Query 037450
Match_columns 224
No_of_seqs 196 out of 1614
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 12:23:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4628 Predicted E3 ubiquitin 99.6 1.7E-16 3.8E-21 141.5 6.7 68 156-223 205-279 (348)
2 PF13639 zf-RING_2: Ring finge 99.6 5.7E-16 1.2E-20 99.2 2.0 44 175-218 1-44 (44)
3 COG5243 HRD1 HRD ubiquitin lig 99.4 1E-13 2.3E-18 123.2 6.3 50 172-221 285-344 (491)
4 COG5540 RING-finger-containing 99.4 1.1E-13 2.3E-18 120.3 4.1 52 172-223 321-373 (374)
5 PF12678 zf-rbx1: RING-H2 zinc 99.3 1.1E-12 2.3E-17 93.1 3.5 46 173-218 18-73 (73)
6 KOG0828 Predicted E3 ubiquitin 99.3 1.2E-12 2.5E-17 120.1 3.8 142 14-223 470-635 (636)
7 PHA02929 N1R/p28-like protein; 99.3 1.9E-12 4E-17 111.0 4.4 65 158-222 150-227 (238)
8 KOG0317 Predicted E3 ubiquitin 99.1 6.5E-11 1.4E-15 102.6 5.3 49 172-223 237-285 (293)
9 PLN03208 E3 ubiquitin-protein 99.1 7.9E-11 1.7E-15 97.5 4.2 49 172-223 16-80 (193)
10 PF13920 zf-C3HC4_3: Zinc fing 99.1 6.7E-11 1.5E-15 77.6 3.0 47 173-222 1-48 (50)
11 cd00162 RING RING-finger (Real 99.0 1.9E-10 4.1E-15 72.2 3.7 44 176-221 1-45 (45)
12 PF13923 zf-C3HC4_2: Zinc fing 99.0 1.5E-10 3.2E-15 72.1 3.0 39 177-217 1-39 (39)
13 KOG0802 E3 ubiquitin ligase [P 98.9 2.7E-10 5.9E-15 108.6 2.1 50 172-221 289-340 (543)
14 KOG0823 Predicted E3 ubiquitin 98.9 5.7E-10 1.2E-14 94.1 3.4 49 172-223 45-96 (230)
15 PF15227 zf-C3HC4_4: zinc fing 98.9 9.8E-10 2.1E-14 69.7 3.0 38 177-217 1-42 (42)
16 PF14634 zf-RING_5: zinc-RING 98.9 1.2E-09 2.5E-14 69.9 3.3 44 176-219 1-44 (44)
17 smart00504 Ubox Modified RING 98.9 2.5E-09 5.5E-14 72.8 4.1 45 175-222 2-46 (63)
18 KOG0320 Predicted E3 ubiquitin 98.9 1.3E-09 2.8E-14 88.6 2.9 51 172-223 129-179 (187)
19 PHA02926 zinc finger-like prot 98.9 1.4E-09 3.1E-14 91.3 3.3 50 172-221 168-229 (242)
20 PF12861 zf-Apc11: Anaphase-pr 98.8 2.4E-09 5.1E-14 77.5 3.5 51 172-222 19-82 (85)
21 PF00097 zf-C3HC4: Zinc finger 98.8 3.2E-09 6.9E-14 66.5 3.2 39 177-217 1-41 (41)
22 smart00184 RING Ring finger. E 98.8 5.7E-09 1.2E-13 63.1 3.2 38 177-217 1-39 (39)
23 KOG1734 Predicted RING-contain 98.8 4E-09 8.7E-14 90.7 2.7 58 164-222 215-281 (328)
24 TIGR00599 rad18 DNA repair pro 98.7 1.3E-08 2.7E-13 93.3 3.5 48 172-222 24-71 (397)
25 COG5574 PEX10 RING-finger-cont 98.5 5.1E-08 1.1E-12 83.8 3.1 49 172-223 213-263 (271)
26 KOG1785 Tyrosine kinase negati 98.5 2.9E-08 6.3E-13 89.6 1.7 150 62-222 260-416 (563)
27 PF13445 zf-RING_UBOX: RING-ty 98.5 7.4E-08 1.6E-12 61.3 2.6 38 177-215 1-43 (43)
28 KOG0287 Postreplication repair 98.4 6.1E-08 1.3E-12 85.9 1.1 48 172-222 21-68 (442)
29 COG5194 APC11 Component of SCF 98.4 2.3E-07 5E-12 65.9 3.2 32 190-221 48-80 (88)
30 smart00744 RINGv The RING-vari 98.4 3.3E-07 7.1E-12 60.0 3.1 42 176-218 1-49 (49)
31 PF04564 U-box: U-box domain; 98.3 2.6E-07 5.7E-12 65.3 2.5 48 173-223 3-51 (73)
32 KOG2164 Predicted E3 ubiquitin 98.3 4.5E-07 9.8E-12 84.3 3.1 48 173-223 185-237 (513)
33 KOG1493 Anaphase-promoting com 98.2 3E-07 6.5E-12 64.8 0.2 50 172-221 18-80 (84)
34 COG5219 Uncharacterized conser 98.2 4.6E-07 1E-11 89.1 0.6 51 172-222 1467-1523(1525)
35 KOG2177 Predicted E3 ubiquitin 98.2 7.5E-07 1.6E-11 76.0 1.7 44 172-218 11-54 (386)
36 COG5432 RAD18 RING-finger-cont 98.2 9.2E-07 2E-11 77.1 2.1 47 172-221 23-69 (391)
37 KOG2930 SCF ubiquitin ligase, 98.1 1.7E-06 3.7E-11 64.4 2.3 49 172-220 44-106 (114)
38 PF11793 FANCL_C: FANCL C-term 98.0 7.4E-07 1.6E-11 62.6 -1.0 49 174-222 2-66 (70)
39 KOG4265 Predicted E3 ubiquitin 97.9 9.7E-06 2.1E-10 72.6 3.3 47 173-222 289-336 (349)
40 PF14835 zf-RING_6: zf-RING of 97.9 2.5E-06 5.5E-11 58.5 -0.6 46 172-221 5-50 (65)
41 KOG0804 Cytoplasmic Zn-finger 97.8 7E-06 1.5E-10 75.4 1.7 49 172-222 173-222 (493)
42 KOG0311 Predicted E3 ubiquitin 97.7 4.1E-06 8.8E-11 74.9 -1.7 49 172-223 41-91 (381)
43 KOG1039 Predicted E3 ubiquitin 97.6 2.9E-05 6.2E-10 70.1 2.3 50 172-221 159-220 (344)
44 KOG0825 PHD Zn-finger protein 97.6 1.5E-05 3.2E-10 77.5 -0.4 50 172-221 121-170 (1134)
45 KOG4159 Predicted E3 ubiquitin 97.4 8.3E-05 1.8E-09 68.4 2.2 48 172-222 82-129 (398)
46 KOG4445 Uncharacterized conser 97.4 5.4E-05 1.2E-09 66.5 0.8 51 172-222 113-186 (368)
47 KOG0297 TNF receptor-associate 97.2 0.00018 4E-09 66.3 2.2 50 171-222 18-67 (391)
48 KOG0978 E3 ubiquitin ligase in 97.1 0.00014 3.1E-09 70.7 0.7 50 171-223 640-690 (698)
49 PF11789 zf-Nse: Zinc-finger o 97.0 0.00037 8.1E-09 46.9 1.9 43 172-216 9-53 (57)
50 KOG4172 Predicted E3 ubiquitin 97.0 0.00017 3.7E-09 47.8 0.2 46 173-221 6-53 (62)
51 KOG1941 Acetylcholine receptor 97.0 0.00022 4.7E-09 64.8 0.6 48 172-219 363-413 (518)
52 KOG2879 Predicted E3 ubiquitin 96.6 0.0018 3.9E-08 56.4 3.4 49 172-222 237-287 (298)
53 KOG2660 Locus-specific chromos 96.5 0.00063 1.4E-08 60.6 -0.1 48 172-221 13-60 (331)
54 PF05883 Baculo_RING: Baculovi 96.4 0.0013 2.8E-08 51.6 0.9 39 174-212 26-70 (134)
55 PF14570 zf-RING_4: RING/Ubox 96.3 0.0019 4.1E-08 41.9 1.4 43 177-220 1-46 (48)
56 KOG0801 Predicted E3 ubiquitin 96.2 0.0017 3.6E-08 52.6 0.7 30 172-201 175-204 (205)
57 COG5152 Uncharacterized conser 96.2 0.0017 3.8E-08 54.1 0.8 44 174-220 196-239 (259)
58 KOG1428 Inhibitor of type V ad 96.1 0.0041 8.8E-08 64.6 3.2 51 172-222 3484-3544(3738)
59 KOG3970 Predicted E3 ubiquitin 96.1 0.0059 1.3E-07 51.9 3.5 49 172-221 48-104 (299)
60 KOG1814 Predicted E3 ubiquitin 96.0 0.0038 8.2E-08 57.2 2.3 47 172-218 182-236 (445)
61 PF10367 Vps39_2: Vacuolar sor 96.0 0.0033 7.2E-08 46.7 1.4 33 172-205 76-108 (109)
62 PHA03096 p28-like protein; Pro 95.9 0.0042 9.1E-08 54.9 1.8 45 175-219 179-231 (284)
63 PF12906 RINGv: RING-variant d 95.8 0.0055 1.2E-07 39.6 1.7 40 177-217 1-47 (47)
64 PHA02825 LAP/PHD finger-like p 95.7 0.0095 2.1E-07 48.1 3.2 46 172-221 6-58 (162)
65 KOG1571 Predicted E3 ubiquitin 95.7 0.0069 1.5E-07 54.6 2.6 48 168-221 299-346 (355)
66 KOG0826 Predicted E3 ubiquitin 95.6 0.023 5.1E-07 50.7 5.5 45 172-218 298-342 (357)
67 KOG0827 Predicted E3 ubiquitin 95.5 0.00078 1.7E-08 61.2 -4.1 51 172-222 194-245 (465)
68 KOG1002 Nucleotide excision re 95.5 0.0057 1.2E-07 57.8 1.4 48 172-222 534-586 (791)
69 KOG1952 Transcription factor N 95.5 0.008 1.7E-07 59.5 2.3 48 172-219 189-244 (950)
70 PHA02862 5L protein; Provision 95.3 0.015 3.3E-07 46.2 3.0 48 174-221 2-52 (156)
71 KOG1813 Predicted E3 ubiquitin 95.2 0.0068 1.5E-07 53.4 0.7 44 175-221 242-285 (313)
72 KOG4692 Predicted E3 ubiquitin 95.1 0.022 4.8E-07 51.5 3.6 48 172-222 420-467 (489)
73 COG5236 Uncharacterized conser 95.0 0.028 6.1E-07 50.7 4.0 46 172-220 59-106 (493)
74 COG5222 Uncharacterized conser 94.7 0.02 4.3E-07 50.7 2.3 43 174-219 274-318 (427)
75 PF14447 Prok-RING_4: Prokaryo 94.6 0.021 4.6E-07 38.0 1.6 45 174-223 7-51 (55)
76 KOG3039 Uncharacterized conser 94.2 0.047 1E-06 47.1 3.4 51 172-222 219-270 (303)
77 KOG2817 Predicted E3 ubiquitin 94.1 0.13 2.8E-06 47.2 6.1 49 172-220 332-383 (394)
78 PF08746 zf-RING-like: RING-li 93.9 0.029 6.3E-07 35.5 1.2 41 177-217 1-43 (43)
79 KOG2114 Vacuolar assembly/sort 93.7 0.034 7.4E-07 55.2 1.7 44 173-221 839-882 (933)
80 KOG1940 Zn-finger protein [Gen 93.5 0.04 8.7E-07 48.5 1.7 47 173-219 157-204 (276)
81 KOG2034 Vacuolar sorting prote 92.7 0.049 1.1E-06 54.3 1.2 36 172-208 815-850 (911)
82 KOG1001 Helicase-like transcri 92.6 0.044 9.6E-07 54.0 0.8 43 175-221 455-499 (674)
83 KOG3268 Predicted E3 ubiquitin 92.4 0.086 1.9E-06 43.5 2.1 51 172-222 163-228 (234)
84 PF04641 Rtf2: Rtf2 RING-finge 91.5 0.22 4.7E-06 43.4 3.7 50 172-222 111-161 (260)
85 PF03854 zf-P11: P-11 zinc fin 91.2 0.07 1.5E-06 34.5 0.2 32 193-224 16-48 (50)
86 KOG4275 Predicted E3 ubiquitin 91.1 0.039 8.5E-07 48.7 -1.3 41 174-221 300-341 (350)
87 KOG3053 Uncharacterized conser 90.9 0.11 2.4E-06 45.1 1.2 49 172-220 18-80 (293)
88 KOG2932 E3 ubiquitin ligase in 90.6 0.11 2.5E-06 46.2 1.2 44 174-221 90-133 (389)
89 PF14446 Prok-RING_1: Prokaryo 90.1 0.33 7.2E-06 32.2 2.7 34 173-206 4-38 (54)
90 KOG0298 DEAD box-containing he 90.0 0.079 1.7E-06 54.9 -0.4 47 172-220 1151-1197(1394)
91 KOG0309 Conserved WD40 repeat- 89.9 0.19 4.2E-06 49.6 2.2 41 175-216 1029-1069(1081)
92 PF14369 zf-RING_3: zinc-finge 88.6 0.19 4.2E-06 30.3 0.7 17 20-36 18-35 (35)
93 KOG2807 RNA polymerase II tran 88.2 0.52 1.1E-05 42.4 3.4 57 164-220 320-376 (378)
94 KOG1812 Predicted E3 ubiquitin 87.2 0.24 5.3E-06 45.7 0.8 40 172-211 144-184 (384)
95 PF10272 Tmpp129: Putative tra 86.5 0.44 9.5E-06 43.5 2.0 28 195-222 311-351 (358)
96 KOG3002 Zn finger protein [Gen 85.2 0.7 1.5E-05 41.3 2.7 45 171-222 45-91 (299)
97 PF05290 Baculo_IE-1: Baculovi 85.0 0.75 1.6E-05 36.2 2.4 50 172-223 78-133 (140)
98 PF02891 zf-MIZ: MIZ/SP-RING z 84.7 0.39 8.4E-06 31.3 0.6 43 175-220 3-50 (50)
99 COG5175 MOT2 Transcriptional r 84.6 0.6 1.3E-05 42.2 2.0 50 172-221 12-63 (480)
100 KOG0802 E3 ubiquitin ligase [P 82.8 0.59 1.3E-05 45.0 1.3 43 172-221 477-519 (543)
101 KOG1100 Predicted E3 ubiquitin 81.7 0.74 1.6E-05 39.0 1.3 39 177-222 161-200 (207)
102 KOG4362 Transcriptional regula 81.5 0.37 8E-06 47.3 -0.7 48 172-222 19-69 (684)
103 KOG1609 Protein involved in mR 81.1 0.86 1.9E-05 40.0 1.6 48 174-221 78-133 (323)
104 COG5220 TFB3 Cdk activating ki 77.1 1.3 2.8E-05 38.3 1.4 47 172-218 8-60 (314)
105 KOG4718 Non-SMC (structural ma 76.4 1.4 3E-05 37.4 1.3 45 172-218 179-223 (235)
106 KOG3899 Uncharacterized conser 75.7 1.6 3.4E-05 38.9 1.5 27 195-221 325-364 (381)
107 KOG1829 Uncharacterized conser 75.3 1 2.2E-05 43.6 0.3 44 172-218 509-557 (580)
108 KOG0269 WD40 repeat-containing 75.0 2.7 5.8E-05 41.8 3.0 42 174-216 779-820 (839)
109 COG5109 Uncharacterized conser 72.9 2.9 6.2E-05 37.6 2.5 48 172-219 334-384 (396)
110 smart00249 PHD PHD zinc finger 71.9 2.6 5.7E-05 25.5 1.5 31 176-206 1-31 (47)
111 PF07975 C1_4: TFIIH C1-like d 70.9 2.4 5.3E-05 27.8 1.2 42 177-218 2-50 (51)
112 COG5183 SSM4 Protein involved 69.6 3.2 7E-05 41.7 2.3 49 172-221 10-65 (1175)
113 PF13901 DUF4206: Domain of un 69.6 3.6 7.9E-05 34.5 2.3 43 172-219 150-197 (202)
114 KOG2066 Vacuolar assembly/sort 66.2 2.4 5.1E-05 42.4 0.6 45 172-217 782-830 (846)
115 PF00628 PHD: PHD-finger; Int 65.6 3 6.5E-05 26.5 0.8 44 176-219 1-50 (51)
116 TIGR00622 ssl1 transcription f 64.6 8 0.00017 29.6 3.1 46 174-219 55-111 (112)
117 KOG0825 PHD Zn-finger protein 63.8 3.2 6.9E-05 41.6 1.0 50 172-221 94-153 (1134)
118 smart00132 LIM Zinc-binding do 62.1 8.9 0.00019 22.2 2.4 38 176-222 1-38 (39)
119 PF07649 C1_3: C1-like domain; 61.1 5.8 0.00013 22.6 1.4 29 176-204 2-30 (30)
120 KOG3161 Predicted E3 ubiquitin 60.2 3.3 7.1E-05 40.6 0.4 41 173-215 10-51 (861)
121 KOG1815 Predicted E3 ubiquitin 60.0 5.4 0.00012 37.4 1.8 38 172-211 68-105 (444)
122 PF13465 zf-H2C2_2: Zinc-finge 58.6 2.3 4.9E-05 23.6 -0.6 16 18-33 10-25 (26)
123 PF13717 zinc_ribbon_4: zinc-r 58.6 5.5 0.00012 24.0 1.0 26 175-200 3-36 (36)
124 KOG1812 Predicted E3 ubiquitin 58.4 4.5 9.8E-05 37.4 0.9 44 173-217 305-351 (384)
125 PF02762 Cbl_N3: CBL proto-onc 57.2 13 0.00027 26.7 2.8 58 62-121 6-64 (86)
126 PF07191 zinc-ribbons_6: zinc- 56.5 3.7 8.1E-05 28.7 0.0 39 175-221 2-40 (70)
127 KOG3579 Predicted E3 ubiquitin 55.8 7.3 0.00016 34.6 1.7 51 172-222 266-328 (352)
128 KOG2068 MOT2 transcription fac 53.5 9 0.00019 34.6 2.0 46 175-221 250-297 (327)
129 PF13719 zinc_ribbon_5: zinc-r 49.1 9.7 0.00021 23.0 1.0 26 175-200 3-36 (37)
130 PF06906 DUF1272: Protein of u 48.9 27 0.00058 23.4 3.2 45 176-222 7-52 (57)
131 KOG3005 GIY-YIG type nuclease 48.0 9.8 0.00021 33.4 1.3 50 172-221 180-242 (276)
132 PF04216 FdhE: Protein involve 46.7 2.3 5.1E-05 37.5 -2.8 48 172-220 170-220 (290)
133 PF06844 DUF1244: Protein of u 46.6 12 0.00027 25.8 1.4 12 198-209 11-22 (68)
134 KOG3842 Adaptor protein Pellin 45.0 21 0.00044 32.3 2.8 50 173-222 340-414 (429)
135 KOG4185 Predicted E3 ubiquitin 44.5 3.8 8.1E-05 36.0 -1.9 46 174-219 207-264 (296)
136 PF06750 DiS_P_DiS: Bacterial 44.4 24 0.00052 25.8 2.7 40 172-223 31-70 (92)
137 PF01363 FYVE: FYVE zinc finge 39.3 13 0.00028 25.1 0.6 37 172-208 7-44 (69)
138 KOG3039 Uncharacterized conser 38.6 24 0.00051 30.9 2.2 36 171-209 40-75 (303)
139 PF15446 zf-PHD-like: PHD/FYVE 38.2 12 0.00025 30.8 0.2 40 5-48 96-146 (175)
140 cd00065 FYVE FYVE domain; Zinc 37.9 24 0.00053 22.6 1.8 36 174-209 2-38 (57)
141 PHA00732 hypothetical protein 37.2 50 0.0011 23.4 3.4 48 21-78 26-73 (79)
142 COG3813 Uncharacterized protei 37.1 22 0.00048 25.1 1.5 24 196-221 28-51 (84)
143 PF03107 C1_2: C1 domain; Int 36.2 23 0.00049 20.2 1.2 28 176-204 2-30 (30)
144 COG4847 Uncharacterized protei 36.0 43 0.00092 24.9 2.8 37 174-211 6-42 (103)
145 KOG1245 Chromatin remodeling c 35.5 12 0.00027 40.2 -0.0 49 172-220 1106-1158(1404)
146 PF13832 zf-HC5HC2H_2: PHD-zin 34.7 38 0.00083 24.9 2.6 33 172-206 53-87 (110)
147 PF00412 LIM: LIM domain; Int 34.7 21 0.00046 22.8 1.0 14 172-185 24-37 (58)
148 PF09723 Zn-ribbon_8: Zinc rib 34.3 13 0.00028 23.0 -0.0 29 190-219 6-34 (42)
149 PF10571 UPF0547: Uncharacteri 33.6 12 0.00027 20.9 -0.2 9 176-184 2-10 (26)
150 PF13913 zf-C2HC_2: zinc-finge 32.1 24 0.00051 19.3 0.8 13 22-34 2-14 (25)
151 PF00096 zf-C2H2: Zinc finger, 30.0 11 0.00024 19.5 -0.8 11 24-34 2-12 (23)
152 KOG2071 mRNA cleavage and poly 29.7 27 0.00058 34.0 1.2 37 172-208 511-557 (579)
153 KOG3113 Uncharacterized conser 28.7 56 0.0012 28.7 2.9 49 172-222 109-158 (293)
154 smart00064 FYVE Protein presen 28.0 44 0.00094 22.4 1.8 37 173-209 9-46 (68)
155 KOG1729 FYVE finger containing 27.7 10 0.00022 33.8 -1.9 41 172-212 212-252 (288)
156 PF14311 DUF4379: Domain of un 27.0 42 0.0009 21.8 1.4 22 195-217 34-55 (55)
157 PF14169 YdjO: Cold-inducible 26.5 35 0.00077 23.0 1.0 12 211-222 39-50 (59)
158 PF14353 CpXC: CpXC protein 26.0 65 0.0014 24.5 2.6 44 175-221 2-48 (128)
159 PRK11827 hypothetical protein; 26.0 24 0.00052 23.9 0.1 18 205-222 2-19 (60)
160 PF04423 Rad50_zn_hook: Rad50 25.3 25 0.00055 22.8 0.1 23 12-34 10-32 (54)
161 PF14569 zf-UDP: Zinc-binding 25.0 73 0.0016 22.8 2.4 49 173-221 8-61 (80)
162 TIGR02605 CxxC_CxxC_SSSS putat 23.3 30 0.00065 22.0 0.2 25 190-219 6-34 (52)
163 PF02318 FYVE_2: FYVE-type zin 22.9 47 0.001 25.2 1.2 46 173-219 53-102 (118)
164 PLN02189 cellulose synthase 22.7 78 0.0017 33.1 3.1 49 173-221 33-86 (1040)
165 PRK03564 formate dehydrogenase 22.4 27 0.00059 31.4 -0.2 46 172-219 185-234 (309)
166 KOG3799 Rab3 effector RIM1 and 22.3 20 0.00044 28.4 -0.9 49 172-220 63-116 (169)
167 cd00350 rubredoxin_like Rubred 22.1 48 0.001 19.2 0.9 12 20-31 15-26 (33)
168 COG3492 Uncharacterized protei 21.8 49 0.0011 24.4 1.1 12 198-209 42-53 (104)
169 KOG1815 Predicted E3 ubiquitin 21.5 29 0.00063 32.5 -0.2 40 172-211 224-268 (444)
170 PF06937 EURL: EURL protein; 21.5 86 0.0019 27.7 2.7 45 172-216 28-75 (285)
171 PF12773 DZR: Double zinc ribb 21.3 67 0.0015 20.1 1.6 11 212-222 30-40 (50)
172 TIGR01562 FdhE formate dehydro 21.1 27 0.00059 31.3 -0.4 47 173-220 183-233 (305)
173 PF10146 zf-C4H2: Zinc finger- 20.9 63 0.0014 27.8 1.8 21 200-220 197-217 (230)
174 KOG3726 Uncharacterized conser 20.7 50 0.0011 32.8 1.2 42 174-218 654-696 (717)
175 PF02591 DUF164: Putative zinc 20.6 49 0.0011 21.5 0.8 27 2-30 26-54 (56)
176 smart00734 ZnF_Rad18 Rad18-lik 20.1 53 0.0011 18.2 0.8 9 213-221 3-11 (26)
177 PF13771 zf-HC5HC2H: PHD-like 20.1 69 0.0015 22.5 1.6 33 172-206 34-68 (90)
No 1
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=1.7e-16 Score=141.49 Aligned_cols=68 Identities=37% Similarity=0.821 Sum_probs=57.6
Q ss_pred ccCChhhhhcCCcccc---cCc---cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC-CCCCcccCCCC
Q 037450 156 AINNKSNVTRLPEKRI---ESE---KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR-SCPLCRNDLPA 223 (224)
Q Consensus 156 ~~~~k~~i~~lp~~~~---~~~---~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~-~CP~CR~~l~~ 223 (224)
....++.+.++|...+ .++ ..|+||+|+|+.|++++.|||+|.||..||++||.+.. .||+||.++++
T Consensus 205 ~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 205 NRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred hhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 3566777888887776 112 38999999999999999999999999999999998885 59999998864
No 2
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.58 E-value=5.7e-16 Score=99.22 Aligned_cols=44 Identities=45% Similarity=1.155 Sum_probs=40.4
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
++|+||+++++.++.+..++|+|.||.+||.+|++.+.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 37999999998888999999999999999999999999999997
No 3
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.45 E-value=1e-13 Score=123.24 Aligned_cols=50 Identities=34% Similarity=0.988 Sum_probs=44.5
Q ss_pred cCccccceeccc-cccC---------CeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDG-IVVG---------QLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~-~~~~---------~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..+..|.||+++ |+.+ .++++|||||++|..|++.|++++++||+||.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence 678899999999 5444 2578999999999999999999999999999985
No 4
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.42 E-value=1.1e-13 Score=120.34 Aligned_cols=52 Identities=38% Similarity=0.979 Sum_probs=48.2
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHh-cCCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLE-KSRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~-~~~~CP~CR~~l~~ 223 (224)
...-+|+|||+.|-.++++++|||+|.||..|+++|+. .++.||+||.++|+
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 45678999999998889999999999999999999998 78899999999986
No 5
>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=1.1e-12 Score=93.11 Aligned_cols=46 Identities=39% Similarity=0.995 Sum_probs=36.9
Q ss_pred CccccceeccccccC----------CeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 173 SEKDCAICLDGIVVG----------QLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 173 ~~~~C~ICle~~~~~----------~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
.+..|+||++.+... -.+...+|+|.||..||..||+.+.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 355699999999321 2355667999999999999999999999998
No 6
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.31 E-value=1.2e-12 Score=120.07 Aligned_cols=142 Identities=23% Similarity=0.470 Sum_probs=90.8
Q ss_pred hhhhhhccCCCCCCCCchhhhhhccccccccCccCCCCCccccccCCcccccchhhhHHHHh--------hHhhhcCcee
Q 037450 14 ILNKVRNQLWDLPNMQPGFIFQLRAHHVINQRATSAKPDTFLYLQADHTLFVTYNNMFHFLS--------NILADEGVTV 85 (224)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~f~~~~~~~lf~t~~~~~~~l~--------~~l~~~~~~~ 85 (224)
+-|++|| |+. +-|-| -|++|+..+|..++-|-+..+.|+....++-.+++.. ++|-.|++
T Consensus 470 v~Nvvrg-~SR-----~Pl~w----~yIlG~Tv~Rl~~plyVF~~s~n~~r~~p~~~f~v~L~lwmlFQv~vLl~Qd~-- 537 (636)
T KOG0828|consen 470 VANVVRG-DSR-----KPLHW----YYILGMTVTRLAIPLYVFGCSENFMRVEPKYFFAVGLVLWMLFQVLVLLVQDY-- 537 (636)
T ss_pred HHHHhcC-CCC-----CCcch----hhhhhHhHHhhhcceEEEecchhhhccCCchhhHHHHHHHHHHHHHHHHHHhh--
Confidence 5688898 554 66899 9999999999777766666677777777754444332 25555554
Q ss_pred cCCC-ccccCCCceeeEecCCCCcccchhhHHHHHHHHHHHHHHHHHHhHhCCCchhhHHhhcCchhhhccccCChhhhh
Q 037450 86 DANG-CFLSDKGLHLLRLDASGGMPIMFPQSVRIYTLTKLVVCVLDYFKRLRTNPSNRFRKFVPIAMDLRMAINNKSNVT 164 (224)
Q Consensus 86 di~g-~f~~~~g~~~l~~d~~gg~~i~~~~~v~i~~l~~l~~~~~~y~~~~~~~~~~~~~r~~~~~~~~~~~~~~k~~i~ 164 (224)
.| |+..++-. +|..+ +|+.... .+..
T Consensus 538 --lGsR~FlPkk~--------------lpe~Y-------------sY~r~l~-----------------------~dh~- 564 (636)
T KOG0828|consen 538 --LGSRCFLPKKF--------------LPEKY-------------SYHRRLQ-----------------------QDHL- 564 (636)
T ss_pred --cccccccchhh--------------Ccccc-------------ccccccc-----------------------cccc-
Confidence 55 44333211 11100 0111100 0000
Q ss_pred cCCcccccCccccceeccccccCC--------------eeEEcCCCCcccHHHHHHHHh-cCCCCCCcccCCCC
Q 037450 165 RLPEKRIESEKDCAICLDGIVVGQ--------------LASCTPCDHVFHKRCIDFWLE-KSRSCPLCRNDLPA 223 (224)
Q Consensus 165 ~lp~~~~~~~~~C~ICle~~~~~~--------------~~~~lpC~H~FH~~CI~~Wl~-~~~~CP~CR~~l~~ 223 (224)
+.-.+...+|+|||..++.-. .++.+||+|+||..|+..|+. .+..||+||.++|+
T Consensus 565 ---~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 565 ---EAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred ---cchhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 001155678999999875311 277889999999999999999 55599999999986
No 7
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.30 E-value=1.9e-12 Score=110.95 Aligned_cols=65 Identities=31% Similarity=0.786 Sum_probs=49.3
Q ss_pred CChhhhhcCCcccc--------cCccccceeccccccCCe-----eEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 158 NNKSNVTRLPEKRI--------ESEKDCAICLDGIVVGQL-----ASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 158 ~~k~~i~~lp~~~~--------~~~~~C~ICle~~~~~~~-----~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
..+..+..+|.... ..+.+|+||++.+...+. ...++|+|.||.+||.+|++.+.+||+||.++.
T Consensus 150 ~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 150 NYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred hhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 35555666665432 457899999998764331 244569999999999999999999999999764
No 8
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.12 E-value=6.5e-11 Score=102.60 Aligned_cols=49 Identities=37% Similarity=0.929 Sum_probs=44.1
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~~ 223 (224)
+.+..|.+|+|.. ..+..+||||+||+.||..|...+..||+||..+++
T Consensus 237 ~a~~kC~LCLe~~---~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 237 EATRKCSLCLENR---SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCCceEEEecCC---CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 5668899999987 456789999999999999999999999999999865
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.09 E-value=7.9e-11 Score=97.51 Aligned_cols=49 Identities=35% Similarity=0.818 Sum_probs=41.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhc----------------CCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEK----------------SRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~----------------~~~CP~CR~~l~~ 223 (224)
.++.+|+||++.++ .+.+++|+|.||..||..|+.. ...||+||..+..
T Consensus 16 ~~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 56789999999884 5577899999999999999853 2479999998853
No 10
>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=99.09 E-value=6.7e-11 Score=77.62 Aligned_cols=47 Identities=28% Similarity=0.889 Sum_probs=39.8
Q ss_pred CccccceeccccccCCeeEEcCCCCc-ccHHHHHHHHhcCCCCCCcccCCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHV-FHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
++..|.||++.. ..+..+||+|. |+.+|+..|++....||+||+++.
T Consensus 1 ~~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 1 EDEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp -HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CcCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 357899999986 45788999999 999999999999999999999874
No 11
>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=99.05 E-value=1.9e-10 Score=72.17 Aligned_cols=44 Identities=43% Similarity=1.117 Sum_probs=36.8
Q ss_pred ccceeccccccCCeeEEcCCCCcccHHHHHHHHhc-CCCCCCcccCC
Q 037450 176 DCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEK-SRSCPLCRNDL 221 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~-~~~CP~CR~~l 221 (224)
+|+||++.+. +....++|+|.||..|++.|++. +..||.||..+
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 5999999982 44555669999999999999998 67899999864
No 12
>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=99.04 E-value=1.5e-10 Score=72.11 Aligned_cols=39 Identities=49% Similarity=1.127 Sum_probs=33.1
Q ss_pred cceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~C 217 (224)
|+||++.+. +.+..++|||.||.+||..|++.+..||+|
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 899999885 344789999999999999999998899998
No 13
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=2.7e-10 Score=108.62 Aligned_cols=50 Identities=38% Similarity=0.979 Sum_probs=44.6
Q ss_pred cCccccceeccccccCCe--eEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQL--ASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~--~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..+..|+||+|++..+.. ++++||+|+||..|+..|++++++||+||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 568899999999976544 78999999999999999999999999999843
No 14
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.93 E-value=5.7e-10 Score=94.13 Aligned_cols=49 Identities=33% Similarity=0.761 Sum_probs=42.4
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC---CCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR---SCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~---~CP~CR~~l~~ 223 (224)
....+|.||+|.- ++++++.|||.||+-||.+||+.+. .||+||..+..
T Consensus 45 ~~~FdCNICLd~a---kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDLA---KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeecccc---CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 6788999999975 5678899999999999999998765 69999998754
No 15
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.90 E-value=9.8e-10 Score=69.68 Aligned_cols=38 Identities=37% Similarity=0.926 Sum_probs=30.4
Q ss_pred cceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC----CCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR----SCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~----~CP~C 217 (224)
|+||++.| .+++.|+|||.|+..||..|.+... .||.|
T Consensus 1 CpiC~~~~---~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF---KDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB----SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh---CCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999 6788999999999999999987653 59987
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.90 E-value=1.2e-09 Score=69.89 Aligned_cols=44 Identities=32% Similarity=0.816 Sum_probs=38.7
Q ss_pred ccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCccc
Q 037450 176 DCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
.|+||++.|.....+..++|+|+||..|+..+......||+||+
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 59999999965667889999999999999999866778999985
No 17
>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=2.5e-09 Score=72.85 Aligned_cols=45 Identities=22% Similarity=0.417 Sum_probs=40.4
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
..|+||.+.++ .+..++|||+|+.+||..|++.+.+||+|+.++.
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 47999999985 3578899999999999999999889999999875
No 18
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.86 E-value=1.3e-09 Score=88.63 Aligned_cols=51 Identities=35% Similarity=0.800 Sum_probs=43.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~~ 223 (224)
+....|+|||+.++.. .+..+.|||+||+.||+.-++....||+||..|..
T Consensus 129 ~~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 5568899999998632 23558899999999999999999999999987753
No 19
>PHA02926 zinc finger-like protein; Provisional
Probab=98.86 E-value=1.4e-09 Score=91.34 Aligned_cols=50 Identities=30% Similarity=0.877 Sum_probs=38.0
Q ss_pred cCccccceeccccccC----C-eeEEc-CCCCcccHHHHHHHHhcC------CCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVG----Q-LASCT-PCDHVFHKRCIDFWLEKS------RSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~----~-~~~~l-pC~H~FH~~CI~~Wl~~~------~~CP~CR~~l 221 (224)
..+.+|+||+|..-.. + ....| +|+|.||..||..|.+.+ .+||+||..+
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f 229 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRF 229 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCccee
Confidence 6688999999976321 1 12344 599999999999999854 3599999875
No 20
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.84 E-value=2.4e-09 Score=77.53 Aligned_cols=51 Identities=31% Similarity=0.720 Sum_probs=39.1
Q ss_pred cCccccceecccccc--------CC-eeEE-cCCCCcccHHHHHHHHhcC---CCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVV--------GQ-LASC-TPCDHVFHKRCIDFWLEKS---RSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~--------~~-~~~~-lpC~H~FH~~CI~~Wl~~~---~~CP~CR~~l~ 222 (224)
..++.|.||...|+. |+ .+.+ -.|+|.||..||.+|++++ ..||+||++..
T Consensus 19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 458889999999862 22 2333 3499999999999999863 58999999753
No 21
>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=98.82 E-value=3.2e-09 Score=66.48 Aligned_cols=39 Identities=44% Similarity=1.060 Sum_probs=33.0
Q ss_pred cceeccccccCCeeEEcCCCCcccHHHHHHHHh--cCCCCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCDHVFHKRCIDFWLE--KSRSCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~--~~~~CP~C 217 (224)
|+||++.++ +....++|+|.||.+||..|++ ....||+|
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999985 3335899999999999999999 44579998
No 22
>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=98.78 E-value=5.7e-09 Score=63.11 Aligned_cols=38 Identities=39% Similarity=1.149 Sum_probs=33.1
Q ss_pred cceeccccccCCeeEEcCCCCcccHHHHHHHHh-cCCCCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCDHVFHKRCIDFWLE-KSRSCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~-~~~~CP~C 217 (224)
|+||++.. ..+..++|+|.||..|++.|++ .+..||+|
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 78999984 5678899999999999999998 55679987
No 23
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.75 E-value=4e-09 Score=90.73 Aligned_cols=58 Identities=36% Similarity=0.781 Sum_probs=45.1
Q ss_pred hcCCcccccCccccceeccccccCC-------eeEEcCCCCcccHHHHHHH--HhcCCCCCCcccCCC
Q 037450 164 TRLPEKRIESEKDCAICLDGIVVGQ-------LASCTPCDHVFHKRCIDFW--LEKSRSCPLCRNDLP 222 (224)
Q Consensus 164 ~~lp~~~~~~~~~C~ICle~~~~~~-------~~~~lpC~H~FH~~CI~~W--l~~~~~CP~CR~~l~ 222 (224)
+.+|++. .++..|+||-..+.... ..-+|.|+|+||..||..| +.++++||.|++.+.
T Consensus 215 ~glPtkh-l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 215 SGLPTKH-LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CCCCCCC-CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3555544 56788999998775433 4567899999999999999 457789999998764
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=98.67 E-value=1.3e-08 Score=93.26 Aligned_cols=48 Identities=33% Similarity=0.699 Sum_probs=42.6
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
+....|+||++.|. .++.++|+|.||..||..|+.....||+||..+.
T Consensus 24 e~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 24 DTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred ccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 66789999999984 4567899999999999999998889999999864
No 25
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.53 E-value=5.1e-08 Score=83.80 Aligned_cols=49 Identities=37% Similarity=0.967 Sum_probs=42.6
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHH-HHhcCCC-CCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDF-WLEKSRS-CPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~-Wl~~~~~-CP~CR~~l~~ 223 (224)
..+..|+||++.. +.+..+||+|+||..||-. |-.++.. ||+||+.+.+
T Consensus 213 ~~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 213 LADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccccceeeeeccc---CCcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 5688999999987 5678899999999999999 9887776 9999997754
No 26
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=98.53 E-value=2.9e-08 Score=89.58 Aligned_cols=150 Identities=18% Similarity=0.338 Sum_probs=96.2
Q ss_pred ccccchhhhHHHHhhHhhhcCceecCCCccccCCCce-eeEecCCCCcccchhhHHHHHHHHHHHHHHHHHHhHhCCCch
Q 037450 62 TLFVTYNNMFHFLSNILADEGVTVDANGCFLSDKGLH-LLRLDASGGMPIMFPQSVRIYTLTKLVVCVLDYFKRLRTNPS 140 (224)
Q Consensus 62 ~lf~t~~~~~~~l~~~l~~~~~~~di~g~f~~~~g~~-~l~~d~~gg~~i~~~~~v~i~~l~~l~~~~~~y~~~~~~~~~ 140 (224)
..|.||+++.+-|.......|..+.+.+|... |+| +......|.+...||....++....-..--+.|..-.+....
T Consensus 260 mAFLTYDEVk~RLqk~~~KpGSYIFRlSCTRl--GQWAIGYVt~dG~IlQTIP~NKpL~QaL~eG~keGFYlyPdGr~~n 337 (563)
T KOG1785|consen 260 MAFLTYDEVKARLQKYIKKPGSYIFRLSCTRL--GQWAIGYVTADGNILQTIPQNKPLFQALLEGHKEGFYLYPDGRDQN 337 (563)
T ss_pred eEEeeHHHHHHHHHHHhcCCCceEEeeccCcc--cceeEEEEcCCCceeeccCCCcHHHHHHHhccccceEECCCCccCC
Confidence 57999999999999999999999998887655 488 777788999998998876554442211111222222222211
Q ss_pred hhHHhhcCchhhhccccCChhhhhc----CCcccccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhc--CCCC
Q 037450 141 NRFRKFVPIAMDLRMAINNKSNVTR----LPEKRIESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEK--SRSC 214 (224)
Q Consensus 141 ~~~~r~~~~~~~~~~~~~~k~~i~~----lp~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~--~~~C 214 (224)
.++... ..+++...-.+.. +-.+....-.-|.||-|. ++.++.-||||..|..|+..|-.. .++|
T Consensus 338 pdLt~l------~~~~p~d~i~VtqEQyeLYceMgsTFeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~C 408 (563)
T KOG1785|consen 338 PDLTGL------CQPPPQDRIKVTQEQYELYCEMGSTFELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTC 408 (563)
T ss_pred CChhhc------cCCCcccceeeeHHHHHHHHHccchHHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCC
Confidence 122111 1112222211111 111111556679999885 356788999999999999999754 4699
Q ss_pred CCcccCCC
Q 037450 215 PLCRNDLP 222 (224)
Q Consensus 215 P~CR~~l~ 222 (224)
|.||.+|.
T Consensus 409 PFCRcEIK 416 (563)
T KOG1785|consen 409 PFCRCEIK 416 (563)
T ss_pred CceeeEec
Confidence 99999873
No 27
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=7.4e-08 Score=61.34 Aligned_cols=38 Identities=37% Similarity=0.832 Sum_probs=23.0
Q ss_pred cceecccccc-CCeeEEcCCCCcccHHHHHHHHhcCC----CCC
Q 037450 177 CAICLDGIVV-GQLASCTPCDHVFHKRCIDFWLEKSR----SCP 215 (224)
Q Consensus 177 C~ICle~~~~-~~~~~~lpC~H~FH~~CI~~Wl~~~~----~CP 215 (224)
|+||.| |.. ...+++|+|||+|+.+||+.+++.+. .||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 643 44578999999999999999998542 576
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.43 E-value=6.1e-08 Score=85.93 Aligned_cols=48 Identities=29% Similarity=0.722 Sum_probs=44.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.....|.||.|.| ..++.+||+|.||.-||...|..+..||.|+.++.
T Consensus 21 D~lLRC~IC~eyf---~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 21 DDLLRCGICFEYF---NIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT 68 (442)
T ss_pred HHHHHHhHHHHHh---cCceeccccchHHHHHHHHHhccCCCCCceecccc
Confidence 5677899999999 56789999999999999999999999999998875
No 29
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.40 E-value=2.3e-07 Score=65.91 Aligned_cols=32 Identities=38% Similarity=0.847 Sum_probs=27.8
Q ss_pred eEEcC-CCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 190 ASCTP-CDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 190 ~~~lp-C~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
+.... |+|.||..||..||..+..||++|++.
T Consensus 48 ~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w 80 (88)
T COG5194 48 PVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTW 80 (88)
T ss_pred eEEEEecchHHHHHHHHHHHhhCCCCCCCCcee
Confidence 34444 999999999999999999999999864
No 30
>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=98.36 E-value=3.3e-07 Score=59.98 Aligned_cols=42 Identities=29% Similarity=0.796 Sum_probs=33.9
Q ss_pred ccceeccccccCCeeEEcCCC-----CcccHHHHHHHHhcCC--CCCCcc
Q 037450 176 DCAICLDGIVVGQLASCTPCD-----HVFHKRCIDFWLEKSR--SCPLCR 218 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~Wl~~~~--~CP~CR 218 (224)
.|.||++ .+.++.+...||. |.+|.+|+..|+..+. +||+|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3899999 3344566789985 8999999999997654 899995
No 31
>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=98.35 E-value=2.6e-07 Score=65.31 Aligned_cols=48 Identities=25% Similarity=0.472 Sum_probs=38.1
Q ss_pred CccccceeccccccCCeeEEcCCCCcccHHHHHHHHhc-CCCCCCcccCCCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEK-SRSCPLCRNDLPA 223 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~-~~~CP~CR~~l~~ 223 (224)
+...|+|+.+.| ..++.+|+||.|...||..|++. ..+||+|+.++..
T Consensus 3 ~~f~CpIt~~lM---~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELM---RDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB----SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHh---hCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 467899999999 56788999999999999999999 7799999998754
No 32
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.28 E-value=4.5e-07 Score=84.29 Aligned_cols=48 Identities=33% Similarity=0.782 Sum_probs=38.7
Q ss_pred CccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC-----CCCCCcccCCCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS-----RSCPLCRNDLPA 223 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~-----~~CP~CR~~l~~ 223 (224)
.+..||||++.. ..+..+.|||+||..||-..+... ..||+||..|..
T Consensus 185 t~~~CPICL~~~---~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 185 TDMQCPICLEPP---SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred cCCcCCcccCCC---CcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 388999999976 455667799999999998877655 269999998754
No 33
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=3e-07 Score=64.82 Aligned_cols=50 Identities=32% Similarity=0.744 Sum_probs=37.8
Q ss_pred cCccccceecccccc--------C-CeeEEcC-CCCcccHHHHHHHHhcCC---CCCCcccCC
Q 037450 172 ESEKDCAICLDGIVV--------G-QLASCTP-CDHVFHKRCIDFWLEKSR---SCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~--------~-~~~~~lp-C~H~FH~~CI~~Wl~~~~---~CP~CR~~l 221 (224)
..+++|.||.-.|.. | +.+.++. |.|.||.-||.+|+.... .||+||++.
T Consensus 18 ~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 18 APDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred CCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 445689999988842 2 2344444 999999999999997544 699999875
No 34
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.17 E-value=4.6e-07 Score=89.08 Aligned_cols=51 Identities=33% Similarity=0.929 Sum_probs=39.9
Q ss_pred cCccccceeccccccCC----eeEEcCCCCcccHHHHHHHHhcCC--CCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQ----LASCTPCDHVFHKRCIDFWLEKSR--SCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~----~~~~lpC~H~FH~~CI~~Wl~~~~--~CP~CR~~l~ 222 (224)
...++||||...+..-+ .-++-.|.|.||..|+.+|.+++. +||+||.++|
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 67889999998774111 113334999999999999998765 7999999986
No 35
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=7.5e-07 Score=76.02 Aligned_cols=44 Identities=36% Similarity=0.780 Sum_probs=38.8
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
.+...|+||++.|... +.+||+|.||..||..+......||.||
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 5788999999999644 8899999999999999988556899999
No 36
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.15 E-value=9.2e-07 Score=77.14 Aligned_cols=47 Identities=36% Similarity=0.697 Sum_probs=41.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.....|-||-+.| ..+..++|+|.||.-||...|..+.-||+||++.
T Consensus 23 Ds~lrC~IC~~~i---~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 23 DSMLRCRICDCRI---SIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred hhHHHhhhhhhee---ecceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 5677899999998 4557789999999999999999999999999864
No 37
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=1.7e-06 Score=64.44 Aligned_cols=49 Identities=33% Similarity=0.733 Sum_probs=37.1
Q ss_pred cCccccceecccc-------------ccCCeeEEcC-CCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 172 ESEKDCAICLDGI-------------VVGQLASCTP-CDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~-------------~~~~~~~~lp-C~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
...+.|+||..-+ ..++...... |+|.||.-||..||++++.||+|..+
T Consensus 44 i~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 44 IVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred eeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence 4567899987533 1123344444 99999999999999999999999765
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.01 E-value=7.4e-07 Score=62.62 Aligned_cols=49 Identities=29% Similarity=0.842 Sum_probs=23.0
Q ss_pred ccccceeccccc-cCCe--eEEc--CCCCcccHHHHHHHHhcC----C-------CCCCcccCCC
Q 037450 174 EKDCAICLDGIV-VGQL--ASCT--PCDHVFHKRCIDFWLEKS----R-------SCPLCRNDLP 222 (224)
Q Consensus 174 ~~~C~ICle~~~-~~~~--~~~l--pC~H~FH~~CI~~Wl~~~----~-------~CP~CR~~l~ 222 (224)
+.+|.||++.+. .++. +..- .|++.||..||..|+... . .||.|+++|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 468999999865 3332 2222 499999999999998631 1 4999999874
No 39
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=9.7e-06 Score=72.62 Aligned_cols=47 Identities=30% Similarity=0.751 Sum_probs=40.2
Q ss_pred CccccceeccccccCCeeEEcCCCCc-ccHHHHHHHHhcCCCCCCcccCCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHV-FHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
...+|.||+.+- ....+|||+|. .|.+|.+..--+++.||+||+++.
T Consensus 289 ~gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 367899999986 45678999998 699999998888889999999874
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.85 E-value=2.5e-06 Score=58.46 Aligned_cols=46 Identities=28% Similarity=0.707 Sum_probs=23.6
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
++...|++|.+.++ +.+....|.|+||+.||..-+. ..||+|+.+-
T Consensus 5 e~lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Pa 50 (65)
T PF14835_consen 5 EELLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPA 50 (65)
T ss_dssp HHTTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT--TB-SSS--B-
T ss_pred HHhcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC--CCCCCcCChH
Confidence 45678999999985 3344566999999999988544 4599998763
No 41
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.83 E-value=7e-06 Score=75.35 Aligned_cols=49 Identities=29% Similarity=0.703 Sum_probs=38.0
Q ss_pred cCccccceeccccccCC-eeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.+.-+|+||+|.+.... -+..+.|.|.||..|+..|-. .+||+||.-..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence 56778999999985432 235566999999999999954 57999997543
No 42
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=4.1e-06 Score=74.86 Aligned_cols=49 Identities=33% Similarity=0.579 Sum_probs=39.8
Q ss_pred cCccccceeccccccCCeeEEcC-CCCcccHHHHHHHHhcC-CCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTP-CDHVFHKRCIDFWLEKS-RSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~Wl~~~-~~CP~CR~~l~~ 223 (224)
..+.-|+||++.++ ..+.++ |.|.||.+||..-++.. +.||.||..+.+
T Consensus 41 ~~~v~c~icl~llk---~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 41 DIQVICPICLSLLK---KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhhhccHHHHHHHH---hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 67888999999985 334444 99999999998888765 589999998754
No 43
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=2.9e-05 Score=70.15 Aligned_cols=50 Identities=40% Similarity=0.868 Sum_probs=37.0
Q ss_pred cCccccceeccccccCC--e--eEEcC-CCCcccHHHHHHHH--hc-----CCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQ--L--ASCTP-CDHVFHKRCIDFWL--EK-----SRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~--~--~~~lp-C~H~FH~~CI~~Wl--~~-----~~~CP~CR~~l 221 (224)
..+..|.||+|..-... . -..+| |.|.||..||..|- .+ ...||.||...
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 56889999999764221 0 12345 99999999999998 44 45799999753
No 44
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.56 E-value=1.5e-05 Score=77.47 Aligned_cols=50 Identities=24% Similarity=0.543 Sum_probs=42.2
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.....|++|+..+-.+.....-+|+|.||..||..|-+..++||+||.++
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF 170 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF 170 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence 45667888888876655556677999999999999999999999999875
No 45
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=8.3e-05 Score=68.42 Aligned_cols=48 Identities=38% Similarity=0.877 Sum_probs=42.7
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
..+..|.||+..+ ..+.++||||.||..||+.-+.+...||.||.+++
T Consensus 82 ~sef~c~vc~~~l---~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRAL---YPPVVTPCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhc---CCCccccccccccHHHHHHHhccCCCCcccccccc
Confidence 6788999999988 45677899999999999998888889999999875
No 46
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.38 E-value=5.4e-05 Score=66.48 Aligned_cols=51 Identities=31% Similarity=0.797 Sum_probs=41.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHH------------------hc-----CCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWL------------------EK-----SRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl------------------~~-----~~~CP~CR~~l~ 222 (224)
.....|.||+--|..++...+++|-|.||..|+...| +. ...||+||..|.
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 4466899999999988889999999999999987755 21 226999999874
No 47
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.19 E-value=0.00018 Score=66.26 Aligned_cols=50 Identities=28% Similarity=0.660 Sum_probs=41.8
Q ss_pred ccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 171 IESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 171 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
..++..|++|...+.+.. ..+.|+|.||..|+..|+..++.||.|+.++.
T Consensus 18 ~~~~l~C~~C~~vl~~p~--~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~ 67 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPV--QTTTCGHRFCAGCLLESLSNHQKCPVCRQELT 67 (391)
T ss_pred CcccccCccccccccCCC--CCCCCCCcccccccchhhccCcCCcccccccc
Confidence 367889999999985332 22589999999999999999999999988764
No 48
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00014 Score=70.66 Aligned_cols=50 Identities=28% Similarity=0.624 Sum_probs=41.0
Q ss_pred ccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC-CCCCcccCCCC
Q 037450 171 IESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR-SCPLCRNDLPA 223 (224)
Q Consensus 171 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~-~CP~CR~~l~~ 223 (224)
+..-..|++|-... .....+.|+|.||..||.+-+..++ .||.|...+.+
T Consensus 640 yK~~LkCs~Cn~R~---Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 640 YKELLKCSVCNTRW---KDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred HHhceeCCCccCch---hhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 37788999999766 3445566999999999999998776 79999998753
No 49
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.03 E-value=0.00037 Score=46.95 Aligned_cols=43 Identities=23% Similarity=0.581 Sum_probs=28.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC--CCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS--RSCPL 216 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~--~~CP~ 216 (224)
.....|+|.+..|+ +-++...|+|+|-.+.|..|++.+ ..||+
T Consensus 9 ~~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 44678999999996 445667899999999999999443 36998
No 50
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00017 Score=47.82 Aligned_cols=46 Identities=22% Similarity=0.539 Sum_probs=33.0
Q ss_pred CccccceeccccccCCeeEEcCCCCc-ccHHHH-HHHHhcCCCCCCcccCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHV-FHKRCI-DFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI-~~Wl~~~~~CP~CR~~l 221 (224)
.+.+|.||+|.- ..-....|+|. .|.+|- ..|-..+..||+||.++
T Consensus 6 ~~dECTICye~p---vdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi 53 (62)
T KOG4172|consen 6 WSDECTICYEHP---VDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI 53 (62)
T ss_pred cccceeeeccCc---chHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence 347899999954 22234459997 577775 55655788999999976
No 51
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.99 E-value=0.00022 Score=64.82 Aligned_cols=48 Identities=40% Similarity=0.863 Sum_probs=40.0
Q ss_pred cCccccceeccccccCC-eeEEcCCCCcccHHHHHHHHhcCC--CCCCccc
Q 037450 172 ESEKDCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWLEKSR--SCPLCRN 219 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl~~~~--~CP~CR~ 219 (224)
+.+.-|..|-|.+-..+ ....|||.|+||..|+...|.++. +||.||+
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 55778999999886543 456799999999999999998775 7999994
No 52
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.63 E-value=0.0018 Score=56.45 Aligned_cols=49 Identities=22% Similarity=0.531 Sum_probs=37.8
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC--CCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS--RSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~--~~CP~CR~~l~ 222 (224)
..+.+|++|-+.-. ......+|+|+||-.||..-.... .+||.|-++++
T Consensus 237 t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCC--CCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 56789999988642 223345699999999999876644 58999998875
No 53
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.50 E-value=0.00063 Score=60.57 Aligned_cols=48 Identities=31% Similarity=0.685 Sum_probs=39.4
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.....|.+|-..|- +.....-|-|.||..||-..+....+||.|...+
T Consensus 13 n~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~i 60 (331)
T KOG2660|consen 13 NPHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLEESKYCPTCDIVI 60 (331)
T ss_pred ccceehhhccceee--cchhHHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence 56778999999984 2223344999999999999999999999998755
No 54
>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=96.37 E-value=0.0013 Score=51.64 Aligned_cols=39 Identities=21% Similarity=0.434 Sum_probs=30.5
Q ss_pred ccccceeccccccCCeeEEcCCC------CcccHHHHHHHHhcCC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCD------HVFHKRCIDFWLEKSR 212 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~------H~FH~~CI~~Wl~~~~ 212 (224)
..+|+||++.+..++-+..++|+ |.||.+|++.|-+.+.
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~ 70 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERN 70 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhcc
Confidence 67899999999774445666775 9999999999954333
No 55
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.33 E-value=0.0019 Score=41.93 Aligned_cols=43 Identities=26% Similarity=0.621 Sum_probs=22.1
Q ss_pred cceeccccccCCeeEEcC--CCCcccHHHHHHHHh-cCCCCCCcccC
Q 037450 177 CAICLDGIVVGQLASCTP--CDHVFHKRCIDFWLE-KSRSCPLCRND 220 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lp--C~H~FH~~CI~~Wl~-~~~~CP~CR~~ 220 (224)
|++|.+++...+ ....| |++..+..|...-++ ....||-||++
T Consensus 1 cp~C~e~~d~~d-~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETD-KDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCC-TT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCC-CccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 789999984333 24466 899999999888876 46689999985
No 56
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.20 E-value=0.0017 Score=52.57 Aligned_cols=30 Identities=30% Similarity=0.834 Sum_probs=28.1
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccH
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHK 201 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~ 201 (224)
....+|.||+|+++.++.+..|||-.+||+
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 667899999999999999999999999996
No 57
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.19 E-value=0.0017 Score=54.11 Aligned_cols=44 Identities=25% Similarity=0.506 Sum_probs=37.4
Q ss_pred ccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
-..|.||.++| +.+.++.|||.||..|.-.-.+....|-+|-..
T Consensus 196 PF~C~iCKkdy---~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 196 PFLCGICKKDY---ESPVVTECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred ceeehhchhhc---cchhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence 34799999999 456788899999999998888888899999653
No 58
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.13 E-value=0.0041 Score=64.56 Aligned_cols=51 Identities=31% Similarity=0.749 Sum_probs=37.8
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC----------CCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR----------SCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~----------~CP~CR~~l~ 222 (224)
..++.|.||+.+--.......|.|+|+||..|....|+.+- +||+|+.++.
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 55777888887643333456788999999999977665443 6999998764
No 59
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0059 Score=51.94 Aligned_cols=49 Identities=22% Similarity=0.680 Sum_probs=40.2
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC--------CCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS--------RSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~--------~~CP~CR~~l 221 (224)
..+..|..|-..+..|+.++ |-|-|.||.+|++.|-..- ..||-|-.+|
T Consensus 48 DY~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 34567999999998888755 6799999999999997642 2699998876
No 60
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.05 E-value=0.0038 Score=57.22 Aligned_cols=47 Identities=30% Similarity=0.629 Sum_probs=37.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC--------CCCCCcc
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS--------RSCPLCR 218 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~--------~~CP~CR 218 (224)
.....|.||+++..-......+||+|.||..|+....... ..||-+.
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 6788999999997544778899999999999999987532 2587654
No 61
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=95.98 E-value=0.0033 Score=46.68 Aligned_cols=33 Identities=27% Similarity=0.655 Sum_probs=28.5
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHH
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCID 205 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~ 205 (224)
.++..|++|-..+.. ....+.||+|+||..|++
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 778889999999865 567789999999999975
No 62
>PHA03096 p28-like protein; Provisional
Probab=95.86 E-value=0.0042 Score=54.92 Aligned_cols=45 Identities=31% Similarity=0.601 Sum_probs=32.6
Q ss_pred cccceeccccccC----CeeEEcC-CCCcccHHHHHHHHhcCC---CCCCccc
Q 037450 175 KDCAICLDGIVVG----QLASCTP-CDHVFHKRCIDFWLEKSR---SCPLCRN 219 (224)
Q Consensus 175 ~~C~ICle~~~~~----~~~~~lp-C~H~FH~~CI~~Wl~~~~---~CP~CR~ 219 (224)
..|.||+|..... .....|+ |.|.||..||..|...+. +||.||.
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 6899999976532 1234566 999999999999976543 4655554
No 63
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.81 E-value=0.0055 Score=39.56 Aligned_cols=40 Identities=35% Similarity=1.042 Sum_probs=27.1
Q ss_pred cceeccccccCCeeEEcCCC-----CcccHHHHHHHHhcC--CCCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCD-----HVFHKRCIDFWLEKS--RSCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~Wl~~~--~~CP~C 217 (224)
|-||++.-+... ....||. -.-|.+|+..|+..+ .+|++|
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 678998765444 5678865 367999999999854 479987
No 64
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.74 E-value=0.0095 Score=48.08 Aligned_cols=46 Identities=30% Similarity=0.747 Sum_probs=34.5
Q ss_pred cCccccceeccccccCCeeEEcCCCC-----cccHHHHHHHHhcCC--CCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDH-----VFHKRCIDFWLEKSR--SCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H-----~FH~~CI~~Wl~~~~--~CP~CR~~l 221 (224)
..+..|=||.++-. + ..-||.- .-|.+|++.|+..+. .|++|+.+.
T Consensus 6 ~~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 6 LMDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 45678999998843 2 2358654 449999999998665 799998864
No 65
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.71 E-value=0.0069 Score=54.62 Aligned_cols=48 Identities=29% Similarity=0.657 Sum_probs=34.7
Q ss_pred cccccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 168 EKRIESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 168 ~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.........|.||+++.+ ...-+||||.-| |..-- +...+||+||..+
T Consensus 299 ~~~~~~p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI 346 (355)
T KOG1571|consen 299 FRELPQPDLCVVCLDEPK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRI 346 (355)
T ss_pred ccccCCCCceEEecCCcc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHH
Confidence 333456778999999874 367899999966 65543 2334599999876
No 66
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=95.63 E-value=0.023 Score=50.75 Aligned_cols=45 Identities=20% Similarity=0.370 Sum_probs=35.5
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
.....|+||+...++.. ...--|-+||..||-..+..++.||+=-
T Consensus 298 ~~~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~ 342 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVVNYGHCPVTG 342 (357)
T ss_pred CccccChhHHhccCCCc--eEEecceEEeHHHHHHHHHhcCCCCccC
Confidence 56788999999875332 2222699999999999999999999743
No 67
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.53 E-value=0.00078 Score=61.19 Aligned_cols=51 Identities=27% Similarity=0.658 Sum_probs=43.6
Q ss_pred cCccccceeccccccC-CeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVG-QLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~-~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.-...|+||.+.++.. +....+-|+|++|.+||.+||.....||.||.+|+
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~ 245 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELP 245 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence 3456799999998755 45666779999999999999999999999999886
No 68
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.53 E-value=0.0057 Score=57.76 Aligned_cols=48 Identities=29% Similarity=0.727 Sum_probs=38.6
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhc-----CCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEK-----SRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~-----~~~CP~CR~~l~ 222 (224)
.++.+|.+|.+.- +.+....|.|.||.-||..+... +.+||.|-..|.
T Consensus 534 k~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 534 KGEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred cCceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 6678899999865 56778899999999999888652 348999977654
No 69
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.49 E-value=0.008 Score=59.48 Aligned_cols=48 Identities=38% Similarity=0.902 Sum_probs=36.8
Q ss_pred cCccccceeccccccCCee-EEcCCCCcccHHHHHHHHhcCC-------CCCCccc
Q 037450 172 ESEKDCAICLDGIVVGQLA-SCTPCDHVFHKRCIDFWLEKSR-------SCPLCRN 219 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~CI~~Wl~~~~-------~CP~CR~ 219 (224)
....+|.||.+.+.....+ ....|=|+||..||..|-++.. .||.|+.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 6788999999998644322 2334779999999999987532 5999984
No 70
>PHA02862 5L protein; Provisional
Probab=95.33 E-value=0.015 Score=46.17 Aligned_cols=48 Identities=27% Similarity=0.636 Sum_probs=31.3
Q ss_pred ccccceeccccccCCee-EEcCCCCcccHHHHHHHHhcCC--CCCCcccCC
Q 037450 174 EKDCAICLDGIVVGQLA-SCTPCDHVFHKRCIDFWLEKSR--SCPLCRNDL 221 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~-~~lpC~H~FH~~CI~~Wl~~~~--~CP~CR~~l 221 (224)
+..|=||.++-+++..+ ....-...-|.+|+..|+..+. .||+|+.+.
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY 52 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY 52 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence 45799999974322100 0000025789999999998655 799999864
No 71
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.21 E-value=0.0068 Score=53.38 Aligned_cols=44 Identities=25% Similarity=0.470 Sum_probs=38.1
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..|-||.+.| ..++++.|+|.||..|-..-++....|++|-...
T Consensus 242 f~c~icr~~f---~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 242 FKCFICRKYF---YRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred cccccccccc---ccchhhcCCceeehhhhccccccCCcceeccccc
Confidence 4599999999 4567889999999999998888889999997654
No 72
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.07 E-value=0.022 Score=51.45 Aligned_cols=48 Identities=27% Similarity=0.589 Sum_probs=41.5
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.++..|+||...- ...+-.||+|.=|.+||.+-+-..+.|=.|+..+.
T Consensus 420 sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 6788999998743 45678999999999999999999999999998653
No 73
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.02 E-value=0.028 Score=50.72 Aligned_cols=46 Identities=30% Similarity=0.740 Sum_probs=38.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHH--HhcCCCCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFW--LEKSRSCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~W--l~~~~~CP~CR~~ 220 (224)
+++..|-||-+.+ .-..++||+|..|.-|.-.. |...+.||+||.+
T Consensus 59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 59 EENMNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred cccceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 6778899999876 34568999999999998553 6778899999985
No 74
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.72 E-value=0.02 Score=50.69 Aligned_cols=43 Identities=30% Similarity=0.617 Sum_probs=34.5
Q ss_pred ccccceeccccccCCeeEEcC-CCCcccHHHHHHHHh-cCCCCCCccc
Q 037450 174 EKDCAICLDGIVVGQLASCTP-CDHVFHKRCIDFWLE-KSRSCPLCRN 219 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~Wl~-~~~~CP~CR~ 219 (224)
...|+.|.-.+. .++++| |+|.||.+||..-|. ....||.|-.
T Consensus 274 ~LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 274 SLKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred cccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 378999998873 456677 999999999987654 5568999965
No 75
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.59 E-value=0.021 Score=38.03 Aligned_cols=45 Identities=27% Similarity=0.676 Sum_probs=33.0
Q ss_pred ccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCCC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLPA 223 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~~ 223 (224)
...|-.|... +.+-.++||+|..+..|.+. +.-+.||+|-.++..
T Consensus 7 ~~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFV---GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEF 51 (55)
T ss_pred ceeEEEcccc---ccccccccccceeeccccCh--hhccCCCCCCCcccC
Confidence 3345556553 34567899999999999766 456689999988754
No 76
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.25 E-value=0.047 Score=47.13 Aligned_cols=51 Identities=20% Similarity=0.345 Sum_probs=42.2
Q ss_pred cCccccceeccccccCCee-EEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLA-SCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.....|+||.+.+.+.-.. ..-||+|+|+.+|.+..+..-..||+|-.++.
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plk 270 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLK 270 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCc
Confidence 3567899999999765443 44559999999999999999999999988764
No 77
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.09 E-value=0.13 Score=47.18 Aligned_cols=49 Identities=18% Similarity=0.345 Sum_probs=41.7
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC---CCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR---SCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~---~CP~CR~~ 220 (224)
.....|||=.+.=.+.+.++.|.|||+...+-|..-.+... .||.|-.+
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 67889999888777777899999999999999999877554 69999654
No 78
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=93.93 E-value=0.029 Score=35.51 Aligned_cols=41 Identities=27% Similarity=0.724 Sum_probs=22.9
Q ss_pred cceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC--CCCCc
Q 037450 177 CAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR--SCPLC 217 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~--~CP~C 217 (224)
|.+|.+..-.|..=....|+=.+|..|++.+++... .||.|
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 678888765443222224888999999999998776 79987
No 79
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.66 E-value=0.034 Score=55.21 Aligned_cols=44 Identities=25% Similarity=0.714 Sum_probs=34.3
Q ss_pred CccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 173 SEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
....|..|--.++.+ .+...|+|.||..|++ .....||.|+.+.
T Consensus 839 q~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 839 QVSKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeeeecccCCccccc--eeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 346899999888533 3456699999999999 5566899998743
No 80
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=93.45 E-value=0.04 Score=48.48 Aligned_cols=47 Identities=30% Similarity=0.726 Sum_probs=38.8
Q ss_pred CccccceeccccccCC-eeEEcCCCCcccHHHHHHHHhcCCCCCCccc
Q 037450 173 SEKDCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
....|+||.|.+-... .+..++|+|.-|..|...-...+-+||+|-.
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 3445999999775543 5678999999999999998888889999976
No 81
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.66 E-value=0.049 Score=54.35 Aligned_cols=36 Identities=25% Similarity=0.627 Sum_probs=29.5
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHH
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWL 208 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl 208 (224)
+..+.|.+|.-.+... .-.+-||+|.||.+||..-.
T Consensus 815 ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred cCccchHHhcchhhcC-cceeeeccchHHHHHHHHHH
Confidence 7889999999987533 45678999999999997653
No 82
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=92.62 E-value=0.044 Score=53.97 Aligned_cols=43 Identities=40% Similarity=0.793 Sum_probs=36.4
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC--CCCCcccCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR--SCPLCRNDL 221 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~--~CP~CR~~l 221 (224)
..|.||++ . +....++|+|.||.+|+..-+.... .||.||..+
T Consensus 455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 89999999 2 6677889999999999988877554 599999765
No 83
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.39 E-value=0.086 Score=43.46 Aligned_cols=51 Identities=25% Similarity=0.727 Sum_probs=35.3
Q ss_pred cCccccceeccccccCCee----EEcCCCCcccHHHHHHHHhcC----C-------CCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLA----SCTPCDHVFHKRCIDFWLEKS----R-------SCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~----~~lpC~H~FH~~CI~~Wl~~~----~-------~CP~CR~~l~ 222 (224)
++...|.||...--.|..+ --..|+.-||.-|+..||+.- + .||.|-.++.
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 4556788887643333221 234599999999999999732 1 5999988764
No 84
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.46 E-value=0.22 Score=43.44 Aligned_cols=50 Identities=22% Similarity=0.454 Sum_probs=38.8
Q ss_pred cCccccceeccccccCCe-eEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQL-ASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~-~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.....|||...+|..... +...||||+|...+|+.-- ....||+|-.++.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence 566789999999943333 3456799999999999973 3568999988764
No 85
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=91.16 E-value=0.07 Score=34.45 Aligned_cols=32 Identities=34% Similarity=0.911 Sum_probs=22.8
Q ss_pred cCC-CCcccHHHHHHHHhcCCCCCCcccCCCCC
Q 037450 193 TPC-DHVFHKRCIDFWLEKSRSCPLCRNDLPAS 224 (224)
Q Consensus 193 lpC-~H~FH~~CI~~Wl~~~~~CP~CR~~l~~~ 224 (224)
..| .|..|..|+..-+..+..||+|..++|++
T Consensus 16 i~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 16 IKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp EE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred eeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 346 49999999999999999999999999874
No 86
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.11 E-value=0.039 Score=48.67 Aligned_cols=41 Identities=29% Similarity=0.742 Sum_probs=29.9
Q ss_pred ccccceeccccccCCeeEEcCCCCcc-cHHHHHHHHhcCCCCCCcccCC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVF-HKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~F-H~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..-|+||++.- ..-..|+|||.- |.+|-+. -+.||+||+-+
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 67899999964 445679999964 6666443 23799999754
No 87
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.90 E-value=0.11 Score=45.12 Aligned_cols=49 Identities=33% Similarity=0.809 Sum_probs=36.0
Q ss_pred cCccccceeccccccCCe-eEEcCCC-----CcccHHHHHHHHhcCC--------CCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQL-ASCTPCD-----HVFHKRCIDFWLEKSR--------SCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~-~~~lpC~-----H~FH~~CI~~Wl~~~~--------~CP~CR~~ 220 (224)
+.+..|-||+..=++.-. .-+-||. |.-|..|+..|+..++ +||.|+.+
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE 80 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE 80 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence 567789999986443222 2456763 8999999999986443 59999975
No 88
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=90.63 E-value=0.11 Score=46.18 Aligned_cols=44 Identities=30% Similarity=0.668 Sum_probs=31.1
Q ss_pred ccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
...|.-|---+. .--+.+||.|+||.+|... ...+.||.|-..|
T Consensus 90 VHfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 90 VHFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred eEeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 455777754442 2347899999999999754 4466899997654
No 89
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.10 E-value=0.33 Score=32.24 Aligned_cols=34 Identities=21% Similarity=0.543 Sum_probs=27.8
Q ss_pred CccccceeccccccCCeeEEcC-CCCcccHHHHHH
Q 037450 173 SEKDCAICLDGIVVGQLASCTP-CDHVFHKRCIDF 206 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~ 206 (224)
....|++|-+.|++++.+++=| |+-.+|.+|.+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3567999999998777776666 999999999544
No 90
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=90.04 E-value=0.079 Score=54.88 Aligned_cols=47 Identities=32% Similarity=0.687 Sum_probs=39.1
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
.....|.||++.+.. .-....|+|.+|..|+..|+..+..||.|++.
T Consensus 1151 ~~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred hcccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence 455589999999862 33456699999999999999999999999853
No 91
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=89.94 E-value=0.19 Score=49.58 Aligned_cols=41 Identities=34% Similarity=0.784 Sum_probs=31.5
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPL 216 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~ 216 (224)
..|+||--.+ .|.......|+|..|.+|...|++....||.
T Consensus 1029 ~~C~~C~l~V-~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAV-RGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeeeEeeEe-eccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 3466665443 3445667789999999999999999999985
No 92
>PF14369 zf-RING_3: zinc-finger
Probab=88.64 E-value=0.19 Score=30.32 Aligned_cols=17 Identities=18% Similarity=0.241 Sum_probs=13.3
Q ss_pred ccCCC-CCCCCchhhhhh
Q 037450 20 NQLWD-LPNMQPGFIFQL 36 (224)
Q Consensus 20 ~~~~~-~~~~~~~~~~~~ 36 (224)
+.+.. ||.|+.|||.||
T Consensus 18 ~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 18 PDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCCCcCCcCCCCcEeEeC
Confidence 34445 999999999875
No 93
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=88.19 E-value=0.52 Score=42.37 Aligned_cols=57 Identities=25% Similarity=0.592 Sum_probs=43.6
Q ss_pred hcCCcccccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 164 TRLPEKRIESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 164 ~~lp~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
.+.|...+.....|-.|.++......++.-.|.|.||.+|=.-.-++-+.||-|.+.
T Consensus 320 ~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~ 376 (378)
T KOG2807|consen 320 VEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEHK 376 (378)
T ss_pred hhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCCC
Confidence 344554445667799998888877888888899999999965555555689999754
No 94
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.23 E-value=0.24 Score=45.67 Aligned_cols=40 Identities=25% Similarity=0.602 Sum_probs=29.0
Q ss_pred cCccccceec-cccccCCeeEEcCCCCcccHHHHHHHHhcC
Q 037450 172 ESEKDCAICL-DGIVVGQLASCTPCDHVFHKRCIDFWLEKS 211 (224)
Q Consensus 172 ~~~~~C~ICl-e~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~ 211 (224)
....+|.||. +..+......+..|+|.||.+|+...+..+
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~ 184 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK 184 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence 3467899999 544433333456699999999999887644
No 95
>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=86.45 E-value=0.44 Score=43.55 Aligned_cols=28 Identities=25% Similarity=0.883 Sum_probs=21.5
Q ss_pred CCCcccHHHHHHHHhcCC-------------CCCCcccCCC
Q 037450 195 CDHVFHKRCIDFWLEKSR-------------SCPLCRNDLP 222 (224)
Q Consensus 195 C~H~FH~~CI~~Wl~~~~-------------~CP~CR~~l~ 222 (224)
|.=..|.+|+-+|+..++ .||+||+.+.
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 556779999988875443 6999999763
No 96
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=85.19 E-value=0.7 Score=41.26 Aligned_cols=45 Identities=24% Similarity=0.558 Sum_probs=34.9
Q ss_pred ccCccccceeccccccCCeeEEcCC--CCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 171 IESEKDCAICLDGIVVGQLASCTPC--DHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 171 ~~~~~~C~ICle~~~~~~~~~~lpC--~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
+.+-.+||||.+.+.... ..| ||+-|..|=. +.++.||.||-+++
T Consensus 45 ~~~lleCPvC~~~l~~Pi----~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPI----FQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred chhhccCchhhccCcccc----eecCCCcEehhhhhh---hhcccCCccccccc
Confidence 367889999999986332 345 6999999965 45678999999886
No 97
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=84.96 E-value=0.75 Score=36.19 Aligned_cols=50 Identities=18% Similarity=0.480 Sum_probs=35.1
Q ss_pred cCccccceeccccccCCeeEEcC---CCCcccHHHHHHHHh---cCCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTP---CDHVFHKRCIDFWLE---KSRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lp---C~H~FH~~CI~~Wl~---~~~~CP~CR~~l~~ 223 (224)
..-.+|-||.|.-. ++...-| ||-..|..|-....+ .+..||+|+.++.+
T Consensus 78 ~~lYeCnIC~etS~--ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 78 PKLYECNICKETSA--EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CCceeccCcccccc--hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 45678999999753 3333334 999999999755444 34589999998753
No 98
>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=84.65 E-value=0.39 Score=31.27 Aligned_cols=43 Identities=21% Similarity=0.556 Sum_probs=21.9
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC-----CCCCcccC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR-----SCPLCRND 220 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~-----~CP~CR~~ 220 (224)
..|+|....++ .-++...|.|.-+.+ ++.||.... .||+|.++
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 46888888775 345667799986554 456665333 69999763
No 99
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=84.62 E-value=0.6 Score=42.24 Aligned_cols=50 Identities=20% Similarity=0.563 Sum_probs=35.0
Q ss_pred cCccccceeccccccCCee-EEcCCCCcccHHHHHHHHhc-CCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLA-SCTPCDHVFHKRCIDFWLEK-SRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~CI~~Wl~~-~~~CP~CR~~l 221 (224)
.+++-|+.|+|++...++- .--|||-..|.-|....-+. +..||-||..-
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y 63 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKY 63 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhc
Confidence 4455599999999766543 23458988888886654333 34799999753
No 100
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.80 E-value=0.59 Score=44.97 Aligned_cols=43 Identities=40% Similarity=0.920 Sum_probs=37.3
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.....|.||.++. ..+..+|. |.-|+..|+..+..||+|+..+
T Consensus 477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~ 519 (543)
T KOG0802|consen 477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYM 519 (543)
T ss_pred cccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhh
Confidence 6788899999987 45677888 9999999999999999998765
No 101
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.70 E-value=0.74 Score=38.95 Aligned_cols=39 Identities=28% Similarity=0.660 Sum_probs=29.1
Q ss_pred cceeccccccCCeeEEcCCCC-cccHHHHHHHHhcCCCCCCcccCCC
Q 037450 177 CAICLDGIVVGQLASCTPCDH-VFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 177 C~ICle~~~~~~~~~~lpC~H-~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
|-.|.+. +..+..+||.| .+|..|=.. -.+||+|+....
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 8888874 35688999986 577788554 446999998653
No 102
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=81.46 E-value=0.37 Score=47.29 Aligned_cols=48 Identities=33% Similarity=0.823 Sum_probs=37.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC---CCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR---SCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~---~CP~CR~~l~ 222 (224)
....+|+||.+-+... ..+.|.|.|+..|+..-+.... .||+|+..++
T Consensus 19 ~k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 19 QKILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 4467899999988533 5677999999999876655444 6999997654
No 103
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=81.06 E-value=0.86 Score=39.98 Aligned_cols=48 Identities=21% Similarity=0.607 Sum_probs=35.8
Q ss_pred ccccceeccccccCCe-eEEcCCC-----CcccHHHHHHHHhcC--CCCCCcccCC
Q 037450 174 EKDCAICLDGIVVGQL-ASCTPCD-----HVFHKRCIDFWLEKS--RSCPLCRNDL 221 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~-~~~lpC~-----H~FH~~CI~~Wl~~~--~~CP~CR~~l 221 (224)
...|-||.++...... ....||. +..|..|++.|+..+ ..|.+|....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~ 133 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF 133 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence 4689999997653321 4677865 667999999999844 4799998754
No 104
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=77.15 E-value=1.3 Score=38.35 Aligned_cols=47 Identities=21% Similarity=0.616 Sum_probs=34.9
Q ss_pred cCccccceeccccccCC--eeEEcC-CCCcccHHHHHHHHhcCC-CCC--Ccc
Q 037450 172 ESEKDCAICLDGIVVGQ--LASCTP-CDHVFHKRCIDFWLEKSR-SCP--LCR 218 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~--~~~~lp-C~H~FH~~CI~~Wl~~~~-~CP--~CR 218 (224)
..+..||||..+--... +.-.-| |-|..|.+|++..+...+ .|| -|-
T Consensus 8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~ 60 (314)
T COG5220 8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG 60 (314)
T ss_pred hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence 34668999998654333 334456 999999999999988776 799 564
No 105
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=76.35 E-value=1.4 Score=37.39 Aligned_cols=45 Identities=29% Similarity=0.825 Sum_probs=37.1
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
..-..|.+|.+..- ..++.-.|+=.+|..|+...++....||.|.
T Consensus 179 dnlk~Cn~Ch~LvI--qg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 179 DNLKNCNLCHCLVI--QGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHHHHHhHhHHHhh--eeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 35678999999764 2346677999999999999999999999993
No 106
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.70 E-value=1.6 Score=38.88 Aligned_cols=27 Identities=26% Similarity=0.844 Sum_probs=21.4
Q ss_pred CCCcccHHHHHHHH-------------hcCCCCCCcccCC
Q 037450 195 CDHVFHKRCIDFWL-------------EKSRSCPLCRNDL 221 (224)
Q Consensus 195 C~H~FH~~CI~~Wl-------------~~~~~CP~CR~~l 221 (224)
|.-..|.+|+..|+ +.+-+||+||+.+
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 66788999998875 4455899999875
No 107
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=75.31 E-value=1 Score=43.64 Aligned_cols=44 Identities=32% Similarity=0.765 Sum_probs=28.0
Q ss_pred cCccccceecc-----ccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 172 ESEKDCAICLD-----GIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 172 ~~~~~C~ICle-----~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
.....|.+|.. .|+.....+...|+++||..|+. ..+..||.|-
T Consensus 509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~---r~s~~CPrC~ 557 (580)
T KOG1829|consen 509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLR---RKSPCCPRCE 557 (580)
T ss_pred cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHh---ccCCCCCchH
Confidence 34455666632 12223345677799999999954 4555699993
No 108
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=75.05 E-value=2.7 Score=41.83 Aligned_cols=42 Identities=26% Similarity=0.528 Sum_probs=31.5
Q ss_pred ccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPL 216 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~ 216 (224)
...|.+|-..+. |..+-.--|+|.-|.+|+.+|+..+.-||.
T Consensus 779 ~~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 779 SAKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred hcCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 447888877652 322333349999999999999999988877
No 109
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.85 E-value=2.9 Score=37.62 Aligned_cols=48 Identities=19% Similarity=0.353 Sum_probs=38.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC---CCCCccc
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR---SCPLCRN 219 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~---~CP~CR~ 219 (224)
.....||+=.|.-.+++.++.|.|||+.-.+-++...+... .||.|-.
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 66788999888776667788999999999999988766443 6999954
No 110
>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 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=70.85 E-value=2.4 Score=27.80 Aligned_cols=42 Identities=29% Similarity=0.598 Sum_probs=21.8
Q ss_pred cceeccccccC-------CeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 177 CAICLDGIVVG-------QLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 177 C~ICle~~~~~-------~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
|.-|+..|..+ ..++.-.|++.|+.+|=.-.-+.-+.||-|-
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 55566666543 2455666999999999443334455899884
No 112
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=69.64 E-value=3.2 Score=41.70 Aligned_cols=49 Identities=27% Similarity=0.727 Sum_probs=36.9
Q ss_pred cCccccceeccccccCCeeEEcCCC-----CcccHHHHHHHHhcCC--CCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCD-----HVFHKRCIDFWLEKSR--SCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~Wl~~~~--~CP~CR~~l 221 (224)
+++..|-||..+=. .+.+-.-||+ ...|.+|+.+|+..+. .|-+|..++
T Consensus 10 ~d~~~CRICr~e~~-~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 10 EDKRSCRICRTEDI-RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred ccchhceeecCCCC-CCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 55678999998643 3445566776 3579999999998665 599998765
No 113
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.63 E-value=3.6 Score=34.49 Aligned_cols=43 Identities=33% Similarity=0.832 Sum_probs=30.5
Q ss_pred cCccccceeccc-----cccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCccc
Q 037450 172 ESEKDCAICLDG-----IVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 172 ~~~~~C~ICle~-----~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
.....|-+|-+. |+.....+.-.|+-.||..|.. +..||-|-.
T Consensus 150 ~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 150 QKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred hCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 446678888752 3333456667799999999966 267999954
No 114
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.21 E-value=2.4 Score=42.35 Aligned_cols=45 Identities=22% Similarity=0.582 Sum_probs=32.7
Q ss_pred cCccccceecccccc-C---CeeEEcCCCCcccHHHHHHHHhcCCCCCCc
Q 037450 172 ESEKDCAICLDGIVV-G---QLASCTPCDHVFHKRCIDFWLEKSRSCPLC 217 (224)
Q Consensus 172 ~~~~~C~ICle~~~~-~---~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~C 217 (224)
..+..|.-|.+..-. + +.+.++.|+|+||..|+..-..+++ |-.|
T Consensus 782 ~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 782 SVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred eehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 556689999986542 2 4577889999999999977655554 5444
No 115
>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=65.61 E-value=3 Score=26.48 Aligned_cols=44 Identities=25% Similarity=0.673 Sum_probs=30.8
Q ss_pred ccceeccccccCCeeEEcCCCCcccHHHHHHHHh------cCCCCCCccc
Q 037450 176 DCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLE------KSRSCPLCRN 219 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~------~~~~CP~CR~ 219 (224)
.|.||...-..++.+.--.|+..||..|+..-.. ..-.||.|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 3889998555555566667999999999865432 2347888753
No 116
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.58 E-value=8 Score=29.57 Aligned_cols=46 Identities=26% Similarity=0.496 Sum_probs=35.0
Q ss_pred ccccceeccccccC-----------CeeEEcCCCCcccHHHHHHHHhcCCCCCCccc
Q 037450 174 EKDCAICLDGIVVG-----------QLASCTPCDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 174 ~~~C~ICle~~~~~-----------~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
...|--|...|... ..++...|++.|+.+|=.-+-+.-+.||-|..
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 45699999987532 12456679999999997777777788999963
No 117
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=63.77 E-value=3.2 Score=41.62 Aligned_cols=50 Identities=8% Similarity=0.162 Sum_probs=34.7
Q ss_pred cCccccceeccccccCC-eeEEcC---CCCcccHHHHHHHHhc------CCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIVVGQ-LASCTP---CDHVFHKRCIDFWLEK------SRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~-~~~~lp---C~H~FH~~CI~~Wl~~------~~~CP~CR~~l 221 (224)
.....|.+|.-++...+ ..-..| |.|.||..||..|..+ +-.|++|.+-|
T Consensus 94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 44567888888776522 122344 9999999999999864 22688887644
No 118
>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=62.07 E-value=8.9 Score=22.17 Aligned_cols=38 Identities=32% Similarity=0.599 Sum_probs=24.2
Q ss_pred ccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 176 DCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.|+.|.+.+..++... ..=+..||.+| ..|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~-~~~~~~~H~~C--------f~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVL-RALGKVWHPEC--------FKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEE-EeCCccccccC--------CCCcccCCcCc
Confidence 3788888876542332 22367888876 35777877664
No 119
>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=61.08 E-value=5.8 Score=22.62 Aligned_cols=29 Identities=31% Similarity=0.729 Sum_probs=12.5
Q ss_pred ccceeccccccCCeeEEcCCCCcccHHHH
Q 037450 176 DCAICLDGIVVGQLASCTPCDHVFHKRCI 204 (224)
Q Consensus 176 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI 204 (224)
.|.+|.+....+..+....|.-.+|.+|+
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 58889888755456788889999999986
No 120
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.24 E-value=3.3 Score=40.60 Aligned_cols=41 Identities=29% Similarity=0.577 Sum_probs=31.0
Q ss_pred CccccceeccccccC-CeeEEcCCCCcccHHHHHHHHhcCCCCC
Q 037450 173 SEKDCAICLDGIVVG-QLASCTPCDHVFHKRCIDFWLEKSRSCP 215 (224)
Q Consensus 173 ~~~~C~ICle~~~~~-~~~~~lpC~H~FH~~CI~~Wl~~~~~CP 215 (224)
+...|+||+.+|... -.++.+-|+|..|..|+..- .+.+||
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp 51 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP 51 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC
Confidence 456799998877543 25667779999999999874 456777
No 121
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.97 E-value=5.4 Score=37.44 Aligned_cols=38 Identities=21% Similarity=0.446 Sum_probs=31.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS 211 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~ 211 (224)
.....|-||.+.+.. ....+.|+|-|+..|+...+..+
T Consensus 68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~k 105 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTK 105 (444)
T ss_pred CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhhe
Confidence 566789999998853 46677899999999999987643
No 122
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=58.64 E-value=2.3 Score=23.57 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=13.3
Q ss_pred hhccCCCCCCCCchhh
Q 037450 18 VRNQLWDLPNMQPGFI 33 (224)
Q Consensus 18 ~~~~~~~~~~~~~~~~ 33 (224)
..+.|..||.|++.|.
T Consensus 10 ~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSSEEESSSSEEES
T ss_pred CCCCCCCCCCCcCeeC
Confidence 3567899999999985
No 123
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.59 E-value=5.5 Score=23.99 Aligned_cols=26 Identities=27% Similarity=0.705 Sum_probs=17.2
Q ss_pred cccceeccccccCC--------eeEEcCCCCccc
Q 037450 175 KDCAICLDGIVVGQ--------LASCTPCDHVFH 200 (224)
Q Consensus 175 ~~C~ICle~~~~~~--------~~~~lpC~H~FH 200 (224)
.+|+=|...|+..+ .++...|+|.|+
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 46888888886544 355555777774
No 124
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.36 E-value=4.5 Score=37.36 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=31.8
Q ss_pred CccccceeccccccCC---eeEEcCCCCcccHHHHHHHHhcCCCCCCc
Q 037450 173 SEKDCAICLDGIVVGQ---LASCTPCDHVFHKRCIDFWLEKSRSCPLC 217 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~---~~~~lpC~H~FH~~CI~~Wl~~~~~CP~C 217 (224)
.-..|+.|.-.++... ..... |+|.||..|...|...+..|..|
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred hcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence 3567999988765433 23333 99999999999998877766444
No 125
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=57.18 E-value=13 Score=26.69 Aligned_cols=58 Identities=19% Similarity=0.270 Sum_probs=43.3
Q ss_pred ccccchhhhHHHHhhHhhhcCceecCCCccccCCCce-eeEecCCCCcccchhhHHHHHHH
Q 037450 62 TLFVTYNNMFHFLSNILADEGVTVDANGCFLSDKGLH-LLRLDASGGMPIMFPQSVRIYTL 121 (224)
Q Consensus 62 ~lf~t~~~~~~~l~~~l~~~~~~~di~g~f~~~~g~~-~l~~d~~gg~~i~~~~~v~i~~l 121 (224)
..|.||+++.+.|.......|..+.+.+|... |+| +......|.+...+|..-.++..
T Consensus 6 ~AFlTYdevk~~L~~~~~kpGsYiFRlSCTrL--GQWAIGyV~~dg~I~QTIPqnk~L~qa 64 (86)
T PF02762_consen 6 MAFLTYDEVKARLQHYRDKPGSYIFRLSCTRL--GQWAIGYVTQDGKILQTIPQNKSLYQA 64 (86)
T ss_dssp ETT--HHHHHHHHGGGTTSTTEEEEEEESSST--TSEEEEEEETTSEEEEE--SSS-HHHH
T ss_pred eEEEeHHHHHHHHHHHhCCcccEEEeeccccc--cceeEEEEcCCCcEEEecCCCchHHHH
Confidence 57999999999999999999999998887654 488 77778888888888887655433
No 126
>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=56.51 E-value=3.7 Score=28.73 Aligned_cols=39 Identities=23% Similarity=0.491 Sum_probs=19.4
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..||.|..+++... +|..|..|-.. +.....||.|..+|
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-
T ss_pred CcCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHH
Confidence 57999998875322 45555555443 24455799998876
No 127
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.83 E-value=7.3 Score=34.60 Aligned_cols=51 Identities=20% Similarity=0.516 Sum_probs=35.8
Q ss_pred cCccccceeccccccCCeeEEcC-CCCcccHHHHHHHHhcCC-----------CCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTP-CDHVFHKRCIDFWLEKSR-----------SCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~Wl~~~~-----------~CP~CR~~l~ 222 (224)
..-..|.+|.|.+|+..-+.+-. =.|.||.-|-.+.++.+. .||+--..+|
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~vP 328 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNVP 328 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCccc
Confidence 44589999999997554333222 479999999998887654 4666655544
No 128
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=53.47 E-value=9 Score=34.58 Aligned_cols=46 Identities=22% Similarity=0.541 Sum_probs=35.9
Q ss_pred cccceeccccccCCeeEEcC--CCCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 175 KDCAICLDGIVVGQLASCTP--CDHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lp--C~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
..|+||-+..... ..-.+| |++..|..|+..-...+..||.||.+.
T Consensus 250 ~s~p~~~~~~~~~-d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 250 PSCPICYEDLDLT-DSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCccccc-ccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence 6799999977332 334566 788888888888888889999999754
No 129
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=49.07 E-value=9.7 Score=22.97 Aligned_cols=26 Identities=31% Similarity=0.704 Sum_probs=17.0
Q ss_pred cccceeccccccCC--------eeEEcCCCCccc
Q 037450 175 KDCAICLDGIVVGQ--------LASCTPCDHVFH 200 (224)
Q Consensus 175 ~~C~ICle~~~~~~--------~~~~lpC~H~FH 200 (224)
..|+-|...|+..+ .++.-.|+|+|.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 46888888886544 344455777774
No 130
>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=48.94 E-value=27 Score=23.41 Aligned_cols=45 Identities=22% Similarity=0.499 Sum_probs=30.2
Q ss_pred ccceeccccccCC-eeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 176 DCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 176 ~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.|-.|-.++..+. .++.=.=...||.+|.+.-| +..||.|--+|.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccc
Confidence 4666777665444 22222223679999999966 778999987764
No 131
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=47.97 E-value=9.8 Score=33.43 Aligned_cols=50 Identities=24% Similarity=0.492 Sum_probs=33.0
Q ss_pred cCccccceeccccc-cCCeeEE---cCCCCcccHHHHHHHHh-c--------CCCCCCcccCC
Q 037450 172 ESEKDCAICLDGIV-VGQLASC---TPCDHVFHKRCIDFWLE-K--------SRSCPLCRNDL 221 (224)
Q Consensus 172 ~~~~~C~ICle~~~-~~~~~~~---lpC~H~FH~~CI~~Wl~-~--------~~~CP~CR~~l 221 (224)
....+|-+|.+++. .+..... .-|+-++|..|+..-+. . ...||.|+.-+
T Consensus 180 ~~~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 180 ALNVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred ccchhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 34568999999984 3332221 11899999999988432 2 22699998743
No 132
>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=46.74 E-value=2.3 Score=37.45 Aligned_cols=48 Identities=19% Similarity=0.294 Sum_probs=22.2
Q ss_pred cCccccceeccccccCCeeEEc---CCCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQLASCT---PCDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~l---pC~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
+....||||-..-..+. ++.- .=.|.+|.-|-..|-..+..||.|-..
T Consensus 170 w~~g~CPvCGs~P~~s~-l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSV-LRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp TT-SS-TTT---EEEEE-EE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred ccCCcCCCCCCcCceEE-EecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 55679999987542211 1111 125678888999998889999999664
No 133
>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=46.57 E-value=12 Score=25.80 Aligned_cols=12 Identities=25% Similarity=0.874 Sum_probs=8.7
Q ss_pred cccHHHHHHHHh
Q 037450 198 VFHKRCIDFWLE 209 (224)
Q Consensus 198 ~FH~~CI~~Wl~ 209 (224)
-||..|+.+|..
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 399999999975
No 134
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=45.04 E-value=21 Score=32.35 Aligned_cols=50 Identities=26% Similarity=0.760 Sum_probs=34.9
Q ss_pred Cccccceeccccc-----cCC-----------eeEEcCCCCcccHHHHHHHHhc---------CCCCCCcccCCC
Q 037450 173 SEKDCAICLDGIV-----VGQ-----------LASCTPCDHVFHKRCIDFWLEK---------SRSCPLCRNDLP 222 (224)
Q Consensus 173 ~~~~C~ICle~~~-----~~~-----------~~~~lpC~H~FH~~CI~~Wl~~---------~~~CP~CR~~l~ 222 (224)
.+.+|++|+..=. .|- ...--||+|+--.+-..-|.+. +..||.|-..|.
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 4778999997421 010 1344689999888888889763 337999987764
No 135
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.52 E-value=3.8 Score=35.99 Aligned_cols=46 Identities=30% Similarity=0.499 Sum_probs=37.3
Q ss_pred ccccceeccccccC---CeeEEcC--------CCCcccHHHHHHHHhcCC-CCCCccc
Q 037450 174 EKDCAICLDGIVVG---QLASCTP--------CDHVFHKRCIDFWLEKSR-SCPLCRN 219 (224)
Q Consensus 174 ~~~C~ICle~~~~~---~~~~~lp--------C~H~FH~~CI~~Wl~~~~-~CP~CR~ 219 (224)
...|.||...++.. ..++++. |+|..+..|++.-+.+.. .||.||.
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~ 264 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTW 264 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccc
Confidence 46799999998732 2456777 999999999999877665 8999986
No 136
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=44.38 E-value=24 Score=25.82 Aligned_cols=40 Identities=20% Similarity=0.370 Sum_probs=31.6
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcccCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLPA 223 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~~ 223 (224)
..-..|+-|...++-.+ ..| |-.|+..+..|..|+++++.
T Consensus 31 ~~rS~C~~C~~~L~~~~---lIP---------i~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWD---LIP---------ILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCCCcCcCCCCcCcccc---cch---------HHHHHHhCCCCcccCCCCCh
Confidence 44578999999885444 344 67899999999999999874
No 137
>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=39.32 E-value=13 Score=25.12 Aligned_cols=37 Identities=19% Similarity=0.473 Sum_probs=19.0
Q ss_pred cCccccceeccccccCC-eeEEcCCCCcccHHHHHHHH
Q 037450 172 ESEKDCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWL 208 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl 208 (224)
.+...|.+|...|..-. ....-.||++|+.+|.....
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 45678999999996432 23344599999999976543
No 138
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.59 E-value=24 Score=30.86 Aligned_cols=36 Identities=19% Similarity=0.276 Sum_probs=30.0
Q ss_pred ccCccccceeccccccCCeeEEcCCCCcccHHHHHHHHh
Q 037450 171 IESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLE 209 (224)
Q Consensus 171 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~ 209 (224)
+..-..|+.|+..+ ..++..|=||+|+.+||-+.+.
T Consensus 40 iK~FdcCsLtLqPc---~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 40 IKPFDCCSLTLQPC---RDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred cCCcceeeeecccc---cCCccCCCCeeeeHHHHHHHHH
Confidence 35677899999988 5678899999999999988754
No 139
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=38.16 E-value=12 Score=30.78 Aligned_cols=40 Identities=28% Similarity=0.452 Sum_probs=33.0
Q ss_pred cccccccc-----------hhhhhhhccCCCCCCCCchhhhhhccccccccCccC
Q 037450 5 ELKLRQDN-----------TILNKVRNQLWDLPNMQPGFIFQLRAHHVINQRATS 48 (224)
Q Consensus 5 ~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (224)
|-|+|++| ..+|-+.+-.+-|-.|.|||-| +|++..+...
T Consensus 96 Ee~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~----~HLP~~~~~~ 146 (175)
T PF15446_consen 96 EEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHF----EHLPPPSGTT 146 (175)
T ss_pred HHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeeh----hhCCCCcCCC
Confidence 45666665 4678899999999999999999 9998877655
No 140
>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=37.94 E-value=24 Score=22.64 Aligned_cols=36 Identities=17% Similarity=0.509 Sum_probs=25.0
Q ss_pred ccccceeccccccCC-eeEEcCCCCcccHHHHHHHHh
Q 037450 174 EKDCAICLDGIVVGQ-LASCTPCDHVFHKRCIDFWLE 209 (224)
Q Consensus 174 ~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~Wl~ 209 (224)
...|.+|-..|.... ....-.|+++|+.+|......
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 357999988885433 223345999999999876543
No 141
>PHA00732 hypothetical protein
Probab=37.18 E-value=50 Score=23.44 Aligned_cols=48 Identities=23% Similarity=0.285 Sum_probs=30.8
Q ss_pred cCCCCCCCCchhhhhhccccccccCccCCCCCccccccCCcccccchhhhHHHHhhHh
Q 037450 21 QLWDLPNMQPGFIFQLRAHHVINQRATSAKPDTFLYLQADHTLFVTYNNMFHFLSNIL 78 (224)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~f~~~~~~~lf~t~~~~~~~l~~~l 78 (224)
.+..|+.|++.|.. +..|. ++.-...-++|-| ||.||.--.++..++.
T Consensus 26 ~~~~C~~CgKsF~~-l~~H~---~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~ 73 (79)
T PHA00732 26 TLTKCPVCNKSYRR-LNQHF---YSQYDIEHLIYCY------LFSTYKLPYHVRLAIK 73 (79)
T ss_pred CCCccCCCCCEeCC-hhhhh---cccCCccceEEeE------eeecCcchHHHHHHHH
Confidence 35589999999984 66665 3333344446667 7888865555555443
No 142
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.14 E-value=22 Score=25.10 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=19.5
Q ss_pred CCcccHHHHHHHHhcCCCCCCcccCC
Q 037450 196 DHVFHKRCIDFWLEKSRSCPLCRNDL 221 (224)
Q Consensus 196 ~H~FH~~CI~~Wl~~~~~CP~CR~~l 221 (224)
.|.||.+|.+. ..+..||.|--++
T Consensus 28 EcTFCadCae~--~l~g~CPnCGGel 51 (84)
T COG3813 28 ECTFCADCAEN--RLHGLCPNCGGEL 51 (84)
T ss_pred eeehhHhHHHH--hhcCcCCCCCchh
Confidence 58899999987 4567899997655
No 143
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=36.23 E-value=23 Score=20.21 Aligned_cols=28 Identities=32% Similarity=0.763 Sum_probs=20.8
Q ss_pred ccceeccccccCC-eeEEcCCCCcccHHHH
Q 037450 176 DCAICLDGIVVGQ-LASCTPCDHVFHKRCI 204 (224)
Q Consensus 176 ~C~ICle~~~~~~-~~~~lpC~H~FH~~CI 204 (224)
.|.||.++. .+. .+....|.-..|..|+
T Consensus 2 ~C~~C~~~~-~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKI-DGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCc-CCCEeEEeCCCCCeEcCccC
Confidence 588997776 444 6777778888888773
No 144
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.97 E-value=43 Score=24.91 Aligned_cols=37 Identities=27% Similarity=0.386 Sum_probs=29.8
Q ss_pred ccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC
Q 037450 174 EKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS 211 (224)
Q Consensus 174 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~ 211 (224)
.-.|+||-+.+..|+.-.-++ .-.-|.+|+..-.+.+
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~k 42 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRKK 42 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhcC
Confidence 347999999999999877777 7778999998765543
No 145
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=35.48 E-value=12 Score=40.16 Aligned_cols=49 Identities=24% Similarity=0.533 Sum_probs=39.9
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC----CCCCcccC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR----SCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~----~CP~CR~~ 220 (224)
.....|.+|....+....+...-|.-.||..|+.+-+..-. .||-||..
T Consensus 1106 ~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred cchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchh
Confidence 56778999999877655556666999999999999887655 69999875
No 146
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=34.74 E-value=38 Score=24.94 Aligned_cols=33 Identities=27% Similarity=0.664 Sum_probs=25.0
Q ss_pred cCccccceeccccccCCeeEEcC--CCCcccHHHHHH
Q 037450 172 ESEKDCAICLDGIVVGQLASCTP--CDHVFHKRCIDF 206 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lp--C~H~FH~~CI~~ 206 (224)
.....|.||... .|..++.-. |...||..|...
T Consensus 53 ~~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 53 RFKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred hcCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHH
Confidence 356789999987 455555554 889999999865
No 147
>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=34.67 E-value=21 Score=22.80 Aligned_cols=14 Identities=14% Similarity=0.263 Sum_probs=6.9
Q ss_pred cCccccceeccccc
Q 037450 172 ESEKDCAICLDGIV 185 (224)
Q Consensus 172 ~~~~~C~ICle~~~ 185 (224)
.+-..|..|...+.
T Consensus 24 ~~Cf~C~~C~~~l~ 37 (58)
T PF00412_consen 24 PECFKCSKCGKPLN 37 (58)
T ss_dssp TTTSBETTTTCBTT
T ss_pred ccccccCCCCCccC
Confidence 34445555555544
No 148
>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=34.26 E-value=13 Score=22.99 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=15.9
Q ss_pred eEEcCCCCcccHHHHHHHHhcCCCCCCccc
Q 037450 190 ASCTPCDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 190 ~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
++...|+|.|-.-.--.= .....||.|..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 455567777754321000 23347999987
No 149
>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=33.57 E-value=12 Score=20.87 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=5.3
Q ss_pred ccceecccc
Q 037450 176 DCAICLDGI 184 (224)
Q Consensus 176 ~C~ICle~~ 184 (224)
.|+-|..++
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 466666654
No 150
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.11 E-value=24 Score=19.35 Aligned_cols=13 Identities=23% Similarity=0.015 Sum_probs=10.6
Q ss_pred CCCCCCCCchhhh
Q 037450 22 LWDLPNMQPGFIF 34 (224)
Q Consensus 22 ~~~~~~~~~~~~~ 34 (224)
.-.||.|+|.|.-
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 4579999999975
No 151
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=30.02 E-value=11 Score=19.55 Aligned_cols=11 Identities=18% Similarity=0.126 Sum_probs=8.9
Q ss_pred CCCCCCchhhh
Q 037450 24 DLPNMQPGFIF 34 (224)
Q Consensus 24 ~~~~~~~~~~~ 34 (224)
.||.|++.|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 58889988875
No 152
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=29.72 E-value=27 Score=34.01 Aligned_cols=37 Identities=24% Similarity=0.489 Sum_probs=25.1
Q ss_pred cCccccceecccccc-----CC-----eeEEcCCCCcccHHHHHHHH
Q 037450 172 ESEKDCAICLDGIVV-----GQ-----LASCTPCDHVFHKRCIDFWL 208 (224)
Q Consensus 172 ~~~~~C~ICle~~~~-----~~-----~~~~lpC~H~FH~~CI~~Wl 208 (224)
+....|+||.|.|+. .+ ....+.=|-+||..|+..-.
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 556789999999963 00 12223258899999986643
No 153
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.65 E-value=56 Score=28.68 Aligned_cols=49 Identities=16% Similarity=0.262 Sum_probs=33.9
Q ss_pred cCccccceeccccccCCe-eEEcCCCCcccHHHHHHHHhcCCCCCCcccCCC
Q 037450 172 ESEKDCAICLDGIVVGQL-ASCTPCDHVFHKRCIDFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~-~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR~~l~ 222 (224)
.....|+|=--+|..... ....+|||+|-..-+.+. ...+|++|.....
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCccc
Confidence 345678887777632222 345669999999888774 3678999987654
No 154
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=27.73 E-value=10 Score=33.75 Aligned_cols=41 Identities=24% Similarity=0.559 Sum_probs=31.0
Q ss_pred cCccccceeccccccCCeeEEcCCCCcccHHHHHHHHhcCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKSR 212 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~~ 212 (224)
.....|.+|+++++.+......-|.-.||..|+-.|+....
T Consensus 212 k~~rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (288)
T KOG1729|consen 212 KPIRVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTGA 252 (288)
T ss_pred CCceecHHHHHHHhcccccchhhcccccccccccccccccc
Confidence 34448999999997655555566666999999999987543
No 156
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=27.03 E-value=42 Score=21.76 Aligned_cols=22 Identities=23% Similarity=0.824 Sum_probs=11.6
Q ss_pred CCCcccHHHHHHHHhcCCCCCCc
Q 037450 195 CDHVFHKRCIDFWLEKSRSCPLC 217 (224)
Q Consensus 195 C~H~FH~~CI~~Wl~~~~~CP~C 217 (224)
|+|.|-.. |..-......||.|
T Consensus 34 Cgh~w~~~-v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 34 CGHEWKAS-VNDRTRRGKGCPYC 55 (55)
T ss_pred CCCeeEcc-HhhhccCCCCCCCC
Confidence 55555332 23222456679988
No 157
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=26.46 E-value=35 Score=23.05 Aligned_cols=12 Identities=33% Similarity=1.021 Sum_probs=9.0
Q ss_pred CCCCCCcccCCC
Q 037450 211 SRSCPLCRNDLP 222 (224)
Q Consensus 211 ~~~CP~CR~~l~ 222 (224)
..+||+|.++..
T Consensus 39 ~p~CPlC~s~M~ 50 (59)
T PF14169_consen 39 EPVCPLCKSPMV 50 (59)
T ss_pred CccCCCcCCccc
Confidence 357999988753
No 158
>PF14353 CpXC: CpXC protein
Probab=26.01 E-value=65 Score=24.50 Aligned_cols=44 Identities=18% Similarity=0.292 Sum_probs=23.5
Q ss_pred cccceeccccccCCeeEEcCCCCcccHHHHHHHHhcC---CCCCCcccCC
Q 037450 175 KDCAICLDGIVVGQLASCTPCDHVFHKRCIDFWLEKS---RSCPLCRNDL 221 (224)
Q Consensus 175 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~Wl~~~---~~CP~CR~~l 221 (224)
.+|+-|...++.... +.-.=.-..+=.+..+... .+||.|.+..
T Consensus 2 itCP~C~~~~~~~v~---~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVW---TSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEE---eEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 468888887743211 1112223344445555333 2799998764
No 159
>PRK11827 hypothetical protein; Provisional
Probab=25.95 E-value=24 Score=23.92 Aligned_cols=18 Identities=33% Similarity=0.647 Sum_probs=13.0
Q ss_pred HHHHhcCCCCCCcccCCC
Q 037450 205 DFWLEKSRSCPLCRNDLP 222 (224)
Q Consensus 205 ~~Wl~~~~~CP~CR~~l~ 222 (224)
++||..-..||.|+.++.
T Consensus 2 d~~LLeILaCP~ckg~L~ 19 (60)
T PRK11827 2 DHRLLEIIACPVCNGKLW 19 (60)
T ss_pred ChHHHhheECCCCCCcCe
Confidence 456666677999988764
No 160
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.26 E-value=25 Score=22.75 Aligned_cols=23 Identities=4% Similarity=-0.084 Sum_probs=14.2
Q ss_pred chhhhhhhccCCCCCCCCchhhh
Q 037450 12 NTILNKVRNQLWDLPNMQPGFIF 34 (224)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~ 34 (224)
+..++.+++..-.||-|+|.|=-
T Consensus 10 ~k~i~~l~~~~~~CPlC~r~l~~ 32 (54)
T PF04423_consen 10 KKYIEELKEAKGCCPLCGRPLDE 32 (54)
T ss_dssp HHHHHHHTT-SEE-TTT--EE-H
T ss_pred HHHHHHHhcCCCcCCCCCCCCCH
Confidence 45677788888899999998865
No 161
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.01 E-value=73 Score=22.79 Aligned_cols=49 Identities=22% Similarity=0.673 Sum_probs=19.5
Q ss_pred CccccceeccccccCC----eeEEcCCCCcccHHHHHHHH-hcCCCCCCcccCC
Q 037450 173 SEKDCAICLDGIVVGQ----LASCTPCDHVFHKRCIDFWL-EKSRSCPLCRNDL 221 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~----~~~~lpC~H~FH~~CI~~Wl-~~~~~CP~CR~~l 221 (224)
....|-||-+++.... -+...-|+---|..|.+-=. .-++.||.|+..-
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 3457999999875432 13344578888889986433 4556899998753
No 162
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=23.30 E-value=30 Score=21.99 Aligned_cols=25 Identities=32% Similarity=0.767 Sum_probs=14.6
Q ss_pred eEEcCCCCcccHHHHHHHHh----cCCCCCCccc
Q 037450 190 ASCTPCDHVFHKRCIDFWLE----KSRSCPLCRN 219 (224)
Q Consensus 190 ~~~lpC~H~FH~~CI~~Wl~----~~~~CP~CR~ 219 (224)
++...|+|.|-. |.. ....||.|..
T Consensus 6 y~C~~Cg~~fe~-----~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEV-----LQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEE-----EEecCCCCCCCCCCCCC
Confidence 345557776643 221 2236999987
No 163
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=22.93 E-value=47 Score=25.20 Aligned_cols=46 Identities=26% Similarity=0.616 Sum_probs=28.2
Q ss_pred Cccccceecccccc--CCeeEEcCCCCcccHHHHHHHHhcCC--CCCCccc
Q 037450 173 SEKDCAICLDGIVV--GQLASCTPCDHVFHKRCIDFWLEKSR--SCPLCRN 219 (224)
Q Consensus 173 ~~~~C~ICle~~~~--~~~~~~lpC~H~FH~~CI~~Wl~~~~--~CP~CR~ 219 (224)
.+..|++|...|.. +.......|+|.+|..|-.. ..... .|-+|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 56789999987642 33456777999999999544 11111 4666643
No 164
>PLN02189 cellulose synthase
Probab=22.67 E-value=78 Score=33.12 Aligned_cols=49 Identities=29% Similarity=0.763 Sum_probs=32.8
Q ss_pred Cccccceecccccc---CCe-eEEcCCCCcccHHHHHHH-HhcCCCCCCcccCC
Q 037450 173 SEKDCAICLDGIVV---GQL-ASCTPCDHVFHKRCIDFW-LEKSRSCPLCRNDL 221 (224)
Q Consensus 173 ~~~~C~ICle~~~~---~~~-~~~lpC~H~FH~~CI~~W-l~~~~~CP~CR~~l 221 (224)
....|.||-+++.. |+. +.+--|+---|..|.+-= -+-++.||.|+..-
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRY 86 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 34579999999753 332 233337777899998432 23456899999753
No 165
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.40 E-value=27 Score=31.38 Aligned_cols=46 Identities=17% Similarity=0.328 Sum_probs=30.9
Q ss_pred cCccccceeccccccCCeeEEc--C--CCCcccHHHHHHHHhcCCCCCCccc
Q 037450 172 ESEKDCAICLDGIVVGQLASCT--P--CDHVFHKRCIDFWLEKSRSCPLCRN 219 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~l--p--C~H~FH~~CI~~Wl~~~~~CP~CR~ 219 (224)
+....||||-..=... +..+ . =.|..|.-|-..|-..+..||.|-.
T Consensus 185 ~~~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 185 EQRQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred cCCCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 3578999998753111 0001 1 2456777888889888999999975
No 166
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.25 E-value=20 Score=28.37 Aligned_cols=49 Identities=27% Similarity=0.612 Sum_probs=28.2
Q ss_pred cCccccceecc-ccccCCeeEEcCCCCcccHHHHHHHH-hcCC---CCCCcccC
Q 037450 172 ESEKDCAICLD-GIVVGQLASCTPCDHVFHKRCIDFWL-EKSR---SCPLCRND 220 (224)
Q Consensus 172 ~~~~~C~ICle-~~~~~~~~~~lpC~H~FH~~CI~~Wl-~~~~---~CP~CR~~ 220 (224)
..+.+|.||+. .|-+|---...-|.-.||..|--... +++. .|-+||..
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 67889999987 44433222333355556666654432 2233 58888753
No 167
>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=22.10 E-value=48 Score=19.24 Aligned_cols=12 Identities=17% Similarity=0.290 Sum_probs=9.8
Q ss_pred ccCCCCCCCCch
Q 037450 20 NQLWDLPNMQPG 31 (224)
Q Consensus 20 ~~~~~~~~~~~~ 31 (224)
..||.||.|..+
T Consensus 15 ~~~~~CP~Cg~~ 26 (33)
T cd00350 15 EAPWVCPVCGAP 26 (33)
T ss_pred cCCCcCcCCCCc
Confidence 379999999763
No 168
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.76 E-value=49 Score=24.43 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=10.5
Q ss_pred cccHHHHHHHHh
Q 037450 198 VFHKRCIDFWLE 209 (224)
Q Consensus 198 ~FH~~CI~~Wl~ 209 (224)
-||..|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999975
No 169
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.54 E-value=29 Score=32.53 Aligned_cols=40 Identities=20% Similarity=0.415 Sum_probs=28.2
Q ss_pred cCccccceeccccccCC-----eeEEcCCCCcccHHHHHHHHhcC
Q 037450 172 ESEKDCAICLDGIVVGQ-----LASCTPCDHVFHKRCIDFWLEKS 211 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~-----~~~~lpC~H~FH~~CI~~Wl~~~ 211 (224)
.....||.|....+... .-...+|.|.||.-|+..|....
T Consensus 224 ~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 224 ANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred ccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 34455999998876443 11223499999999999997764
No 170
>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=21.53 E-value=86 Score=27.71 Aligned_cols=45 Identities=24% Similarity=0.438 Sum_probs=27.2
Q ss_pred cCccccceeccccccCCeeEEcC-CC-CcccHHHHHHH-HhcCCCCCC
Q 037450 172 ESEKDCAICLDGIVVGQLASCTP-CD-HVFHKRCIDFW-LEKSRSCPL 216 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~lp-C~-H~FH~~CI~~W-l~~~~~CP~ 216 (224)
+.-..|.||+|.--+|..-.-|. =. =.-|.+|.++| +--++.||-
T Consensus 28 ~tLsfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~pr 75 (285)
T PF06937_consen 28 ETLSFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCPR 75 (285)
T ss_pred cceeecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCCc
Confidence 45567888888654433211111 11 14689999999 455668983
No 171
>PF12773 DZR: Double zinc ribbon
Probab=21.30 E-value=67 Score=20.06 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=7.3
Q ss_pred CCCCCcccCCC
Q 037450 212 RSCPLCRNDLP 222 (224)
Q Consensus 212 ~~CP~CR~~l~ 222 (224)
..||.|.+.++
T Consensus 30 ~~C~~Cg~~~~ 40 (50)
T PF12773_consen 30 KICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCCc
Confidence 35777777664
No 172
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=21.12 E-value=27 Score=31.29 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=30.0
Q ss_pred CccccceeccccccCCeeEE----cCCCCcccHHHHHHHHhcCCCCCCcccC
Q 037450 173 SEKDCAICLDGIVVGQLASC----TPCDHVFHKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 173 ~~~~C~ICle~~~~~~~~~~----lpC~H~FH~~CI~~Wl~~~~~CP~CR~~ 220 (224)
....||||-..=..+. ++. -.=.|..|.-|-..|-..+..||.|-..
T Consensus 183 ~~~~CPvCGs~P~~s~-~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 183 SRTLCPACGSPPVASM-VRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCcCCCCCChhhhhh-hcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 4558999987531110 110 0023556777888898889999999763
No 173
>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=20.90 E-value=63 Score=27.76 Aligned_cols=21 Identities=24% Similarity=0.651 Sum_probs=15.4
Q ss_pred cHHHHHHHHhcCCCCCCcccC
Q 037450 200 HKRCIDFWLEKSRSCPLCRND 220 (224)
Q Consensus 200 H~~CI~~Wl~~~~~CP~CR~~ 220 (224)
|..|-...-+....||+|+..
T Consensus 197 C~sC~qqIHRNAPiCPlCK~K 217 (230)
T PF10146_consen 197 CQSCHQQIHRNAPICPLCKAK 217 (230)
T ss_pred hHhHHHHHhcCCCCCcccccc
Confidence 456666666677899999864
No 174
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.68 E-value=50 Score=32.82 Aligned_cols=42 Identities=17% Similarity=0.343 Sum_probs=30.1
Q ss_pred ccccceeccccc-cCCeeEEcCCCCcccHHHHHHHHhcCCCCCCcc
Q 037450 174 EKDCAICLDGIV-VGQLASCTPCDHVFHKRCIDFWLEKSRSCPLCR 218 (224)
Q Consensus 174 ~~~C~ICle~~~-~~~~~~~lpC~H~FH~~CI~~Wl~~~~~CP~CR 218 (224)
...|-+|...-. ..+..+.+.|+-.||.+| |+.-.+.||+|-
T Consensus 654 ~r~C~vcq~pedse~~v~rt~~C~~~~C~~c---~~~~~~~~~vC~ 696 (717)
T KOG3726|consen 654 IRTCKVCQLPEDSETDVCRTTFCYTPYCVAC---SLDYASISEVCG 696 (717)
T ss_pred HHHHHHhcCCcCccccccCccccCCcchHhh---hhhhhccCcccC
Confidence 567889976422 223445667999999988 777788899994
No 175
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.62 E-value=49 Score=21.52 Aligned_cols=27 Identities=30% Similarity=0.471 Sum_probs=17.1
Q ss_pred Ccccccccccchhhhhhhcc--CCCCCCCCc
Q 037450 2 SNCELKLRQDNTILNKVRNQ--LWDLPNMQP 30 (224)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 30 (224)
+.|-++|.. ..+++++.. .--||+|+|
T Consensus 26 ~gC~~~l~~--~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 26 SGCHMELPP--QELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred CCCCEEcCH--HHHHHHHcCCCeEECcCCCc
Confidence 346666643 345555544 778999987
No 176
>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=20.13 E-value=53 Score=18.17 Aligned_cols=9 Identities=33% Similarity=1.265 Sum_probs=5.8
Q ss_pred CCCCcccCC
Q 037450 213 SCPLCRNDL 221 (224)
Q Consensus 213 ~CP~CR~~l 221 (224)
.||+|...+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 477776654
No 177
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=20.13 E-value=69 Score=22.53 Aligned_cols=33 Identities=27% Similarity=0.662 Sum_probs=23.3
Q ss_pred cCccccceeccccccCCeeEE--cCCCCcccHHHHHH
Q 037450 172 ESEKDCAICLDGIVVGQLASC--TPCDHVFHKRCIDF 206 (224)
Q Consensus 172 ~~~~~C~ICle~~~~~~~~~~--lpC~H~FH~~CI~~ 206 (224)
.....|.+|... .|..+.. -.|.-.||..|...
T Consensus 34 ~~~~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 34 RRKLKCSICKKK--GGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred HhCCCCcCCCCC--CCeEEEEeCCCCCcEEChHHHcc
Confidence 456789999975 2444432 33999999999754
Done!