Query 038790
Match_columns 139
No_of_seqs 115 out of 1423
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 03:19:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038790.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038790hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4628 Predicted E3 ubiquitin 99.8 2E-19 4.2E-24 138.8 6.9 85 31-116 204-288 (348)
2 PF13639 zf-RING_2: Ring finge 99.7 2.1E-17 4.5E-22 92.6 1.9 44 57-102 1-44 (44)
3 COG5540 RING-finger-containing 99.5 7.1E-15 1.5E-19 110.8 2.8 55 53-108 320-374 (374)
4 PF12678 zf-rbx1: RING-H2 zinc 99.5 2.9E-14 6.2E-19 88.1 3.9 45 56-102 19-73 (73)
5 KOG0317 Predicted E3 ubiquitin 99.5 1.2E-13 2.5E-18 103.6 6.5 54 52-110 235-288 (293)
6 PHA02929 N1R/p28-like protein; 99.4 9.2E-14 2E-18 103.1 4.5 52 53-106 171-227 (238)
7 COG5243 HRD1 HRD ubiquitin lig 99.4 2.3E-13 5E-18 105.2 3.1 51 53-105 284-344 (491)
8 KOG1734 Predicted RING-contain 99.3 2.1E-13 4.5E-18 101.4 1.4 68 53-120 221-295 (328)
9 PF12861 zf-Apc11: Anaphase-pr 99.3 1E-12 2.2E-17 82.5 3.1 54 55-108 20-84 (85)
10 KOG0823 Predicted E3 ubiquitin 99.2 7.9E-12 1.7E-16 91.3 3.9 54 52-108 43-97 (230)
11 PF13923 zf-C3HC4_2: Zinc fing 99.2 8.1E-12 1.8E-16 68.0 2.9 39 59-101 1-39 (39)
12 PLN03208 E3 ubiquitin-protein 99.2 1.3E-11 2.9E-16 88.5 4.2 54 53-109 15-82 (193)
13 cd00162 RING RING-finger (Real 99.2 1.7E-11 3.6E-16 67.7 3.2 45 58-105 1-45 (45)
14 PF13920 zf-C3HC4_3: Zinc fing 99.2 2.7E-11 5.9E-16 69.4 3.3 46 56-106 2-48 (50)
15 PHA02926 zinc finger-like prot 99.1 5.1E-11 1.1E-15 86.8 4.3 55 52-106 166-230 (242)
16 KOG0802 E3 ubiquitin ligase [P 99.1 3.2E-11 6.9E-16 99.5 2.2 58 54-113 289-348 (543)
17 PF00097 zf-C3HC4: Zinc finger 99.1 1.1E-10 2.3E-15 64.0 2.9 41 59-101 1-41 (41)
18 PF14634 zf-RING_5: zinc-RING 99.0 1.6E-10 3.4E-15 64.5 3.0 44 58-103 1-44 (44)
19 KOG0320 Predicted E3 ubiquitin 99.0 1.3E-10 2.8E-15 81.9 2.5 55 52-109 127-181 (187)
20 KOG1493 Anaphase-promoting com 99.0 5.4E-11 1.2E-15 72.5 0.3 53 55-107 19-82 (84)
21 PF15227 zf-C3HC4_4: zinc fing 99.0 3.6E-10 7.9E-15 62.4 3.2 40 59-101 1-42 (42)
22 COG5194 APC11 Component of SCF 99.0 5.1E-10 1.1E-14 68.8 3.0 52 57-110 21-85 (88)
23 smart00504 Ubox Modified RING 98.9 1.8E-09 3.8E-14 64.3 3.6 48 57-109 2-49 (63)
24 smart00184 RING Ring finger. E 98.9 1.7E-09 3.7E-14 57.5 2.8 39 59-101 1-39 (39)
25 KOG0828 Predicted E3 ubiquitin 98.9 2.9E-09 6.2E-14 85.3 4.7 53 54-107 569-635 (636)
26 TIGR00599 rad18 DNA repair pro 98.8 4.2E-09 9.1E-14 83.5 3.5 51 53-108 23-73 (397)
27 smart00744 RINGv The RING-vari 98.7 1E-08 2.2E-13 58.4 2.9 44 58-102 1-49 (49)
28 COG5574 PEX10 RING-finger-cont 98.7 9.5E-09 2.1E-13 76.6 2.3 53 54-110 213-266 (271)
29 COG5219 Uncharacterized conser 98.6 6.3E-09 1.4E-13 88.7 -0.8 70 37-106 1450-1523(1525)
30 PF11793 FANCL_C: FANCL C-term 98.6 1.6E-08 3.4E-13 61.9 0.8 53 56-108 2-68 (70)
31 PF13445 zf-RING_UBOX: RING-ty 98.5 8.3E-08 1.8E-12 53.1 2.6 40 59-99 1-43 (43)
32 KOG0804 Cytoplasmic Zn-finger 98.5 5.7E-08 1.2E-12 77.1 2.3 49 54-106 173-222 (493)
33 KOG2164 Predicted E3 ubiquitin 98.5 8.1E-08 1.7E-12 77.4 3.0 52 56-110 186-240 (513)
34 PF04564 U-box: U-box domain; 98.5 1.8E-07 4E-12 57.6 3.3 55 55-113 3-57 (73)
35 KOG2930 SCF ubiquitin ligase, 98.4 8.1E-08 1.8E-12 62.0 1.6 52 55-108 45-110 (114)
36 COG5432 RAD18 RING-finger-cont 98.4 7.9E-08 1.7E-12 72.8 1.1 55 54-113 23-77 (391)
37 TIGR00570 cdk7 CDK-activating 98.4 2.7E-07 5.8E-12 70.9 3.8 54 55-109 2-57 (309)
38 KOG0287 Postreplication repair 98.3 1.7E-07 3.8E-12 72.2 1.2 50 54-108 21-70 (442)
39 KOG0827 Predicted E3 ubiquitin 98.3 3.5E-07 7.6E-12 71.6 2.0 47 56-102 4-52 (465)
40 KOG2177 Predicted E3 ubiquitin 98.2 5.8E-07 1.3E-11 67.4 1.5 45 53-102 10-54 (386)
41 KOG4265 Predicted E3 ubiquitin 98.2 1.3E-06 2.8E-11 67.8 2.8 51 54-109 288-339 (349)
42 PF11789 zf-Nse: Zinc-finger o 98.0 4.3E-06 9.3E-11 49.0 2.7 45 54-100 9-53 (57)
43 PF14835 zf-RING_6: zf-RING of 98.0 1.3E-06 2.8E-11 52.0 -0.1 45 56-106 7-51 (65)
44 KOG1645 RING-finger-containing 98.0 4.8E-06 1E-10 65.7 2.8 49 55-103 3-53 (463)
45 KOG2879 Predicted E3 ubiquitin 97.9 3.8E-05 8.3E-10 57.9 7.0 57 49-107 232-288 (298)
46 KOG0824 Predicted E3 ubiquitin 97.9 5.2E-06 1.1E-10 63.2 1.7 50 54-107 5-54 (324)
47 KOG1039 Predicted E3 ubiquitin 97.9 5.5E-06 1.2E-10 64.8 1.7 52 54-105 159-220 (344)
48 KOG0825 PHD Zn-finger protein 97.9 3.1E-06 6.6E-11 71.5 0.2 52 56-109 123-174 (1134)
49 KOG4172 Predicted E3 ubiquitin 97.9 2.5E-06 5.3E-11 49.0 -0.3 47 56-106 7-54 (62)
50 KOG0311 Predicted E3 ubiquitin 97.8 2.7E-06 5.8E-11 66.0 -1.2 59 54-115 41-99 (381)
51 KOG0978 E3 ubiquitin ligase in 97.8 5.4E-06 1.2E-10 69.7 0.0 51 56-110 643-693 (698)
52 PHA02825 LAP/PHD finger-like p 97.7 3.2E-05 7E-10 54.0 3.5 55 53-111 5-64 (162)
53 KOG0297 TNF receptor-associate 97.7 1.7E-05 3.6E-10 63.4 1.6 56 53-112 18-73 (391)
54 KOG1941 Acetylcholine receptor 97.6 1.7E-05 3.6E-10 62.5 0.9 49 55-103 364-413 (518)
55 PHA02862 5L protein; Provision 97.6 4.2E-05 9E-10 52.5 2.5 52 56-111 2-58 (156)
56 KOG0801 Predicted E3 ubiquitin 97.6 1.8E-05 3.8E-10 55.4 0.3 41 43-83 164-204 (205)
57 PF12906 RINGv: RING-variant d 97.5 4.4E-05 9.5E-10 43.0 1.1 42 59-101 1-47 (47)
58 KOG4445 Uncharacterized conser 97.5 4.6E-05 9.9E-10 58.2 1.2 58 52-109 111-189 (368)
59 KOG4159 Predicted E3 ubiquitin 97.4 0.00011 2.4E-09 58.7 2.6 50 53-107 81-130 (398)
60 KOG1785 Tyrosine kinase negati 97.4 7.1E-05 1.5E-09 59.3 1.5 48 55-105 368-415 (563)
61 PF05883 Baculo_RING: Baculovi 97.3 7.8E-05 1.7E-09 50.7 1.1 36 56-91 26-67 (134)
62 KOG3970 Predicted E3 ubiquitin 97.3 0.0002 4.4E-09 52.7 3.1 57 55-112 49-111 (299)
63 KOG1428 Inhibitor of type V ad 97.3 0.00018 3.9E-09 64.8 2.7 53 54-106 3484-3544(3738)
64 PF10367 Vps39_2: Vacuolar sor 97.0 0.00027 5.9E-09 46.0 1.1 34 53-87 75-108 (109)
65 KOG0826 Predicted E3 ubiquitin 97.0 0.0033 7.2E-08 48.7 6.8 51 51-105 295-345 (357)
66 KOG2660 Locus-specific chromos 97.0 9.6E-05 2.1E-09 57.0 -1.5 56 52-111 11-66 (331)
67 KOG3039 Uncharacterized conser 96.9 0.001 2.2E-08 49.7 3.3 53 55-109 220-273 (303)
68 PF04641 Rtf2: Rtf2 RING-finge 96.8 0.0026 5.7E-08 48.2 5.3 55 53-110 110-165 (260)
69 PF08746 zf-RING-like: RING-li 96.8 0.00051 1.1E-08 37.9 0.9 43 59-101 1-43 (43)
70 PF14570 zf-RING_4: RING/Ubox 96.8 0.0012 2.7E-08 37.1 2.3 46 59-105 1-47 (48)
71 KOG1002 Nucleotide excision re 96.7 0.00045 9.8E-09 56.6 0.2 58 52-112 532-592 (791)
72 KOG1814 Predicted E3 ubiquitin 96.6 0.001 2.2E-08 52.9 1.8 50 54-103 182-237 (445)
73 KOG4739 Uncharacterized protei 96.6 0.0011 2.3E-08 49.3 1.5 52 57-113 4-55 (233)
74 KOG3268 Predicted E3 ubiquitin 96.6 0.0014 3.1E-08 46.7 2.1 36 75-110 188-232 (234)
75 COG5152 Uncharacterized conser 96.5 0.00096 2.1E-08 48.4 0.9 45 56-105 196-240 (259)
76 KOG1952 Transcription factor N 96.5 0.0015 3.2E-08 56.2 1.8 52 52-103 187-244 (950)
77 PF14447 Prok-RING_4: Prokaryo 96.4 0.0016 3.4E-08 37.6 1.0 47 56-109 7-53 (55)
78 KOG4185 Predicted E3 ubiquitin 96.2 0.0031 6.8E-08 48.4 2.4 49 56-105 3-54 (296)
79 KOG4275 Predicted E3 ubiquitin 96.2 0.0014 3.1E-08 50.0 0.5 41 56-105 300-341 (350)
80 COG5236 Uncharacterized conser 96.2 0.005 1.1E-07 48.2 3.2 55 49-106 54-108 (493)
81 PHA03096 p28-like protein; Pro 95.7 0.0055 1.2E-07 47.1 1.7 47 57-103 179-231 (284)
82 KOG1571 Predicted E3 ubiquitin 95.7 0.0078 1.7E-07 47.2 2.5 49 50-106 299-347 (355)
83 KOG1813 Predicted E3 ubiquitin 95.7 0.0041 8.8E-08 47.6 0.7 46 56-106 241-286 (313)
84 KOG0827 Predicted E3 ubiquitin 95.6 0.00066 1.4E-08 53.6 -3.8 52 55-108 195-247 (465)
85 PF07800 DUF1644: Protein of u 95.5 0.013 2.8E-07 41.0 2.8 72 55-129 1-119 (162)
86 KOG1001 Helicase-like transcri 95.4 0.016 3.5E-07 49.5 3.5 52 57-112 455-506 (674)
87 PF10272 Tmpp129: Putative tra 95.0 0.034 7.4E-07 44.0 4.0 66 41-106 255-351 (358)
88 COG5183 SSM4 Protein involved 94.9 0.021 4.6E-07 49.3 2.7 67 54-121 10-81 (1175)
89 KOG4692 Predicted E3 ubiquitin 94.9 0.025 5.3E-07 44.6 2.9 50 53-107 419-468 (489)
90 KOG1609 Protein involved in mR 94.8 0.02 4.3E-07 44.0 2.3 52 56-107 78-135 (323)
91 KOG2114 Vacuolar assembly/sort 94.8 0.014 3.1E-07 50.3 1.6 41 56-103 840-880 (933)
92 PF14446 Prok-RING_1: Prokaryo 94.6 0.039 8.4E-07 31.8 2.5 31 55-85 4-35 (54)
93 KOG1940 Zn-finger protein [Gen 94.6 0.021 4.5E-07 43.6 1.9 47 55-103 157-204 (276)
94 KOG2817 Predicted E3 ubiquitin 94.6 0.083 1.8E-06 42.1 5.2 51 53-103 331-382 (394)
95 PF03854 zf-P11: P-11 zinc fin 94.3 0.017 3.8E-07 32.2 0.6 44 58-108 4-48 (50)
96 KOG2034 Vacuolar sorting prote 94.1 0.025 5.3E-07 49.1 1.5 37 54-91 815-851 (911)
97 COG5222 Uncharacterized conser 93.7 0.034 7.4E-07 42.9 1.4 45 56-103 274-318 (427)
98 KOG2932 E3 ubiquitin ligase in 93.7 0.028 6.1E-07 43.5 0.9 42 58-105 92-133 (389)
99 COG5175 MOT2 Transcriptional r 93.6 0.051 1.1E-06 42.7 2.3 51 54-108 12-66 (480)
100 KOG1812 Predicted E3 ubiquitin 93.3 0.17 3.8E-06 40.5 4.9 38 54-91 144-182 (384)
101 KOG3800 Predicted E3 ubiquitin 92.6 0.11 2.3E-06 39.9 2.7 47 58-105 2-50 (300)
102 KOG0309 Conserved WD40 repeat- 92.4 0.078 1.7E-06 45.6 1.8 39 59-100 1031-1069(1081)
103 KOG0298 DEAD box-containing he 91.5 0.044 9.6E-07 49.4 -0.6 45 55-103 1152-1196(1394)
104 PF05290 Baculo_IE-1: Baculovi 91.2 0.19 4E-06 34.3 2.3 55 54-110 78-136 (140)
105 KOG3053 Uncharacterized conser 90.9 0.12 2.7E-06 39.0 1.3 54 53-106 17-82 (293)
106 KOG3899 Uncharacterized conser 90.7 0.13 2.8E-06 39.6 1.3 31 77-107 325-366 (381)
107 KOG3113 Uncharacterized conser 90.5 0.25 5.3E-06 37.3 2.6 60 55-118 110-170 (293)
108 KOG3002 Zn finger protein [Gen 90.4 0.19 4E-06 39.0 2.0 48 53-109 45-94 (299)
109 PF02891 zf-MIZ: MIZ/SP-RING z 90.0 0.5 1.1E-05 26.6 3.1 45 57-104 3-50 (50)
110 KOG4367 Predicted Zn-finger pr 89.8 0.32 7E-06 39.6 2.9 35 54-91 2-36 (699)
111 COG5220 TFB3 Cdk activating ki 89.4 0.18 3.8E-06 37.9 1.1 49 54-103 8-61 (314)
112 KOG1100 Predicted E3 ubiquitin 89.1 0.27 6E-06 36.1 1.9 40 59-107 161-201 (207)
113 KOG1815 Predicted E3 ubiquitin 88.9 0.46 9.9E-06 38.8 3.3 38 53-92 67-104 (444)
114 KOG4718 Non-SMC (structural ma 87.6 0.3 6.6E-06 35.9 1.3 44 56-103 181-224 (235)
115 smart00249 PHD PHD zinc finger 86.7 0.32 6.9E-06 25.9 0.8 31 58-88 1-31 (47)
116 PF13901 DUF4206: Domain of un 86.3 0.65 1.4E-05 33.9 2.5 42 55-103 151-197 (202)
117 KOG0802 E3 ubiquitin ligase [P 85.6 0.43 9.3E-06 39.9 1.4 53 54-115 477-529 (543)
118 KOG3005 GIY-YIG type nuclease 84.3 0.77 1.7E-05 35.0 2.1 51 56-106 182-243 (276)
119 KOG1829 Uncharacterized conser 84.1 0.34 7.4E-06 40.8 0.2 44 55-103 510-558 (580)
120 KOG3161 Predicted E3 ubiquitin 84.0 0.3 6.6E-06 41.4 -0.1 43 56-103 11-54 (861)
121 KOG4362 Transcriptional regula 82.7 0.32 6.8E-06 41.6 -0.5 51 55-108 20-71 (684)
122 KOG0825 PHD Zn-finger protein 80.7 1.1 2.3E-05 39.2 1.9 52 55-106 95-154 (1134)
123 PF14569 zf-UDP: Zinc-binding 80.0 2 4.4E-05 26.6 2.5 52 54-106 7-62 (80)
124 COG5109 Uncharacterized conser 79.8 4.2 9E-05 31.9 4.6 50 52-101 332-382 (396)
125 KOG3842 Adaptor protein Pellin 79.1 2.7 5.8E-05 33.0 3.4 59 54-112 339-420 (429)
126 KOG0269 WD40 repeat-containing 78.4 2.2 4.8E-05 37.0 3.0 42 56-100 779-820 (839)
127 PF00628 PHD: PHD-finger; Int 76.3 1.1 2.4E-05 24.8 0.5 45 58-102 1-49 (51)
128 PF04423 Rad50_zn_hook: Rad50 75.5 0.87 1.9E-05 25.9 -0.1 16 94-109 19-34 (54)
129 PF01363 FYVE: FYVE zinc finge 72.5 1.7 3.7E-05 25.7 0.7 37 54-90 7-44 (69)
130 KOG2066 Vacuolar assembly/sort 71.6 1.5 3.3E-05 38.1 0.4 45 54-101 782-830 (846)
131 PF04710 Pellino: Pellino; In 70.2 1.4 3.1E-05 35.4 0.0 57 55-111 327-406 (416)
132 PLN02189 cellulose synthase 69.6 5.3 0.00011 36.1 3.3 52 54-106 32-87 (1040)
133 PF10497 zf-4CXXC_R1: Zinc-fin 69.3 8.3 0.00018 25.2 3.5 48 55-103 6-69 (105)
134 PLN02195 cellulose synthase A 69.0 5.5 0.00012 35.7 3.3 52 54-106 4-59 (977)
135 PF10571 UPF0547: Uncharacteri 68.9 2.5 5.4E-05 20.5 0.7 22 58-81 2-24 (26)
136 PLN02436 cellulose synthase A 67.7 6.1 0.00013 35.8 3.3 52 54-106 34-89 (1094)
137 KOG2979 Protein involved in DN 65.8 3.6 7.7E-05 31.2 1.3 44 56-101 176-219 (262)
138 KOG2068 MOT2 transcription fac 65.7 5.7 0.00012 31.2 2.5 49 56-106 249-298 (327)
139 COG4847 Uncharacterized protei 65.4 6.6 0.00014 25.3 2.3 36 55-91 5-40 (103)
140 PLN02915 cellulose synthase A 65.1 8.1 0.00018 35.0 3.5 53 53-106 12-68 (1044)
141 PF07191 zinc-ribbons_6: zinc- 64.4 0.54 1.2E-05 28.5 -2.6 40 57-106 2-41 (70)
142 PLN02638 cellulose synthase A 63.6 8.7 0.00019 34.9 3.5 52 54-106 15-70 (1079)
143 PF06844 DUF1244: Protein of u 62.5 4.8 0.0001 24.1 1.2 12 80-91 11-22 (68)
144 KOG1812 Predicted E3 ubiquitin 62.4 3.8 8.1E-05 33.0 1.0 44 56-101 306-351 (384)
145 COG4469 CoiA Competence protei 61.6 3.1 6.6E-05 32.8 0.3 49 86-134 15-64 (342)
146 smart00064 FYVE Protein presen 61.1 8.4 0.00018 22.6 2.2 37 55-91 9-46 (68)
147 smart00132 LIM Zinc-binding do 58.6 5.5 0.00012 20.0 0.9 36 59-105 2-37 (39)
148 PF10886 DUF2685: Protein of u 58.5 4.5 9.8E-05 23.2 0.6 23 97-119 3-25 (54)
149 PLN02400 cellulose synthase 58.4 9.4 0.0002 34.7 2.8 52 54-106 34-89 (1085)
150 KOG2807 RNA polymerase II tran 58.0 9.2 0.0002 30.2 2.4 48 54-103 328-375 (378)
151 KOG1729 FYVE finger containing 57.5 2.1 4.5E-05 33.1 -1.2 34 58-91 216-249 (288)
152 PF07649 C1_3: C1-like domain; 57.2 10 0.00022 18.6 1.8 29 58-86 2-30 (30)
153 PF06906 DUF1272: Protein of u 57.1 18 0.00039 21.0 2.9 47 57-108 6-54 (57)
154 cd00065 FYVE FYVE domain; Zinc 56.0 9.7 0.00021 21.3 1.8 35 57-91 3-38 (57)
155 PF13717 zinc_ribbon_4: zinc-r 55.4 9.2 0.0002 19.9 1.4 25 58-82 4-36 (36)
156 PF09889 DUF2116: Uncharacteri 55.4 6.3 0.00014 23.1 0.9 16 94-109 2-17 (59)
157 PHA02446 hypothetical protein 53.1 4 8.6E-05 27.4 -0.3 16 120-136 87-102 (166)
158 PF05605 zf-Di19: Drought indu 52.8 1.3 2.9E-05 25.1 -2.3 39 56-104 2-40 (54)
159 PF00412 LIM: LIM domain; Int 51.9 21 0.00045 19.8 2.7 40 59-109 1-40 (58)
160 PF13832 zf-HC5HC2H_2: PHD-zin 51.5 11 0.00025 24.2 1.7 32 55-88 54-87 (110)
161 PF09943 DUF2175: Uncharacteri 50.2 18 0.00038 23.6 2.4 34 57-91 3-36 (101)
162 PF13771 zf-HC5HC2H: PHD-like 48.5 11 0.00025 23.2 1.4 31 56-88 36-68 (90)
163 TIGR00622 ssl1 transcription f 46.3 24 0.00053 23.4 2.7 45 56-102 55-110 (112)
164 COG3813 Uncharacterized protei 45.3 22 0.00048 21.7 2.2 44 59-106 8-52 (84)
165 COG4357 Zinc finger domain con 44.5 15 0.00033 23.7 1.4 29 77-108 65-93 (105)
166 PF13719 zinc_ribbon_5: zinc-r 44.3 18 0.00039 18.8 1.5 12 58-69 4-15 (37)
167 KOG3039 Uncharacterized conser 43.8 25 0.00055 26.8 2.7 36 53-91 40-75 (303)
168 PHA02610 uvsY.-2 hypothetical 42.7 9.2 0.0002 21.7 0.2 22 97-118 3-24 (53)
169 smart00746 TRASH metallochaper 42.1 12 0.00026 17.8 0.6 9 98-106 1-9 (39)
170 PF04216 FdhE: Protein involve 42.0 2.4 5.1E-05 32.6 -3.1 42 55-103 171-219 (290)
171 PRK11827 hypothetical protein; 42.0 8.5 0.00018 22.6 -0.0 18 88-107 3-20 (60)
172 PF00130 C1_1: Phorbol esters/ 41.0 24 0.00053 19.3 1.8 35 54-88 9-45 (53)
173 cd00350 rubredoxin_like Rubred 40.9 12 0.00027 18.8 0.5 10 94-103 16-25 (33)
174 PF09237 GAGA: GAGA factor; I 40.5 5.5 0.00012 22.7 -0.9 12 96-107 25-36 (54)
175 PF07975 C1_4: TFIIH C1-like d 39.8 19 0.00042 20.4 1.2 42 59-102 2-50 (51)
176 PF15353 HECA: Headcase protei 38.7 32 0.0007 22.6 2.3 16 76-91 39-54 (107)
177 KOG0956 PHD finger protein AF1 38.0 17 0.00037 31.7 1.1 53 54-106 115-182 (900)
178 PF04890 DUF648: Family of unk 37.9 38 0.00082 26.7 2.9 25 1-25 64-88 (328)
179 PF05715 zf-piccolo: Piccolo Z 37.7 19 0.00041 21.1 1.0 12 95-106 2-13 (61)
180 PRK11088 rrmA 23S rRNA methylt 37.0 25 0.00054 26.4 1.9 26 57-82 3-28 (272)
181 PF02318 FYVE_2: FYVE-type zin 36.9 12 0.00027 24.7 0.2 48 55-103 53-102 (118)
182 KOG2462 C2H2-type Zn-finger pr 36.9 14 0.00031 28.4 0.5 56 56-111 161-231 (279)
183 smart00734 ZnF_Rad18 Rad18-lik 36.7 15 0.00032 17.6 0.4 10 96-105 2-11 (26)
184 KOG4185 Predicted E3 ubiquitin 36.1 4.9 0.00011 30.7 -2.1 49 55-104 206-265 (296)
185 COG5627 MMS21 DNA repair prote 34.3 20 0.00044 27.0 1.0 43 56-100 189-231 (275)
186 PF14311 DUF4379: Domain of un 34.3 24 0.00051 19.9 1.1 23 76-101 33-55 (55)
187 COG3492 Uncharacterized protei 33.7 21 0.00045 22.8 0.8 12 80-91 42-53 (104)
188 COG4068 Uncharacterized protei 33.5 21 0.00046 20.9 0.8 17 94-110 7-23 (64)
189 KOG4218 Nuclear hormone recept 33.5 16 0.00034 29.2 0.3 49 54-103 13-75 (475)
190 COG2835 Uncharacterized conser 32.1 20 0.00043 21.1 0.5 15 95-109 8-22 (60)
191 PF09986 DUF2225: Uncharacteri 32.0 21 0.00045 26.3 0.7 22 94-115 4-25 (214)
192 KOG3579 Predicted E3 ubiquitin 31.8 31 0.00066 26.9 1.6 36 55-91 267-304 (352)
193 cd00029 C1 Protein kinase C co 31.6 33 0.00071 18.3 1.3 34 55-88 10-45 (50)
194 KOG1512 PHD Zn-finger protein 31.5 21 0.00045 27.8 0.6 34 55-88 313-346 (381)
195 KOG2231 Predicted E3 ubiquitin 30.8 46 0.001 28.9 2.6 47 58-107 2-53 (669)
196 PF13913 zf-C2HC_2: zinc-finge 30.7 14 0.00031 17.4 -0.2 13 96-108 3-15 (25)
197 PF12088 DUF3565: Protein of u 29.7 42 0.00091 19.7 1.6 15 68-82 8-22 (61)
198 PF03884 DUF329: Domain of unk 29.6 23 0.00049 20.6 0.4 12 96-107 3-14 (57)
199 PF14169 YdjO: Cold-inducible 29.1 50 0.0011 19.3 1.8 17 54-70 37-53 (59)
200 PF03119 DNA_ligase_ZBD: NAD-d 28.7 27 0.00059 17.0 0.6 10 97-106 1-10 (28)
201 cd00729 rubredoxin_SM Rubredox 28.6 26 0.00057 17.9 0.5 9 95-103 18-26 (34)
202 PF11376 DUF3179: Protein of u 28.5 21 0.00046 27.3 0.3 42 96-138 63-108 (266)
203 PF06054 CoiA: Competence prot 28.3 31 0.00067 27.6 1.2 20 94-113 29-48 (375)
204 PF06676 DUF1178: Protein of u 28.0 23 0.00049 24.7 0.3 22 77-103 10-40 (148)
205 KOG2071 mRNA cleavage and poly 27.7 36 0.00078 29.0 1.5 36 54-89 511-556 (579)
206 smart00109 C1 Protein kinase C 27.4 45 0.00097 17.5 1.4 34 55-88 10-44 (49)
207 TIGR02652 conserved hypothetic 26.9 27 0.00058 24.2 0.5 13 94-106 8-20 (163)
208 PF10170 C6_DPF: Cysteine-rich 26.8 64 0.0014 20.8 2.2 36 55-91 48-83 (97)
209 PF09654 DUF2396: Protein of u 26.7 27 0.00059 24.1 0.5 13 94-106 5-17 (161)
210 COG4768 Uncharacterized protei 26.7 87 0.0019 21.5 2.9 18 1-18 2-19 (139)
211 PF11290 DUF3090: Protein of u 26.7 34 0.00075 24.4 1.0 15 94-108 153-167 (171)
212 PRK01343 zinc-binding protein; 26.5 30 0.00066 20.1 0.6 13 94-106 8-20 (57)
213 COG1545 Predicted nucleic-acid 26.1 30 0.00066 23.7 0.7 20 76-105 34-53 (140)
214 PF13453 zf-TFIIB: Transcripti 25.9 26 0.00057 18.5 0.2 14 97-110 1-14 (41)
215 PRK03564 formate dehydrogenase 24.4 33 0.00071 26.9 0.6 42 55-103 186-234 (309)
216 PRK00418 DNA gyrase inhibitor; 24.2 41 0.00089 19.9 0.9 12 95-106 6-17 (62)
217 smart00647 IBR In Between Ring 23.8 20 0.00044 20.2 -0.5 15 76-90 45-59 (64)
218 TIGR03847 conserved hypothetic 23.5 43 0.00093 24.0 1.0 15 94-108 155-169 (177)
219 PF08209 Sgf11: Sgf11 (transcr 23.4 31 0.00067 17.7 0.2 15 95-109 4-18 (33)
220 PLN02248 cellulose synthase-li 23.3 1.8E+02 0.0038 27.1 4.9 28 77-106 150-177 (1135)
221 PF15616 TerY-C: TerY-C metal 23.2 36 0.00078 23.2 0.6 46 54-110 75-120 (131)
222 KOG4577 Transcription factor L 22.9 21 0.00046 27.7 -0.6 41 56-107 92-132 (383)
223 KOG0824 Predicted E3 ubiquitin 22.9 30 0.00065 27.1 0.2 48 54-105 103-150 (324)
224 CHL00031 psbT photosystem II p 22.9 1.1E+02 0.0023 15.7 2.1 19 2-20 4-22 (33)
225 PRK11875 psbT photosystem II r 22.7 1.2E+02 0.0026 15.2 2.6 19 2-20 4-22 (31)
226 KOG4451 Uncharacterized conser 22.6 54 0.0012 24.7 1.4 21 82-104 252-272 (286)
227 PF00096 zf-C2H2: Zinc finger, 22.2 14 0.0003 16.4 -1.2 9 98-106 3-11 (23)
228 PF10146 zf-C4H2: Zinc finger- 22.1 60 0.0013 24.3 1.6 20 82-103 197-216 (230)
229 PF06645 SPC12: Microsomal sig 21.6 1.3E+02 0.0029 18.2 2.9 25 2-26 13-37 (76)
230 PRK11595 DNA utilization prote 21.4 71 0.0015 23.5 1.9 37 58-104 7-43 (227)
231 PF07282 OrfB_Zn_ribbon: Putat 21.1 91 0.002 18.0 2.0 32 55-86 27-61 (69)
232 PRK05978 hypothetical protein; 21.0 56 0.0012 22.8 1.2 29 78-113 42-70 (148)
233 PF06170 DUF983: Protein of un 21.0 36 0.00078 21.4 0.2 22 88-111 3-24 (86)
234 KOG4443 Putative transcription 21.0 54 0.0012 28.4 1.3 28 76-103 40-70 (694)
235 KOG1538 Uncharacterized conser 20.9 43 0.00092 29.4 0.7 28 77-106 1050-1077(1081)
236 PHA03164 hypothetical protein; 20.8 1.9E+02 0.0041 17.9 3.3 24 3-26 59-82 (88)
237 KOG1818 Membrane trafficking a 20.7 40 0.00086 29.1 0.5 52 55-106 164-222 (634)
238 PF05115 PetL: Cytochrome B6-F 20.5 1.4E+02 0.003 15.1 2.4 18 2-19 5-22 (31)
239 PHA02909 hypothetical protein; 20.4 1E+02 0.0022 17.9 1.9 15 1-15 35-49 (72)
240 KOG2555 AICAR transformylase/I 20.1 35 0.00075 28.2 0.0 12 127-139 453-464 (588)
241 PF12907 zf-met2: Zinc-binding 20.0 28 0.00061 18.7 -0.4 11 96-106 2-12 (40)
No 1
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.79 E-value=2e-19 Score=138.79 Aligned_cols=85 Identities=24% Similarity=0.547 Sum_probs=61.4
Q ss_pred CCCCChhhhhhhhhccccccCCCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 31 MHGVPAEIGEELLTVGRYERNNDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
...........++...+...........|+||+|+|..|+++++|||+|.||..||++||.+ .+..||+||+.......
T Consensus 204 ~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~-~r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 204 RNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQ-TRTFCPVCKRDIRTDSG 282 (348)
T ss_pred hhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhh-cCccCCCCCCcCCCCCC
Confidence 33444444555555555544333333699999999999999999999999999999999982 34669999998765555
Q ss_pred cccCCc
Q 038790 111 VVENGI 116 (139)
Q Consensus 111 ~~~~~~ 116 (139)
.....+
T Consensus 283 ~~~~~e 288 (348)
T KOG4628|consen 283 SEPVSE 288 (348)
T ss_pred CCCccC
Confidence 444333
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=99.67 E-value=2.1e-17 Score=92.55 Aligned_cols=44 Identities=48% Similarity=1.256 Sum_probs=39.6
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
++|+||++++..++.+..++|+|.||.+||..|++ .+.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~--~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLK--RNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHH--HSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHH--hCCcCCccC
Confidence 36999999999888889999999999999999999 778999997
No 3
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.51 E-value=7.1e-15 Score=110.78 Aligned_cols=55 Identities=35% Similarity=0.850 Sum_probs=49.6
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
...+.+|+|||++|..+++++.+||+|.||..|+++|+. +.+..||+||.+++|.
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~-~y~~~CPvCrt~iPPp 374 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL-GYSNKCPVCRTAIPPP 374 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHh-hhcccCCccCCCCCCC
Confidence 345789999999999999999999999999999999997 5788999999998863
No 4
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.49 E-value=2.9e-14 Score=88.11 Aligned_cols=45 Identities=42% Similarity=0.895 Sum_probs=35.6
Q ss_pred CcccccccccccC----------CCeeEEcCCCCcccHHHHHHHHccCCcccccccc
Q 038790 56 AVECAVCLCEIEE----------GEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 56 ~~~C~ICl~~~~~----------~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
++.|+||++++.. +-.+...+|+|.||..||.+|++ .+.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~--~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK--QNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT--TSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh--cCCcCCCCC
Confidence 5569999999932 12344558999999999999999 888999997
No 5
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.46 E-value=1.2e-13 Score=103.64 Aligned_cols=54 Identities=26% Similarity=0.733 Sum_probs=45.3
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
.......|.+||+..+.. ..+||||+||+.||..|.. .+..||+||..+.++..
T Consensus 235 i~~a~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~--ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRSNP---SATPCGHIFCWSCILEWCS--EKAECPLCREKFQPSKV 288 (293)
T ss_pred CCCCCCceEEEecCCCCC---CcCcCcchHHHHHHHHHHc--cccCCCcccccCCCcce
Confidence 345568899999987643 3689999999999999998 78889999999888754
No 6
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.44 E-value=9.2e-14 Score=103.13 Aligned_cols=52 Identities=31% Similarity=0.717 Sum_probs=42.5
Q ss_pred CCCCcccccccccccCCCe-----eEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEE-----IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~-----~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
...+.+|+||++.+..+.. ...++|+|.||.+||.+|+. .+.+||+||.++.
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~--~~~tCPlCR~~~~ 227 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK--EKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh--cCCCCCCCCCEee
Confidence 3457899999999775431 23448999999999999998 8999999999775
No 7
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.38 E-value=2.3e-13 Score=105.18 Aligned_cols=51 Identities=35% Similarity=0.893 Sum_probs=43.2
Q ss_pred CCCCccccccccc-ccCCC---------eeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 53 DNEAVECAVCLCE-IEEGE---------EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 53 ~~~~~~C~ICl~~-~~~~~---------~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
.+++..|+||||+ |+++. ....+||||++|.+|++.|++ ++++||+||.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E--RqQTCPICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE--RQQTCPICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH--hccCCCcccCcc
Confidence 5678899999999 55441 234679999999999999999 999999999985
No 8
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.35 E-value=2.1e-13 Score=101.42 Aligned_cols=68 Identities=28% Similarity=0.604 Sum_probs=58.9
Q ss_pred CCCCcccccccccccCCC-------eeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcccccCCceEEE
Q 038790 53 DNEAVECAVCLCEIEEGE-------EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENGIEILV 120 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~-------~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~ 120 (139)
..++..|++|-..+.... ++..+.|+|+||..||+.|.-.+++++||.|+..++.++...++.+++++
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnpWekph~ 295 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNPWEKPHV 295 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCccccchh
Confidence 456889999998886544 56678999999999999999778999999999999999999998888764
No 9
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.32 E-value=1e-12 Score=82.46 Aligned_cols=54 Identities=24% Similarity=0.690 Sum_probs=41.8
Q ss_pred CCccccccccccc--------CCCe--eEEcCCCCcccHHHHHHHHccC-CcccccccccccccC
Q 038790 55 EAVECAVCLCEIE--------EGEE--IRELRCDHIFHRVCLDQWVGLF-RRVTCPLCRDFLDSR 108 (139)
Q Consensus 55 ~~~~C~ICl~~~~--------~~~~--~~~l~C~H~fh~~Ci~~Wl~~~-~~~~CP~Cr~~~~~~ 108 (139)
.++.|.||...|+ +|+. +..-.|+|.||..||.+|+++. .+..||+||+++..+
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 4788999999887 3332 2233799999999999999852 468999999987543
No 10
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.23 E-value=7.9e-12 Score=91.32 Aligned_cols=54 Identities=26% Similarity=0.658 Sum_probs=42.4
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc-CCcccccccccccccC
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL-FRRVTCPLCRDFLDSR 108 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~-~~~~~CP~Cr~~~~~~ 108 (139)
......+|.||+|.-+ +.|. +.|||.||+.||.+||.. .....||+||..+..+
T Consensus 43 ~~~~~FdCNICLd~ak--dPVv-TlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAK--DPVV-TLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCCCceeeeeeccccC--CCEE-eecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 3567889999999844 6654 459999999999999974 3567889999876443
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=99.22 E-value=8.1e-12 Score=67.95 Aligned_cols=39 Identities=28% Similarity=0.963 Sum_probs=33.4
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
|+||++.+. +.+..++|||.|+..||.+|++ .+..||+|
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~--~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLE--KNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHH--CTSB-TTT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHH--CcCCCcCC
Confidence 899999987 5667889999999999999999 68999997
No 12
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.21 E-value=1.3e-11 Score=88.50 Aligned_cols=54 Identities=20% Similarity=0.645 Sum_probs=41.9
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc--------------CCcccccccccccccCc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL--------------FRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~--------------~~~~~CP~Cr~~~~~~~ 109 (139)
..++.+|+||++.+. +. ..++|+|.||..||..|+.. +....||+||.++....
T Consensus 15 ~~~~~~CpICld~~~--dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 15 SGGDFDCNICLDQVR--DP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCCccCCccCCCcCC--Cc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 346789999999876 43 35789999999999999852 13468999999885433
No 13
>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=99.19 E-value=1.7e-11 Score=67.71 Aligned_cols=45 Identities=44% Similarity=1.067 Sum_probs=37.1
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
+|+||++.+. +.+...+|+|.||..|++.|++. .+..||+|+..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~-~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS-GKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh-CcCCCCCCCCcC
Confidence 5999999983 55556679999999999999982 378899999753
No 14
>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=99.16 E-value=2.7e-11 Score=69.35 Aligned_cols=46 Identities=28% Similarity=0.834 Sum_probs=38.6
Q ss_pred CcccccccccccCCCeeEEcCCCCc-ccHHHHHHHHccCCcccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHI-FHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~-fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
+..|.||++... .+..+||||. |+..|+..|+. ....||+||+++.
T Consensus 2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 578999999854 3567799999 99999999999 9999999999875
No 15
>PHA02926 zinc finger-like protein; Provisional
Probab=99.13 E-value=5.1e-11 Score=86.78 Aligned_cols=55 Identities=25% Similarity=0.625 Sum_probs=40.4
Q ss_pred CCCCCcccccccccccCC-----CeeEEc-CCCCcccHHHHHHHHccC----Ccccccccccccc
Q 038790 52 NDNEAVECAVCLCEIEEG-----EEIREL-RCDHIFHRVCLDQWVGLF----RRVTCPLCRDFLD 106 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~-----~~~~~l-~C~H~fh~~Ci~~Wl~~~----~~~~CP~Cr~~~~ 106 (139)
..+.+.+|+|||+..-.+ ....++ +|+|.||..||..|...+ ...+||+||..+.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 455678999999986422 122344 899999999999999731 2356999998664
No 16
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.10 E-value=3.2e-11 Score=99.51 Aligned_cols=58 Identities=36% Similarity=0.749 Sum_probs=47.9
Q ss_pred CCCcccccccccccCCCe--eEEcCCCCcccHHHHHHHHccCCcccccccccccccCccccc
Q 038790 54 NEAVECAVCLCEIEEGEE--IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~--~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~ 113 (139)
..+..|+||+|++..+.+ ...++|+|+||..|+++|++ +..+||+||..+......+.
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e--r~qtCP~CR~~~~~~~~~~~ 348 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE--RQQTCPTCRTVLYDYVLWQI 348 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHH--HhCcCCcchhhhhccccccc
Confidence 458899999999997654 56789999999999999999 99999999996654444443
No 17
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=99.07 E-value=1.1e-10 Score=64.01 Aligned_cols=41 Identities=41% Similarity=0.983 Sum_probs=35.7
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
|+||++.+. +....++|+|.|+..||..|++......||+|
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 899999987 55567899999999999999985577889987
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.05 E-value=1.6e-10 Score=64.49 Aligned_cols=44 Identities=36% Similarity=0.905 Sum_probs=38.6
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.|.||.+.|.+.....+++|||+|+..|+..... ....||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~--~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKG--KSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcC--CCCCCcCCCC
Confidence 4999999996666777889999999999999974 7899999985
No 19
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.03 E-value=1.3e-10 Score=81.87 Aligned_cols=55 Identities=22% Similarity=0.671 Sum_probs=44.5
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
...+.+.|+|||+++.....+ .+.|||+||..||+.-++ ....||+|++.+..+.
T Consensus 127 ~~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk--~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALK--NTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccccccCCCceecchhhcccc-ccccchhHHHHHHHHHHH--hCCCCCCcccccchhh
Confidence 344568899999999854432 368999999999999998 8999999998665543
No 20
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=5.4e-11 Score=72.53 Aligned_cols=53 Identities=25% Similarity=0.696 Sum_probs=41.1
Q ss_pred CCccccccccccc--------CCCeeEEc--CCCCcccHHHHHHHHcc-CCccccccccccccc
Q 038790 55 EAVECAVCLCEIE--------EGEEIREL--RCDHIFHRVCLDQWVGL-FRRVTCPLCRDFLDS 107 (139)
Q Consensus 55 ~~~~C~ICl~~~~--------~~~~~~~l--~C~H~fh~~Ci~~Wl~~-~~~~~CP~Cr~~~~~ 107 (139)
.++.|.||..+|+ +++...++ .|.|.||..||.+|+++ ..+..||+||+.+..
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 3558999999886 44443333 69999999999999984 356899999997653
No 21
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.00 E-value=3.6e-10 Score=62.40 Aligned_cols=40 Identities=33% Similarity=0.811 Sum_probs=28.9
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCc--cccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRR--VTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~--~~CP~C 101 (139)
|+||++-|. +++ .++|||.|+..||..|.+.... ..||.|
T Consensus 1 CpiC~~~~~--~Pv-~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK--DPV-SLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S--SEE-E-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC--Ccc-ccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999988 554 5799999999999999984222 479987
No 22
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.96 E-value=5.1e-10 Score=68.84 Aligned_cols=52 Identities=31% Similarity=0.689 Sum_probs=38.5
Q ss_pred cccccccccc-----------cCCCeeEEc--CCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 57 VECAVCLCEI-----------EEGEEIREL--RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 57 ~~C~ICl~~~-----------~~~~~~~~l--~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
+.|+||...+ .++++.... .|+|.||..||..||. .+..||++|+.+...+.
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~--Tk~~CPld~q~w~~~~~ 85 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLD--TKGVCPLDRQTWVLADG 85 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHh--hCCCCCCCCceeEEecc
Confidence 4566665544 355543333 6999999999999999 79999999998765543
No 23
>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=98.89 E-value=1.8e-09 Score=64.34 Aligned_cols=48 Identities=17% Similarity=0.342 Sum_probs=40.5
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
..|+||.+.+.. + ..++|||+|++.||.+|+. .+.+||+|+.++....
T Consensus 2 ~~Cpi~~~~~~~--P-v~~~~G~v~~~~~i~~~~~--~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMKD--P-VILPSGQTYERRAIEKWLL--SHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCCC--C-EECCCCCEEeHHHHHHHHH--HCCCCCCCcCCCChhh
Confidence 469999999884 4 3579999999999999998 6889999999875433
No 24
>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=98.87 E-value=1.7e-09 Score=57.48 Aligned_cols=39 Identities=38% Similarity=1.036 Sum_probs=32.3
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
|+||++.. .....++|+|.||..|++.|+. ..+..||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHH-hCcCCCCCC
Confidence 78999882 4456779999999999999997 356789987
No 25
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.86 E-value=2.9e-09 Score=85.27 Aligned_cols=53 Identities=34% Similarity=0.812 Sum_probs=40.8
Q ss_pred CCCcccccccccccCCC--------------eeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGE--------------EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~--------------~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
....+|+|||.+++--. .-..+||+|+||..|+.+|+.+ .+..||+||.++++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-YKLICPVCRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-hcccCCccCCCCCC
Confidence 34668999998875111 1113599999999999999983 67799999999875
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.79 E-value=4.2e-09 Score=83.53 Aligned_cols=51 Identities=22% Similarity=0.596 Sum_probs=42.6
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
......|+||++.|. +.+ +++|+|.||..||..|+. ....||+|+..+...
T Consensus 23 Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~--~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLS--NQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHh--CCCCCCCCCCccccc
Confidence 456789999999987 333 679999999999999998 677999999877543
No 27
>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=98.72 E-value=1e-08 Score=58.42 Aligned_cols=44 Identities=27% Similarity=0.697 Sum_probs=33.8
Q ss_pred ccccccccccCCCeeEEcCCC-----CcccHHHHHHHHccCCcccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCD-----HIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~-----H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
.|.||++..++ +...+.||. |.+|..|+.+|+..+.+.+||+|+
T Consensus 1 ~CrIC~~~~~~-~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDE-GDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCC-CCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 48999984333 334467885 789999999999755677999995
No 28
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=9.5e-09 Score=76.57 Aligned_cols=53 Identities=30% Similarity=0.602 Sum_probs=41.9
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHH-HHccCCcccccccccccccCcc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQ-WVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~-Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
..+..|+||++..... ..++|||+||..||.. |-. ++-..||+||+...++..
T Consensus 213 ~~d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~-~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTK-KKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCCc---ccccccchhhHHHHHHHHHh-hccccCchhhhhccchhh
Confidence 5688999999986632 3678999999999999 866 244559999997776543
No 29
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.59 E-value=6.3e-09 Score=88.70 Aligned_cols=70 Identities=26% Similarity=0.506 Sum_probs=50.2
Q ss_pred hhhhhhhhccccccCCCCCCccccccccccc-CCCe---eEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 37 EIGEELLTVGRYERNNDNEAVECAVCLCEIE-EGEE---IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~-~~~~---~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
...+.+..+.+.-....++..+|+||...++ .+.. -+.-.|.|.||..|+.+|++...+.+||+||..++
T Consensus 1450 s~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1450 SFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3444444555555556678899999998766 1111 11224999999999999999778999999997664
No 30
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.57 E-value=1.6e-08 Score=61.89 Aligned_cols=53 Identities=28% Similarity=0.677 Sum_probs=25.8
Q ss_pred CcccccccccccCCCeeEEc-----CCCCcccHHHHHHHHcc---CC------cccccccccccccC
Q 038790 56 AVECAVCLCEIEEGEEIREL-----RCDHIFHRVCLDQWVGL---FR------RVTCPLCRDFLDSR 108 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l-----~C~H~fh~~Ci~~Wl~~---~~------~~~CP~Cr~~~~~~ 108 (139)
+.+|.||++.+..++....+ .|+..||..|+.+||.. .+ ...||.|+.++..+
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 46799999987633322222 58899999999999973 11 24799999988654
No 31
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=8.3e-08 Score=53.11 Aligned_cols=40 Identities=30% Similarity=0.686 Sum_probs=22.4
Q ss_pred cccccccccCCC-eeEEcCCCCcccHHHHHHHHccC--Cccccc
Q 038790 59 CAVCLCEIEEGE-EIRELRCDHIFHRVCLDQWVGLF--RRVTCP 99 (139)
Q Consensus 59 C~ICl~~~~~~~-~~~~l~C~H~fh~~Ci~~Wl~~~--~~~~CP 99 (139)
|+||.+ |...+ ....|+|||+|+.+||++++..+ ....||
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 76544 34567999999999999999832 355676
No 32
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.49 E-value=5.7e-08 Score=77.10 Aligned_cols=49 Identities=35% Similarity=0.843 Sum_probs=40.0
Q ss_pred CCCcccccccccccCCCe-eEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEE-IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~-~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.+-.+|++||+.+++... +....|.|.||..|+..| ...+||+||.-..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w----~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW----WDSSCPVCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhc----ccCcChhhhhhcC
Confidence 356689999999986653 234479999999999999 6789999998655
No 33
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.49 E-value=8.1e-08 Score=77.39 Aligned_cols=52 Identities=25% Similarity=0.655 Sum_probs=40.7
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccC---CcccccccccccccCcc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLF---RRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~---~~~~CP~Cr~~~~~~~~ 110 (139)
+..|+||++.... .+ .+.|||+||..||-+++++. ....||+|+..+.++..
T Consensus 186 ~~~CPICL~~~~~--p~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl 240 (513)
T KOG2164|consen 186 DMQCPICLEPPSV--PV-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDL 240 (513)
T ss_pred CCcCCcccCCCCc--cc-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccce
Confidence 7889999998653 33 33599999999999999853 45799999987766433
No 34
>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=98.45 E-value=1.8e-07 Score=57.56 Aligned_cols=55 Identities=16% Similarity=0.360 Sum_probs=40.3
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCccccc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~ 113 (139)
+...|+|+.+-|. +++ ++++||.|.+.+|..|+. .++.+||+|+.++......++
T Consensus 3 ~~f~CpIt~~lM~--dPV-i~~~G~tyer~~I~~~l~-~~~~~~P~t~~~l~~~~l~pn 57 (73)
T PF04564_consen 3 DEFLCPITGELMR--DPV-ILPSGHTYERSAIERWLE-QNGGTDPFTRQPLSESDLIPN 57 (73)
T ss_dssp GGGB-TTTSSB-S--SEE-EETTSEEEEHHHHHHHHC-TTSSB-TTT-SB-SGGGSEE-
T ss_pred cccCCcCcCcHhh--Cce-eCCcCCEEcHHHHHHHHH-cCCCCCCCCCCcCCcccceEC
Confidence 4678999999998 555 578999999999999998 248999999998877655443
No 35
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.44 E-value=8.1e-08 Score=61.97 Aligned_cols=52 Identities=31% Similarity=0.606 Sum_probs=37.4
Q ss_pred CCccccccccccc------------CCCe--eEEcCCCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 55 EAVECAVCLCEIE------------EGEE--IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 55 ~~~~C~ICl~~~~------------~~~~--~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
.-+.|+||..-+- ..++ +.---|+|.||..||.+||+ .+..||+|-++...+
T Consensus 45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlk--tr~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLK--TRNVCPLDNKEWVFQ 110 (114)
T ss_pred eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHh--hcCcCCCcCcceeEe
Confidence 3567999875431 1122 22226999999999999999 899999998766543
No 36
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.41 E-value=7.9e-08 Score=72.76 Aligned_cols=55 Identities=27% Similarity=0.667 Sum_probs=43.6
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~ 113 (139)
.....|.||-+-+... ..++|||.||.-||+..|. .+..||+||.+....+...+
T Consensus 23 Ds~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~--~qp~CP~Cr~~~~esrlr~~ 77 (391)
T COG5432 23 DSMLRCRICDCRISIP---CETTCGHTFCSLCIRRHLG--TQPFCPVCREDPCESRLRGS 77 (391)
T ss_pred hhHHHhhhhhheeecc---eecccccchhHHHHHHHhc--CCCCCccccccHHhhhcccc
Confidence 3456799999988732 3568999999999999999 99999999986654444433
No 37
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.40 E-value=2.7e-07 Score=70.88 Aligned_cols=54 Identities=19% Similarity=0.399 Sum_probs=39.5
Q ss_pred CCcccccccccccCCCeeE--EcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 55 EAVECAVCLCEIEEGEEIR--ELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~--~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
++..|++|..+--....+. +.+|||.||..||+..+. .....||.|+.++....
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~-~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV-RGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc-CCCCCCCCCCCccchhh
Confidence 3568999998633333322 228999999999999765 26679999998776654
No 38
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.32 E-value=1.7e-07 Score=72.24 Aligned_cols=50 Identities=18% Similarity=0.592 Sum_probs=41.6
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
..-..|.||.+-|... .++||+|.||.-||+..|. .+..||.|+.++..+
T Consensus 21 D~lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~--~~p~CP~C~~~~~Es 70 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLS--YKPQCPTCCVTVTES 70 (442)
T ss_pred HHHHHHhHHHHHhcCc---eeccccchHHHHHHHHHhc--cCCCCCceecccchh
Confidence 4456799999998743 3679999999999999999 999999998766443
No 39
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.28 E-value=3.5e-07 Score=71.62 Aligned_cols=47 Identities=34% Similarity=0.858 Sum_probs=35.4
Q ss_pred CcccccccccccCCCeeEEc-CCCCcccHHHHHHHHccCCc-ccccccc
Q 038790 56 AVECAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWVGLFRR-VTCPLCR 102 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~-~~CP~Cr 102 (139)
...|.||.+-+.....+..+ .|||+||..|+.+|++.-.. ..||+|+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 46799995554444444444 59999999999999984333 5899998
No 40
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=5.8e-07 Score=67.41 Aligned_cols=45 Identities=36% Similarity=0.759 Sum_probs=40.1
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
..+...|+||++.|... .+++|+|.||..||..++. ....||.||
T Consensus 10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC--CCcCCcccC
Confidence 45678899999999965 6789999999999999987 778999999
No 41
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=1.3e-06 Score=67.80 Aligned_cols=51 Identities=25% Similarity=0.595 Sum_probs=41.3
Q ss_pred CCCcccccccccccCCCeeEEcCCCC-cccHHHHHHHHccCCcccccccccccccCc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDH-IFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H-~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
..+.+|.||+.+-. .+.+|||.| ..|..|.+.--- +++.||+||+++..-.
T Consensus 288 ~~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~--q~n~CPICRqpi~~ll 339 (349)
T KOG4265|consen 288 ESGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRY--QTNNCPICRQPIEELL 339 (349)
T ss_pred cCCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHH--hhcCCCccccchHhhh
Confidence 44789999998744 456899998 789999998765 7899999999886543
No 42
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.03 E-value=4.3e-06 Score=49.03 Aligned_cols=45 Identities=20% Similarity=0.569 Sum_probs=32.4
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPL 100 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~ 100 (139)
.-...|+|.+..|+ ++++...|+|+|-+..|.+++.......||+
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 34678999999988 7888889999999999999995447789998
No 43
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.99 E-value=1.3e-06 Score=51.98 Aligned_cols=45 Identities=27% Similarity=0.727 Sum_probs=23.4
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
...|.+|.+-++ +++....|.|+|+..||..-+. ..||+|+.+-.
T Consensus 7 lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~----~~CPvC~~Paw 51 (65)
T PF14835_consen 7 LLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG----SECPVCHTPAW 51 (65)
T ss_dssp TTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT----TB-SSS--B-S
T ss_pred hcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC----CCCCCcCChHH
Confidence 456999999987 6666668999999999988554 34999987653
No 44
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=4.8e-06 Score=65.72 Aligned_cols=49 Identities=31% Similarity=0.889 Sum_probs=39.9
Q ss_pred CCcccccccccccCCCe--eEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEEGEE--IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~--~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.+..|+||++++...-. +..+.|+|.|..+||.+|+.......||.|..
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ 53 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG 53 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence 46789999999985544 44558999999999999997446789999964
No 45
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.94 E-value=3.8e-05 Score=57.88 Aligned_cols=57 Identities=23% Similarity=0.418 Sum_probs=44.7
Q ss_pred ccCCCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 49 ERNNDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 49 ~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
+......+.+|++|-+.-. -+..+.+|+|+||..||..=+......+||.|-.+..+
T Consensus 232 sss~~t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 232 SSSTGTSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred ccccccCCceeeccCCCCC--CCeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence 4445567899999998844 55667789999999999997764456899999886653
No 46
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=5.2e-06 Score=63.21 Aligned_cols=50 Identities=28% Similarity=0.519 Sum_probs=40.1
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
....+|+||+....- + ..++|+|.||.-||+.=.. ..+.+|++||.+++.
T Consensus 5 ~~~~eC~IC~nt~n~--P-v~l~C~HkFCyiCiKGsy~-ndk~~CavCR~pids 54 (324)
T KOG0824|consen 5 TKKKECLICYNTGNC--P-VNLYCFHKFCYICIKGSYK-NDKKTCAVCRFPIDS 54 (324)
T ss_pred ccCCcceeeeccCCc--C-ccccccchhhhhhhcchhh-cCCCCCceecCCCCc
Confidence 346789999988653 2 4689999999999998765 267789999998864
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=5.5e-06 Score=64.82 Aligned_cols=52 Identities=29% Similarity=0.710 Sum_probs=39.0
Q ss_pred CCCcccccccccccCCC----eeEEc-CCCCcccHHHHHHHHccCC-----ccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGE----EIREL-RCDHIFHRVCLDQWVGLFR-----RVTCPLCRDFL 105 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~----~~~~l-~C~H~fh~~Ci~~Wl~~~~-----~~~CP~Cr~~~ 105 (139)
..+.+|.|||+...... ...++ +|.|.||..||..|-...+ ...||.||...
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 45889999999876432 12344 5999999999999984224 58999999643
No 48
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.88 E-value=3.1e-06 Score=71.51 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=40.9
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
...|++|+..+..+......+|+|.||..||..|-+ .-.+||+||..+..-.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR--~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR--CAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh--hcccCchhhhhhheee
Confidence 446888887776554444558999999999999988 8999999998775433
No 49
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=2.5e-06 Score=48.99 Aligned_cols=47 Identities=21% Similarity=0.499 Sum_probs=33.4
Q ss_pred CcccccccccccCCCeeEEcCCCC-cccHHHHHHHHccCCcccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDH-IFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H-~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
+++|.||+|.-. +.+ +-.||| ..+..|-..-++ ..+..||+||+++.
T Consensus 7 ~dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~-~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKK-ALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHH-ccCCcCcchhhHHH
Confidence 478999998744 322 226998 567777655444 37899999999764
No 50
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=2.7e-06 Score=66.01 Aligned_cols=59 Identities=25% Similarity=0.491 Sum_probs=47.4
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcccccCC
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENG 115 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~~~ 115 (139)
..+..|+||++-+.. .+....|.|.||.+||..-++ ..+..||.||+.+...+..+...
T Consensus 41 ~~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r-~gn~ecptcRk~l~SkrsLr~Dp 99 (381)
T KOG0311|consen 41 DIQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALR-SGNNECPTCRKKLVSKRSLRIDP 99 (381)
T ss_pred hhhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHH-hcCCCCchHHhhccccccCCCCc
Confidence 457789999998773 333447999999999999987 47889999999998888776543
No 51
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=5.4e-06 Score=69.70 Aligned_cols=51 Identities=22% Similarity=0.604 Sum_probs=41.9
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
-..|+.|...+. + ++++.|+|+||..||..-+.+ ++..||.|-.+|++...
T Consensus 643 ~LkCs~Cn~R~K--d-~vI~kC~H~FC~~Cvq~r~et-RqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 643 LLKCSVCNTRWK--D-AVITKCGHVFCEECVQTRYET-RQRKCPKCNAAFGANDV 693 (698)
T ss_pred ceeCCCccCchh--h-HHHHhcchHHHHHHHHHHHHH-hcCCCCCCCCCCCcccc
Confidence 457999997655 3 346689999999999999974 88999999999987643
No 52
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=97.75 E-value=3.2e-05 Score=53.96 Aligned_cols=55 Identities=20% Similarity=0.564 Sum_probs=41.8
Q ss_pred CCCCcccccccccccCCCeeEEcCCC--C---cccHHHHHHHHccCCcccccccccccccCccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCD--H---IFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~--H---~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~ 111 (139)
...+..|-||.++-. +. .-||. . ..|.+|++.|+..++...|++|..++......
T Consensus 5 s~~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~ 64 (162)
T PHA02825 5 SLMDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNY 64 (162)
T ss_pred CCCCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEec
Confidence 456788999998843 22 23654 3 67999999999877889999999988766444
No 53
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.69 E-value=1.7e-05 Score=63.41 Aligned_cols=56 Identities=23% Similarity=0.613 Sum_probs=46.3
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVV 112 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~ 112 (139)
..++..|++|+..+.+ ++..+.|+|.||..|+..|+. .+..||.|+..+.......
T Consensus 18 ~~~~l~C~~C~~vl~~--p~~~~~cgh~fC~~C~~~~~~--~~~~cp~~~~~~~~~~~~~ 73 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRD--PVQTTTCGHRFCAGCLLESLS--NHQKCPVCRQELTQAEELP 73 (391)
T ss_pred CcccccCccccccccC--CCCCCCCCCcccccccchhhc--cCcCCcccccccchhhccC
Confidence 4567899999999884 444468999999999999999 7999999998887665554
No 54
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.63 E-value=1.7e-05 Score=62.53 Aligned_cols=49 Identities=31% Similarity=0.668 Sum_probs=40.8
Q ss_pred CCcccccccccccCCC-eeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEEGE-EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~-~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.+.-|..|-+.+...+ ....+||.|+||..|+...|.+....+||-||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 3567999999987554 456779999999999999998556789999994
No 55
>PHA02862 5L protein; Provisional
Probab=97.62 E-value=4.2e-05 Score=52.54 Aligned_cols=52 Identities=19% Similarity=0.580 Sum_probs=39.4
Q ss_pred CcccccccccccCCCeeEEcCCC-----CcccHHHHHHHHccCCcccccccccccccCccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCD-----HIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~-----H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~ 111 (139)
+..|-||.++-+ +. .-||. ...|.+|+.+|++..++..||+|+.++.-....
T Consensus 2 ~diCWIC~~~~~--e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~y 58 (156)
T PHA02862 2 SDICWICNDVCD--ER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTY 58 (156)
T ss_pred CCEEEEecCcCC--CC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEcc
Confidence 467999999843 32 24654 588999999999877889999999887544333
No 56
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=1.8e-05 Score=55.43 Aligned_cols=41 Identities=27% Similarity=0.613 Sum_probs=34.0
Q ss_pred hhccccccCCCCCCcccccccccccCCCeeEEcCCCCcccH
Q 038790 43 LTVGRYERNNDNEAVECAVCLCEIEEGEEIRELRCDHIFHR 83 (139)
Q Consensus 43 ~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~ 83 (139)
+.+.+.+.....+..+|.||+|+++.++.+..|||-.+||+
T Consensus 164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 44455555556678899999999999999999999999996
No 57
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=97.49 E-value=4.4e-05 Score=42.95 Aligned_cols=42 Identities=33% Similarity=0.790 Sum_probs=28.6
Q ss_pred cccccccccCCCeeEEcCCC-----CcccHHHHHHHHccCCccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCD-----HIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~-----H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
|-||+++-..++. -+.||+ ...|..|+..|+..+.+.+|++|
T Consensus 1 CrIC~~~~~~~~~-li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEP-LISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCc-eecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 7899988665552 345664 37899999999986567789887
No 58
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.46 E-value=4.6e-05 Score=58.20 Aligned_cols=58 Identities=24% Similarity=0.640 Sum_probs=46.5
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc---------------------CCcccccccccccccCc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL---------------------FRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~---------------------~~~~~CP~Cr~~~~~~~ 109 (139)
.......|.|||=-|..++....++|.|.||..|+..+|+. .....||+||..+....
T Consensus 111 nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 111 NNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred CCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 34457789999999999888888999999999999998862 11257999998775443
No 59
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=0.00011 Score=58.69 Aligned_cols=50 Identities=34% Similarity=0.680 Sum_probs=41.9
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
...+.+|.||+.-+.. .+ .+||||.|+..||+.-+. +...||.||.++..
T Consensus 81 ~~sef~c~vc~~~l~~--pv-~tpcghs~c~~Cl~r~ld--~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYP--PV-VTPCGHSFCLECLDRSLD--QETECPLCRDELVE 130 (398)
T ss_pred ccchhhhhhhHhhcCC--Cc-cccccccccHHHHHHHhc--cCCCCccccccccc
Confidence 3568899999988763 33 559999999999999777 89999999998875
No 60
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.38 E-value=7.1e-05 Score=59.26 Aligned_cols=48 Identities=25% Similarity=0.648 Sum_probs=38.1
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
...-|.||-+. +..+.+-||||..|..|+..|-......+||.||..+
T Consensus 368 TFeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 368 TFELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred hHHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 45579999865 2456677999999999999997533478999999766
No 61
>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=97.34 E-value=7.8e-05 Score=50.74 Aligned_cols=36 Identities=22% Similarity=0.607 Sum_probs=30.0
Q ss_pred CcccccccccccCCCeeEEcCCC------CcccHHHHHHHHc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCD------HIFHRVCLDQWVG 91 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~------H~fh~~Ci~~Wl~ 91 (139)
..+|+||++.+..++.+..++|+ |.||.+|++.|-+
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 67899999999985566667776 7999999999943
No 62
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.32 E-value=0.0002 Score=52.74 Aligned_cols=57 Identities=25% Similarity=0.561 Sum_probs=44.2
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccC------CcccccccccccccCcccc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLF------RRVTCPLCRDFLDSRRAVV 112 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~------~~~~CP~Cr~~~~~~~~~~ 112 (139)
....|.+|.-.+..++.++. -|-|.||++|++.|...- ..-.||-|..++.+.....
T Consensus 49 Y~pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nlv 111 (299)
T KOG3970|consen 49 YNPNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLV 111 (299)
T ss_pred CCCCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcccc
Confidence 35569999999999887764 599999999999998631 2358999998876654433
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.26 E-value=0.00018 Score=64.77 Aligned_cols=53 Identities=25% Similarity=0.638 Sum_probs=41.2
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccC--------Ccccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLF--------RRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~--------~~~~CP~Cr~~~~ 106 (139)
..++.|.||..+--...+...+.|+|+||.+|.+.-|+.+ +-.+||+|+.++.
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 4578899999776555677788999999999999877621 1269999987663
No 64
>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=97.01 E-value=0.00027 Score=45.96 Aligned_cols=34 Identities=24% Similarity=0.595 Sum_probs=28.0
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHH
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLD 87 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~ 87 (139)
..++..|++|-..+.. ......||||+||..|++
T Consensus 75 i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 3457789999999886 456677999999999975
No 65
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=96.98 E-value=0.0033 Score=48.74 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=39.0
Q ss_pred CCCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 51 NNDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 51 ~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
........|++|+....++.. ...=|=+||..||-+++. .+..||+=-.+.
T Consensus 295 ~l~~~~~~CpvClk~r~Nptv--l~vSGyVfCY~Ci~~Yv~--~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 295 LLPPDREVCPVCLKKRQNPTV--LEVSGYVFCYPCIFSYVV--NYGHCPVTGYPA 345 (357)
T ss_pred cCCCccccChhHHhccCCCce--EEecceEEeHHHHHHHHH--hcCCCCccCCcc
Confidence 344567789999998775443 333488999999999999 899999865544
No 66
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.98 E-value=9.6e-05 Score=57.03 Aligned_cols=56 Identities=18% Similarity=0.488 Sum_probs=44.9
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCccc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~ 111 (139)
..+....|.+|-.-|- +...+.-|-|.||+.||-..+. ...+||.|...+......
T Consensus 11 ~~n~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~--~~~~CP~C~i~ih~t~pl 66 (331)
T KOG2660|consen 11 ELNPHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLE--ESKYCPTCDIVIHKTHPL 66 (331)
T ss_pred hcccceehhhccceee--cchhHHHHHHHHHHHHHHHHHH--HhccCCccceeccCcccc
Confidence 3456778999999887 4445668999999999999999 799999998766554433
No 67
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.89 E-value=0.001 Score=49.75 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=46.5
Q ss_pred CCcccccccccccCCCeeEEc-CCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 55 EAVECAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
..+.|++|.+.+.+......| ||||+|..+|+...+. ....||+|-.++....
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir--~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR--KDMVDPVTDKPLKDRD 273 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc--ccccccCCCCcCcccc
Confidence 467899999999988887777 9999999999999998 8999999988775543
No 68
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.84 E-value=0.0026 Score=48.16 Aligned_cols=55 Identities=18% Similarity=0.388 Sum_probs=43.4
Q ss_pred CCCCcccccccccccCCCeeEEc-CCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 53 DNEAVECAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
......|+|...+|........+ ||||+|-..+|+.- . ....||+|-.++.....
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k--~~~~Cp~c~~~f~~~Di 165 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-K--KSKKCPVCGKPFTEEDI 165 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-c--ccccccccCCccccCCE
Confidence 45678999999999765555555 99999999999996 2 36779999998875533
No 69
>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=96.81 E-value=0.00051 Score=37.88 Aligned_cols=43 Identities=21% Similarity=0.617 Sum_probs=23.2
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
|.+|.+-...|..-..-.|+-.+|..|++.++.......||.|
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 6678777665543333358889999999999984334479987
No 70
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.77 E-value=0.0012 Score=37.10 Aligned_cols=46 Identities=24% Similarity=0.590 Sum_probs=22.4
Q ss_pred cccccccccCCC-eeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 59 CAVCLCEIEEGE-EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 59 C~ICl~~~~~~~-~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
|++|.+++...+ ...--+|+...+..|...-++ .....||-||+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~-~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE-NEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT-SS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh-ccCCCCCCCCCCC
Confidence 789999985433 222235788889999887765 2588999999875
No 71
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.69 E-value=0.00045 Score=56.63 Aligned_cols=58 Identities=31% Similarity=0.607 Sum_probs=42.9
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc---CCcccccccccccccCcccc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL---FRRVTCPLCRDFLDSRRAVV 112 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~---~~~~~CP~Cr~~~~~~~~~~ 112 (139)
...+..+|.+|-++-+ +. ....|.|.||+-||..+..- ..+.+||+|..++.-..+.+
T Consensus 532 enk~~~~C~lc~d~ae--d~-i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~ 592 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAE--DY-IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEP 592 (791)
T ss_pred cccCceeecccCChhh--hh-HhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccch
Confidence 3456778999998743 33 35679999999999888762 35689999988776554433
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.001 Score=52.95 Aligned_cols=50 Identities=24% Similarity=0.586 Sum_probs=38.7
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc---C---Cccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL---F---RRVTCPLCRD 103 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~---~---~~~~CP~Cr~ 103 (139)
....+|.||+++.........+||+|+||+.|.+.++.. + +...||-++-
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 457789999999765567778899999999999999973 2 2356766643
No 73
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.58 E-value=0.0011 Score=49.33 Aligned_cols=52 Identities=23% Similarity=0.483 Sum_probs=37.5
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCccccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~ 113 (139)
..|.-|...-. ++...++.|+|+||..|...= ....||+|++.+-......+
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~----~~~~C~lCkk~ir~i~l~~s 55 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS----SPDVCPLCKKSIRIIQLNRS 55 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccC----Cccccccccceeeeeecccc
Confidence 35777776544 677888899999999997652 23399999998655444444
No 74
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0014 Score=46.69 Aligned_cols=36 Identities=31% Similarity=0.854 Sum_probs=27.8
Q ss_pred cCCCCcccHHHHHHHHcc---CCc------ccccccccccccCcc
Q 038790 75 LRCDHIFHRVCLDQWVGL---FRR------VTCPLCRDFLDSRRA 110 (139)
Q Consensus 75 l~C~H~fh~~Ci~~Wl~~---~~~------~~CP~Cr~~~~~~~~ 110 (139)
..|+..||.-|+..||+. .++ ..||+|..++..+.+
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 369999999999999972 122 589999998865443
No 75
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.52 E-value=0.00096 Score=48.36 Aligned_cols=45 Identities=20% Similarity=0.506 Sum_probs=37.3
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
...|.||-++|.. ++ .+.|||.||..|...-+. ....|-+|-+..
T Consensus 196 PF~C~iCKkdy~s--pv-vt~CGH~FC~~Cai~~y~--kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES--PV-VTECGHSFCSLCAIRKYQ--KGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc--hh-hhhcchhHHHHHHHHHhc--cCCcceecchhh
Confidence 5579999999984 33 457999999999988887 889999997643
No 76
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=96.46 E-value=0.0015 Score=56.16 Aligned_cols=52 Identities=27% Similarity=0.687 Sum_probs=38.3
Q ss_pred CCCCCcccccccccccCCCeeEE-cCCCCcccHHHHHHHHccC-----Cccccccccc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRE-LRCDHIFHRVCLDQWVGLF-----RRVTCPLCRD 103 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~-l~C~H~fh~~Ci~~Wl~~~-----~~~~CP~Cr~ 103 (139)
.....++|.||.+.+...+.+=. ..|-|+||..||..|.... ..=.||.|..
T Consensus 187 l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 187 LSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred HhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 34568899999999986654322 2588999999999999731 1237999974
No 77
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.35 E-value=0.0016 Score=37.60 Aligned_cols=47 Identities=23% Similarity=0.512 Sum_probs=34.4
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
...|..|... +.+...+||+|..+..|...+ +-+-||+|-+++....
T Consensus 7 ~~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~----rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFV---GTKGTVLPCGHLICDNCFPGE----RYNGCPFCGTPFEFDD 53 (55)
T ss_pred ceeEEEcccc---ccccccccccceeeccccChh----hccCCCCCCCcccCCC
Confidence 3345555543 233457799999999998875 7788999999887654
No 78
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.0031 Score=48.36 Aligned_cols=49 Identities=29% Similarity=0.719 Sum_probs=39.9
Q ss_pred CcccccccccccCCCe---eEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 56 AVECAVCLCEIEEGEE---IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~---~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
...|-||-++|+.++. .+.+.|||.++..|+..-+. .....||.||.+.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-NSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc-CceeeccCCCCcc
Confidence 3579999999987642 45668999999999999886 3667899999874
No 79
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.24 E-value=0.0014 Score=50.02 Aligned_cols=41 Identities=29% Similarity=0.710 Sum_probs=30.0
Q ss_pred CcccccccccccCCCeeEEcCCCC-cccHHHHHHHHccCCccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDH-IFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H-~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
..-|+|||+... ....|+||| +-|.+|- ++...||+||+.+
T Consensus 300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CG------krm~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPR---DCVFLECGHMVTCTKCG------KRMNECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCc---ceEEeecCcEEeehhhc------cccccCchHHHHH
Confidence 667999998743 345789999 4566672 3566899999854
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.17 E-value=0.005 Score=48.25 Aligned_cols=55 Identities=24% Similarity=0.583 Sum_probs=40.4
Q ss_pred ccCCCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 49 ERNNDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 49 ~~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
..+.+++...|.||-+.+. ....+||+|..|.-|--.--.+-....||+||....
T Consensus 54 addtDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 54 ADDTDEENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred ccccccccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 4455667888999998754 556789999999998655322225788999997543
No 81
>PHA03096 p28-like protein; Provisional
Probab=95.73 E-value=0.0055 Score=47.08 Aligned_cols=47 Identities=26% Similarity=0.422 Sum_probs=32.5
Q ss_pred cccccccccccCCC----eeEEc-CCCCcccHHHHHHHHccC-Cccccccccc
Q 038790 57 VECAVCLCEIEEGE----EIREL-RCDHIFHRVCLDQWVGLF-RRVTCPLCRD 103 (139)
Q Consensus 57 ~~C~ICl~~~~~~~----~~~~l-~C~H~fh~~Ci~~Wl~~~-~~~~CP~Cr~ 103 (139)
..|.||++...... .-.+| .|.|.|+..||..|-... ...+||.|+.
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 78999999876432 22244 699999999999998732 2345555544
No 82
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.72 E-value=0.0078 Score=47.20 Aligned_cols=49 Identities=24% Similarity=0.440 Sum_probs=34.7
Q ss_pred cCCCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 50 RNNDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 50 ~~~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....-...|.||+++..+ ...+||||.-+ |..--. ...+||+||+.+.
T Consensus 299 ~~~~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~---~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 299 FRELPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSK---HLPQCPVCRQRIR 347 (355)
T ss_pred ccccCCCCceEEecCCccc---eeeecCCcEEE--chHHHh---hCCCCchhHHHHH
Confidence 3445567789999998663 45679999865 544432 4667999998764
No 83
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.65 E-value=0.0041 Score=47.61 Aligned_cols=46 Identities=20% Similarity=0.468 Sum_probs=38.1
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
...|.||...|. .+| .+.|+|.||..|...=+. ....|++|.++..
T Consensus 241 Pf~c~icr~~f~--~pV-vt~c~h~fc~~ca~~~~q--k~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPV-VTKCGHYFCEVCALKPYQ--KGEKCYVCSQQTH 286 (313)
T ss_pred Cccccccccccc--cch-hhcCCceeehhhhccccc--cCCcceecccccc
Confidence 556999999998 443 467999999999988887 7899999987553
No 84
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.00066 Score=53.64 Aligned_cols=52 Identities=23% Similarity=0.592 Sum_probs=43.5
Q ss_pred CCcccccccccccCC-CeeEEcCCCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 55 EAVECAVCLCEIEEG-EEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~-~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
.-..|+||.+++... +++..+-|+|.+|.+||.+|+. ....||.|++.++..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~--~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLA--TKRKLPSCRRELPKN 247 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHH--HHHHhHHHHhhhhhh
Confidence 355699999999865 5566678999999999999999 689999999877543
No 85
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=95.52 E-value=0.013 Score=41.03 Aligned_cols=72 Identities=28% Similarity=0.590 Sum_probs=44.1
Q ss_pred CCcccccccccccCCCeeEEc------C-----CCC-cccHHHHHHHHccC-----------------------------
Q 038790 55 EAVECAVCLCEIEEGEEIREL------R-----CDH-IFHRVCLDQWVGLF----------------------------- 93 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l------~-----C~H-~fh~~Ci~~Wl~~~----------------------------- 93 (139)
++..|+||||--. +.|-++ . |+- .-|..|+++.-+..
T Consensus 1 ed~~CpICme~PH--NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (162)
T PF07800_consen 1 EDVTCPICMEHPH--NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ 78 (162)
T ss_pred CCccCceeccCCC--ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence 4678999999866 333222 1 443 34778999986520
Q ss_pred Cccccccccccc------ccCcccccCCceEEEeecccccCC
Q 038790 94 RRVTCPLCRDFL------DSRRAVVENGIEILVFKRFCYLSS 129 (139)
Q Consensus 94 ~~~~CP~Cr~~~------~~~~~~~~~~~~~~~~~~~~~~~~ 129 (139)
.+..||+||..+ .+.+..-+...+.=..+ .|++.|
T Consensus 79 ~~L~CPLCRG~V~GWtvve~AR~~LN~K~RsC~~e-~C~F~G 119 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVEPARRFLNAKKRSCSQE-SCSFSG 119 (162)
T ss_pred ccccCccccCceeceEEchHHHHHhccCCccCccc-cccccc
Confidence 135799999765 34444555555554444 666665
No 86
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=95.40 E-value=0.016 Score=49.46 Aligned_cols=52 Identities=27% Similarity=0.584 Sum_probs=40.4
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVV 112 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~ 112 (139)
..|.||++ .+...+++|+|.|+..|+..-+.......||+||..+.......
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence 88999999 25556778999999999999987544557999998665444433
No 87
>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=94.99 E-value=0.034 Score=44.04 Aligned_cols=66 Identities=21% Similarity=0.513 Sum_probs=39.3
Q ss_pred hhhhccccccC-CCCCCccccccccccc-------------CCC------eeEEcCCCCcccHHHHHHHHccC-------
Q 038790 41 ELLTVGRYERN-NDNEAVECAVCLCEIE-------------EGE------EIRELRCDHIFHRVCLDQWVGLF------- 93 (139)
Q Consensus 41 ~~~~~~~~~~~-~~~~~~~C~ICl~~~~-------------~~~------~~~~l~C~H~fh~~Ci~~Wl~~~------- 93 (139)
+....+.+... ...+.+.|.-|+..-. .|. ......|...+|.+|+.+|+..+
T Consensus 255 ~V~~Np~y~~~~~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~ 334 (358)
T PF10272_consen 255 QVEQNPRYSYPESGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPE 334 (358)
T ss_pred HHHhCCccccCCCccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChh
Confidence 33344444332 4566778888996532 010 01111255677899999999632
Q ss_pred ----Ccccccccccccc
Q 038790 94 ----RRVTCPLCRDFLD 106 (139)
Q Consensus 94 ----~~~~CP~Cr~~~~ 106 (139)
++.+||.||+.+-
T Consensus 335 ~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 335 TWLSGKCPCPTCRAKFC 351 (358)
T ss_pred hhhcCCCCCCCCcccce
Confidence 3469999999764
No 88
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=94.90 E-value=0.021 Score=49.29 Aligned_cols=67 Identities=21% Similarity=0.463 Sum_probs=50.6
Q ss_pred CCCcccccccccccCCCeeEEcCCC-----CcccHHHHHHHHccCCcccccccccccccCcccccCCceEEEe
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCD-----HIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENGIEILVF 121 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~-----H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~~ 121 (139)
+++..|.||..+=.++++. --||+ ...|.+|+.+|+..+....|-+|+.++.-+....+.-++..++
T Consensus 10 ~d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~~IPf 81 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQIIPF 81 (1175)
T ss_pred ccchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCcccce
Confidence 4568899999775555532 12665 3689999999998778889999999998888777766665443
No 89
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.90 E-value=0.025 Score=44.60 Aligned_cols=50 Identities=20% Similarity=0.362 Sum_probs=39.6
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
..++..|+||...-- . ....||+|.=|..||.+-+- +...|=.|+..+..
T Consensus 419 ~sEd~lCpICyA~pi--~-Avf~PC~H~SC~~CI~qHlm--N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPI--N-AVFAPCSHRSCYGCITQHLM--NCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecccc--h-hhccCCCCchHHHHHHHHHh--cCCeeeEecceeee
Confidence 357888999996522 1 23459999999999999998 88899999986653
No 90
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=94.82 E-value=0.02 Score=43.98 Aligned_cols=52 Identities=29% Similarity=0.722 Sum_probs=38.8
Q ss_pred CcccccccccccCCCe-eEEcCCC-----CcccHHHHHHHHccCCccccccccccccc
Q 038790 56 AVECAVCLCEIEEGEE-IRELRCD-----HIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~-~~~l~C~-----H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
+..|.||.++...... .-..||. +..|+.|++.|+..++...|.+|...+..
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 4789999987654321 2345764 57799999999987788999999875543
No 91
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.82 E-value=0.014 Score=50.34 Aligned_cols=41 Identities=24% Similarity=0.745 Sum_probs=33.6
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
...|..|--.++ -++....|+|.||..|+. . ....||-|+-
T Consensus 840 ~skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e---~--~~~~CP~C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLD--LPFVHFLCGHSYHQHCLE---D--KEDKCPKCLP 880 (933)
T ss_pred eeeecccCCccc--cceeeeecccHHHHHhhc---c--CcccCCccch
Confidence 368999998877 445566799999999988 3 7889999986
No 92
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=94.61 E-value=0.039 Score=31.80 Aligned_cols=31 Identities=32% Similarity=0.801 Sum_probs=25.8
Q ss_pred CCcccccccccccCCCeeEEc-CCCCcccHHH
Q 038790 55 EAVECAVCLCEIEEGEEIREL-RCDHIFHRVC 85 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~C 85 (139)
....|++|-+.|.+++.+.+- .|+-.||++|
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C 35 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDC 35 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHH
Confidence 456799999999877766665 6999999999
No 93
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.60 E-value=0.021 Score=43.63 Aligned_cols=47 Identities=26% Similarity=0.665 Sum_probs=38.0
Q ss_pred CCcccccccccccCCCe-eEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEEGEE-IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~-~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
....|+||.+.+..... +..++|+|.-|..|+..... .+-+||+|.+
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~--~~y~CP~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC--EGYTCPICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc--cCCCCCcccc
Confidence 44559999998876554 44569999999999999887 5599999988
No 94
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.58 E-value=0.083 Score=42.09 Aligned_cols=51 Identities=18% Similarity=0.320 Sum_probs=40.0
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccC-Cccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLF-RRVTCPLCRD 103 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~-~~~~CP~Cr~ 103 (139)
...-..|||=.+.-.++.+...|.|||+..++-+.+-.+.+ +...||+|=.
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 34567899988887777777788999999999999988731 2378999943
No 95
>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=94.25 E-value=0.017 Score=32.25 Aligned_cols=44 Identities=25% Similarity=0.667 Sum_probs=25.1
Q ss_pred ccccccccccCCCeeEEcCCC-CcccHHHHHHHHccCCcccccccccccccC
Q 038790 58 ECAVCLCEIEEGEEIRELRCD-HIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~-H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
.|.-|+-..+ . ...|+ |..+..|+..-+. ....||+|..+++.+
T Consensus 4 nCKsCWf~~k--~---Li~C~dHYLCl~CLt~ml~--~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFANK--G---LIKCSDHYLCLNCLTLMLS--RSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S--S--S---EEE-SS-EEEHHHHHHT-S--SSSEETTTTEE----
T ss_pred cChhhhhcCC--C---eeeecchhHHHHHHHHHhc--cccCCCcccCcCccc
Confidence 4556664322 2 34575 9999999999988 999999999988754
No 96
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.15 E-value=0.025 Score=49.13 Aligned_cols=37 Identities=27% Similarity=0.453 Sum_probs=29.5
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
.....|.+|...+-. .+....||||.||++||..-..
T Consensus 815 ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHH
Confidence 457789999988775 3555679999999999987653
No 97
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.68 E-value=0.034 Score=42.89 Aligned_cols=45 Identities=22% Similarity=0.676 Sum_probs=35.7
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
...|+.|..-+. ..+..-.|+|.|+.+||..-|. .....||.|.+
T Consensus 274 ~LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~-dsDf~CpnC~r 318 (427)
T COG5222 274 SLKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALL-DSDFKCPNCSR 318 (427)
T ss_pred cccCcchhhhhh--CcccCccccchHHHHHHhhhhh-hccccCCCccc
Confidence 378999988766 4444446899999999998876 47889999965
No 98
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=93.67 E-value=0.028 Score=43.51 Aligned_cols=42 Identities=31% Similarity=0.583 Sum_probs=30.0
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
-|--|-..+. -..+.+||+|+||.+|... .....||.|...+
T Consensus 92 fCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~----~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIA--IYGRMIPCKHVFCLECARS----DSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcce--eeecccccchhhhhhhhhc----CccccCcCcccHH
Confidence 3555655544 4556779999999999665 2567999997655
No 99
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.64 E-value=0.051 Score=42.67 Aligned_cols=51 Identities=22% Similarity=0.507 Sum_probs=32.6
Q ss_pred CCCcccccccccccCCCe-eEEcCCCCcccHHH---HHHHHccCCcccccccccccccC
Q 038790 54 NEAVECAVCLCEIEEGEE-IRELRCDHIFHRVC---LDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~-~~~l~C~H~fh~~C---i~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
.+++-|++|+++++-.++ ..-.|||-..|.-| |++= -+..||-||+.+...
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~----lngrcpacrr~y~de 66 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN----LNGRCPACRRKYDDE 66 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhh----ccCCChHhhhhcccc
Confidence 344459999999986554 22346775444444 4443 357899999866543
No 100
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.31 E-value=0.17 Score=40.51 Aligned_cols=38 Identities=26% Similarity=0.626 Sum_probs=28.2
Q ss_pred CCCccccccc-ccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 54 NEAVECAVCL-CEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 54 ~~~~~C~ICl-~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
....+|.||+ +.....+......|+|.|+.+|..+.+.
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 3477899999 4444333333457999999999999987
No 101
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=92.62 E-value=0.11 Score=39.90 Aligned_cols=47 Identities=21% Similarity=0.598 Sum_probs=34.8
Q ss_pred ccccccccccCCCeeEEc--CCCCcccHHHHHHHHccCCccccccccccc
Q 038790 58 ECAVCLCEIEEGEEIREL--RCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l--~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
.|++|..+.-.+..+..+ +|+|..|..|++.-+. .+...||-|-..+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-LGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-cCCCCCCcccchh
Confidence 488888654433333333 8999999999999986 3788999996644
No 102
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=92.38 E-value=0.078 Score=45.65 Aligned_cols=39 Identities=26% Similarity=0.635 Sum_probs=26.3
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPL 100 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~ 100 (139)
|+||--.+.... .....|+|+.|.+|.+.|+. ....||.
T Consensus 1031 C~~C~l~V~gss-~~Cg~C~Hv~H~sc~~eWf~--~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVRGSS-NFCGTCGHVGHTSCMMEWFR--TGDVCPS 1069 (1081)
T ss_pred eeeEeeEeeccc-hhhccccccccHHHHHHHHh--cCCcCCC
Confidence 555544433211 12235999999999999999 6778874
No 103
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=91.51 E-value=0.044 Score=49.40 Aligned_cols=45 Identities=22% Similarity=0.571 Sum_probs=38.0
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
+...|.||++.+.. ...+..|+|.++..|+..|+. .+..||.|+.
T Consensus 1152 ~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~--~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLY--ASSRCPICKS 1196 (1394)
T ss_pred cccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHH--HhccCcchhh
Confidence 45589999999883 234567999999999999999 9999999984
No 104
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=91.24 E-value=0.19 Score=34.33 Aligned_cols=55 Identities=22% Similarity=0.422 Sum_probs=36.9
Q ss_pred CCCcccccccccccCCCeeEEcC---CCCcccHHH-HHHHHccCCcccccccccccccCcc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELR---CDHIFHRVC-LDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~---C~H~fh~~C-i~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
..-.+|.||.|.-.+ +.-..| ||=..|.-| ..-|-...-++.||+|+..+-.+..
T Consensus 78 ~~lYeCnIC~etS~e--e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 78 PKLYECNICKETSAE--ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CCceeccCcccccch--hhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 367899999987442 212223 787777765 5556443478999999998766544
No 105
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.86 E-value=0.12 Score=38.99 Aligned_cols=54 Identities=22% Similarity=0.542 Sum_probs=36.5
Q ss_pred CCCCcccccccccccCCCeeE-EcCCC-----CcccHHHHHHHHccC------Ccccccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGEEIR-ELRCD-----HIFHRVCLDQWVGLF------RRVTCPLCRDFLD 106 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~-~l~C~-----H~fh~~Ci~~Wl~~~------~~~~CP~Cr~~~~ 106 (139)
...+..|-||+..=+++.... .-||. |-.|..|+..|+..+ +..+||-|+.++.
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 345678999998744322111 12663 789999999999632 2368999988654
No 106
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.69 E-value=0.13 Score=39.61 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=23.9
Q ss_pred CCCcccHHHHHHHHcc-----------CCccccccccccccc
Q 038790 77 CDHIFHRVCLDQWVGL-----------FRRVTCPLCRDFLDS 107 (139)
Q Consensus 77 C~H~fh~~Ci~~Wl~~-----------~~~~~CP~Cr~~~~~ 107 (139)
|...+|.+|+.+|+.. +++.+||+||+.+-.
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci 366 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI 366 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence 5578889999999863 245799999997643
No 107
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.46 E-value=0.25 Score=37.34 Aligned_cols=60 Identities=22% Similarity=0.383 Sum_probs=44.8
Q ss_pred CCcccccccccccCCCeeEEc-CCCCcccHHHHHHHHccCCcccccccccccccCcccccCCceE
Q 038790 55 EAVECAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENGIEI 118 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~~~~~~ 118 (139)
....|+|-.-+|...-....+ +|||+|-..-+++- ...+|++|-.++.......-.+.++
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei----kas~C~~C~a~y~~~dvIvlNg~~E 170 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI----KASVCHVCGAAYQEDDVIVLNGTEE 170 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHh----hhccccccCCcccccCeEeeCCCHH
Confidence 456799988888765554445 99999998887774 6789999999887766665555443
No 108
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=90.40 E-value=0.19 Score=39.04 Aligned_cols=48 Identities=25% Similarity=0.627 Sum_probs=36.8
Q ss_pred CCCCcccccccccccCCCeeEEcCC--CCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRC--DHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C--~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
..+-.+|+||.+.+... +..| ||..|..|-.+ ....||.||.+++..+
T Consensus 45 ~~~lleCPvC~~~l~~P----i~QC~nGHlaCssC~~~-----~~~~CP~Cr~~~g~~R 94 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP----IFQCDNGHLACSSCRTK-----VSNKCPTCRLPIGNIR 94 (299)
T ss_pred chhhccCchhhccCccc----ceecCCCcEehhhhhhh-----hcccCCccccccccHH
Confidence 44567899999998843 5567 69999888553 6788999999887543
No 109
>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=89.98 E-value=0.5 Score=26.65 Aligned_cols=45 Identities=20% Similarity=0.517 Sum_probs=21.6
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHcc---CCcccccccccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL---FRRVTCPLCRDF 104 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~---~~~~~CP~Cr~~ 104 (139)
..|+|....+. -+++...|.|.-+- -+..|+.. ...-.||+|.++
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CF-Dl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCF-DLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--E-EHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE--eCccCCcCcccceE-CHHHHHHHhhccCCeECcCCcCc
Confidence 46888888877 67788899997331 24445541 234579999764
No 110
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.77 E-value=0.32 Score=39.56 Aligned_cols=35 Identities=26% Similarity=0.493 Sum_probs=28.2
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
+++..|+||..=|.+ + .++||+|..|.-|...=+.
T Consensus 2 eeelkc~vc~~f~~e--p-iil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYRE--P-IILPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhccC--c-eEeecccHHHHHHHHhhcc
Confidence 356789999988773 3 5789999999999887665
No 111
>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=89.38 E-value=0.18 Score=37.90 Aligned_cols=49 Identities=27% Similarity=0.542 Sum_probs=36.5
Q ss_pred CCCcccccccccccCCCeeEEc--C-CCCcccHHHHHHHHccCCccccc--cccc
Q 038790 54 NEAVECAVCLCEIEEGEEIREL--R-CDHIFHRVCLDQWVGLFRRVTCP--LCRD 103 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l--~-C~H~fh~~Ci~~Wl~~~~~~~CP--~Cr~ 103 (139)
..+..|+||..+--.+..+..+ | |-|..|.+|++.-+. .....|| -|-+
T Consensus 8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-~GpAqCP~~gC~k 61 (314)
T COG5220 8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-RGPAQCPYKGCGK 61 (314)
T ss_pred hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-CCCCCCCCccHHH
Confidence 3466899999765444444444 6 999999999999997 3678999 7743
No 112
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.06 E-value=0.27 Score=36.10 Aligned_cols=40 Identities=28% Similarity=0.612 Sum_probs=27.8
Q ss_pred cccccccccCCCeeEEcCCCC-cccHHHHHHHHccCCccccccccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDH-IFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H-~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
|..|.+. +..|..+||.| .+|..|=.. -..||+|+.+...
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~------~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES------LRICPICRSPKTS 201 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc------CccCCCCcChhhc
Confidence 8888865 23466779986 777888222 5679999886543
No 113
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.86 E-value=0.46 Score=38.76 Aligned_cols=38 Identities=29% Similarity=0.689 Sum_probs=31.8
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL 92 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~ 92 (139)
......|.||.+.+.. ....+.|+|.|+..|...++++
T Consensus 67 ~~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 4557889999999875 4556699999999999999985
No 114
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=87.56 E-value=0.3 Score=35.89 Aligned_cols=44 Identities=34% Similarity=0.850 Sum_probs=34.8
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
-..|.+|..-.-. .++.-.|+-.+|..|+..++. +...||.|-.
T Consensus 181 lk~Cn~Ch~LvIq--g~rCg~c~i~~h~~c~qty~q--~~~~cphc~d 224 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQ--GIRCGSCNIQYHRGCIQTYLQ--RRDICPHCGD 224 (235)
T ss_pred HHHHhHhHHHhhe--eeccCcccchhhhHHHHHHhc--ccCcCCchhc
Confidence 4579999977553 334447888999999999998 7999999954
No 115
>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 PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=86.27 E-value=0.65 Score=33.91 Aligned_cols=42 Identities=24% Similarity=0.817 Sum_probs=27.6
Q ss_pred CCccccccccc-----ccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCE-----IEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~-----~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.+..|.+|.++ |+.+..++--.|+.+||..|.. ...||-|.+
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-------~~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-------KKSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-------CCCCCCcHh
Confidence 36788899852 2332222333699999999944 356999954
No 117
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.60 E-value=0.43 Score=39.94 Aligned_cols=53 Identities=28% Similarity=0.750 Sum_probs=40.2
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcccccCC
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVENG 115 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~~~ 115 (139)
.....|.||+.++ ..+..+|. |..|...|+. .+..||+|+..+.......+..
T Consensus 477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~--~~~~~pl~~~~~~~~~~~~~~~ 529 (543)
T KOG0802|consen 477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLY--VQEVCPLCHTYMKEDDFLSKNS 529 (543)
T ss_pred cccCcchHHHHHH----Hhcccccc---chhHHHhhhh--hccccCCCchhhhcccccCccc
Confidence 3567899999997 33566787 9999999998 8999999988665544444433
No 118
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=84.33 E-value=0.77 Score=34.96 Aligned_cols=51 Identities=35% Similarity=0.621 Sum_probs=37.0
Q ss_pred CcccccccccccCCCeeEEc----CCCCcccHHHHHHHHccC-------Ccccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIREL----RCDHIFHRVCLDQWVGLF-------RRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l----~C~H~fh~~Ci~~Wl~~~-------~~~~CP~Cr~~~~ 106 (139)
..+|.+|.+++.+.+..+.. .|+-.+|..|+..-+.+. ....||.|++-+.
T Consensus 182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 36899999999654544433 388899999999955421 2479999988553
No 119
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=84.08 E-value=0.34 Score=40.75 Aligned_cols=44 Identities=27% Similarity=0.690 Sum_probs=26.9
Q ss_pred CCcccccccc-----cccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLC-----EIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~-----~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.+..|.+|-. +|+.....+...|+++||..|... ...-||.|-+
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r-----~s~~CPrC~R 558 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR-----KSPCCPRCER 558 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc-----cCCCCCchHH
Confidence 3567888832 122111222336999999999655 4455999954
No 120
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.04 E-value=0.3 Score=41.44 Aligned_cols=43 Identities=21% Similarity=0.502 Sum_probs=31.2
Q ss_pred CcccccccccccCCCe-eEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 56 AVECAVCLCEIEEGEE-IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~-~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
-..|.||+..|....- .+-+.|||..|+.|+..- .+.+|| |++
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l----yn~scp-~~~ 54 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL----YNASCP-TKR 54 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH----hhccCC-CCc
Confidence 4569999887764432 234579999999999885 467788 644
No 121
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=82.74 E-value=0.32 Score=41.60 Aligned_cols=51 Identities=33% Similarity=0.802 Sum_probs=38.4
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHcc-CCcccccccccccccC
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL-FRRVTCPLCRDFLDSR 108 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~-~~~~~CP~Cr~~~~~~ 108 (139)
...+|+||...+... ..+.|.|.|+..|+..-+.- .....||+|+..+...
T Consensus 20 k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 20 KILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 367899999998854 35689999999998877651 2356899998755443
No 122
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=80.71 E-value=1.1 Score=39.18 Aligned_cols=52 Identities=13% Similarity=0.118 Sum_probs=37.5
Q ss_pred CCcccccccccccCCCe-eEEcC---CCCcccHHHHHHHHcc----CCcccccccccccc
Q 038790 55 EAVECAVCLCEIEEGEE-IRELR---CDHIFHRVCLDQWVGL----FRRVTCPLCRDFLD 106 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~-~~~l~---C~H~fh~~Ci~~Wl~~----~~~~~CP~Cr~~~~ 106 (139)
+...|.+|..++..++. ..++| |.|.||..||..|... ..+..|++|...|.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~ 154 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG 154 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence 35568888877775322 23445 9999999999999863 34678899987664
No 123
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=80.00 E-value=2 Score=26.56 Aligned_cols=52 Identities=17% Similarity=0.327 Sum_probs=21.7
Q ss_pred CCCcccccccccccCCCe---eE-EcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEE---IR-ELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~---~~-~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....|.||-+++..... .. ..-|+--.++.|..-=.+ ..+..||-|+.++.
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErk-eg~q~CpqCkt~yk 62 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERK-EGNQVCPQCKTRYK 62 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHH-TS-SB-TTT--B--
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhh-cCcccccccCCCcc
Confidence 457789999998754332 11 124666778889876655 47889999998775
No 124
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.82 E-value=4.2 Score=31.93 Aligned_cols=50 Identities=18% Similarity=0.284 Sum_probs=37.2
Q ss_pred CCCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccC-Cccccccc
Q 038790 52 NDNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLF-RRVTCPLC 101 (139)
Q Consensus 52 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~-~~~~CP~C 101 (139)
....-..|++--+.-....+...+.|||+.-..-++.-.+++ ....||+|
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYC 382 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYC 382 (396)
T ss_pred cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCC
Confidence 344567899877766555666677999999999998877632 35789999
No 125
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=79.08 E-value=2.7 Score=32.99 Aligned_cols=59 Identities=19% Similarity=0.534 Sum_probs=39.3
Q ss_pred CCCccccccccc--c-------------cCCCeeEE-cCCCCcccHHHHHHHHcc-------CCcccccccccccccCcc
Q 038790 54 NEAVECAVCLCE--I-------------EEGEEIRE-LRCDHIFHRVCLDQWVGL-------FRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 54 ~~~~~C~ICl~~--~-------------~~~~~~~~-l~C~H~fh~~Ci~~Wl~~-------~~~~~CP~Cr~~~~~~~~ 110 (139)
..+.+|++|+.. + +.+..... .||||+--.+-..-|... .-+..||.|-+.+.....
T Consensus 339 ~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~ 418 (429)
T KOG3842|consen 339 QRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQG 418 (429)
T ss_pred cccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCCc
Confidence 347789999853 1 11222112 389999888888888763 235789999888876555
Q ss_pred cc
Q 038790 111 VV 112 (139)
Q Consensus 111 ~~ 112 (139)
..
T Consensus 419 ~i 420 (429)
T KOG3842|consen 419 YI 420 (429)
T ss_pred eE
Confidence 43
No 126
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=78.38 E-value=2.2 Score=37.04 Aligned_cols=42 Identities=24% Similarity=0.456 Sum_probs=29.9
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPL 100 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~ 100 (139)
...|++|-..+.. ..+-.-.|+|.-|.+|+++|+. ...-||.
T Consensus 779 ~~~CtVC~~vi~G-~~~~c~~C~H~gH~sh~~sw~~--~~s~ca~ 820 (839)
T KOG0269|consen 779 SAKCTVCDLVIRG-VDVWCQVCGHGGHDSHLKSWFF--KASPCAK 820 (839)
T ss_pred hcCceeecceeee-eEeecccccccccHHHHHHHHh--cCCCCcc
Confidence 4468888766542 1111225999999999999998 7888866
No 127
>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=76.31 E-value=1.1 Score=24.81 Aligned_cols=45 Identities=27% Similarity=0.560 Sum_probs=27.8
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHcc----CCcccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGL----FRRVTCPLCR 102 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~----~~~~~CP~Cr 102 (139)
.|.||...-..++-+.--.|+..||..|+..=... ...-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 38889984333333322378999999998764331 1245677775
No 128
>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=75.54 E-value=0.87 Score=25.91 Aligned_cols=16 Identities=38% Similarity=0.785 Sum_probs=7.9
Q ss_pred CcccccccccccccCc
Q 038790 94 RRVTCPLCRDFLDSRR 109 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~~ 109 (139)
.+..||+|.++|+...
T Consensus 19 ~~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 19 AKGCCPLCGRPLDEEH 34 (54)
T ss_dssp -SEE-TTT--EE-HHH
T ss_pred CCCcCCCCCCCCCHHH
Confidence 3449999999887543
No 129
>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=72.46 E-value=1.7 Score=25.69 Aligned_cols=37 Identities=19% Similarity=0.403 Sum_probs=18.4
Q ss_pred CCCcccccccccccCCCeeEEc-CCCCcccHHHHHHHH
Q 038790 54 NEAVECAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWV 90 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl 90 (139)
.+...|.+|...|..-..-..- .||++|+..|.....
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 4467799999999754332222 699999998876543
No 130
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.58 E-value=1.5 Score=38.13 Aligned_cols=45 Identities=20% Similarity=0.500 Sum_probs=32.1
Q ss_pred CCCcccccccccccCC----CeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 54 NEAVECAVCLCEIEEG----EEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~----~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
..+..|..|.+..... +.+..+.|+|.||..|+..-.. ++. |-.|
T Consensus 782 ~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~--~~~-~~~~ 830 (846)
T KOG2066|consen 782 SVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESL--RNA-CNIE 830 (846)
T ss_pred eehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHH--hcc-cChh
Confidence 3455799999876532 3456678999999999998876 333 5444
No 131
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=70.19 E-value=1.4 Score=35.37 Aligned_cols=57 Identities=19% Similarity=0.433 Sum_probs=0.0
Q ss_pred CCccccccccccc-------------C--CCeeE-EcCCCCcccHHHHHHHHcc-------CCcccccccccccccCccc
Q 038790 55 EAVECAVCLCEIE-------------E--GEEIR-ELRCDHIFHRVCLDQWVGL-------FRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 55 ~~~~C~ICl~~~~-------------~--~~~~~-~l~C~H~fh~~Ci~~Wl~~-------~~~~~CP~Cr~~~~~~~~~ 111 (139)
...+|++|+..=. . +.... --||||+--....+-|.+. .-+..||.|-.+|......
T Consensus 327 ~~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~ 406 (416)
T PF04710_consen 327 RSRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGY 406 (416)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCCCCc
Confidence 3778999995311 1 11111 2289999888889999763 1246899999888754443
No 132
>PLN02189 cellulose synthase
Probab=69.63 E-value=5.3 Score=36.09 Aligned_cols=52 Identities=19% Similarity=0.403 Sum_probs=35.1
Q ss_pred CCCcccccccccccCC---CeeEEc-CCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEG---EEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~---~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....|.||-+++... +..+.. -|+=-.|+.|.+ +=..+.++.||-|+..+.
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-yer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-YERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccCCchh
Confidence 4566899999997632 322222 366668999983 332247899999998764
No 133
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=69.31 E-value=8.3 Score=25.19 Aligned_cols=48 Identities=23% Similarity=0.379 Sum_probs=30.1
Q ss_pred CCcccccccccccCCCeeEE------cCC---CCcccHHHHHHHHcc-------CCccccccccc
Q 038790 55 EAVECAVCLCEIEEGEEIRE------LRC---DHIFHRVCLDQWVGL-------FRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~------l~C---~H~fh~~Ci~~Wl~~-------~~~~~CP~Cr~ 103 (139)
.+..|..|...-. +..+.- ..| .-.|+..|+..++.+ ..+-.||.||.
T Consensus 6 ~g~~CHqCrqKt~-~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 6 NGKTCHQCRQKTL-DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCchhhcCCCC-CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 4556777775422 112221 345 668999999998863 23457999986
No 134
>PLN02195 cellulose synthase A
Probab=69.04 E-value=5.5 Score=35.72 Aligned_cols=52 Identities=23% Similarity=0.376 Sum_probs=35.8
Q ss_pred CCCcccccccccccCCC---e-eEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGE---E-IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~---~-~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
+....|.||-+++..+. . ++.--|+--.|+.|- .+=+.+.+..||-|+..+.
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccCCCccccchh-hhhhhcCCccCCccCCccc
Confidence 44668999999876433 2 222257777899997 3332247889999998887
No 135
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=68.95 E-value=2.5 Score=20.48 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=10.9
Q ss_pred ccccccccccCCCeeEEcC-CCCcc
Q 038790 58 ECAVCLCEIEEGEEIRELR-CDHIF 81 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~-C~H~f 81 (139)
.|+-|...+.... ..-| |||.|
T Consensus 2 ~CP~C~~~V~~~~--~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESA--KFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhc--CcCCCCCCCC
Confidence 3666666654322 2223 66665
No 136
>PLN02436 cellulose synthase A
Probab=67.67 E-value=6.1 Score=35.84 Aligned_cols=52 Identities=25% Similarity=0.531 Sum_probs=35.0
Q ss_pred CCCccccccccccc---CCCeeEEc-CCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIE---EGEEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~---~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....|.||-|++. .|+..... -|+=-.|+.|.+ +=..+.+..||-|+..+.
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-yer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YERREGNQACPQCKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccCCchh
Confidence 45668999999974 33332222 366668999984 333247899999998764
No 137
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=65.76 E-value=3.6 Score=31.24 Aligned_cols=44 Identities=16% Similarity=0.294 Sum_probs=33.9
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
+..|+|-..++. .+++-..|+|+|-++-|...+.-.....||+=
T Consensus 176 s~rdPis~~~I~--nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~ 219 (262)
T KOG2979|consen 176 SNRDPISKKPIV--NPVISKKCGHVYDRDSIMQILCDEITIRCPVL 219 (262)
T ss_pred cccCchhhhhhh--chhhhcCcCcchhhhhHHHHhccCceeecccc
Confidence 446888887777 45566689999999999999973346778874
No 138
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=65.70 E-value=5.7 Score=31.20 Aligned_cols=49 Identities=16% Similarity=0.416 Sum_probs=34.6
Q ss_pred CcccccccccccCCCeeE-EcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIR-ELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~-~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
...|+||.++....+... -.||++..|..|...=.. .+..||.||.+..
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~--~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD--GDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc--cCCCCCccCCccc
Confidence 468999999875444322 235777777777766655 8899999997653
No 139
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=65.42 E-value=6.6 Score=25.27 Aligned_cols=36 Identities=25% Similarity=0.379 Sum_probs=29.3
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
....|.+|-+++..|+...-++ .-..|.+|+..=..
T Consensus 5 kewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~ 40 (103)
T COG4847 5 KEWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKR 40 (103)
T ss_pred ceeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHh
Confidence 3567999999999999877677 67899999877544
No 140
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=65.08 E-value=8.1 Score=34.96 Aligned_cols=53 Identities=21% Similarity=0.398 Sum_probs=35.6
Q ss_pred CCCCcccccccccccCCC---ee-EEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 53 DNEAVECAVCLCEIEEGE---EI-RELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~---~~-~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.-....|.||-+++.... .. +.--|+--.|+.|.+ +=..+.+..||.|+.++.
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye-ye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE-YERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchhh-hhhhcCCccCCccCCchh
Confidence 345778999999876433 22 212466668999984 322247889999998765
No 141
>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=64.37 E-value=0.54 Score=28.52 Aligned_cols=40 Identities=25% Similarity=0.571 Sum_probs=19.9
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
..|+.|-.+++... ++.++..|-... . ....||-|.+++.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~~-~--~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKDY-K--KEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--EE-E--EEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-------CEEECccccccc-e--ecccCCCcccHHH
Confidence 46899988876433 344444454332 2 5788999988764
No 142
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=63.62 E-value=8.7 Score=34.89 Aligned_cols=52 Identities=15% Similarity=0.344 Sum_probs=34.5
Q ss_pred CCCcccccccccccCCC---ee-EEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGE---EI-RELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~---~~-~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....|.||-+++.... .. +.--|+=-.|+.|- .+=+.+.++.||-|+..+.
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCchh
Confidence 34668999999976433 22 21246656899997 3322247889999988664
No 143
>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=62.53 E-value=4.8 Score=24.10 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=9.0
Q ss_pred cccHHHHHHHHc
Q 038790 80 IFHRVCLDQWVG 91 (139)
Q Consensus 80 ~fh~~Ci~~Wl~ 91 (139)
.||+.|+..|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 599999999986
No 144
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.44 E-value=3.8 Score=32.97 Aligned_cols=44 Identities=30% Similarity=0.594 Sum_probs=29.6
Q ss_pred CcccccccccccCCCeeE--EcCCCCcccHHHHHHHHccCCccccccc
Q 038790 56 AVECAVCLCEIEEGEEIR--ELRCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~--~l~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
-..|+.|.-.++...... ...|+|.|+..|...|.. .+..|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~--~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKT--HNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhh--CCccccCc
Confidence 456888876654333222 225899999999999987 66666444
No 145
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=61.61 E-value=3.1 Score=32.77 Aligned_cols=49 Identities=14% Similarity=0.221 Sum_probs=38.3
Q ss_pred HHHHHccC-CcccccccccccccCcccccCCceEEEeecccccCCCCCCc
Q 038790 86 LDQWVGLF-RRVTCPLCRDFLDSRRAVVENGIEILVFKRFCYLSSSSDRD 134 (139)
Q Consensus 86 i~~Wl~~~-~~~~CP~Cr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (139)
++.|.++. +...||.|..++.-+.+......=.+...+.|.+..|.|+.
T Consensus 15 l~~~~k~~~~~ffCPaC~~~l~lK~G~~k~pHFAHk~l~~C~~~~EnES~ 64 (342)
T COG4469 15 LTALQKTQLQRFFCPACGSQLILKQGLIKIPHFAHKSLKACAFFNENESE 64 (342)
T ss_pred hhhHHHhhhhccccCCCCCeeeeecCccccchhhhhhhhhccccCCCCCH
Confidence 45565521 24699999999999999888888888888789999987764
No 146
>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 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=58.57 E-value=5.5 Score=20.02 Aligned_cols=36 Identities=31% Similarity=0.600 Sum_probs=22.0
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
|+.|.+.+..++.. ...=+..||.+| ..|..|..+|
T Consensus 2 C~~C~~~i~~~~~~-~~~~~~~~H~~C----------f~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGELV-LRALGKVWHPEC----------FKCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCcEE-EEeCCccccccC----------CCCcccCCcC
Confidence 77888887765222 222367888755 3466666654
No 148
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=58.47 E-value=4.5 Score=23.21 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=17.0
Q ss_pred cccccccccccCcccccCCceEE
Q 038790 97 TCPLCRDFLDSRRAVVENGIEIL 119 (139)
Q Consensus 97 ~CP~Cr~~~~~~~~~~~~~~~~~ 119 (139)
.|.+|++++.+.......+...+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH 25 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVH 25 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccC
Confidence 58888888888777777666554
No 149
>PLN02400 cellulose synthase
Probab=58.44 E-value=9.4 Score=34.70 Aligned_cols=52 Identities=17% Similarity=0.367 Sum_probs=34.2
Q ss_pred CCCcccccccccccCCC---e-eEEcCCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGE---E-IRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~---~-~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
.....|.||-|++.... . ++.--|+=-.|+.|-. +=+.+.++.||-|+..+.
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCCCccccchhh-eecccCCccCcccCCccc
Confidence 45668999999976432 2 2222466668888973 322246789999988664
No 150
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=58.00 E-value=9.2 Score=30.17 Aligned_cols=48 Identities=23% Similarity=0.380 Sum_probs=33.2
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
.++..|..|.++.......+.-.|.+.||.+|=.---+ .--.||-|..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHe--sLh~CpgCeh 375 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHE--SLHNCPGCEH 375 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeeccchHHHHh--hhhcCCCcCC
Confidence 34556999987776655555557999999999333222 4457999964
No 151
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=57.51 E-value=2.1 Score=33.13 Aligned_cols=34 Identities=26% Similarity=0.671 Sum_probs=28.7
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
+|.+|+++|..+.......|..+||..|+..|++
T Consensus 216 vC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~ 249 (288)
T KOG1729|consen 216 VCDICFEELEKGARGDREDSLPVFHGKCYPNWLT 249 (288)
T ss_pred ecHHHHHHHhcccccchhhccccccccccccccc
Confidence 8999999998655556666766999999999998
No 152
>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=57.24 E-value=10 Score=18.58 Aligned_cols=29 Identities=31% Similarity=0.555 Sum_probs=10.1
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHH
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCL 86 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci 86 (139)
.|.+|.+....+..-.-..|.-.+|..|+
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 47888887665222333478888898885
No 153
>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=57.13 E-value=18 Score=20.97 Aligned_cols=47 Identities=21% Similarity=0.482 Sum_probs=33.0
Q ss_pred cccccccccccCCCeeEEcCCC--CcccHHHHHHHHccCCcccccccccccccC
Q 038790 57 VECAVCLCEIEEGEEIRELRCD--HIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~--H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
..|-.|-.++.++..-+.. |. ..|+.+|...-| +..||.|-..+..+
T Consensus 6 pnCE~C~~dLp~~s~~A~I-CSfECTFC~~C~e~~l----~~~CPNCgGelv~R 54 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYI-CSFECTFCADCAETML----NGVCPNCGGELVRR 54 (57)
T ss_pred CCccccCCCCCCCCCcceE-EeEeCcccHHHHHHHh----cCcCcCCCCccccC
Confidence 4577888888776633333 43 579999998864 57899998776543
No 154
>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=55.95 E-value=9.7 Score=21.33 Aligned_cols=35 Identities=17% Similarity=0.340 Sum_probs=23.7
Q ss_pred cccccccccccCCCeeEE-cCCCCcccHHHHHHHHc
Q 038790 57 VECAVCLCEIEEGEEIRE-LRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~-l~C~H~fh~~Ci~~Wl~ 91 (139)
..|.+|-..|.....-.. -.||++|+..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 468899888875432222 26999999999765543
No 155
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=55.44 E-value=9.2 Score=19.86 Aligned_cols=25 Identities=32% Similarity=0.809 Sum_probs=14.2
Q ss_pred ccccccccccCCCe--------eEEcCCCCccc
Q 038790 58 ECAVCLCEIEEGEE--------IRELRCDHIFH 82 (139)
Q Consensus 58 ~C~ICl~~~~~~~~--------~~~l~C~H~fh 82 (139)
+|+=|...|..++. ++-..|+|.|+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 57777777764432 22235667663
No 156
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=55.37 E-value=6.3 Score=23.08 Aligned_cols=16 Identities=19% Similarity=0.592 Sum_probs=12.4
Q ss_pred CcccccccccccccCc
Q 038790 94 RRVTCPLCRDFLDSRR 109 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~~ 109 (139)
.|..||+|-.++++++
T Consensus 2 ~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCcCCcCCCcCCcch
Confidence 5788999988887643
No 157
>PHA02446 hypothetical protein
Probab=53.10 E-value=4 Score=27.45 Aligned_cols=16 Identities=31% Similarity=0.625 Sum_probs=8.4
Q ss_pred EeecccccCCCCCCccc
Q 038790 120 VFKRFCYLSSSSDRDSW 136 (139)
Q Consensus 120 ~~~~~~~~~~~~~~~~~ 136 (139)
+++ -|+|++.+-...|
T Consensus 87 l~q-ecplsgqsv~tdw 102 (166)
T PHA02446 87 LLQ-ECPLSGQSVATDW 102 (166)
T ss_pred HHH-hCCCCCCccccch
Confidence 344 5666665544444
No 158
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=52.75 E-value=1.3 Score=25.07 Aligned_cols=39 Identities=26% Similarity=0.555 Sum_probs=20.5
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDF 104 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~ 104 (139)
...|+.|.+.++.. .| +.|+ .+.=........||+|...
T Consensus 2 ~f~CP~C~~~~~~~----~L-~~H~-----~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGFSES----SL-VEHC-----EDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCccCHH----HH-HHHH-----HhHCcCCCCCccCCCchhh
Confidence 46789998865532 22 2232 1111111246789999763
No 159
>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=51.86 E-value=21 Score=19.81 Aligned_cols=40 Identities=25% Similarity=0.465 Sum_probs=27.6
Q ss_pred cccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCc
Q 038790 59 CAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRR 109 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~ 109 (139)
|+-|.+.+..++.+. ..-+..||..| ..|-.|+.++....
T Consensus 1 C~~C~~~I~~~~~~~-~~~~~~~H~~C----------f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIVI-KAMGKFWHPEC----------FKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEEE-EETTEEEETTT----------SBETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEEE-EeCCcEEEccc----------cccCCCCCccCCCe
Confidence 677888887655432 23578888644 56888988887766
No 160
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=51.50 E-value=11 Score=24.23 Aligned_cols=32 Identities=25% Similarity=0.592 Sum_probs=22.3
Q ss_pred CCcccccccccccCCCeeEEc--CCCCcccHHHHHH
Q 038790 55 EAVECAVCLCEIEEGEEIREL--RCDHIFHRVCLDQ 88 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l--~C~H~fh~~Ci~~ 88 (139)
....|.||... .|..+.-. .|...||..|...
T Consensus 54 ~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHH
Confidence 46789999987 33333222 3888999999765
No 161
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=50.17 E-value=18 Score=23.61 Aligned_cols=34 Identities=21% Similarity=0.338 Sum_probs=26.5
Q ss_pred cccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
-.|.||-+++..|+...-++ +-..|..|+..=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~-kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTK-KGPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEec-CCcEeHHHHHHHHh
Confidence 36999999999988765553 36789999987654
No 162
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=48.53 E-value=11 Score=23.18 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=21.0
Q ss_pred CcccccccccccCCCeeE--EcCCCCcccHHHHHH
Q 038790 56 AVECAVCLCEIEEGEEIR--ELRCDHIFHRVCLDQ 88 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~--~l~C~H~fh~~Ci~~ 88 (139)
...|.+|.... |.-+. .-.|...||..|...
T Consensus 36 ~~~C~~C~~~~--Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKG--GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCC--CeEEEEeCCCCCcEEChHHHcc
Confidence 55799999762 33222 225888999999654
No 163
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.35 E-value=24 Score=23.39 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=30.5
Q ss_pred CcccccccccccCCC---------e--eEEcCCCCcccHHHHHHHHccCCcccccccc
Q 038790 56 AVECAVCLCEIEEGE---------E--IRELRCDHIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~---------~--~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
...|.-|...|.... . -+-..|++.|+.+|=.-+-+ .--+||-|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe--~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE--SLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh--hccCCcCCC
Confidence 456999999886431 1 11226899999999665555 556799885
No 164
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.35 E-value=22 Score=21.72 Aligned_cols=44 Identities=18% Similarity=0.396 Sum_probs=28.0
Q ss_pred cccccccccCCCeeEEc-CCCCcccHHHHHHHHccCCcccccccccccc
Q 038790 59 CAVCLCEIEEGEEIREL-RCDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 59 C~ICl~~~~~~~~~~~l-~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
|--|-.++.++..-..+ .=.+.|+.+|...- -+..||.|-..+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~----l~g~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENR----LHGLCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHh----hcCcCCCCCchhh
Confidence 55566666544332222 22478999998865 4678999976554
No 165
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=44.54 E-value=15 Score=23.72 Aligned_cols=29 Identities=14% Similarity=0.345 Sum_probs=19.8
Q ss_pred CCCcccHHHHHHHHccCCcccccccccccccC
Q 038790 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSR 108 (139)
Q Consensus 77 C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~ 108 (139)
||+.-|.--+.++.. -..||.|+.++.+.
T Consensus 65 CGvC~~~LT~~EY~~---~~~Cp~C~spFNp~ 93 (105)
T COG4357 65 CGVCRKLLTRAEYGM---CGSCPYCQSPFNPG 93 (105)
T ss_pred hhhhhhhhhHHHHhh---cCCCCCcCCCCCcc
Confidence 666555555556543 56799999988764
No 166
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=44.28 E-value=18 Score=18.79 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=7.6
Q ss_pred ccccccccccCC
Q 038790 58 ECAVCLCEIEEG 69 (139)
Q Consensus 58 ~C~ICl~~~~~~ 69 (139)
.|+-|-..|..+
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 577777766533
No 167
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.78 E-value=25 Score=26.77 Aligned_cols=36 Identities=11% Similarity=0.136 Sum_probs=28.6
Q ss_pred CCCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 53 DNEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 53 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
.....-|.+|+.++. +++ ++|=||+|++.||..++.
T Consensus 40 iK~FdcCsLtLqPc~--dPv-it~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 40 IKPFDCCSLTLQPCR--DPV-ITPDGYLFDREAILEYIL 75 (303)
T ss_pred cCCcceeeeeccccc--CCc-cCCCCeeeeHHHHHHHHH
Confidence 345677999999987 333 567799999999999985
No 168
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=42.70 E-value=9.2 Score=21.73 Aligned_cols=22 Identities=14% Similarity=0.371 Sum_probs=15.3
Q ss_pred cccccccccccCcccccCCceE
Q 038790 97 TCPLCRDFLDSRRAVVENGIEI 118 (139)
Q Consensus 97 ~CP~Cr~~~~~~~~~~~~~~~~ 118 (139)
.|++|++++......+....-.
T Consensus 3 iCvvCK~Pi~~al~v~T~~Gpv 24 (53)
T PHA02610 3 ICVVCKQPIEKALVVETEKGPV 24 (53)
T ss_pred eeeeeCCchhhceEEecCCCCC
Confidence 5888888887776666655444
No 169
>smart00746 TRASH metallochaperone-like domain.
Probab=42.14 E-value=12 Score=17.79 Aligned_cols=9 Identities=22% Similarity=0.755 Sum_probs=7.2
Q ss_pred ccccccccc
Q 038790 98 CPLCRDFLD 106 (139)
Q Consensus 98 CP~Cr~~~~ 106 (139)
||+|...+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788888776
No 170
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=42.03 E-value=2.4 Score=32.58 Aligned_cols=42 Identities=29% Similarity=0.619 Sum_probs=17.6
Q ss_pred CCccccccccccc-----CCC--eeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIE-----EGE--EIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~-----~~~--~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
....|++|-..-. .++ ..+ +.+|.-|-..|-- ....||.|-.
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R-----~L~Cs~C~t~W~~--~R~~Cp~Cg~ 219 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKR-----YLHCSLCGTEWRF--VRIKCPYCGN 219 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EE-----EEEETTT--EEE----TTS-TTT--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccE-----EEEcCCCCCeeee--cCCCCcCCCC
Confidence 4578999997643 111 123 4455556667755 7889999965
No 171
>PRK11827 hypothetical protein; Provisional
Probab=41.99 E-value=8.5 Score=22.62 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=11.7
Q ss_pred HHHccCCccccccccccccc
Q 038790 88 QWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 88 ~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
++|. .--.||+|+.++..
T Consensus 3 ~~LL--eILaCP~ckg~L~~ 20 (60)
T PRK11827 3 HRLL--EIIACPVCNGKLWY 20 (60)
T ss_pred hHHH--hheECCCCCCcCeE
Confidence 3444 55678888877654
No 172
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=41.04 E-value=24 Score=19.35 Aligned_cols=35 Identities=26% Similarity=0.465 Sum_probs=24.0
Q ss_pred CCCcccccccccc--cCCCeeEEcCCCCcccHHHHHH
Q 038790 54 NEAVECAVCLCEI--EEGEEIRELRCDHIFHRVCLDQ 88 (139)
Q Consensus 54 ~~~~~C~ICl~~~--~~~~~~~~l~C~H~fh~~Ci~~ 88 (139)
.....|.+|.+.+ ...+..+-.-|+-..|..|++.
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 4567899999998 3344455557999999999654
No 173
>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=40.93 E-value=12 Score=18.83 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=7.2
Q ss_pred Cccccccccc
Q 038790 94 RRVTCPLCRD 103 (139)
Q Consensus 94 ~~~~CP~Cr~ 103 (139)
....||+|..
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4568999865
No 174
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=40.48 E-value=5.5 Score=22.73 Aligned_cols=12 Identities=33% Similarity=1.041 Sum_probs=5.1
Q ss_pred cccccccccccc
Q 038790 96 VTCPLCRDFLDS 107 (139)
Q Consensus 96 ~~CP~Cr~~~~~ 107 (139)
.+||+|.+.+..
T Consensus 25 atCP~C~a~~~~ 36 (54)
T PF09237_consen 25 ATCPICGAVIRQ 36 (54)
T ss_dssp EE-TTT--EESS
T ss_pred CCCCcchhhccc
Confidence 467777655443
No 175
>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=39.81 E-value=19 Score=20.39 Aligned_cols=42 Identities=29% Similarity=0.605 Sum_probs=19.8
Q ss_pred cccccccccCCCe-----eEE--cCCCCcccHHHHHHHHccCCcccccccc
Q 038790 59 CAVCLCEIEEGEE-----IRE--LRCDHIFHRVCLDQWVGLFRRVTCPLCR 102 (139)
Q Consensus 59 C~ICl~~~~~~~~-----~~~--l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr 102 (139)
|.-|+..|..+.. .+. -.|++.|+.+| +-.+- +.--+||-|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiH-E~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC-DVFIH-ETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHH-HHTTT-TTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCc-Chhhh-ccccCCcCCC
Confidence 5567777665421 222 26999999999 33322 2345788773
No 176
>PF15353 HECA: Headcase protein family homologue
Probab=38.70 E-value=32 Score=22.59 Aligned_cols=16 Identities=25% Similarity=0.821 Sum_probs=13.3
Q ss_pred CCCCcccHHHHHHHHc
Q 038790 76 RCDHIFHRVCLDQWVG 91 (139)
Q Consensus 76 ~C~H~fh~~Ci~~Wl~ 91 (139)
|.++..|.+|++.|=.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4578999999999943
No 177
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=38.00 E-value=17 Score=31.66 Aligned_cols=53 Identities=19% Similarity=0.311 Sum_probs=33.9
Q ss_pred CCCcccccccccccCCCe--eEEc-----CCCCcccHHHHHHHHcc--------CCcccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEE--IREL-----RCDHIFHRVCLDQWVGL--------FRRVTCPLCRDFLD 106 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~--~~~l-----~C~H~fh~~Ci~~Wl~~--------~~~~~CP~Cr~~~~ 106 (139)
.-...|.||-|.=.+.+. .+.+ .|...||..|.+.-=.+ .+-..|.+|+..+.
T Consensus 115 RfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 115 RFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred hhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 346789999987443321 2223 36789999998763211 23479999987654
No 178
>PF04890 DUF648: Family of unknown function (DUF648) ; InterPro: IPR006974 This is a family of hypothetical proteins from Chlamydia pneumoniae.
Probab=37.87 E-value=38 Score=26.74 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=20.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhc
Q 038790 1 MLSYIVSVSTHLKWACKFLIQNSLF 25 (139)
Q Consensus 1 ~~~~i~l~~~~l~~~~~~~~~~~~~ 25 (139)
|++|+.+.+.++++++.+++...+-
T Consensus 64 ILSyll~PivLIAL~lR~lLH~~l~ 88 (328)
T PF04890_consen 64 ILSYLLFPIVLIALLLRYLLHRKLH 88 (328)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5799999999999999888876554
No 179
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=37.65 E-value=19 Score=21.12 Aligned_cols=12 Identities=42% Similarity=1.157 Sum_probs=9.3
Q ss_pred cccccccccccc
Q 038790 95 RVTCPLCRDFLD 106 (139)
Q Consensus 95 ~~~CP~Cr~~~~ 106 (139)
+..||+|+..+.
T Consensus 2 k~~CPlCkt~~n 13 (61)
T PF05715_consen 2 KSLCPLCKTTLN 13 (61)
T ss_pred CccCCcccchhh
Confidence 467999998764
No 180
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=37.04 E-value=25 Score=26.45 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=17.8
Q ss_pred cccccccccccCCCeeEEcCCCCccc
Q 038790 57 VECAVCLCEIEEGEEIRELRCDHIFH 82 (139)
Q Consensus 57 ~~C~ICl~~~~~~~~~~~l~C~H~fh 82 (139)
..|++|...+...+..-..+.+|.|-
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~fd 28 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQFD 28 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCCc
Confidence 46999999997655433335578873
No 181
>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=36.87 E-value=12 Score=24.68 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=27.3
Q ss_pred CCcccccccccccC--CCeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEE--GEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~--~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
+...|++|..+|.. +....-..|+|.+|..|-.. ......-.|-+|..
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 56789999988753 23344447888888887433 11011225777754
No 182
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=36.85 E-value=14 Score=28.35 Aligned_cols=56 Identities=18% Similarity=0.377 Sum_probs=31.7
Q ss_pred CcccccccccccCCC------eeEEcCCCCcccHHHH-HHHHcc--------CCcccccccccccccCccc
Q 038790 56 AVECAVCLCEIEEGE------EIRELRCDHIFHRVCL-DQWVGL--------FRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~------~~~~l~C~H~fh~~Ci-~~Wl~~--------~~~~~CP~Cr~~~~~~~~~ 111 (139)
...|.+|-..|..=- .+-.|+|...+|..-+ .+||.+ ++-..||.|.+.|..+...
T Consensus 161 a~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNL 231 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNL 231 (279)
T ss_pred cccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHH
Confidence 345666666554110 1113455555554443 489975 2347999999988665543
No 183
>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=36.65 E-value=15 Score=17.64 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.6
Q ss_pred cccccccccc
Q 038790 96 VTCPLCRDFL 105 (139)
Q Consensus 96 ~~CP~Cr~~~ 105 (139)
..||+|.+.+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 3699997766
No 184
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.10 E-value=4.9 Score=30.70 Aligned_cols=49 Identities=20% Similarity=0.401 Sum_probs=36.9
Q ss_pred CCcccccccccccCCC-e--eEEcC--------CCCcccHHHHHHHHccCCcccccccccc
Q 038790 55 EAVECAVCLCEIEEGE-E--IRELR--------CDHIFHRVCLDQWVGLFRRVTCPLCRDF 104 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~-~--~~~l~--------C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~ 104 (139)
....|.||...+...+ . .+.+. |+|..+..|++.-+.+ ....||.|+..
T Consensus 206 ~~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~-~~~~cp~~~~~ 265 (296)
T KOG4185|consen 206 IEKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQ-AGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHH-hhhcCCcccce
Confidence 3467999999998432 1 22335 9999999999999873 23799999874
No 185
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=34.34 E-value=20 Score=27.03 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=29.5
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPL 100 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~ 100 (139)
+..|+|-+.++. -++.-..|+|.|-.+-|...+...-...||.
T Consensus 189 ~nrCpitl~p~~--~pils~kcnh~~e~D~I~~~lq~~~trvcp~ 231 (275)
T COG5627 189 SNRCPITLNPDF--YPILSSKCNHKPEMDLINKKLQVECTRVCPR 231 (275)
T ss_pred cccCCcccCcch--hHHHHhhhcccccHHHHHHHhcCCceeecch
Confidence 456999877655 2222337999999999999987223445553
No 186
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=34.30 E-value=24 Score=19.87 Aligned_cols=23 Identities=26% Similarity=0.783 Sum_probs=13.1
Q ss_pred CCCCcccHHHHHHHHccCCccccccc
Q 038790 76 RCDHIFHRVCLDQWVGLFRRVTCPLC 101 (139)
Q Consensus 76 ~C~H~fh~~Ci~~Wl~~~~~~~CP~C 101 (139)
.|+|.|-.. |..-.. ....||.|
T Consensus 33 ~Cgh~w~~~-v~~R~~--~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKAS-VNDRTR--RGKGCPYC 55 (55)
T ss_pred CCCCeeEcc-Hhhhcc--CCCCCCCC
Confidence 467766543 222223 67788887
No 187
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.73 E-value=21 Score=22.84 Aligned_cols=12 Identities=42% Similarity=0.902 Sum_probs=11.1
Q ss_pred cccHHHHHHHHc
Q 038790 80 IFHRVCLDQWVG 91 (139)
Q Consensus 80 ~fh~~Ci~~Wl~ 91 (139)
.||+.|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 699999999997
No 188
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=33.54 E-value=21 Score=20.87 Aligned_cols=17 Identities=12% Similarity=0.393 Sum_probs=13.1
Q ss_pred CcccccccccccccCcc
Q 038790 94 RRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~~~ 110 (139)
.|..||+|.+++++.+.
T Consensus 7 PH~HC~VCg~aIp~de~ 23 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CCccccccCCcCCCccc
Confidence 57789999888876554
No 189
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=33.47 E-value=16 Score=29.20 Aligned_cols=49 Identities=24% Similarity=0.465 Sum_probs=26.4
Q ss_pred CCCcccccccccccCCCeeEEc---CCCCccc--------HHHHHHHHcc---CCccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIREL---RCDHIFH--------RVCLDQWVGL---FRRVTCPLCRD 103 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l---~C~H~fh--------~~Ci~~Wl~~---~~~~~CP~Cr~ 103 (139)
..++-|++|-+..+. =.-..+ .|+-.|. ..|+..---. .++..||.||-
T Consensus 13 dl~ElCPVCGDkVSG-YHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRF 75 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSG-YHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRF 75 (475)
T ss_pred ccccccccccCcccc-ceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhH
Confidence 457789999988653 222334 4554443 2343321000 13467999984
No 190
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=32.13 E-value=20 Score=21.06 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=10.8
Q ss_pred cccccccccccccCc
Q 038790 95 RVTCPLCRDFLDSRR 109 (139)
Q Consensus 95 ~~~CP~Cr~~~~~~~ 109 (139)
--.||+||.++...+
T Consensus 8 iLaCP~~kg~L~~~~ 22 (60)
T COG2835 8 ILACPVCKGPLVYDE 22 (60)
T ss_pred eeeccCcCCcceEec
Confidence 457999999865433
No 191
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=32.00 E-value=21 Score=26.25 Aligned_cols=22 Identities=18% Similarity=0.622 Sum_probs=15.8
Q ss_pred CcccccccccccccCcccccCC
Q 038790 94 RRVTCPLCRDFLDSRRAVVENG 115 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~~~~~~~~ 115 (139)
...+||+|.+.+..........
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~ 25 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKI 25 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCc
Confidence 5678999988887665555444
No 192
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.81 E-value=31 Score=26.86 Aligned_cols=36 Identities=17% Similarity=0.355 Sum_probs=26.1
Q ss_pred CCcccccccccccCCCeeEEcC--CCCcccHHHHHHHHc
Q 038790 55 EAVECAVCLCEIEEGEEIRELR--CDHIFHRVCLDQWVG 91 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~--C~H~fh~~Ci~~Wl~ 91 (139)
....|++|.|.+++. .....| =.|.||-.|-++-++
T Consensus 267 apLcCTLC~ERLEDT-HFVQCPSVp~HKFCFPCSResIK 304 (352)
T KOG3579|consen 267 APLCCTLCHERLEDT-HFVQCPSVPSHKFCFPCSRESIK 304 (352)
T ss_pred CceeehhhhhhhccC-ceeecCCCcccceecccCHHHHH
Confidence 457899999998853 222222 169999999988887
No 193
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=31.58 E-value=33 Score=18.28 Aligned_cols=34 Identities=26% Similarity=0.449 Sum_probs=23.2
Q ss_pred CCcccccccccccCC--CeeEEcCCCCcccHHHHHH
Q 038790 55 EAVECAVCLCEIEEG--EEIRELRCDHIFHRVCLDQ 88 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~--~~~~~l~C~H~fh~~Ci~~ 88 (139)
....|.+|.+.+... ...+-..|+-..|..|...
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 355699999887642 2233336888999999654
No 194
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=31.50 E-value=21 Score=27.81 Aligned_cols=34 Identities=26% Similarity=0.490 Sum_probs=23.0
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHH
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQ 88 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~ 88 (139)
+...|.||+.+-.+.+.+-.=-|...||.-|+.-
T Consensus 313 ~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL 346 (381)
T KOG1512|consen 313 SCELCRICLGPVIESEHLFCDVCDRGPHTLCVGL 346 (381)
T ss_pred ccHhhhccCCcccchheeccccccCCCCcccccc
Confidence 4567899998876655333225778888888753
No 195
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.78 E-value=46 Score=28.90 Aligned_cols=47 Identities=21% Similarity=0.526 Sum_probs=32.9
Q ss_pred ccccccccccCCCeeEEcCCCC-cccHHHHHHHHccCC----ccccccccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDH-IFHRVCLDQWVGLFR----RVTCPLCRDFLDS 107 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H-~fh~~Ci~~Wl~~~~----~~~CP~Cr~~~~~ 107 (139)
.|+||-..++. +..-.|+| ..+..|...-..... ...||+||..+..
T Consensus 2 ~c~ic~~s~~~---~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 2 SCAICAFSPDF---VGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred CcceeecCccc---cccccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 58999877553 22347999 889999887654323 5677999986643
No 196
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.71 E-value=14 Score=17.42 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=8.3
Q ss_pred ccccccccccccC
Q 038790 96 VTCPLCRDFLDSR 108 (139)
Q Consensus 96 ~~CP~Cr~~~~~~ 108 (139)
..||.|.+.+.+.
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 3577887766543
No 197
>PF12088 DUF3565: Protein of unknown function (DUF3565); InterPro: IPR021948 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Probab=29.69 E-value=42 Score=19.69 Aligned_cols=15 Identities=47% Similarity=0.813 Sum_probs=11.8
Q ss_pred CCCeeEEcCCCCccc
Q 038790 68 EGEEIRELRCDHIFH 82 (139)
Q Consensus 68 ~~~~~~~l~C~H~fh 82 (139)
++.-++.|.|||.=|
T Consensus 8 e~hWVA~L~CGH~QH 22 (61)
T PF12088_consen 8 EGHWVAELSCGHTQH 22 (61)
T ss_pred cCCEEEEeccccccc
Confidence 556789999998655
No 198
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=29.59 E-value=23 Score=20.59 Aligned_cols=12 Identities=33% Similarity=0.938 Sum_probs=5.9
Q ss_pred cccccccccccc
Q 038790 96 VTCPLCRDFLDS 107 (139)
Q Consensus 96 ~~CP~Cr~~~~~ 107 (139)
..||.|++++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468999887665
No 199
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=29.14 E-value=50 Score=19.31 Aligned_cols=17 Identities=24% Similarity=0.602 Sum_probs=10.0
Q ss_pred CCCcccccccccccCCC
Q 038790 54 NEAVECAVCLCEIEEGE 70 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~ 70 (139)
.+...|++|..++..+.
T Consensus 37 ~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSGT 53 (59)
T ss_pred CCCccCCCcCCccccce
Confidence 34456777776666443
No 200
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=28.67 E-value=27 Score=17.02 Aligned_cols=10 Identities=50% Similarity=1.072 Sum_probs=5.2
Q ss_pred cccccccccc
Q 038790 97 TCPLCRDFLD 106 (139)
Q Consensus 97 ~CP~Cr~~~~ 106 (139)
+||.|-..+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899987765
No 201
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.61 E-value=26 Score=17.86 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=6.6
Q ss_pred ccccccccc
Q 038790 95 RVTCPLCRD 103 (139)
Q Consensus 95 ~~~CP~Cr~ 103 (139)
-..||+|..
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 458888865
No 202
>PF11376 DUF3179: Protein of unknown function (DUF3179); InterPro: IPR021516 This family of proteins has no known function.
Probab=28.47 E-value=21 Score=27.26 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=21.1
Q ss_pred ccccccccccccCcccccCC----ceEEEeecccccCCCCCCccccc
Q 038790 96 VTCPLCRDFLDSRRAVVENG----IEILVFKRFCYLSSSSDRDSWWL 138 (139)
Q Consensus 96 ~~CP~Cr~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 138 (139)
..||+|...+.-.+...... ..=.+.+ ..-+--+.++++||-
T Consensus 63 TyCplc~s~~~f~~~v~g~~l~fgvsG~L~n-snlvmyDr~T~S~W~ 108 (266)
T PF11376_consen 63 TYCPLCGSGMAFDRRVDGQVLTFGVSGKLYN-SNLVMYDRETESLWQ 108 (266)
T ss_pred EECccCCCceEEecccCCCcceEEeecceec-CccEEEECCCCChhh
Confidence 58999988665444322211 1111111 222223378899993
No 203
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=28.30 E-value=31 Score=27.62 Aligned_cols=20 Identities=15% Similarity=0.370 Sum_probs=9.9
Q ss_pred CcccccccccccccCccccc
Q 038790 94 RRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~~~~~~ 113 (139)
..-.||.|..++..+.+...
T Consensus 29 ~~~~CP~C~~~v~lk~G~~k 48 (375)
T PF06054_consen 29 GKYFCPGCGEPVILKKGKKK 48 (375)
T ss_pred CcEECCCCCCeeEEEEcCcc
Confidence 34455555555555444333
No 204
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=27.98 E-value=23 Score=24.73 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=14.8
Q ss_pred CCCcccHHHHHHHHcc---------CCccccccccc
Q 038790 77 CDHIFHRVCLDQWVGL---------FRRVTCPLCRD 103 (139)
Q Consensus 77 C~H~fh~~Ci~~Wl~~---------~~~~~CP~Cr~ 103 (139)
++|.| ..||.. .+..+||+|-.
T Consensus 10 ~gH~F-----EgWF~ss~~fd~Q~~~glv~CP~Cgs 40 (148)
T PF06676_consen 10 NGHEF-----EGWFRSSAAFDRQQARGLVSCPVCGS 40 (148)
T ss_pred CCCcc-----ceecCCHHHHHHHHHcCCccCCCCCC
Confidence 46776 568763 24579999953
No 205
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.73 E-value=36 Score=28.95 Aligned_cols=36 Identities=25% Similarity=0.554 Sum_probs=23.4
Q ss_pred CCCcccccccccccC----C-C-----eeEEcCCCCcccHHHHHHH
Q 038790 54 NEAVECAVCLCEIEE----G-E-----EIRELRCDHIFHRVCLDQW 89 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~----~-~-----~~~~l~C~H~fh~~Ci~~W 89 (139)
.....|+||.|.|+. . + ....+-=|-+||..|+..=
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~ 556 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEK 556 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchH
Confidence 556789999999861 0 1 0112224789999997653
No 206
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=27.42 E-value=45 Score=17.50 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=23.2
Q ss_pred CCcccccccccccCCC-eeEEcCCCCcccHHHHHH
Q 038790 55 EAVECAVCLCEIEEGE-EIRELRCDHIFHRVCLDQ 88 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~-~~~~l~C~H~fh~~Ci~~ 88 (139)
....|.+|.+.+.... ...-..|+-..|..|...
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 3556999998877432 222235788999999765
No 207
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=26.94 E-value=27 Score=24.24 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=10.4
Q ss_pred Ccccccccccccc
Q 038790 94 RRVTCPLCRDFLD 106 (139)
Q Consensus 94 ~~~~CP~Cr~~~~ 106 (139)
....||.||+.++
T Consensus 8 pei~CPhCRQ~ip 20 (163)
T TIGR02652 8 PEIRCPHCRQNIP 20 (163)
T ss_pred CcCcCchhhcccc
Confidence 5778999998663
No 208
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=26.77 E-value=64 Score=20.84 Aligned_cols=36 Identities=14% Similarity=0.320 Sum_probs=24.6
Q ss_pred CCcccccccccccCCCeeEEcCCCCcccHHHHHHHHc
Q 038790 55 EAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVG 91 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~ 91 (139)
-+..|.+|....-.++....-. ...||..|...+++
T Consensus 48 LGa~CS~C~~~VC~~~~CSlFY-tkrFC~pC~~~~~~ 83 (97)
T PF10170_consen 48 LGAPCSICGKPVCVGQDCSLFY-TKRFCLPCVKRNLK 83 (97)
T ss_pred ECccccccCCceEcCCCccEEe-eCceeHHHHHHHHH
Confidence 4678999987766554332222 24699999999876
No 209
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=26.70 E-value=27 Score=24.14 Aligned_cols=13 Identities=31% Similarity=0.943 Sum_probs=10.3
Q ss_pred Ccccccccccccc
Q 038790 94 RRVTCPLCRDFLD 106 (139)
Q Consensus 94 ~~~~CP~Cr~~~~ 106 (139)
....||.||+.++
T Consensus 5 pei~CPhCRq~ip 17 (161)
T PF09654_consen 5 PEIQCPHCRQTIP 17 (161)
T ss_pred CcCcCchhhcccc
Confidence 5678999998653
No 210
>COG4768 Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]
Probab=26.69 E-value=87 Score=21.52 Aligned_cols=18 Identities=11% Similarity=0.217 Sum_probs=13.5
Q ss_pred ChhHHHHHHHHHHHHHHH
Q 038790 1 MLSYIVSVSTHLKWACKF 18 (139)
Q Consensus 1 ~~~~i~l~~~~l~~~~~~ 18 (139)
+|.||.+++++++|++.-
T Consensus 2 ~ilyIs~~iiAiAf~vL~ 19 (139)
T COG4768 2 IILYISLAIIAIAFLVLV 19 (139)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 467888888888887443
No 211
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.69 E-value=34 Score=24.42 Aligned_cols=15 Identities=47% Similarity=0.977 Sum_probs=13.1
Q ss_pred CcccccccccccccC
Q 038790 94 RRVTCPLCRDFLDSR 108 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~ 108 (139)
....||+|-.++.+.
T Consensus 153 GRP~CPlCg~PlDP~ 167 (171)
T PF11290_consen 153 GRPPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCCCC
Confidence 789999999998765
No 212
>PRK01343 zinc-binding protein; Provisional
Probab=26.46 E-value=30 Score=20.08 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=10.2
Q ss_pred Ccccccccccccc
Q 038790 94 RRVTCPLCRDFLD 106 (139)
Q Consensus 94 ~~~~CP~Cr~~~~ 106 (139)
....||+|++++.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 4578999998764
No 213
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.07 E-value=30 Score=23.68 Aligned_cols=20 Identities=25% Similarity=0.781 Sum_probs=16.8
Q ss_pred CCCCcccHHHHHHHHccCCccccccccccc
Q 038790 76 RCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 76 ~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
.|||+|+. .+..||.|...-
T Consensus 34 ~CG~v~~P----------Pr~~Cp~C~~~~ 53 (140)
T COG1545 34 KCGRVYFP----------PRAYCPKCGSET 53 (140)
T ss_pred CCCeEEcC----------CcccCCCCCCCC
Confidence 68999986 788999998764
No 214
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=25.88 E-value=26 Score=18.46 Aligned_cols=14 Identities=36% Similarity=0.767 Sum_probs=9.8
Q ss_pred cccccccccccCcc
Q 038790 97 TCPLCRDFLDSRRA 110 (139)
Q Consensus 97 ~CP~Cr~~~~~~~~ 110 (139)
.||.|+..+.....
T Consensus 1 ~CP~C~~~l~~~~~ 14 (41)
T PF13453_consen 1 KCPRCGTELEPVRL 14 (41)
T ss_pred CcCCCCcccceEEE
Confidence 49999887664443
No 215
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.38 E-value=33 Score=26.90 Aligned_cols=42 Identities=26% Similarity=0.559 Sum_probs=26.8
Q ss_pred CCcccccccccccCC-------CeeEEcCCCCcccHHHHHHHHccCCccccccccc
Q 038790 55 EAVECAVCLCEIEEG-------EEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~-------~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
....|++|-..-... +..+.+ +|.-|-..|-- .+..||.|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL-----~CslC~teW~~--~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYL-----HCNLCESEWHV--VRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEE-----EcCCCCCcccc--cCccCCCCCC
Confidence 467899998763211 223333 44446666755 7889999975
No 216
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.18 E-value=41 Score=19.88 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=9.3
Q ss_pred cccccccccccc
Q 038790 95 RVTCPLCRDFLD 106 (139)
Q Consensus 95 ~~~CP~Cr~~~~ 106 (139)
...||.|++++.
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 467999998764
No 217
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.85 E-value=20 Score=20.23 Aligned_cols=15 Identities=27% Similarity=0.698 Sum_probs=12.4
Q ss_pred CCCCcccHHHHHHHH
Q 038790 76 RCDHIFHRVCLDQWV 90 (139)
Q Consensus 76 ~C~H~fh~~Ci~~Wl 90 (139)
.|++.|+..|-..|-
T Consensus 45 ~C~~~fC~~C~~~~H 59 (64)
T smart00647 45 KCGFSFCFRCKVPWH 59 (64)
T ss_pred CCCCeECCCCCCcCC
Confidence 689999999988773
No 218
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=23.46 E-value=43 Score=24.02 Aligned_cols=15 Identities=40% Similarity=0.868 Sum_probs=13.0
Q ss_pred CcccccccccccccC
Q 038790 94 RRVTCPLCRDFLDSR 108 (139)
Q Consensus 94 ~~~~CP~Cr~~~~~~ 108 (139)
....||+|-.++.+.
T Consensus 155 GRP~CPlCg~PldP~ 169 (177)
T TIGR03847 155 GRPPCPLCGRPIDPD 169 (177)
T ss_pred CCCCCCCCCCCCCCC
Confidence 689999999999764
No 219
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=23.38 E-value=31 Score=17.65 Aligned_cols=15 Identities=33% Similarity=0.691 Sum_probs=9.4
Q ss_pred cccccccccccccCc
Q 038790 95 RVTCPLCRDFLDSRR 109 (139)
Q Consensus 95 ~~~CP~Cr~~~~~~~ 109 (139)
...||.|.+.+...+
T Consensus 4 ~~~C~nC~R~v~a~R 18 (33)
T PF08209_consen 4 YVECPNCGRPVAASR 18 (33)
T ss_dssp EEE-TTTSSEEEGGG
T ss_pred eEECCCCcCCcchhh
Confidence 457888887775543
No 220
>PLN02248 cellulose synthase-like protein
Probab=23.28 E-value=1.8e+02 Score=27.14 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=23.8
Q ss_pred CCCcccHHHHHHHHccCCcccccccccccc
Q 038790 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 77 C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
|+...|++|-..-++ ....||-|+.++.
T Consensus 150 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 177 (1135)
T PLN02248 150 CGFKICRDCYIDAVK--SGGICPGCKEPYK 177 (1135)
T ss_pred ccchhHHhHhhhhhh--cCCCCCCCccccc
Confidence 567889999999888 6889999998773
No 221
>PF15616 TerY-C: TerY-C metal binding domain
Probab=23.15 E-value=36 Score=23.25 Aligned_cols=46 Identities=24% Similarity=0.372 Sum_probs=31.7
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccccccCcc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRA 110 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~ 110 (139)
.+...||-|-..+. .+.-.|+++||. +. ....+||-|.+.......
T Consensus 75 ~g~PgCP~CGn~~~----fa~C~CGkl~Ci---~g----~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 75 IGAPGCPHCGNQYA----FAVCGCGKLFCI---DG----EGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred cCCCCCCCCcChhc----EEEecCCCEEEe---CC----CCCEECCCCCCeeeeccc
Confidence 34578999997744 345589999863 33 267899999886654433
No 222
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=22.93 E-value=21 Score=27.75 Aligned_cols=41 Identities=24% Similarity=0.670 Sum_probs=25.7
Q ss_pred CcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccccc
Q 038790 56 AVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFLDS 107 (139)
Q Consensus 56 ~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~ 107 (139)
+..|.-|.+.+.+.+.|+.. =.|+||.+|+. |-+|++.+..
T Consensus 92 GTKCsaC~~GIpPtqVVRkA-qd~VYHl~CF~----------C~iC~R~L~T 132 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKA-QDFVYHLHCFA----------CFICKRQLAT 132 (383)
T ss_pred CCcchhhcCCCChHHHHHHh-hcceeehhhhh----------hHhhhccccc
Confidence 55678887777665544433 46888887743 5566655543
No 223
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.91 E-value=30 Score=27.06 Aligned_cols=48 Identities=25% Similarity=0.481 Sum_probs=35.9
Q ss_pred CCCcccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCccccccccccc
Q 038790 54 NEAVECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDFL 105 (139)
Q Consensus 54 ~~~~~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~ 105 (139)
.....|.||..-+.... +.=.|.|.|+..|-..|.+ ....||.|+...
T Consensus 103 ~~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~--~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 103 QDHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFA--MGNDCPDCRGKI 150 (324)
T ss_pred CCccceeeeeeeEEecc--cccCceeeeeecCCchhhh--hhhccchhhcCc
Confidence 34567888887766332 1225999999999999998 888899997643
No 224
>CHL00031 psbT photosystem II protein T
Probab=22.86 E-value=1.1e+02 Score=15.68 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=11.2
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q 038790 2 LSYIVSVSTHLKWACKFLI 20 (139)
Q Consensus 2 ~~~i~l~~~~l~~~~~~~~ 20 (139)
+.|..++...|..+++.+.
T Consensus 4 lvYtfll~~tlgilFFAI~ 22 (33)
T CHL00031 4 LVYTFLLVSTLGIIFFAIF 22 (33)
T ss_pred hHHHHHHHHHHHHHHHhhe
Confidence 4576776666666544433
No 225
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=22.65 E-value=1.2e+02 Score=15.25 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=11.2
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q 038790 2 LSYIVSVSTHLKWACKFLI 20 (139)
Q Consensus 2 ~~~i~l~~~~l~~~~~~~~ 20 (139)
+.|..++...|..+++.++
T Consensus 4 l~Ytfll~~tlgiiFFAIf 22 (31)
T PRK11875 4 FAYILILTLALVTLFFAIA 22 (31)
T ss_pred HHHHHHHHHHHHHHHHhhh
Confidence 4576666666666544443
No 226
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=22.60 E-value=54 Score=24.70 Aligned_cols=21 Identities=29% Similarity=0.555 Sum_probs=13.3
Q ss_pred cHHHHHHHHccCCcccccccccc
Q 038790 82 HRVCLDQWVGLFRRVTCPLCRDF 104 (139)
Q Consensus 82 h~~Ci~~Wl~~~~~~~CP~Cr~~ 104 (139)
|..|-.+--+ +-+.||+|+..
T Consensus 252 ClsChqqIHR--NAPiCPlCKaK 272 (286)
T KOG4451|consen 252 CLSCHQQIHR--NAPICPLCKAK 272 (286)
T ss_pred HHHHHHHHhc--CCCCCcchhhc
Confidence 3444444333 78999999863
No 227
>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=22.23 E-value=14 Score=16.44 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=4.9
Q ss_pred ccccccccc
Q 038790 98 CPLCRDFLD 106 (139)
Q Consensus 98 CP~Cr~~~~ 106 (139)
||.|.+.+.
T Consensus 3 C~~C~~~f~ 11 (23)
T PF00096_consen 3 CPICGKSFS 11 (23)
T ss_dssp ETTTTEEES
T ss_pred CCCCCCccC
Confidence 566655444
No 228
>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=22.13 E-value=60 Score=24.29 Aligned_cols=20 Identities=30% Similarity=0.699 Sum_probs=12.9
Q ss_pred cHHHHHHHHccCCccccccccc
Q 038790 82 HRVCLDQWVGLFRRVTCPLCRD 103 (139)
Q Consensus 82 h~~Ci~~Wl~~~~~~~CP~Cr~ 103 (139)
|..|-..=-+ +-+.||+|+.
T Consensus 197 C~sC~qqIHR--NAPiCPlCK~ 216 (230)
T PF10146_consen 197 CQSCHQQIHR--NAPICPLCKA 216 (230)
T ss_pred hHhHHHHHhc--CCCCCccccc
Confidence 3444444333 7799999986
No 229
>PF06645 SPC12: Microsomal signal peptidase 12 kDa subunit (SPC12); InterPro: IPR009542 This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12).; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=21.61 E-value=1.3e+02 Score=18.23 Aligned_cols=25 Identities=16% Similarity=0.442 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcc
Q 038790 2 LSYIVSVSTHLKWACKFLIQNSLFG 26 (139)
Q Consensus 2 ~~~i~l~~~~l~~~~~~~~~~~~~~ 26 (139)
+.++.+...+++++..|+.+.....
T Consensus 13 ~~~il~~~~iisfi~Gy~~q~~~~~ 37 (76)
T PF06645_consen 13 MQYILIISAIISFIVGYITQSFSYT 37 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777888888888888776654
No 230
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.40 E-value=71 Score=23.49 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=19.2
Q ss_pred ccccccccccCCCeeEEcCCCCcccHHHHHHHHccCCcccccccccc
Q 038790 58 ECAVCLCEIEEGEEIRELRCDHIFHRVCLDQWVGLFRRVTCPLCRDF 104 (139)
Q Consensus 58 ~C~ICl~~~~~~~~~~~l~C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~ 104 (139)
.|.+|-+.+..+. ...|..|...+-. -...||.|-.+
T Consensus 7 ~C~~C~~~~~~~~--------~~lC~~C~~~l~~--~~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSH--------WGICSVCSRALRT--LKTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCC--------CcccHHHHhhCCc--ccCcCccCCCc
Confidence 4777776553211 2356666655432 23456766554
No 231
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.14 E-value=91 Score=18.05 Aligned_cols=32 Identities=13% Similarity=0.231 Sum_probs=19.7
Q ss_pred CCcccccccccccC--CCeeEEcC-CCCcccHHHH
Q 038790 55 EAVECAVCLCEIEE--GEEIRELR-CDHIFHRVCL 86 (139)
Q Consensus 55 ~~~~C~ICl~~~~~--~~~~~~l~-C~H~fh~~Ci 86 (139)
....|+.|-..... ....-..+ ||+.+|.+-.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcHHH
Confidence 46679999877665 22222334 8877776643
No 232
>PRK05978 hypothetical protein; Provisional
Probab=21.00 E-value=56 Score=22.78 Aligned_cols=29 Identities=17% Similarity=0.338 Sum_probs=21.4
Q ss_pred CCcccHHHHHHHHccCCcccccccccccccCccccc
Q 038790 78 DHIFHRVCLDQWVGLFRRVTCPLCRDFLDSRRAVVE 113 (139)
Q Consensus 78 ~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~~~~~~~~ 113 (139)
|+.|+ .+++ -+..||.|-.++...+...-
T Consensus 42 G~LF~-----g~Lk--v~~~C~~CG~~~~~~~a~Dg 70 (148)
T PRK05978 42 GKLFR-----AFLK--PVDHCAACGEDFTHHRADDL 70 (148)
T ss_pred Ccccc-----cccc--cCCCccccCCccccCCcccc
Confidence 36665 6777 89999999988877665543
No 233
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=20.99 E-value=36 Score=21.38 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=16.0
Q ss_pred HHHccCCcccccccccccccCccc
Q 038790 88 QWVGLFRRVTCPLCRDFLDSRRAV 111 (139)
Q Consensus 88 ~Wl~~~~~~~CP~Cr~~~~~~~~~ 111 (139)
.+++ -...||.|..++...+..
T Consensus 3 g~Lk--~~~~C~~CG~d~~~~~ad 24 (86)
T PF06170_consen 3 GYLK--VAPRCPHCGLDYSHARAD 24 (86)
T ss_pred cccc--CCCcccccCCccccCCcC
Confidence 3555 788999998888766653
No 234
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=20.97 E-value=54 Score=28.41 Aligned_cols=28 Identities=29% Similarity=0.799 Sum_probs=21.2
Q ss_pred CCCCcccHHHHHHHHcc---CCccccccccc
Q 038790 76 RCDHIFHRVCLDQWVGL---FRRVTCPLCRD 103 (139)
Q Consensus 76 ~C~H~fh~~Ci~~Wl~~---~~~~~CP~Cr~ 103 (139)
.|+..||..|+..|+.- .+.-.||-||.
T Consensus 40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 58899999999999861 12346888875
No 235
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=20.93 E-value=43 Score=29.42 Aligned_cols=28 Identities=32% Similarity=0.685 Sum_probs=21.4
Q ss_pred CCCcccHHHHHHHHccCCcccccccccccc
Q 038790 77 CDHIFHRVCLDQWVGLFRRVTCPLCRDFLD 106 (139)
Q Consensus 77 C~H~fh~~Ci~~Wl~~~~~~~CP~Cr~~~~ 106 (139)
|...||.+=...-.. ++..||.||....
T Consensus 1050 C~~~F~~eDFEl~vL--qKGHCPFCrTS~d 1077 (1081)
T KOG1538|consen 1050 CFQMFHSEDFELLVL--QKGHCPFCRTSKD 1077 (1081)
T ss_pred HHhhhccchhhHHHH--hcCCCCccccccc
Confidence 667788777776666 8899999998544
No 236
>PHA03164 hypothetical protein; Provisional
Probab=20.76 E-value=1.9e+02 Score=17.86 Aligned_cols=24 Identities=8% Similarity=0.174 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcc
Q 038790 3 SYIVSVSTHLKWACKFLIQNSLFG 26 (139)
Q Consensus 3 ~~i~l~~~~l~~~~~~~~~~~~~~ 26 (139)
+|+++-..+++++++..+--..|.
T Consensus 59 tFlvLtgLaIamILfiifvlyvFn 82 (88)
T PHA03164 59 TFLVLTGLAIAMILFIIFVLYVFN 82 (88)
T ss_pred ehHHHHHHHHHHHHHHHHHHHhee
Confidence 566666666666655555444443
No 237
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.74 E-value=40 Score=29.07 Aligned_cols=52 Identities=19% Similarity=0.425 Sum_probs=35.1
Q ss_pred CCcccccccccccCCCe-eEEcCCCCcccHHHHHHHHcc------CCcccccccccccc
Q 038790 55 EAVECAVCLCEIEEGEE-IRELRCDHIFHRVCLDQWVGL------FRRVTCPLCRDFLD 106 (139)
Q Consensus 55 ~~~~C~ICl~~~~~~~~-~~~l~C~H~fh~~Ci~~Wl~~------~~~~~CP~Cr~~~~ 106 (139)
+..+|-.|...|..-.. ...-.||.+||..|-..-+.. +...+|-.|-..+.
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~ 222 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLT 222 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhh
Confidence 45889999999874432 223369999999997766543 23467888844333
No 238
>PF05115 PetL: Cytochrome B6-F complex subunit VI (PetL); InterPro: IPR007802 This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in a number of plant species. PetL is one of the small subunits which make up the cytochrome b(6)f complex. PetL is not absolutely required for either the accumulation or for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro. It has been suggested that the N terminus of the protein is likely to lie in the thylakoid lumen [].; GO: 0009055 electron carrier activity, 0009512 cytochrome b6f complex; PDB: 2ZT9_E 1Q90_L.
Probab=20.46 E-value=1.4e+02 Score=15.08 Aligned_cols=18 Identities=17% Similarity=0.224 Sum_probs=11.9
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 038790 2 LSYIVSVSTHLKWACKFL 19 (139)
Q Consensus 2 ~~~i~l~~~~l~~~~~~~ 19 (139)
++|+.++..++.+....+
T Consensus 5 isYf~fL~~al~~t~~lf 22 (31)
T PF05115_consen 5 ISYFGFLLAALTLTLVLF 22 (31)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 678777777776664443
No 239
>PHA02909 hypothetical protein; Provisional
Probab=20.37 E-value=1e+02 Score=17.91 Aligned_cols=15 Identities=33% Similarity=0.403 Sum_probs=9.0
Q ss_pred ChhHHHHHHHHHHHH
Q 038790 1 MLSYIVSVSTHLKWA 15 (139)
Q Consensus 1 ~~~~i~l~~~~l~~~ 15 (139)
|++||.++++.|++.
T Consensus 35 mvsfilfviiflsmf 49 (72)
T PHA02909 35 MVSFILFVIIFLSMF 49 (72)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456766666665543
No 240
>KOG2555 consensus AICAR transformylase/IMP cyclohydrolase/methylglyoxal synthase [Nucleotide transport and metabolism]
Probab=20.14 E-value=35 Score=28.16 Aligned_cols=12 Identities=50% Similarity=1.348 Sum_probs=9.2
Q ss_pred cCCCCCCcccccC
Q 038790 127 LSSSSDRDSWWLR 139 (139)
Q Consensus 127 ~~~~~~~~~~~~~ 139 (139)
|-+ +..|+||||
T Consensus 453 lAg-dkadnwwlr 464 (588)
T KOG2555|consen 453 LAG-DKADNWWLR 464 (588)
T ss_pred ccc-ccccchhhh
Confidence 344 788999997
No 241
>PF12907 zf-met2: Zinc-binding
Probab=20.03 E-value=28 Score=18.67 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=7.8
Q ss_pred ccccccccccc
Q 038790 96 VTCPLCRDFLD 106 (139)
Q Consensus 96 ~~CP~Cr~~~~ 106 (139)
..|++||+.+.
T Consensus 2 i~C~iC~qtF~ 12 (40)
T PF12907_consen 2 IICKICRQTFM 12 (40)
T ss_pred cCcHHhhHHHH
Confidence 46899986553
Done!