score=70.19 Aligned_cols=47 Identities=36% Similarity=0.868 Sum_probs=35.2
Q ss_pred cccccccccccccCc----eeEEeC-cCCeecHHHHHHHhh--c-----CCCCCCcCCC
Q 041990 178 QCLCAICLQEFVVGL----QVTRLP-CSHIFHGDCVLNWLT--K-----SKSCPLCRSE 224 (225)
Q Consensus 178 ~c~C~ICLee~~~g~----~~~~lp-C~H~FH~~CI~~WL~--~-----~~sCPlCR~~ 224 (225)
+..|.||++...... ..+++| |.|.||..||.+|-+ + ...||.||..
T Consensus 161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~ 219 (344)
T KOG1039|consen 161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVP 219 (344)
T ss_pred cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCc
Confidence 346899999765432 123444 999999999999973 3 5789999975
No 43
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.43 E-value=3.5e-05 Score=68.80 Aligned_cols=39 Identities=33% Similarity=0.634 Sum_probs=33.1
Q ss_pred ccccccccccccccccccCceeEEeCcCCeecHHHHHHHhh
Q 041990 173 RLRRQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT 213 (225)
Q Consensus 173 ~~~~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~ 213 (225)
+....+| .|||--|..+....+++|-|.||..|+.++|.
T Consensus 112 n~p~gqC--vICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~ 150 (368)
T KOG4445|consen 112 NHPNGQC--VICLYGFASSPAFTVTACDHYMHFACLARYLT 150 (368)
T ss_pred CCCCCce--EEEEEeecCCCceeeehhHHHHHHHHHHHHHH
Confidence 3335555 99999999999899999999999999988873
No 44
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00019 Score=66.99 Aligned_cols=46 Identities=33% Similarity=0.767 Sum_probs=38.5
Q ss_pred ccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.+.+|.||+..+..+ +.+||||.||..||.+-+..+..||.||.++
T Consensus 83 sef~c~vc~~~l~~p---v~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l 128 (398)
T KOG4159|consen 83 SEFECCVCSRALYPP---VVTPCGHSFCLECLDRSLDQETECPLCRDEL 128 (398)
T ss_pred chhhhhhhHhhcCCC---ccccccccccHHHHHHHhccCCCCccccccc
Confidence 344789998887644 6679999999999999888888999999764
No 45
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.16 E-value=0.00011 Score=67.69 Aligned_cols=44 Identities=39% Similarity=0.904 Sum_probs=36.7
Q ss_pred cccccccccccC-ceeEEeCcCCeecHHHHHHHhhcC--CCCCCcCC
Q 041990 180 LCAICLQEFVVG-LQVTRLPCSHIFHGDCVLNWLTKS--KSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g-~~~~~lpC~H~FH~~CI~~WL~~~--~sCPlCR~ 223 (225)
-|..|=+.+... +....|||+|+||..|+...|.++ .+||.||+
T Consensus 367 ~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 367 YCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 589998877654 456778999999999999999875 48999993
No 46
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.16 E-value=0.00012 Score=67.74 Aligned_cols=43 Identities=35% Similarity=1.001 Sum_probs=34.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc--CCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCPlCR~~l 225 (225)
.|-||-+. ...+.+-||||..|..|+..|-.. ..+||.||.+|
T Consensus 371 LCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 371 LCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred HHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 48999865 234566699999999999999754 57899999865
No 47
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.15 E-value=0.00019 Score=66.95 Aligned_cols=47 Identities=36% Similarity=0.859 Sum_probs=39.1
Q ss_pred ccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
....|++|...+..+.. .+.|+|.||..|+.+|+..+..||.||..+
T Consensus 20 ~~l~C~~C~~vl~~p~~--~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~ 66 (391)
T KOG0297|consen 20 ENLLCPICMSVLRDPVQ--TTTCGHRFCAGCLLESLSNHQKCPVCRQEL 66 (391)
T ss_pred ccccCccccccccCCCC--CCCCCCcccccccchhhccCcCCccccccc
Confidence 33578999998876533 268999999999999999999999998753
No 48
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.14 E-value=0.00032 Score=48.08 Aligned_cols=40 Identities=35% Similarity=0.747 Sum_probs=28.0
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc--CCCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--SKSCPL 220 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCPl 220 (225)
..|||.+..|+ +.++...|+|+|-...|.+||++ ...||+
T Consensus 12 ~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 12 LKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred cCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 36899999987 44666789999999999999954 446998
No 49
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=7.7e-05 Score=50.55 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=31.7
Q ss_pred ccccccccccccCceeEEeCcCCe-ecHHHHHHHhh-cCCCCCCcCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHI-FHGDCVLNWLT-KSKSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~-FH~~CI~~WL~-~~~sCPlCR~~l 225 (225)
.+|.||++.-.. .+...|||. .|..|-.+-++ .+..||+||.++
T Consensus 8 dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI 53 (62)
T ss_pred cceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence 378999985432 234489996 57788666555 688999999864
No 50
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00028 Score=69.62 Aligned_cols=46 Identities=22% Similarity=0.664 Sum_probs=36.6
Q ss_pred ccccccccccccccCceeEEeCcCCeecHHHHHHHhhc-CCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~l 225 (225)
+-+.|++|-.-++. ++.+.|+|+||..||..-+.+ +..||.|-..+
T Consensus 642 ~~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAF 688 (698)
T ss_pred hceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCC
Confidence 34579999866543 356689999999999999986 67899997653
No 51
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.88 E-value=0.00031 Score=57.72 Aligned_cols=40 Identities=35% Similarity=0.816 Sum_probs=32.0
Q ss_pred cccccccccccccccccccccccccCceeEEeCcCCeecH
Q 041990 166 RVQIDEDRLRRQQCLCAICLQEFVVGLQVTRLPCSHIFHG 205 (225)
Q Consensus 166 ~~~~~~~~~~~~~c~C~ICLee~~~g~~~~~lpC~H~FH~ 205 (225)
++.+.++-...+.-+|.||||++..|+.+.+|||-.+||.
T Consensus 165 rlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 165 RLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 3344445455556689999999999999999999999995
No 52
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.56 E-value=0.0014 Score=43.02 Aligned_cols=40 Identities=28% Similarity=0.779 Sum_probs=27.1
Q ss_pred ccccccccccCceeEEeCcC--C---eecHHHHHHHhhc--CCCCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCS--H---IFHGDCVLNWLTK--SKSCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~--H---~FH~~CI~~WL~~--~~sCPlC 221 (225)
|-||++.-.... ..+.||. - ..|..|+.+|+.. +.+|++|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 689998766544 4556763 3 7899999999985 5679988
No 53
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.42 E-value=0.00065 Score=61.37 Aligned_cols=44 Identities=30% Similarity=0.683 Sum_probs=34.9
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
-.|.+|---|-. ..++.-|-|.||..||.+.|..+.+||.|.-.
T Consensus 16 itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ 59 (331)
T KOG2660|consen 16 ITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEESKYCPTCDIV 59 (331)
T ss_pred eehhhccceeec--chhHHHHHHHHHHHHHHHHHHHhccCCcccee
Confidence 368999765543 23344699999999999999999999999753
No 54
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.24 E-value=0.003 Score=66.33 Aligned_cols=73 Identities=27% Similarity=0.600 Sum_probs=51.0
Q ss_pred CCCCCHHHHHhccccccccccc-ccccccccccccccccCceeEEeCcCCeecHHHHHHHhhcC----------CCCCCc
Q 041990 153 AEGASREAIERLERVQIDEDRL-RRQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS----------KSCPLC 221 (225)
Q Consensus 153 ~~~as~~~i~~L~~~~~~~~~~-~~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~----------~sCPlC 221 (225)
+-|.-+.....||-..-+.... ...+..|.||+.+--......+|.|+|.||..|...-|+++ -+||+|
T Consensus 3460 ~CGGvkNEE~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC 3539 (3738)
T KOG1428|consen 3460 PCGGVKNEEHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPIC 3539 (3738)
T ss_pred cccCccchhhcccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccc
Confidence 3344455556677665433322 23344689999876666778889999999999998877652 269999
Q ss_pred CCCC
Q 041990 222 RSEL 225 (225)
Q Consensus 222 R~~l 225 (225)
+.+|
T Consensus 3540 ~n~I 3543 (3738)
T KOG1428|consen 3540 KNKI 3543 (3738)
T ss_pred cchh
Confidence 9865
No 55
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.22 E-value=0.0019 Score=48.42 Aligned_cols=30 Identities=23% Similarity=0.644 Sum_probs=25.2
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHH
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVL 209 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~ 209 (225)
..|++|-..+.. ......||+|+||..|+.
T Consensus 79 ~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 458999999876 566778999999999975
No 56
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.22 E-value=0.0044 Score=54.89 Aligned_cols=47 Identities=23% Similarity=0.474 Sum_probs=35.7
Q ss_pred cccccccccccccccCceeEEeCcCCeecHHHHHHHhhc--CCCCCCcCCC
Q 041990 176 RQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--SKSCPLCRSE 224 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCPlCR~~ 224 (225)
..+.+|++|-+.-..+ -...+|+|+||+-||..=+.. +.+||.|-.+
T Consensus 237 t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGEN 285 (298)
T ss_pred cCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCC
Confidence 4556899998765433 344579999999999987765 4789999764
No 57
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.20 E-value=0.0048 Score=54.01 Aligned_cols=49 Identities=18% Similarity=0.421 Sum_probs=43.2
Q ss_pred ccccccccccccccCceeEEe-CcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRL-PCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~l-pC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
....||||.+.+.+......| ||||+|+.+|+.+.+.....||+|-.++
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~pl 269 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPL 269 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcC
Confidence 445799999999988777777 8999999999999999999999997654
No 58
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.14 E-value=0.0036 Score=41.46 Aligned_cols=44 Identities=23% Similarity=0.505 Sum_probs=22.6
Q ss_pred cccccccccc-CceeEEeCcCCeecHHHHHHHhh-cCCCCCCcCCC
Q 041990 181 CAICLQEFVV-GLQVTRLPCSHIFHGDCVLNWLT-KSKSCPLCRSE 224 (225)
Q Consensus 181 C~ICLee~~~-g~~~~~lpC~H~FH~~CI~~WL~-~~~sCPlCR~~ 224 (225)
|++|.+++.. +....--+|++..+..|-.+-++ ..+.||-||.+
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 6999999833 22333346899999999888886 47899999975
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=96.12 E-value=0.003 Score=50.49 Aligned_cols=35 Identities=23% Similarity=0.495 Sum_probs=28.8
Q ss_pred ccccccccccccCceeEEeCcC------CeecHHHHHHHhh
Q 041990 179 CLCAICLQEFVVGLQVTRLPCS------HIFHGDCVLNWLT 213 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~------H~FH~~CI~~WL~ 213 (225)
-+|+||++.+.....++.++|+ |.||.+|+.+|-+
T Consensus 27 ~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 27 VECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred eeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 3799999999884456777885 8999999999943
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.12 E-value=0.0018 Score=54.95 Aligned_cols=42 Identities=26% Similarity=0.686 Sum_probs=37.1
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.|.||-.+|..+ +.+.|||.||..|..+=.++...|-+|-..
T Consensus 198 ~C~iCKkdy~sp---vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 198 LCGICKKDYESP---VVTECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred eehhchhhccch---hhhhcchhHHHHHHHHHhccCCcceecchh
Confidence 689999999766 678899999999999999999999999653
No 61
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.92 E-value=0.0052 Score=53.15 Aligned_cols=45 Identities=33% Similarity=0.766 Sum_probs=36.9
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc--------CCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--------SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--------~~sCPlCR~~l 225 (225)
-|..|-..+..|+. ++|-|-|+||+.|+..|-.. ...||-|..+|
T Consensus 52 NC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 52 NCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 57999888877754 67899999999999999764 34699998765
No 62
>PHA03096 p28-like protein; Provisional
Probab=95.86 E-value=0.0039 Score=55.88 Aligned_cols=45 Identities=27% Similarity=0.510 Sum_probs=32.1
Q ss_pred ccccccccccccCc----eeEEe-CcCCeecHHHHHHHhhc---CCCCCCcCC
Q 041990 179 CLCAICLQEFVVGL----QVTRL-PCSHIFHGDCVLNWLTK---SKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~----~~~~l-pC~H~FH~~CI~~WL~~---~~sCPlCR~ 223 (225)
-.|.|||+...... .-..| .|.|.||..||..|-.. ..+||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46899999776532 23455 49999999999999864 334555553
No 63
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.78 E-value=0.0052 Score=57.17 Aligned_cols=44 Identities=32% Similarity=0.679 Sum_probs=35.5
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc--------CCCCCCcC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--------SKSCPLCR 222 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--------~~sCPlCR 222 (225)
..|.||+++.....-...+||+|+||..|...++.. .-.||-+.
T Consensus 185 f~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 185 FDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred ccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 368999999876677888999999999999999863 22587654
No 64
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.69 E-value=0.0071 Score=55.44 Aligned_cols=46 Identities=28% Similarity=0.661 Sum_probs=37.4
Q ss_pred cccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 176 RQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.++..|+||.-. +-.++..||+|.-|..||.+-+.+.+.|=.|+.+
T Consensus 420 sEd~lCpICyA~---pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktT 465 (489)
T KOG4692|consen 420 SEDNLCPICYAG---PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTT 465 (489)
T ss_pred cccccCcceecc---cchhhccCCCCchHHHHHHHHHhcCCeeeEecce
Confidence 344579999743 2345667999999999999999999999999875
No 65
>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=95.67 E-value=0.0072 Score=39.00 Aligned_cols=41 Identities=24% Similarity=0.718 Sum_probs=24.1
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhhcCC--CCCCc
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSK--SCPLC 221 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~--sCPlC 221 (225)
|.+|.+....|..-..-.|+=.+|..|+.++++... .||.|
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 678888777664333334999999999999998865 79988
No 66
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.66 E-value=0.004 Score=55.66 Aligned_cols=42 Identities=29% Similarity=0.607 Sum_probs=37.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.|-||...|..+ +++.|+|.||..|..+=+++...|++|-++
T Consensus 243 ~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~ 284 (313)
T KOG1813|consen 243 KCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGEKCYVCSQQ 284 (313)
T ss_pred cccccccccccc---hhhcCCceeehhhhccccccCCcceecccc
Confidence 479999999765 778999999999999999999999999775
No 67
>PF04641 Rtf2: Rtf2 RING-finger
Probab=95.45 E-value=0.016 Score=51.06 Aligned_cols=48 Identities=27% Similarity=0.614 Sum_probs=37.8
Q ss_pred cccccccccccccccCceeEEe-CcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 176 RQQCLCAICLQEFVVGLQVTRL-PCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 176 ~~~c~C~ICLee~~~g~~~~~l-pC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.....|||...+|......+.+ ||||+|-..+|..- .....||+|-.+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~ 159 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKP 159 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCc
Confidence 3445789999999665565555 99999999999887 336689999765
No 68
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.42 E-value=0.0064 Score=60.97 Aligned_cols=49 Identities=31% Similarity=0.714 Sum_probs=37.0
Q ss_pred ccccccccccccccccCceeE-EeCcCCeecHHHHHHHhhcC-------CCCCCcCC
Q 041990 175 RRQQCLCAICLQEFVVGLQVT-RLPCSHIFHGDCVLNWLTKS-------KSCPLCRS 223 (225)
Q Consensus 175 ~~~~c~C~ICLee~~~g~~~~-~lpC~H~FH~~CI~~WL~~~-------~sCPlCR~ 223 (225)
.+...+|.||++.+.....+. ...|-|+||..||.+|-++. -.||.|..
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 355568999999987655443 33699999999999998651 15999973
No 69
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.22 E-value=0.0089 Score=54.73 Aligned_cols=40 Identities=35% Similarity=0.897 Sum_probs=29.4
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|.||+++..+ ..-+||||+=| |+.- -+...+||+||+.|
T Consensus 307 lcVVcl~e~~~---~~fvpcGh~cc--ct~c-s~~l~~CPvCR~rI 346 (355)
T KOG1571|consen 307 LCVVCLDEPKS---AVFVPCGHVCC--CTLC-SKHLPQCPVCRQRI 346 (355)
T ss_pred ceEEecCCccc---eeeecCCcEEE--chHH-HhhCCCCchhHHHH
Confidence 58999998754 57789999976 5433 23455699999853
No 70
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.14 E-value=0.0035 Score=56.03 Aligned_cols=41 Identities=32% Similarity=0.750 Sum_probs=30.0
Q ss_pred cccccccccccccCceeEEeCcCCe-ecHHHHHHHhhcCCCCCCcCCCC
Q 041990 178 QCLCAICLQEFVVGLQVTRLPCSHI-FHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
...|+|||+.- .....|+|||. -|..|-.. -+.||+||+.|
T Consensus 300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHH
Confidence 44699999764 45578899995 47777644 34899999753
No 71
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=95.13 E-value=0.016 Score=52.56 Aligned_cols=47 Identities=15% Similarity=0.413 Sum_probs=36.2
Q ss_pred ccccccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 175 RRQQCLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 175 ~~~~c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
....+.||||+..-.++ .+...-|-+||+.||.+.+.+.+.||+=-.
T Consensus 297 ~~~~~~CpvClk~r~Np--tvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~ 343 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNP--TVLEVSGYVFCYPCIFSYVVNYGHCPVTGY 343 (357)
T ss_pred CCccccChhHHhccCCC--ceEEecceEEeHHHHHHHHHhcCCCCccCC
Confidence 35566899999876544 233346999999999999999999998443
No 72
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.80 E-value=0.0097 Score=57.13 Aligned_cols=43 Identities=21% Similarity=0.636 Sum_probs=33.4
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc-----CCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-----SKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-----~~sCPlCR~~ 224 (225)
-+|.+|-+.-+ ......|.|.||+-||..++.. +-+||.|-..
T Consensus 537 ~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~ 584 (791)
T KOG1002|consen 537 VECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIG 584 (791)
T ss_pred eeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccc
Confidence 46899987643 3356789999999999998763 4589999654
No 73
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.49 E-value=0.0024 Score=58.98 Aligned_cols=46 Identities=28% Similarity=0.706 Sum_probs=40.1
Q ss_pred cccccccccccC-ceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVG-LQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g-~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|+||.+.++.. .+...+-|+|.+|..||.+||.+...||-||+++
T Consensus 198 sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel 244 (465)
T KOG0827|consen 198 SLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRREL 244 (465)
T ss_pred hhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhh
Confidence 579999999876 5566678999999999999999999999999864
No 74
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.31 E-value=0.022 Score=50.80 Aligned_cols=44 Identities=25% Similarity=0.750 Sum_probs=37.4
Q ss_pred cccccccccccCc-eeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQEFVVGL-QVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.||||.+.+..+. .+..++|||.-|..|.......+.+||+|..
T Consensus 160 ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 160 NCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 3799999887765 4577899999999999988888899999975
No 75
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.14 E-value=0.029 Score=47.04 Aligned_cols=46 Identities=28% Similarity=0.746 Sum_probs=31.1
Q ss_pred cccccccccccCcee----EEeCcCCeecHHHHHHHhhc-----------CCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQV----TRLPCSHIFHGDCVLNWLTK-----------SKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~----~~lpC~H~FH~~CI~~WL~~-----------~~sCPlCR~~l 225 (225)
.|.||+----.|... --..|+.-||.-|+..||+. -..||.|..++
T Consensus 167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi 227 (234)
T KOG3268|consen 167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI 227 (234)
T ss_pred cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence 357776433333221 22479999999999999974 12599998764
No 76
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.01 E-value=0.041 Score=45.22 Aligned_cols=48 Identities=27% Similarity=0.627 Sum_probs=29.2
Q ss_pred ccccccccccccccCceeEEe-CcCCeecHHHHHHHhhc--CCCCCCcCCC
Q 041990 177 QQCLCAICLQEFVVGLQVTRL-PCSHIFHGDCVLNWLTK--SKSCPLCRSE 224 (225)
Q Consensus 177 ~~c~C~ICLee~~~g~~~~~l-pC~H~FH~~CI~~WL~~--~~sCPlCR~~ 224 (225)
....|-||.++-......-.- .-...-|.+|+.+|+.. ..+||+|+++
T Consensus 7 ~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~ 57 (162)
T PHA02825 7 MDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGP 57 (162)
T ss_pred CCCeeEecCCCCCCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCe
Confidence 344689999874311000000 00015699999999986 4479999875
No 77
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.70 E-value=0.024 Score=56.42 Aligned_cols=42 Identities=29% Similarity=0.636 Sum_probs=34.7
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc--CCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK--SKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCPlCR~~ 224 (225)
..|.||++ ......++|+|.||..|+.+-++. ...||+||..
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~ 498 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNV 498 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHH
Confidence 57899998 356688899999999999998875 3369999964
No 78
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.48 E-value=0.049 Score=49.21 Aligned_cols=39 Identities=26% Similarity=0.714 Sum_probs=32.2
Q ss_pred cccccccccccCceeEEeCc--CCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPC--SHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC--~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
+||||.+.+..+ .+.| ||.-|..|-. +.++.||.||.+|
T Consensus 50 eCPvC~~~l~~P----i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~ 90 (299)
T KOG3002|consen 50 DCPVCFNPLSPP----IFQCDNGHLACSSCRT---KVSNKCPTCRLPI 90 (299)
T ss_pred cCchhhccCccc----ceecCCCcEehhhhhh---hhcccCCcccccc
Confidence 689999998765 5677 7999999975 3688899999875
No 79
>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=93.15 E-value=0.06 Score=49.77 Aligned_cols=27 Identities=26% Similarity=0.934 Sum_probs=22.1
Q ss_pred cCCeecHHHHHHHhhc-------------CCCCCCcCCCC
Q 041990 199 CSHIFHGDCVLNWLTK-------------SKSCPLCRSEL 225 (225)
Q Consensus 199 C~H~FH~~CI~~WL~~-------------~~sCPlCR~~l 225 (225)
|.-.+|.+|+.+||.. +-+||.||+++
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 7888899999999963 33699999864
No 80
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=92.87 E-value=0.052 Score=36.90 Aligned_cols=33 Identities=30% Similarity=0.853 Sum_probs=25.2
Q ss_pred CceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 191 GLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 191 g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
+.+...+||+|+.+..|-.- +.-+.||+|-+++
T Consensus 17 ~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~ 49 (55)
T PF14447_consen 17 GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPF 49 (55)
T ss_pred ccccccccccceeeccccCh--hhccCCCCCCCcc
Confidence 34557789999999999544 3667899998764
No 81
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=92.72 E-value=0.047 Score=49.35 Aligned_cols=40 Identities=30% Similarity=0.790 Sum_probs=26.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.|--|=-.+ .-..+..||+|+||.+|... ..-+.||+|-.
T Consensus 92 fCd~Cd~PI--~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d 131 (389)
T KOG2932|consen 92 FCDRCDFPI--AIYGRMIPCKHVFCLECARS--DSDKICPLCDD 131 (389)
T ss_pred eecccCCcc--eeeecccccchhhhhhhhhc--CccccCcCccc
Confidence 356663322 22334559999999999743 34678999964
No 82
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.55 E-value=0.11 Score=47.64 Aligned_cols=43 Identities=37% Similarity=0.802 Sum_probs=33.8
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHH--hhcCCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNW--LTKSKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~W--L~~~~sCPlCR~~ 224 (225)
-.|.||-+.+ ....++||+|.-|--|..+. |-+.+.||+||.+
T Consensus 62 ~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 62 MNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 3589998765 35578899999999998664 4468899999974
No 83
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.85 E-value=0.084 Score=53.27 Aligned_cols=40 Identities=25% Similarity=0.708 Sum_probs=31.4
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
..|..|--.+..+ .+-.-|+|.||.+|+. .+...||-|+-
T Consensus 841 skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKEDKCPKCLP 880 (933)
T ss_pred eeecccCCccccc--eeeeecccHHHHHhhc---cCcccCCccch
Confidence 4689997766533 4556799999999998 56778999985
No 84
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.65 E-value=0.1 Score=47.14 Aligned_cols=42 Identities=26% Similarity=0.637 Sum_probs=32.3
Q ss_pred ccccccccccccCceeEEeC-cCCeecHHHHHHHhh-cCCCCCCcCC
Q 041990 179 CLCAICLQEFVVGLQVTRLP-CSHIFHGDCVLNWLT-KSKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lp-C~H~FH~~CI~~WL~-~~~sCPlCR~ 223 (225)
-.|+.|--.+... ..+| |+|.||.+||..-|. ....||.|.+
T Consensus 275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 4689998776554 4455 899999999997765 4678999976
No 85
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=89.73 E-value=0.093 Score=55.08 Aligned_cols=42 Identities=36% Similarity=0.705 Sum_probs=36.5
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.|.||++.+.. ...+..|+|.+|..|+..|+..+..||.|..
T Consensus 1155 ~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1155 VCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred chHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence 68999999872 2356789999999999999999999999964
No 86
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.26 E-value=0.25 Score=44.52 Aligned_cols=27 Identities=26% Similarity=0.803 Sum_probs=21.8
Q ss_pred cCCeecHHHHHHHhh-------------cCCCCCCcCCCC
Q 041990 199 CSHIFHGDCVLNWLT-------------KSKSCPLCRSEL 225 (225)
Q Consensus 199 C~H~FH~~CI~~WL~-------------~~~sCPlCR~~l 225 (225)
|...+|.+|+.+|+. ++-+||.||+.+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~f 364 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNF 364 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhce
Confidence 678889999999984 345799999853
No 87
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.50 E-value=0.26 Score=50.04 Aligned_cols=34 Identities=26% Similarity=0.714 Sum_probs=26.8
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhh
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT 213 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~ 213 (225)
..|.+|...+... .-...||+|.||+.||.+-..
T Consensus 818 d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 818 DSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cchHHhcchhhcC-cceeeeccchHHHHHHHHHHH
Confidence 3589999887643 456679999999999988753
No 88
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=86.96 E-value=0.25 Score=43.78 Aligned_cols=47 Identities=28% Similarity=0.656 Sum_probs=34.4
Q ss_pred cccccccccccccCce-eEEeCcC-----CeecHHHHHHHhh--cCCCCCCcCCC
Q 041990 178 QCLCAICLQEFVVGLQ-VTRLPCS-----HIFHGDCVLNWLT--KSKSCPLCRSE 224 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~-~~~lpC~-----H~FH~~CI~~WL~--~~~sCPlCR~~ 224 (225)
+..|-||..+...... ...+||. +..|..|+.+|+. .+..|.+|.+.
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~ 132 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSF 132 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccc
Confidence 3468999997654322 4556874 6779999999998 45679999763
No 89
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=86.89 E-value=0.39 Score=48.21 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=24.0
Q ss_pred eeEEeCcCCeecHHHHHHHhhcCCCCCC
Q 041990 193 QVTRLPCSHIFHGDCVLNWLTKSKSCPL 220 (225)
Q Consensus 193 ~~~~lpC~H~FH~~CI~~WL~~~~sCPl 220 (225)
...+..|+|+-|.+|...|++....||-
T Consensus 1042 s~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1042 SNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred chhhccccccccHHHHHHHHhcCCcCCC
Confidence 3345679999999999999999999984
No 90
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.46 E-value=0.54 Score=31.86 Aligned_cols=30 Identities=33% Similarity=0.882 Sum_probs=25.5
Q ss_pred ccccccccccccCceeEEeC-cCCeecHHHH
Q 041990 179 CLCAICLQEFVVGLQVTRLP-CSHIFHGDCV 208 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lp-C~H~FH~~CI 208 (225)
..|++|-+.|..++.+++-| |+-.||+.|-
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 46899999998777777775 9999999994
No 91
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.10 E-value=0.25 Score=43.61 Aligned_cols=45 Identities=29% Similarity=0.710 Sum_probs=31.0
Q ss_pred cccccccccccCc-eeEEeCc-----CCeecHHHHHHHhhcC--------CCCCCcCCC
Q 041990 180 LCAICLQEFVVGL-QVTRLPC-----SHIFHGDCVLNWLTKS--------KSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~-~~~~lpC-----~H~FH~~CI~~WL~~~--------~sCPlCR~~ 224 (225)
.|=||+.-=++.. ..-+-|| .|..|..|+..|+..+ -+||-|+.+
T Consensus 22 ~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE 80 (293)
T KOG3053|consen 22 CCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE 80 (293)
T ss_pred eEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence 4899987533321 2234477 5899999999999542 269999874
No 92
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.87 E-value=0.95 Score=42.22 Aligned_cols=44 Identities=18% Similarity=0.408 Sum_probs=36.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcC---CCCCCcCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS---KSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~---~sCPlCR~ 223 (225)
.|||=-+.=...+....|.|||+-..+=|.+..++. ..||.|=.
T Consensus 336 ~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 336 ICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred ecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 689988877777888999999999999999987763 36999943
No 93
>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=83.30 E-value=0.51 Score=31.18 Aligned_cols=29 Identities=31% Similarity=0.835 Sum_probs=22.3
Q ss_pred eCc-CCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 197 LPC-SHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 197 lpC-~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
..| .|..|..|+...|..+..||+|..++
T Consensus 16 i~C~dHYLCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 16 IKCSDHYLCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp EE-SS-EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred eeecchhHHHHHHHHHhccccCCCcccCcC
Confidence 457 59999999999999999999998764
No 94
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.30 E-value=0.49 Score=44.18 Aligned_cols=37 Identities=30% Similarity=0.506 Sum_probs=27.1
Q ss_pred cccccccccccccC-ceeEEeCcCCeecHHHHHHHhhc
Q 041990 178 QCLCAICLQEFVVG-LQVTRLPCSHIFHGDCVLNWLTK 214 (225)
Q Consensus 178 ~c~C~ICLee~~~g-~~~~~lpC~H~FH~~CI~~WL~~ 214 (225)
..+|.||+.+...+ .......|+|.||.+|..+.++.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev 183 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV 183 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence 34789999544444 33344579999999999998874
No 95
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=81.70 E-value=0.78 Score=42.22 Aligned_cols=45 Identities=22% Similarity=0.564 Sum_probs=31.9
Q ss_pred cccccccccccCce-eEEeCcCCeecHHHHHHHhhc-CCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQ-VTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~-~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~ 224 (225)
-|+.|++++...++ ..-.|||-..|.-|-..--+. ++.||-||+.
T Consensus 16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~ 62 (480)
T COG5175 16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRK 62 (480)
T ss_pred cCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhh
Confidence 48999999877654 344588987777774433332 7789999974
No 96
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.75 E-value=0.62 Score=45.28 Aligned_cols=38 Identities=45% Similarity=1.053 Sum_probs=32.7
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
.|+||+++. ..+..+|. |..|..+|+..+..||+|+..
T Consensus 481 ~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~ 518 (543)
T KOG0802|consen 481 VCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTY 518 (543)
T ss_pred cchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchh
Confidence 579999987 44667888 899999999999999999864
No 97
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.68 E-value=1 Score=38.62 Aligned_cols=37 Identities=38% Similarity=0.868 Sum_probs=25.7
Q ss_pred ccccccccccCceeEEeCcCCe-ecHHHHHHHhhcCCCCCCcCCC
Q 041990 181 CAICLQEFVVGLQVTRLPCSHI-FHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
|-.|-+. +..+..+||.|. +|..|-.. -..||+|+..
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~ 198 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSP 198 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcCh
Confidence 6888654 345777899764 66678543 4569999864
No 98
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=74.41 E-value=1.6 Score=37.61 Aligned_cols=41 Identities=24% Similarity=0.712 Sum_probs=33.5
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCc
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLC 221 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlC 221 (225)
..|.+|-...-.| .+.=.|+-.+|..|+...++....||.|
T Consensus 182 k~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc 222 (235)
T KOG4718|consen 182 KNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHC 222 (235)
T ss_pred HHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCch
Confidence 3689998766544 2333799999999999999999999999
No 99
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.30 E-value=1.6 Score=44.23 Aligned_cols=45 Identities=11% Similarity=0.205 Sum_probs=32.4
Q ss_pred ccccccccccccCc-eeEEeC---cCCeecHHHHHHHhhc------CCCCCCcCC
Q 041990 179 CLCAICLQEFVVGL-QVTRLP---CSHIFHGDCVLNWLTK------SKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~-~~~~lp---C~H~FH~~CI~~WL~~------~~sCPlCR~ 223 (225)
-.|.||.-++.... ....+| |.|.||..||..|..+ +..|++|..
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~ 151 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEE 151 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHH
Confidence 35788888777632 223445 9999999999999864 446888864
No 100
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=72.95 E-value=3 Score=42.10 Aligned_cols=40 Identities=25% Similarity=0.520 Sum_probs=29.3
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPL 220 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPl 220 (225)
.|.+|--.+. |..+..=.|+|.=|.+|+.+|+.++..||.
T Consensus 781 ~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 781 KCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred Cceeecceee-eeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 5788854432 333333359999999999999999888876
No 101
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=72.44 E-value=0.98 Score=45.01 Aligned_cols=42 Identities=36% Similarity=0.800 Sum_probs=34.1
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc---CCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK---SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~---~~sCPlCR~~ 224 (225)
+|+||++-+... ..+.|.|.|+..|+..-|.. ...||+|+..
T Consensus 23 Ec~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~ 67 (684)
T KOG4362|consen 23 ECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSD 67 (684)
T ss_pred cCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhh
Confidence 789999988765 56789999999998877754 4479999853
No 102
>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=71.93 E-value=2.8 Score=28.02 Aligned_cols=42 Identities=29% Similarity=0.534 Sum_probs=22.2
Q ss_pred ccccccccccCc------eeEEe-CcCCeecHHHHHHHhhcCCCCCCcC
Q 041990 181 CAICLQEFVVGL------QVTRL-PCSHIFHGDCVLNWLTKSKSCPLCR 222 (225)
Q Consensus 181 C~ICLee~~~g~------~~~~l-pC~H~FH~~CI~~WL~~~~sCPlCR 222 (225)
|--|+..|..+. ...+- .|++.|+.+|=.--=++-++||-|-
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 455777776652 22233 4999999999644445677899884
No 103
>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=71.57 E-value=6 Score=27.03 Aligned_cols=44 Identities=25% Similarity=0.501 Sum_probs=31.3
Q ss_pred cccccccccccCc-eeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGL-QVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.|-.|-.++.... .+.+-.=...||.+|...-| ++.||.|..++
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCcc
Confidence 3567777777655 44443445689999998876 78899997643
No 104
>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=69.06 E-value=6.4 Score=25.93 Aligned_cols=42 Identities=24% Similarity=0.574 Sum_probs=19.2
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc-----CCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK-----SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~-----~~sCPlCR~~ 224 (225)
.|+|....+.. .++-..|.|.-+.+ +..||.. .-.||+|.++
T Consensus 4 ~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 47888877654 45566899985543 3345543 2269999864
No 105
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=67.87 E-value=3.8 Score=37.51 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=34.2
Q ss_pred ccccccccccccC-ceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 179 CLCAICLQEFVVG-LQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g-~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
..|+||-+..... ....-.||++.-|..|...-...+..||.||.+
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~ 296 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKP 296 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCc
Confidence 3689999876332 233444688888888888877889999999964
No 106
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=67.35 E-value=3.7 Score=34.89 Aligned_cols=39 Identities=36% Similarity=0.894 Sum_probs=25.4
Q ss_pred cccccccc-----cccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQE-----FVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee-----~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.|.||-.. |......+.-.|+-+||..|.. +..||-|-+
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 67888752 2221222333699999999964 377999954
No 107
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.17 E-value=2.6 Score=39.92 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=28.5
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK 214 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~ 214 (225)
-.|.||.+.+.. ....+.|+|.|+..|....+.+
T Consensus 71 ~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 71 VQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred ccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 368999998765 5677799999999999888865
No 108
>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 PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=66.19 E-value=3.9 Score=32.83 Aligned_cols=43 Identities=26% Similarity=0.583 Sum_probs=31.5
Q ss_pred ccccccccccccCceeEEe-C---cCCeecHHHHHHHhhc---CCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVTRL-P---CSHIFHGDCVLNWLTK---SKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~l-p---C~H~FH~~CI~~WL~~---~~sCPlCR~~ 224 (225)
.+|.||.|...+. +-| | ||-.-|..|-....+. ...||+|+..
T Consensus 81 YeCnIC~etS~ee---~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTS 130 (140)
T PF05290_consen 81 YECNICKETSAEE---RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTS 130 (140)
T ss_pred eeccCcccccchh---hcCCcccccchHHHHHHHHHHHHHcccCCCCCccccc
Confidence 4789998875443 223 4 8999999987766554 6689999875
No 110
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=64.96 E-value=2.1 Score=42.03 Aligned_cols=25 Identities=36% Similarity=0.857 Sum_probs=19.0
Q ss_pred EEeCcCCeecHHHHHHHhhcCCCCCCcC
Q 041990 195 TRLPCSHIFHGDCVLNWLTKSKSCPLCR 222 (225)
Q Consensus 195 ~~lpC~H~FH~~CI~~WL~~~~sCPlCR 222 (225)
+...|+++||..|.. .++.-||.|-
T Consensus 533 rC~~C~avfH~~C~~---r~s~~CPrC~ 557 (580)
T KOG1829|consen 533 RCSTCLAVFHKKCLR---RKSPCCPRCE 557 (580)
T ss_pred eHHHHHHHHHHHHHh---ccCCCCCchH
Confidence 445799999999953 3556699994
No 111
>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=64.83 E-value=3.6 Score=26.49 Aligned_cols=43 Identities=28% Similarity=0.513 Sum_probs=29.1
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhh------cCCCCCCcCC
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT------KSKSCPLCRS 223 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~------~~~sCPlCR~ 223 (225)
|.||...-..+..+..-.|+..||..|+..=.. ..-.||.|+.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 789988444444444447999999999876543 1346887763
No 112
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.88 E-value=4.1 Score=38.07 Aligned_cols=41 Identities=29% Similarity=0.573 Sum_probs=28.5
Q ss_pred cccccccccc--cCc-eeEEeCcCCeecHHHHHHHhhcCCCCCCc
Q 041990 180 LCAICLQEFV--VGL-QVTRLPCSHIFHGDCVLNWLTKSKSCPLC 221 (225)
Q Consensus 180 ~C~ICLee~~--~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCPlC 221 (225)
.|++|.-.+. .|- .+.. .|+|.||+.|...|...+..|..|
T Consensus 308 ~CpkC~~~ie~~~GCnhm~C-rC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 308 QCPKCKFMIELSEGCNHMTC-RCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcccceeeeecCCcceEEe-eccccchhhcCcchhhCCccccCc
Confidence 5688866443 332 2333 499999999999998888877443
No 113
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=63.44 E-value=4.6 Score=37.05 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=22.2
Q ss_pred EEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 195 TRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 195 ~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
+.-.|+++||.+|=.---+.-+.||-|-.
T Consensus 347 ~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 347 RCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred EchhccceeeccchHHHHhhhhcCCCcCC
Confidence 33369999999997665566778999964
No 114
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=61.93 E-value=4.1 Score=36.30 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=31.2
Q ss_pred cccccccccccCce-eEEe---CcCCeecHHHHHHHhhc---------CCCCCCcCC
Q 041990 180 LCAICLQEFVVGLQ-VTRL---PCSHIFHGDCVLNWLTK---------SKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~~-~~~l---pC~H~FH~~CI~~WL~~---------~~sCPlCR~ 223 (225)
+|-+|.+++.+... .... -|.-++|..|+..-+.. ...||.|++
T Consensus 184 ~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~ 240 (276)
T KOG3005|consen 184 ECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEK 240 (276)
T ss_pred hhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhc
Confidence 68999999943332 2222 29999999999984432 457999986
No 115
>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=59.39 E-value=3.1 Score=39.06 Aligned_cols=41 Identities=34% Similarity=0.730 Sum_probs=0.0
Q ss_pred cccccccccccCc-----------eeEEeCcCCeecHHHHHHHhhc------CCCCCCcCC
Q 041990 180 LCAICLQEFVVGL-----------QVTRLPCSHIFHGDCVLNWLTK------SKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~-----------~~~~lpC~H~FH~~CI~~WL~~------~~sCPlCR~ 223 (225)
.||+=|.-+..+. .-+-|.|||++.. ..|-.. ..+||+||.
T Consensus 279 QCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~ 336 (416)
T PF04710_consen 279 QCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQ 336 (416)
T ss_dssp -------------------------------------------------------------
T ss_pred CCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCccc
Confidence 4588776554432 2345689999875 468642 558999996
No 116
>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=59.19 E-value=8.5 Score=22.57 Aligned_cols=36 Identities=25% Similarity=0.558 Sum_probs=22.1
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
|+.|-+.+..+.. ....=+..||..|. .|..|+.+|
T Consensus 2 C~~C~~~i~~~~~-~~~~~~~~~H~~Cf--------~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGEL-VLRALGKVWHPECF--------KCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCcE-EEEeCCccccccCC--------CCcccCCcC
Confidence 6788877765422 22234778888774 466676543
No 117
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=52.25 E-value=5.8 Score=40.25 Aligned_cols=41 Identities=20% Similarity=0.586 Sum_probs=29.6
Q ss_pred cccccccccccC----ceeEEeCcCCeecHHHHHHHhhcCCCCCCc
Q 041990 180 LCAICLQEFVVG----LQVTRLPCSHIFHGDCVLNWLTKSKSCPLC 221 (225)
Q Consensus 180 ~C~ICLee~~~g----~~~~~lpC~H~FH~~CI~~WL~~~~sCPlC 221 (225)
.|.-|.+..... ..++++.|+|.||..|+..-..++. |-.|
T Consensus 786 rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 786 RCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred hhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 578998865532 4568889999999999977655544 4433
No 118
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.67 E-value=16 Score=32.51 Aligned_cols=44 Identities=16% Similarity=0.369 Sum_probs=31.0
Q ss_pred ccccccccccccCceeE-EeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 179 CLCAICLQEFVVGLQVT-RLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~-~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
-.|||=--+|.....-. ..+|||+|-..-+.+- +..+|++|-..
T Consensus 112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~ 156 (293)
T KOG3113|consen 112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAA 156 (293)
T ss_pred eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCc
Confidence 36788766665444433 3499999998777664 57889999763
No 119
>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=51.60 E-value=8.7 Score=27.10 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=8.7
Q ss_pred eecHHHHHHHhh
Q 041990 202 IFHGDCVLNWLT 213 (225)
Q Consensus 202 ~FH~~CI~~WL~ 213 (225)
-||+.|+.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 399999999985
No 120
>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=50.27 E-value=4.6 Score=26.75 Aligned_cols=9 Identities=56% Similarity=1.368 Sum_probs=4.3
Q ss_pred CCCCcCCCC
Q 041990 217 SCPLCRSEL 225 (225)
Q Consensus 217 sCPlCR~~l 225 (225)
.||+|.++|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 788887753
No 121
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=49.01 E-value=17 Score=27.22 Aligned_cols=30 Identities=30% Similarity=0.572 Sum_probs=21.3
Q ss_pred cccccccccccCceeEEeC--cCCeecHHHHHHH
Q 041990 180 LCAICLQEFVVGLQVTRLP--CSHIFHGDCVLNW 211 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lp--C~H~FH~~CI~~W 211 (225)
.|.||... .|..+.... |...||..|..+.
T Consensus 57 ~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 57 KCSICGKS--GGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHC
Confidence 68999876 343333333 8889999998664
No 122
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=48.31 E-value=3.3 Score=37.30 Aligned_cols=35 Identities=40% Similarity=0.874 Sum_probs=29.5
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK 214 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~ 214 (225)
.|.+|++++..+.......|--+||..|+..|+.+
T Consensus 216 vC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 (288)
T KOG1729|consen 216 VCDICFEELEKGARGDREDSLPVFHGKCYPNWLTT 250 (288)
T ss_pred ecHHHHHHHhcccccchhhcccccccccccccccc
Confidence 78999999987666666666669999999999976
No 123
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.06 E-value=14 Score=32.75 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=26.1
Q ss_pred ccccccccccCceeEEeCcCCeecHHHHHHHhh
Q 041990 181 CAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLT 213 (225)
Q Consensus 181 C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~ 213 (225)
|+.||+.+..+ +++|=||+|+++||...+.
T Consensus 46 CsLtLqPc~dP---vit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 46 CSLTLQPCRDP---VITPDGYLFDREAILEYIL 75 (303)
T ss_pred eeeecccccCC---ccCCCCeeeeHHHHHHHHH
Confidence 89999988655 7789999999999999874
No 124
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.71 E-value=20 Score=27.94 Aligned_cols=44 Identities=23% Similarity=0.440 Sum_probs=33.2
Q ss_pred cccccccccccCc-----------eeEEeCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 180 LCAICLQEFVVGL-----------QVTRLPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g~-----------~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
.|--|+..|..+. .-..-.|++.|+.+|=.-+-+.-++||-|-.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 4788888776431 1123369999999999888888899999964
No 125
>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=42.36 E-value=5.1 Score=35.67 Aligned_cols=45 Identities=18% Similarity=0.372 Sum_probs=19.8
Q ss_pred ccccccccccccCceeEEe--CcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 179 CLCAICLQEFVVGLQVTRL--PCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~l--pC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
-.||||=..-..+.-...- .=.|.+|.-|-..|--....||.|-.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 3689996543322100000 02567777888889888889999954
No 126
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=42.11 E-value=13 Score=25.58 Aligned_cols=16 Identities=38% Similarity=1.209 Sum_probs=11.6
Q ss_pred HHhhc------CCCCCCcCCCC
Q 041990 210 NWLTK------SKSCPLCRSEL 225 (225)
Q Consensus 210 ~WL~~------~~sCPlCR~~l 225 (225)
.|.+. ...||+|..+|
T Consensus 28 gWmR~nFs~~~~p~CPlC~s~M 49 (59)
T PF14169_consen 28 GWMRDNFSFEEEPVCPLCKSPM 49 (59)
T ss_pred cccccccccCCCccCCCcCCcc
Confidence 47664 45799998865
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.66 E-value=5.2 Score=22.19 Aligned_cols=12 Identities=42% Similarity=0.933 Sum_probs=6.7
Q ss_pred cCCCCCCcCCCC
Q 041990 214 KSKSCPLCRSEL 225 (225)
Q Consensus 214 ~~~sCPlCR~~l 225 (225)
..+.||.|..+|
T Consensus 12 ~~~fC~~CG~~l 23 (23)
T PF13240_consen 12 DAKFCPNCGTPL 23 (23)
T ss_pred cCcchhhhCCcC
Confidence 344566666553
No 128
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.61 E-value=20 Score=21.95 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=15.7
Q ss_pred cccccccccccCc--------eeEEeCcCCeec
Q 041990 180 LCAICLQEFVVGL--------QVTRLPCSHIFH 204 (225)
Q Consensus 180 ~C~ICLee~~~g~--------~~~~lpC~H~FH 204 (225)
+|+=|...|...+ .+....|+|+|+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 4677777666542 344446888885
No 129
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.09 E-value=22 Score=32.60 Aligned_cols=44 Identities=18% Similarity=0.400 Sum_probs=32.3
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhc---CCCCCCcC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK---SKSCPLCR 222 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~---~~sCPlCR 222 (225)
-.||+=-+.-...+...-|.|||+.-..-+.+.-++ ...||.|-
T Consensus 337 FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 367876666555567788899999999888776544 33599994
No 130
>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=37.24 E-value=4.7 Score=28.76 Aligned_cols=38 Identities=29% Similarity=0.523 Sum_probs=19.2
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
.||.|-.++.... +|.+|..|-.. +.....||-|..+|
T Consensus 3 ~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHH
Confidence 4788887764322 56666666543 44566788887764
No 131
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=37.04 E-value=28 Score=31.99 Aligned_cols=28 Identities=29% Similarity=0.826 Sum_probs=22.1
Q ss_pred eCcCCeecHHHHHHHhhc---------CCCCCCcCCC
Q 041990 197 LPCSHIFHGDCVLNWLTK---------SKSCPLCRSE 224 (225)
Q Consensus 197 lpC~H~FH~~CI~~WL~~---------~~sCPlCR~~ 224 (225)
.||+|+--..-..-|-+. +..||.|-..
T Consensus 376 ~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~ 412 (429)
T KOG3842|consen 376 NPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQ 412 (429)
T ss_pred CCcccccchhhhhHhhcCcCCCccccccccCcchhhh
Confidence 489999988888889764 3369999664
No 132
>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=36.55 E-value=22 Score=21.19 Aligned_cols=20 Identities=30% Similarity=0.861 Sum_probs=12.0
Q ss_pred CcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 198 PCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 198 pC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
-|||+|-..- ....||+|..
T Consensus 6 ~CGy~y~~~~------~~~~CP~Cg~ 25 (33)
T cd00350 6 VCGYIYDGEE------APWVCPVCGA 25 (33)
T ss_pred CCCCEECCCc------CCCcCcCCCC
Confidence 3566554432 3457999975
No 133
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=36.19 E-value=17 Score=26.11 Aligned_cols=29 Identities=31% Similarity=0.600 Sum_probs=20.0
Q ss_pred cccccccccccCceeEEe--CcCCeecHHHHHH
Q 041990 180 LCAICLQEFVVGLQVTRL--PCSHIFHGDCVLN 210 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~l--pC~H~FH~~CI~~ 210 (225)
.|.+|-... |-.+... .|.-.||..|..+
T Consensus 38 ~C~~C~~~~--Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 38 KCSICKKKG--GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCcCCCCCC--CeEEEEeCCCCCcEEChHHHcc
Confidence 689998652 3222222 5999999999865
No 134
>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=35.44 E-value=22 Score=24.28 Aligned_cols=35 Identities=17% Similarity=0.395 Sum_probs=17.6
Q ss_pred cccccccccccccCcee-EEeCcCCeecHHHHHHHh
Q 041990 178 QCLCAICLQEFVVGLQV-TRLPCSHIFHGDCVLNWL 212 (225)
Q Consensus 178 ~c~C~ICLee~~~g~~~-~~lpC~H~FH~~CI~~WL 212 (225)
...|.+|...|..-..- -.-.||++|+..|.....
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 34689999999654322 223699999999986554
No 135
>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=32.52 E-value=33 Score=19.75 Aligned_cols=29 Identities=21% Similarity=0.437 Sum_probs=10.4
Q ss_pred cccccccccccCceeEEeCcCCeecHHHH
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCV 208 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI 208 (225)
.|.+|-.....+..-....|.-.+|..|+
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 36888777654223344579999999886
No 136
>PF10572 UPF0556: Uncharacterised protein family UPF0556; InterPro: IPR018887 This family of proteins has no known function.
Probab=31.89 E-value=55 Score=26.94 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=20.3
Q ss_pred chhhhcccccccccccccccceEEEEEEEeeeeC
Q 041990 7 DYCEIWAENAKSIEDEVRASVTFSLVFHVSFIHL 40 (225)
Q Consensus 7 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~ 40 (225)
+.|+|||++ .+|-.||-+|++...-.
T Consensus 75 ~sC~I~RPq--------gkSYL~F~qFkaev~G~ 100 (158)
T PF10572_consen 75 YSCIIWRPQ--------GKSYLFFTQFKAEVKGA 100 (158)
T ss_pred eEEEEECCC--------CCcEEEEEEEEEEEecc
Confidence 459999982 37789999999877654
No 137
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.72 E-value=7.8 Score=34.30 Aligned_cols=44 Identities=25% Similarity=0.551 Sum_probs=34.1
Q ss_pred cccccccccccC-c--eeEEeC--------cCCeecHHHHHHHhhcC-CCCCCcCC
Q 041990 180 LCAICLQEFVVG-L--QVTRLP--------CSHIFHGDCVLNWLTKS-KSCPLCRS 223 (225)
Q Consensus 180 ~C~ICLee~~~g-~--~~~~lp--------C~H~FH~~CI~~WL~~~-~sCPlCR~ 223 (225)
.|.||...+... . ....+. |+|..+..|+..-+.+. -.||.||.
T Consensus 209 ~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~ 264 (296)
T KOG4185|consen 209 LCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTW 264 (296)
T ss_pred HHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccc
Confidence 589999998832 2 224445 99999999999998764 48999985
No 138
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.93 E-value=52 Score=24.95 Aligned_cols=34 Identities=21% Similarity=0.342 Sum_probs=28.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhc
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTK 214 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~ 214 (225)
.|.||-..+..|++-+-++ .-..|++|+..=..+
T Consensus 8 kC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~ 41 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRK 41 (103)
T ss_pred eEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhc
Confidence 5899999999999988888 778899999775443
No 139
>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=29.88 E-value=14 Score=21.06 Aligned_cols=22 Identities=27% Similarity=0.469 Sum_probs=12.4
Q ss_pred cccccccccccCceeEEeC-cCCee
Q 041990 180 LCAICLQEFVVGLQVTRLP-CSHIF 203 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lp-C~H~F 203 (225)
.||-|-..+.. ....-| |||.|
T Consensus 2 ~CP~C~~~V~~--~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE--SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh--hcCcCCCCCCCC
Confidence 36777766542 233334 77766
No 140
>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=29.39 E-value=25 Score=22.76 Aligned_cols=12 Identities=25% Similarity=0.556 Sum_probs=5.9
Q ss_pred cccccccccccC
Q 041990 180 LCAICLQEFVVG 191 (225)
Q Consensus 180 ~C~ICLee~~~g 191 (225)
.|..|-..+..+
T Consensus 28 ~C~~C~~~l~~~ 39 (58)
T PF00412_consen 28 KCSKCGKPLNDG 39 (58)
T ss_dssp BETTTTCBTTTS
T ss_pred ccCCCCCccCCC
Confidence 455555554443
No 141
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=29.37 E-value=38 Score=22.33 Aligned_cols=23 Identities=26% Similarity=0.783 Sum_probs=13.6
Q ss_pred CcCCeecHHHHHHHhhcCCCCCCc
Q 041990 198 PCSHIFHGDCVLNWLTKSKSCPLC 221 (225)
Q Consensus 198 pC~H~FH~~CI~~WL~~~~sCPlC 221 (225)
.|+|.|-..=- .-......||.|
T Consensus 33 ~Cgh~w~~~v~-~R~~~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKASVN-DRTRRGKGCPYC 55 (55)
T ss_pred CCCCeeEccHh-hhccCCCCCCCC
Confidence 36776665422 222456789998
No 142
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=29.06 E-value=39 Score=20.62 Aligned_cols=25 Identities=32% Similarity=0.654 Sum_probs=15.9
Q ss_pred cccccccccccCc--------eeEEeCcCCeec
Q 041990 180 LCAICLQEFVVGL--------QVTRLPCSHIFH 204 (225)
Q Consensus 180 ~C~ICLee~~~g~--------~~~~lpC~H~FH 204 (225)
.||-|-..|.... .++.-.|+|+|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 4677877776543 333345888885
No 143
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.40 E-value=60 Score=23.43 Aligned_cols=42 Identities=24% Similarity=0.470 Sum_probs=27.5
Q ss_pred ccccccccccCce-eEEeCcCCeecHHHHHHHhhcCCCCCCcCCC
Q 041990 181 CAICLQEFVVGLQ-VTRLPCSHIFHGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 181 C~ICLee~~~g~~-~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~ 224 (225)
|--|-.++..++. +.+..=.|.||.+|...- -+..||.|-.+
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~--l~g~CPnCGGe 50 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENR--LHGLCPNCGGE 50 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHh--hcCcCCCCCch
Confidence 3446666655433 333344789999998753 47789999654
No 144
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.87 E-value=19 Score=34.08 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=25.1
Q ss_pred cccccccccccCce---eEE--eCcCCeecHHHHHHHhhc
Q 041990 180 LCAICLQEFVVGLQ---VTR--LPCSHIFHGDCVLNWLTK 214 (225)
Q Consensus 180 ~C~ICLee~~~g~~---~~~--lpC~H~FH~~CI~~WL~~ 214 (225)
.||.|...++.... ... .+|.|.||..|+..|-..
T Consensus 228 ~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 228 ECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred cCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 58999987765431 122 259999999998888654
No 145
>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=26.73 E-value=48 Score=25.24 Aligned_cols=24 Identities=33% Similarity=0.739 Sum_probs=19.2
Q ss_pred CCeecHHHHHHHhhc---------CCCCCCcCC
Q 041990 200 SHIFHGDCVLNWLTK---------SKSCPLCRS 223 (225)
Q Consensus 200 ~H~FH~~CI~~WL~~---------~~sCPlCR~ 223 (225)
.-.||..||..++.. +-.||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 788999999998753 336999984
No 146
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=25.98 E-value=32 Score=34.46 Aligned_cols=26 Identities=38% Similarity=1.002 Sum_probs=21.1
Q ss_pred CcCCeecHHHHHHHhhc---CC--CCCCcCC
Q 041990 198 PCSHIFHGDCVLNWLTK---SK--SCPLCRS 223 (225)
Q Consensus 198 pC~H~FH~~CI~~WL~~---~~--sCPlCR~ 223 (225)
.|+-.||..|+.-|++. .+ .||-||.
T Consensus 40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 58999999999999875 22 4888874
No 147
>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=25.69 E-value=42 Score=21.79 Aligned_cols=34 Identities=24% Similarity=0.474 Sum_probs=24.4
Q ss_pred cccccccccccCcee-EEeCcCCeecHHHHHHHhh
Q 041990 180 LCAICLQEFVVGLQV-TRLPCSHIFHGDCVLNWLT 213 (225)
Q Consensus 180 ~C~ICLee~~~g~~~-~~lpC~H~FH~~CI~~WL~ 213 (225)
.|.+|-..|...... ....||++|+..|......
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 479998888764322 2236999999999876654
No 148
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.61 E-value=35 Score=25.66 Aligned_cols=12 Identities=33% Similarity=0.872 Sum_probs=10.3
Q ss_pred eecHHHHHHHhh
Q 041990 202 IFHGDCVLNWLT 213 (225)
Q Consensus 202 ~FH~~CI~~WL~ 213 (225)
-||+.|+.+|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 488999999986
No 149
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=24.27 E-value=64 Score=23.56 Aligned_cols=45 Identities=20% Similarity=0.494 Sum_probs=18.8
Q ss_pred cccccccccccCce----eEEeCcCCeecHHHHHHHhhc-CCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQ----VTRLPCSHIFHGDCVLNWLTK-SKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~----~~~lpC~H~FH~~CI~~WL~~-~~sCPlCR~~ 224 (225)
.|.||=+++..... +...-|+--.|+.|..-=.+. +..||-|+.+
T Consensus 11 iCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 11 ICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B
T ss_pred ccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCC
Confidence 57999988764321 334468888888997654443 7789999864
No 150
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=24.14 E-value=21 Score=33.18 Aligned_cols=44 Identities=30% Similarity=0.561 Sum_probs=23.2
Q ss_pred cccccccccccCceeEEe---CcCCeec--------HHHHHHHh-----hcCCCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRL---PCSHIFH--------GDCVLNWL-----TKSKSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~l---pC~H~FH--------~~CI~~WL-----~~~~sCPlCR~~ 224 (225)
.||+|=+..+.=.. ..| .|+-.|. +.|+..-- ..++.||.||+.
T Consensus 17 lCPVCGDkVSGYHY-GLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 17 LCPVCGDKVSGYHY-GLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccCcccccee-eeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 57999776543222 223 4555443 34443211 014569999973
No 151
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=24.02 E-value=24 Score=38.45 Aligned_cols=45 Identities=29% Similarity=0.478 Sum_probs=35.6
Q ss_pred cccccccccccCceeEEeCcCCeecHHHHHHHhhcC----CCCCCcCCC
Q 041990 180 LCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKS----KSCPLCRSE 224 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~----~sCPlCR~~ 224 (225)
.|.||.........+...-|.-.||.-|+..-+... =.||-||.+
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchh
Confidence 689999887665555555799999999999988763 379999864
No 152
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=23.75 E-value=41 Score=28.83 Aligned_cols=20 Identities=30% Similarity=0.760 Sum_probs=14.5
Q ss_pred HHHHHHHhh-cCCCCCCcCCC
Q 041990 205 GDCVLNWLT-KSKSCPLCRSE 224 (225)
Q Consensus 205 ~~CI~~WL~-~~~sCPlCR~~ 224 (225)
..||.+-=. ..+-||+||-+
T Consensus 97 ktCIrkn~~~~gnpCPICRDe 117 (239)
T KOG4021|consen 97 KTCIRKNGRFLGNPCPICRDE 117 (239)
T ss_pred hHHHhhcCeecCCCCCccccc
Confidence 568887543 46789999963
No 153
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=23.57 E-value=44 Score=34.55 Aligned_cols=24 Identities=33% Similarity=1.007 Sum_probs=19.6
Q ss_pred CeecHHHHHHHhhcC--CCCCCcCCC
Q 041990 201 HIFHGDCVLNWLTKS--KSCPLCRSE 224 (225)
Q Consensus 201 H~FH~~CI~~WL~~~--~sCPlCR~~ 224 (225)
..-|.+|+..|+.-+ ..|-+|.++
T Consensus 39 kYiH~eCL~eW~~~s~~~kCdiChy~ 64 (1175)
T COG5183 39 KYIHRECLMEWMECSGTKKCDICHYE 64 (1175)
T ss_pred HHHHHHHHHHHHhcCCCcceeeecce
Confidence 456899999999864 469999875
No 154
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.40 E-value=38 Score=30.70 Aligned_cols=35 Identities=20% Similarity=0.359 Sum_probs=26.2
Q ss_pred cccccccccccCceeEEeC--cCCeecHHHHHHHhhcC
Q 041990 180 LCAICLQEFVVGLQVTRLP--CSHIFHGDCVLNWLTKS 215 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~lp--C~H~FH~~CI~~WL~~~ 215 (225)
.|.+|.|-++.-.- +..| =+|.||..|-+.-++.+
T Consensus 270 cCTLC~ERLEDTHF-VQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 270 CCTLCHERLEDTHF-VQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred eehhhhhhhccCce-eecCCCcccceecccCHHHHHhh
Confidence 58999998876433 2222 38999999999988763
No 155
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.12 E-value=30 Score=21.76 Aligned_cols=26 Identities=27% Similarity=0.470 Sum_probs=14.5
Q ss_pred eCcCCeecHHHHHHHhhcCCCCCCcCC
Q 041990 197 LPCSHIFHGDCVLNWLTKSKSCPLCRS 223 (225)
Q Consensus 197 lpC~H~FH~~CI~~WL~~~~sCPlCR~ 223 (225)
..|+|.|-..--..= .....||.|..
T Consensus 9 ~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 9 EECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred CCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 458888874211000 12447999987
No 156
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=22.11 E-value=44 Score=18.89 Aligned_cols=7 Identities=43% Similarity=1.388 Sum_probs=3.8
Q ss_pred CCCCcCC
Q 041990 217 SCPLCRS 223 (225)
Q Consensus 217 sCPlCR~ 223 (225)
.||+|-+
T Consensus 3 ~CPiC~~ 9 (26)
T smart00734 3 QCPVCFR 9 (26)
T ss_pred cCCCCcC
Confidence 3666644
No 157
>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=21.75 E-value=61 Score=28.24 Aligned_cols=21 Identities=24% Similarity=0.667 Sum_probs=14.8
Q ss_pred cHHHHHHHhhcCCCCCCcCCC
Q 041990 204 HGDCVLNWLTKSKSCPLCRSE 224 (225)
Q Consensus 204 H~~CI~~WL~~~~sCPlCR~~ 224 (225)
|..|-.+--++-..||+|+..
T Consensus 197 C~sC~qqIHRNAPiCPlCK~K 217 (230)
T PF10146_consen 197 CQSCHQQIHRNAPICPLCKAK 217 (230)
T ss_pred hHhHHHHHhcCCCCCcccccc
Confidence 456665555677899999864
No 158
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.46 E-value=21 Score=28.81 Aligned_cols=48 Identities=27% Similarity=0.538 Sum_probs=24.4
Q ss_pred ccccccccccc-ccccCceeEEeCcCCeecHHHHHHHhhc-CC---CCCCcCC
Q 041990 176 RQQCLCAICLQ-EFVVGLQVTRLPCSHIFHGDCVLNWLTK-SK---SCPLCRS 223 (225)
Q Consensus 176 ~~~c~C~ICLe-e~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~---sCPlCR~ 223 (225)
+++..|.||+. .|..|---...=|.-.||..|--+--.+ ++ .|-+||.
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRK 115 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcH
Confidence 44557999986 4555522222223444555554433222 22 4778775
No 159
>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=20.20 E-value=77 Score=28.45 Aligned_cols=41 Identities=27% Similarity=0.570 Sum_probs=27.6
Q ss_pred cccccccccccCceeEEe--CcCCeecHHHHHHHh-hcCCCCCC
Q 041990 180 LCAICLQEFVVGLQVTRL--PCSHIFHGDCVLNWL-TKSKSCPL 220 (225)
Q Consensus 180 ~C~ICLee~~~g~~~~~l--pC~H~FH~~CI~~WL-~~~~sCPl 220 (225)
-|.||++.--.|.....| .=+=.=|++|..+|- -.+..||.
T Consensus 32 fChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~pr 75 (285)
T PF06937_consen 32 FCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCPR 75 (285)
T ss_pred ecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCCc
Confidence 689999977666443333 223345699999994 34777884
No 160
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.09 E-value=33 Score=22.59 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=14.4
Q ss_pred eEEe-CcCCeecHHHHHHH
Q 041990 194 VTRL-PCSHIFHGDCVLNW 211 (225)
Q Consensus 194 ~~~l-pC~H~FH~~CI~~W 211 (225)
.+.- .|+|.||..|...|
T Consensus 40 ~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eeECCCCCCeECCCCCCcC
Confidence 3444 69999999998888
No 161
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=20.03 E-value=59 Score=24.32 Aligned_cols=35 Identities=17% Similarity=0.537 Sum_probs=24.9
Q ss_pred ccccccccccccCceeEEeCcCCeecHHHHHHHhhcCCCCCCcCCCC
Q 041990 179 CLCAICLQEFVVGLQVTRLPCSHIFHGDCVLNWLTKSKSCPLCRSEL 225 (225)
Q Consensus 179 c~C~ICLee~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCPlCR~~l 225 (225)
..|.||-..... =+|.||..|..+ ...|.+|-..|
T Consensus 45 ~~C~~CK~~v~q--------~g~~YCq~CAYk----kGiCamCGKki 79 (90)
T PF10235_consen 45 SKCKICKTKVHQ--------PGAKYCQTCAYK----KGICAMCGKKI 79 (90)
T ss_pred cccccccccccc--------CCCccChhhhcc----cCcccccCCee
Confidence 357999755432 368899999654 77899997653
Done!