Query 039088
Match_columns 409
No_of_seqs 403 out of 1962
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:11:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06547 DUF1117: Protein of u 100.0 4.9E-35 1.1E-39 243.5 6.6 113 283-395 1-116 (117)
2 KOG4628 Predicted E3 ubiquitin 99.6 2.2E-16 4.7E-21 157.9 5.4 78 184-261 203-282 (348)
3 PF14369 zf-RING_3: zinc-finge 99.6 1.2E-15 2.7E-20 104.6 3.0 34 8-41 1-35 (35)
4 PF13639 zf-RING_2: Ring finge 99.5 2.1E-14 4.6E-19 102.9 1.7 44 210-253 1-44 (44)
5 COG5243 HRD1 HRD ubiquitin lig 99.2 1.3E-11 2.8E-16 123.1 5.3 72 188-260 267-348 (491)
6 COG5540 RING-finger-containing 99.2 7.3E-12 1.6E-16 122.0 3.1 50 209-258 323-373 (374)
7 PHA02929 N1R/p28-like protein; 99.2 1.1E-11 2.4E-16 119.2 3.7 72 187-258 149-228 (238)
8 PF12678 zf-rbx1: RING-H2 zinc 99.2 1.6E-11 3.5E-16 97.6 3.4 45 209-253 19-73 (73)
9 KOG0823 Predicted E3 ubiquitin 98.9 5E-10 1.1E-14 106.1 3.0 54 207-263 45-101 (230)
10 PLN03208 E3 ubiquitin-protein 98.9 1.3E-09 2.8E-14 101.5 3.3 51 208-261 17-83 (193)
11 KOG0317 Predicted E3 ubiquitin 98.8 1.4E-09 3.1E-14 105.8 2.7 51 207-260 237-287 (293)
12 cd00162 RING RING-finger (Real 98.8 2.1E-09 4.6E-14 75.0 2.8 44 211-256 1-45 (45)
13 PF13920 zf-C3HC4_3: Zinc fing 98.8 2.1E-09 4.6E-14 79.0 2.8 46 209-257 2-48 (50)
14 PF13923 zf-C3HC4_2: Zinc fing 98.8 3.8E-09 8.3E-14 73.8 2.3 39 212-252 1-39 (39)
15 KOG0802 E3 ubiquitin ligase [P 98.7 3.8E-09 8.2E-14 113.0 2.3 53 208-260 290-344 (543)
16 PF12861 zf-Apc11: Anaphase-pr 98.7 1.3E-08 2.8E-13 83.0 2.6 50 208-257 20-82 (85)
17 smart00504 Ubox Modified RING 98.6 3.9E-08 8.4E-13 74.9 3.7 47 210-259 2-48 (63)
18 PF15227 zf-C3HC4_4: zinc fing 98.6 3E-08 6.4E-13 70.8 2.7 38 212-252 1-42 (42)
19 KOG0320 Predicted E3 ubiquitin 98.6 2E-08 4.2E-13 91.9 2.0 50 209-259 131-180 (187)
20 PF14634 zf-RING_5: zinc-RING 98.6 3.4E-08 7.3E-13 70.9 2.4 44 211-254 1-44 (44)
21 smart00184 RING Ring finger. E 98.5 4.9E-08 1.1E-12 65.7 2.5 38 212-252 1-39 (39)
22 PF00097 zf-C3HC4: Zinc finger 98.5 6E-08 1.3E-12 68.0 2.6 39 212-252 1-41 (41)
23 PHA02926 zinc finger-like prot 98.5 5.5E-08 1.2E-12 92.0 2.6 50 208-257 169-230 (242)
24 TIGR00599 rad18 DNA repair pro 98.4 1.3E-07 2.9E-12 97.2 3.7 50 207-259 24-73 (397)
25 COG5194 APC11 Component of SCF 98.3 2.4E-07 5.2E-12 74.3 2.4 49 210-258 21-82 (88)
26 smart00744 RINGv The RING-vari 98.2 7.9E-07 1.7E-11 65.5 2.1 42 211-253 1-49 (49)
27 KOG1493 Anaphase-promoting com 98.2 6.1E-07 1.3E-11 71.4 0.9 49 209-257 20-81 (84)
28 KOG1734 Predicted RING-contain 98.1 6.4E-07 1.4E-11 86.7 0.5 53 208-260 223-284 (328)
29 COG5574 PEX10 RING-finger-cont 98.1 1.2E-06 2.6E-11 84.8 1.7 50 208-260 214-265 (271)
30 KOG0828 Predicted E3 ubiquitin 98.1 1.2E-06 2.6E-11 90.7 1.3 50 209-258 571-635 (636)
31 PF13445 zf-RING_UBOX: RING-ty 98.0 2.2E-06 4.7E-11 61.6 2.0 38 212-250 1-43 (43)
32 KOG2164 Predicted E3 ubiquitin 98.0 2.3E-06 5E-11 89.3 2.3 49 209-260 186-239 (513)
33 KOG0287 Postreplication repair 98.0 1.7E-06 3.7E-11 86.1 0.9 48 210-260 24-71 (442)
34 PF04564 U-box: U-box domain; 98.0 4.2E-06 9E-11 66.5 2.5 48 209-259 4-52 (73)
35 COG5432 RAD18 RING-finger-cont 97.9 3.4E-06 7.4E-11 82.5 1.9 47 209-258 25-71 (391)
36 KOG2930 SCF ubiquitin ligase, 97.9 3.9E-06 8.5E-11 70.5 1.3 27 230-256 81-107 (114)
37 COG5219 Uncharacterized conser 97.9 2.5E-06 5.5E-11 93.7 0.0 50 208-257 1468-1523(1525)
38 TIGR00570 cdk7 CDK-activating 97.8 1.3E-05 2.9E-10 79.8 3.4 52 209-260 3-57 (309)
39 KOG2177 Predicted E3 ubiquitin 97.8 6.8E-06 1.5E-10 77.6 1.3 43 208-253 12-54 (386)
40 KOG4265 Predicted E3 ubiquitin 97.7 1.7E-05 3.7E-10 79.8 2.4 47 209-258 290-337 (349)
41 PF11793 FANCL_C: FANCL C-term 97.7 1.1E-05 2.3E-10 63.8 0.5 48 210-257 3-66 (70)
42 KOG0804 Cytoplasmic Zn-finger 97.7 1.7E-05 3.6E-10 81.7 2.0 47 209-257 175-222 (493)
43 KOG0311 Predicted E3 ubiquitin 97.6 6.9E-06 1.5E-10 82.3 -1.7 59 199-260 33-93 (381)
44 KOG4445 Uncharacterized conser 97.6 3.1E-05 6.8E-10 76.2 2.1 92 163-260 75-189 (368)
45 KOG0825 PHD Zn-finger protein 97.5 2E-05 4.4E-10 85.5 0.2 50 209-258 123-172 (1134)
46 KOG0824 Predicted E3 ubiquitin 97.5 3.4E-05 7.4E-10 76.0 1.7 48 209-259 7-55 (324)
47 PF14835 zf-RING_6: zf-RING of 97.4 0.0001 2.2E-09 57.2 2.0 46 210-260 8-54 (65)
48 KOG0827 Predicted E3 ubiquitin 97.4 7.3E-05 1.6E-09 75.8 1.5 51 210-260 5-59 (465)
49 KOG1039 Predicted E3 ubiquitin 97.1 0.00022 4.7E-09 72.5 1.9 53 208-260 160-224 (344)
50 KOG4172 Predicted E3 ubiquitin 96.9 0.00018 3.9E-09 54.0 -0.3 46 209-257 7-54 (62)
51 KOG1645 RING-finger-containing 96.9 0.00043 9.3E-09 70.8 2.2 47 210-256 5-55 (463)
52 KOG4159 Predicted E3 ubiquitin 96.8 0.00063 1.4E-08 70.4 2.2 50 207-259 82-131 (398)
53 KOG1785 Tyrosine kinase negati 96.8 0.00055 1.2E-08 69.9 1.6 48 210-260 370-419 (563)
54 KOG0801 Predicted E3 ubiquitin 96.7 0.00061 1.3E-08 61.9 1.2 40 197-236 164-204 (205)
55 KOG0978 E3 ubiquitin ligase in 96.6 0.00056 1.2E-08 74.7 0.5 47 210-259 644-691 (698)
56 KOG0297 TNF receptor-associate 96.5 0.0016 3.4E-08 67.5 3.1 52 206-260 18-70 (391)
57 PF11789 zf-Nse: Zinc-finger o 96.3 0.0019 4.2E-08 49.1 1.7 41 209-251 11-53 (57)
58 KOG3970 Predicted E3 ubiquitin 96.3 0.0028 6.1E-08 60.5 2.7 51 208-259 49-107 (299)
59 KOG1941 Acetylcholine receptor 96.2 0.0012 2.6E-08 67.3 0.1 49 208-256 364-415 (518)
60 KOG1428 Inhibitor of type V ad 96.1 0.003 6.4E-08 72.7 2.5 67 192-258 3467-3545(3738)
61 PF12906 RINGv: RING-variant d 96.1 0.0037 8.1E-08 45.6 2.1 40 212-252 1-47 (47)
62 KOG1002 Nucleotide excision re 96.0 0.0042 9E-08 65.6 2.8 50 208-260 535-589 (791)
63 COG5152 Uncharacterized conser 96.0 0.0026 5.7E-08 59.6 1.0 44 210-256 197-240 (259)
64 KOG2660 Locus-specific chromos 95.7 0.0024 5.2E-08 63.9 -0.4 49 207-257 13-61 (331)
65 KOG4692 Predicted E3 ubiquitin 95.7 0.0072 1.6E-07 61.1 2.7 49 208-259 421-469 (489)
66 PF05883 Baculo_RING: Baculovi 95.6 0.0039 8.5E-08 55.2 0.4 34 210-243 27-66 (134)
67 PHA02862 5L protein; Provision 95.5 0.008 1.7E-07 53.8 2.0 47 209-259 2-55 (156)
68 KOG2879 Predicted E3 ubiquitin 95.4 0.013 2.8E-07 57.5 3.3 50 207-258 237-288 (298)
69 PF10367 Vps39_2: Vacuolar sor 95.2 0.0094 2E-07 49.6 1.5 32 208-240 77-108 (109)
70 KOG1571 Predicted E3 ubiquitin 95.1 0.012 2.6E-07 59.7 2.1 43 209-257 305-347 (355)
71 PHA02825 LAP/PHD finger-like p 95.0 0.016 3.4E-07 52.8 2.6 49 207-259 6-61 (162)
72 KOG0827 Predicted E3 ubiquitin 95.0 0.0015 3.3E-08 66.5 -4.4 51 209-259 196-247 (465)
73 KOG1814 Predicted E3 ubiquitin 95.0 0.0063 1.4E-07 62.6 -0.2 47 208-254 183-237 (445)
74 KOG3039 Uncharacterized conser 94.7 0.033 7.1E-07 54.0 3.9 53 209-261 221-274 (303)
75 KOG1813 Predicted E3 ubiquitin 94.6 0.014 3E-07 57.9 1.1 45 210-257 242-286 (313)
76 KOG1952 Transcription factor N 94.3 0.021 4.5E-07 63.4 1.9 46 209-254 191-244 (950)
77 PF08746 zf-RING-like: RING-li 94.3 0.021 4.6E-07 40.9 1.3 41 212-252 1-43 (43)
78 COG5222 Uncharacterized conser 94.1 0.031 6.7E-07 55.5 2.3 42 210-254 275-318 (427)
79 PF14570 zf-RING_4: RING/Ubox 93.8 0.045 9.8E-07 40.3 2.2 44 212-256 1-47 (48)
80 PF10272 Tmpp129: Putative tra 93.8 0.093 2E-06 53.8 5.2 30 230-259 311-353 (358)
81 PF04641 Rtf2: Rtf2 RING-finge 93.6 0.11 2.3E-06 51.0 5.1 54 207-261 111-165 (260)
82 PHA03096 p28-like protein; Pro 93.5 0.03 6.6E-07 55.7 1.2 45 210-254 179-231 (284)
83 KOG4739 Uncharacterized protei 93.5 0.028 6E-07 54.3 0.8 47 210-260 4-51 (233)
84 KOG4185 Predicted E3 ubiquitin 93.0 0.068 1.5E-06 52.8 2.7 47 210-256 4-54 (296)
85 COG5236 Uncharacterized conser 92.8 0.054 1.2E-06 54.8 1.7 46 208-256 60-107 (493)
86 KOG4275 Predicted E3 ubiquitin 92.3 0.03 6.4E-07 55.5 -0.8 42 209-257 300-342 (350)
87 PF14447 Prok-RING_4: Prokaryo 92.2 0.11 2.3E-06 39.3 2.2 47 209-260 7-53 (55)
88 KOG2114 Vacuolar assembly/sort 91.9 0.064 1.4E-06 59.7 1.0 44 210-258 841-884 (933)
89 COG0375 HybF Zn finger protein 91.8 0.099 2.2E-06 45.3 1.9 34 7-42 68-101 (115)
90 KOG0826 Predicted E3 ubiquitin 91.7 0.12 2.5E-06 52.1 2.5 48 208-258 299-347 (357)
91 KOG1940 Zn-finger protein [Gen 91.7 0.087 1.9E-06 52.2 1.6 45 210-254 159-204 (276)
92 KOG2932 E3 ubiquitin ligase in 90.2 0.12 2.5E-06 51.8 0.9 42 211-256 92-133 (389)
93 PF14446 Prok-RING_1: Prokaryo 90.0 0.19 4.1E-06 37.9 1.7 39 209-251 5-44 (54)
94 KOG3268 Predicted E3 ubiquitin 89.4 0.2 4.3E-06 46.5 1.7 50 210-259 166-230 (234)
95 KOG3053 Uncharacterized conser 89.1 0.14 2.9E-06 50.1 0.4 53 206-258 17-83 (293)
96 KOG0298 DEAD box-containing he 89.1 0.26 5.7E-06 57.3 2.8 43 210-254 1154-1196(1394)
97 COG2093 DNA-directed RNA polym 89.0 0.2 4.4E-06 38.7 1.3 27 12-42 7-34 (64)
98 KOG1001 Helicase-like transcri 88.7 0.14 3.1E-06 56.7 0.3 50 210-263 455-506 (674)
99 PRK00398 rpoP DNA-directed RNA 87.5 0.65 1.4E-05 33.4 3.0 34 8-41 2-35 (46)
100 KOG0802 E3 ubiquitin ligase [P 86.8 0.37 8.1E-06 52.1 2.1 48 208-262 478-525 (543)
101 PF03854 zf-P11: P-11 zinc fin 86.5 0.25 5.4E-06 36.3 0.4 44 211-259 4-48 (50)
102 PRK03681 hypA hydrogenase nick 85.2 0.71 1.5E-05 39.8 2.6 34 7-41 68-101 (114)
103 COG5175 MOT2 Transcriptional r 84.9 0.46 9.9E-06 48.2 1.5 53 208-260 13-67 (480)
104 TIGR00100 hypA hydrogenase nic 84.4 0.8 1.7E-05 39.6 2.6 33 7-41 68-100 (115)
105 COG1996 RPC10 DNA-directed RNA 84.3 0.61 1.3E-05 34.5 1.5 35 6-40 3-37 (49)
106 PF07754 DUF1610: Domain of un 84.1 0.6 1.3E-05 29.6 1.2 23 12-34 1-23 (24)
107 KOG1100 Predicted E3 ubiquitin 84.1 0.59 1.3E-05 44.6 1.8 39 212-257 161-200 (207)
108 KOG1609 Protein involved in mR 83.9 0.53 1.2E-05 46.4 1.5 51 209-259 78-136 (323)
109 KOG0309 Conserved WD40 repeat- 83.4 0.59 1.3E-05 51.8 1.7 40 211-251 1030-1069(1081)
110 KOG3161 Predicted E3 ubiquitin 83.3 0.34 7.5E-06 52.7 -0.1 42 210-254 12-54 (861)
111 KOG2034 Vacuolar sorting prote 83.3 0.46 1E-05 53.4 0.8 36 207-243 815-850 (911)
112 PRK00564 hypA hydrogenase nick 83.1 0.9 1.9E-05 39.4 2.4 34 7-41 69-102 (117)
113 KOG3800 Predicted E3 ubiquitin 82.5 0.81 1.8E-05 45.5 2.1 50 211-260 2-54 (300)
114 PF07800 DUF1644: Protein of u 82.5 1.1 2.4E-05 41.0 2.7 32 209-243 2-46 (162)
115 PRK12380 hydrogenase nickel in 82.3 1.1 2.4E-05 38.6 2.6 33 7-41 68-100 (113)
116 COG5183 SSM4 Protein involved 82.0 0.83 1.8E-05 51.0 2.1 50 208-258 11-67 (1175)
117 KOG3002 Zn finger protein [Gen 81.8 0.99 2.2E-05 45.4 2.5 41 210-257 49-91 (299)
118 PF05290 Baculo_IE-1: Baculovi 80.9 1.1 2.3E-05 40.0 2.0 50 209-260 80-135 (140)
119 KOG1812 Predicted E3 ubiquitin 80.7 1.2 2.6E-05 46.3 2.7 51 209-259 146-205 (384)
120 KOG2817 Predicted E3 ubiquitin 80.6 1.5 3.2E-05 45.5 3.2 48 207-254 332-382 (394)
121 PF01155 HypA: Hydrogenase exp 79.9 0.95 2.1E-05 38.9 1.4 33 7-41 68-100 (113)
122 PF10571 UPF0547: Uncharacteri 79.7 1 2.2E-05 28.9 1.2 23 12-38 3-25 (26)
123 PRK03824 hypA hydrogenase nick 79.7 1.4 3.1E-05 39.1 2.5 34 7-40 68-120 (135)
124 PF03604 DNA_RNApol_7kD: DNA d 78.8 1.7 3.7E-05 29.3 2.0 27 10-37 1-27 (32)
125 PF13240 zinc_ribbon_2: zinc-r 77.7 1.2 2.6E-05 27.7 1.0 23 11-37 1-23 (23)
126 smart00659 RPOLCX RNA polymera 76.0 2.4 5.1E-05 30.6 2.3 31 9-40 2-32 (44)
127 KOG4367 Predicted Zn-finger pr 74.2 1.4 3.1E-05 46.1 1.1 34 208-244 3-36 (699)
128 PRK00762 hypA hydrogenase nick 74.1 2 4.4E-05 37.6 1.9 34 7-41 68-106 (124)
129 smart00834 CxxC_CXXC_SSSS Puta 72.5 3.1 6.7E-05 28.5 2.2 28 8-35 4-34 (41)
130 COG5220 TFB3 Cdk activating ki 71.0 2 4.3E-05 41.8 1.2 48 209-256 10-63 (314)
131 COG5270 PUA domain (predicted 70.5 2.5 5.5E-05 39.6 1.7 32 8-46 13-44 (202)
132 KOG0825 PHD Zn-finger protein 69.9 2.2 4.8E-05 47.7 1.3 48 210-257 97-154 (1134)
133 KOG4362 Transcriptional regula 69.8 1.2 2.7E-05 49.1 -0.6 48 209-259 21-71 (684)
134 KOG3899 Uncharacterized conser 69.3 2 4.3E-05 43.0 0.8 31 230-260 325-368 (381)
135 PF13248 zf-ribbon_3: zinc-rib 68.9 2.6 5.6E-05 26.8 1.0 23 10-36 3-25 (26)
136 KOG0269 WD40 repeat-containing 68.5 3.3 7.1E-05 46.2 2.3 41 210-251 780-820 (839)
137 KOG4718 Non-SMC (structural ma 68.1 2.2 4.9E-05 40.8 0.8 43 210-254 182-224 (235)
138 smart00249 PHD PHD zinc finger 67.3 2.4 5.2E-05 29.0 0.7 31 211-241 1-31 (47)
139 KOG1829 Uncharacterized conser 65.9 2 4.3E-05 46.8 0.1 42 209-253 511-557 (580)
140 KOG1815 Predicted E3 ubiquitin 64.6 4.8 0.0001 42.5 2.6 36 208-245 69-104 (444)
141 KOG1812 Predicted E3 ubiquitin 64.5 3.5 7.6E-05 42.9 1.5 44 209-252 306-351 (384)
142 smart00132 LIM Zinc-binding do 63.3 4.9 0.00011 26.5 1.6 38 211-257 1-38 (39)
143 PF02891 zf-MIZ: MIZ/SP-RING z 62.8 5 0.00011 29.5 1.7 42 210-254 3-49 (50)
144 PRK06266 transcription initiat 62.1 5.1 0.00011 37.2 2.0 35 5-39 113-148 (178)
145 PF06906 DUF1272: Protein of u 58.6 17 0.00036 27.8 3.8 48 210-259 6-54 (57)
146 PF08792 A2L_zn_ribbon: A2L zi 58.0 6.5 0.00014 26.7 1.4 28 10-37 4-31 (33)
147 smart00661 RPOL9 RNA polymeras 57.1 8.5 0.00018 27.8 2.1 30 11-42 2-33 (52)
148 TIGR02605 CxxC_CxxC_SSSS putat 57.0 12 0.00026 27.1 2.9 34 8-41 4-40 (52)
149 PF13901 DUF4206: Domain of un 55.9 7.1 0.00015 36.9 1.8 40 209-254 152-197 (202)
150 KOG3005 GIY-YIG type nuclease 54.3 5.2 0.00011 39.6 0.7 47 210-256 183-242 (276)
151 PF08772 NOB1_Zn_bind: Nin one 53.9 8.4 0.00018 30.9 1.7 31 10-43 10-40 (73)
152 KOG3579 Predicted E3 ubiquitin 53.9 6.3 0.00014 39.4 1.1 38 209-247 268-307 (352)
153 KOG2066 Vacuolar assembly/sort 53.7 5.4 0.00012 44.7 0.7 45 209-254 784-832 (846)
154 KOG3993 Transcription factor ( 53.3 6.8 0.00015 41.1 1.3 22 13-39 286-307 (500)
155 KOG4317 Predicted Zn-finger pr 53.0 8.5 0.00018 39.0 1.9 28 4-37 2-29 (383)
156 PF09723 Zn-ribbon_8: Zinc rib 52.8 16 0.00035 25.8 2.8 33 8-40 4-39 (42)
157 PF00628 PHD: PHD-finger; Int 52.7 6.5 0.00014 28.2 0.8 43 211-253 1-49 (51)
158 KOG3113 Uncharacterized conser 52.0 19 0.00041 35.5 4.0 51 210-262 112-163 (293)
159 TIGR00373 conserved hypothetic 51.6 7 0.00015 35.6 1.0 37 5-42 105-142 (158)
160 KOG2169 Zn-finger transcriptio 50.6 11 0.00023 41.9 2.4 88 163-259 260-358 (636)
161 KOG2068 MOT2 transcription fac 49.6 16 0.00034 37.3 3.2 50 210-259 250-300 (327)
162 PF07975 C1_4: TFIIH C1-like d 48.7 11 0.00023 28.2 1.4 42 212-253 2-50 (51)
163 PF07191 zinc-ribbons_6: zinc- 48.6 4.1 8.8E-05 32.4 -0.9 40 210-257 2-41 (70)
164 PF00412 LIM: LIM domain; Int 46.3 15 0.00033 26.7 1.9 39 212-259 1-39 (58)
165 smart00531 TFIIE Transcription 45.6 11 0.00024 33.7 1.3 36 5-40 95-136 (147)
166 KOG2807 RNA polymerase II tran 45.2 18 0.00039 36.9 2.8 45 210-254 331-375 (378)
167 KOG0824 Predicted E3 ubiquitin 45.2 10 0.00022 38.3 1.0 49 206-256 102-150 (324)
168 TIGR02098 MJ0042_CXXC MJ0042 f 45.0 14 0.0003 25.1 1.5 29 10-38 3-36 (38)
169 TIGR00155 pqiA_fam integral me 44.9 12 0.00026 39.1 1.7 27 11-37 15-43 (403)
170 KOG2041 WD40 repeat protein [G 44.8 22 0.00047 40.0 3.6 44 209-256 1131-1184(1189)
171 PRK06393 rpoE DNA-directed RNA 44.3 12 0.00026 29.3 1.2 19 12-36 8-26 (64)
172 PF01363 FYVE: FYVE zinc finge 43.3 15 0.00033 28.1 1.6 36 209-244 9-45 (69)
173 COG5109 Uncharacterized conser 42.4 18 0.00039 36.7 2.4 47 207-253 334-383 (396)
174 KOG3799 Rab3 effector RIM1 and 42.4 8 0.00017 34.6 -0.1 51 205-255 61-116 (169)
175 PF08271 TF_Zn_Ribbon: TFIIB z 41.0 21 0.00046 25.1 1.9 31 10-41 1-32 (43)
176 smart00647 IBR In Between Ring 40.8 20 0.00043 26.5 1.9 34 8-41 17-54 (64)
177 PLN02189 cellulose synthase 40.2 30 0.00064 40.4 3.9 50 210-259 35-89 (1040)
178 smart00154 ZnF_AN1 AN1-like Zi 40.0 16 0.00035 25.5 1.1 26 12-41 1-26 (39)
179 PRK08351 DNA-directed RNA poly 39.8 16 0.00034 28.3 1.2 19 11-35 5-23 (61)
180 TIGR00622 ssl1 transcription f 39.7 34 0.00074 29.7 3.3 44 210-253 56-110 (112)
181 PRK14890 putative Zn-ribbon RN 38.4 23 0.00051 27.2 1.9 29 7-35 5-33 (59)
182 PF09538 FYDLN_acid: Protein o 37.8 27 0.00058 30.0 2.4 32 7-40 7-39 (108)
183 smart00064 FYVE Protein presen 37.6 8.8 0.00019 29.4 -0.5 35 210-244 11-46 (68)
184 PF01485 IBR: IBR domain; Int 37.4 19 0.00041 26.6 1.3 28 10-37 19-50 (64)
185 PF05191 ADK_lid: Adenylate ki 37.3 23 0.00051 24.4 1.6 31 9-39 1-33 (36)
186 PF04216 FdhE: Protein involve 36.5 8 0.00017 38.4 -1.2 45 210-254 173-219 (290)
187 PF05605 zf-Di19: Drought indu 35.6 19 0.00042 26.5 1.1 12 27-38 2-13 (54)
188 KOG1729 FYVE finger containing 35.5 12 0.00025 37.6 -0.2 38 210-247 215-252 (288)
189 PRK15103 paraquat-inducible me 35.2 22 0.00047 37.5 1.8 28 10-37 11-40 (419)
190 PF09297 zf-NADH-PPase: NADH p 34.7 28 0.00061 22.9 1.7 25 11-35 5-29 (32)
191 TIGR02300 FYDLN_acid conserved 34.4 31 0.00066 30.6 2.3 32 7-40 7-39 (129)
192 PLN02436 cellulose synthase A 34.1 48 0.001 39.0 4.3 49 210-258 37-90 (1094)
193 PF06750 DiS_P_DiS: Bacterial 33.5 39 0.00084 28.0 2.7 39 209-259 33-71 (92)
194 PF03811 Zn_Tnp_IS1: InsA N-te 33.3 19 0.00042 24.9 0.7 10 27-36 5-14 (36)
195 KOG4185 Predicted E3 ubiquitin 33.1 9.2 0.0002 37.7 -1.4 46 210-255 208-265 (296)
196 PF06844 DUF1244: Protein of u 32.5 21 0.00045 28.1 0.8 13 233-245 11-23 (68)
197 cd00065 FYVE FYVE domain; Zinc 32.2 27 0.00058 25.5 1.4 35 210-244 3-38 (57)
198 PF07191 zinc-ribbons_6: zinc- 32.0 28 0.00061 27.7 1.5 23 8-35 16-38 (70)
199 TIGR00155 pqiA_fam integral me 31.9 24 0.00051 37.0 1.4 24 11-37 217-240 (403)
200 TIGR01053 LSD1 zinc finger dom 31.7 36 0.00077 22.8 1.7 24 11-34 3-26 (31)
201 COG4391 Uncharacterized protei 31.6 28 0.0006 27.1 1.3 15 24-38 45-59 (62)
202 KOG3039 Uncharacterized conser 31.6 24 0.00053 34.7 1.3 33 210-245 44-76 (303)
203 PLN02400 cellulose synthase 30.9 48 0.001 39.0 3.6 50 209-258 36-90 (1085)
204 KOG3842 Adaptor protein Pellin 30.7 46 0.001 34.0 3.1 51 209-259 341-416 (429)
205 cd04718 BAH_plant_2 BAH, or Br 30.5 28 0.00062 31.6 1.5 27 234-260 2-32 (148)
206 KOG1815 Predicted E3 ubiquitin 30.4 20 0.00043 37.9 0.5 37 210-246 227-268 (444)
207 PF13913 zf-C2HC_2: zinc-finge 30.3 19 0.00041 22.6 0.2 14 27-40 2-15 (25)
208 COG1198 PriA Primosomal protei 30.2 26 0.00057 39.5 1.5 31 6-41 459-489 (730)
209 PF03107 C1_2: C1 domain; Int 29.6 33 0.00071 22.4 1.3 22 10-34 1-22 (30)
210 PF14569 zf-UDP: Zinc-binding 28.9 72 0.0016 26.0 3.3 51 209-259 9-64 (80)
211 PF06943 zf-LSD1: LSD1 zinc fi 28.0 50 0.0011 21.1 1.8 23 12-34 1-23 (25)
212 PF04423 Rad50_zn_hook: Rad50 27.4 20 0.00044 26.4 -0.0 11 248-258 22-32 (54)
213 PLN02638 cellulose synthase A 27.2 75 0.0016 37.4 4.4 50 209-258 17-71 (1079)
214 PF13717 zinc_ribbon_4: zinc-r 27.2 38 0.00081 23.2 1.3 27 11-37 4-35 (36)
215 PRK15103 paraquat-inducible me 27.2 34 0.00075 36.0 1.6 24 10-37 222-245 (419)
216 PRK10220 hypothetical protein; 27.2 40 0.00086 29.2 1.7 28 12-40 6-33 (111)
217 PF10122 Mu-like_Com: Mu-like 26.7 25 0.00053 26.3 0.3 30 8-37 3-34 (51)
218 PF06827 zf-FPG_IleRS: Zinc fi 26.1 26 0.00056 22.7 0.3 23 12-34 4-28 (30)
219 KOG1245 Chromatin remodeling c 25.6 22 0.00048 43.0 -0.2 48 209-256 1108-1159(1404)
220 PRK00432 30S ribosomal protein 25.3 32 0.0007 25.4 0.7 15 27-41 20-34 (50)
221 cd07973 Spt4 Transcription elo 25.1 37 0.0008 28.7 1.1 27 11-39 5-31 (98)
222 PHA00616 hypothetical protein 25.0 19 0.00041 26.1 -0.6 13 28-40 2-14 (44)
223 PF11023 DUF2614: Protein of u 24.9 53 0.0012 28.5 2.1 23 241-263 80-102 (114)
224 KOG4443 Putative transcription 24.5 35 0.00076 37.8 1.1 25 230-254 41-70 (694)
225 PF14353 CpXC: CpXC protein 24.3 40 0.00086 29.1 1.2 17 27-43 1-17 (128)
226 PF12773 DZR: Double zinc ribb 24.1 49 0.0011 23.6 1.5 26 9-35 12-37 (50)
227 PF02148 zf-UBP: Zn-finger in 23.6 28 0.00062 26.4 0.2 17 4-20 44-60 (63)
228 PF14968 CCDC84: Coiled coil p 23.4 35 0.00077 35.0 0.8 32 5-42 54-85 (336)
229 KOG2932 E3 ubiquitin ligase in 23.3 33 0.00072 34.8 0.6 12 25-36 121-132 (389)
230 PF14803 Nudix_N_2: Nudix N-te 23.2 45 0.00097 22.8 1.0 24 11-34 2-29 (34)
231 PF14787 zf-CCHC_5: GAG-polypr 23.0 39 0.00085 23.5 0.7 12 28-39 3-14 (36)
232 PF13719 zinc_ribbon_5: zinc-r 22.5 55 0.0012 22.4 1.4 26 12-37 5-35 (37)
233 KOG4323 Polycomb-like PHD Zn-f 22.5 29 0.00063 37.1 0.0 47 209-255 168-224 (464)
234 KOG0956 PHD finger protein AF1 22.3 40 0.00086 37.7 1.0 47 210-256 118-181 (900)
235 PF06677 Auto_anti-p27: Sjogre 22.2 71 0.0015 22.7 1.9 23 11-34 19-41 (41)
236 PRK04338 N(2),N(2)-dimethylgua 21.6 70 0.0015 33.2 2.6 30 8-38 243-272 (382)
237 PF08274 PhnA_Zn_Ribbon: PhnA 21.5 49 0.0011 22.0 0.9 23 12-35 5-27 (30)
238 PRK13794 hypothetical protein; 21.0 58 0.0013 34.9 1.9 23 8-36 9-31 (479)
239 PF12760 Zn_Tnp_IS1595: Transp 21.0 23 0.00051 25.3 -0.7 11 26-36 17-27 (46)
240 PF13832 zf-HC5HC2H_2: PHD-zin 20.9 56 0.0012 27.2 1.4 32 209-242 55-88 (110)
241 KOG2071 mRNA cleavage and poly 20.2 68 0.0015 35.2 2.2 36 207-242 511-556 (579)
242 COG1885 Uncharacterized protei 20.1 65 0.0014 27.7 1.6 18 18-37 42-59 (115)
No 1
>PF06547 DUF1117: Protein of unknown function (DUF1117); InterPro: IPR010543 This entry represents the C terminus of a number of hypothetical plant proteins.
Probab=100.00 E-value=4.9e-35 Score=243.51 Aligned_cols=113 Identities=72% Similarity=1.157 Sum_probs=96.5
Q ss_pred cccceeeecCCCccccccccCCCCCCccccCceeecCCCCCCCC-CCCccccCCCCCCCCcccCCcchHHhhhhhhcccc
Q 039088 283 AVGLTIWRLPGGGFAVGRFSGGRRGGERELPVVYTEMDGGFNNG-GLPRRVSWGSRGSRGRERGGGFVGRFVRSLFGCFG 361 (409)
Q Consensus 283 ~~g~ti~~lPggg~avgr~~g~rr~~er~~Pv~~~e~dg~~n~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 361 (409)
++|||||+||+||||||||+|++|++|++|||||||||||+||+ ++||+|||++++.+++++.||.|+|+|||||+||+
T Consensus 1 avGLTIWRLPGGGFAVGRF~GgrR~gErelPvVyTEmDGgfn~~~g~PRRisW~~r~~r~~~~~gg~~~R~frn~fs~f~ 80 (117)
T PF06547_consen 1 AVGLTIWRLPGGGFAVGRFSGGRRAGERELPVVYTEMDGGFNNGGGAPRRISWSSRGGRSRERRGGGFRRVFRNLFSCFG 80 (117)
T ss_pred CcceEEEEcCCCceEEeeecCCCcCCcccCCEEEEEecCCccCCCCCceeeeecccCCcccccccchHHHHHHHHHHHhc
Confidence 47999999999999999999999999999999999999999988 99999999999999999966669999999999999
Q ss_pred CCCCCCCCCCCCCc--ccccCCCCCcceeeecCCcc
Q 039088 362 GGSGSSSTSGSSDS--RIRRRGTSRAVSLFNVSSRR 395 (409)
Q Consensus 362 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 395 (409)
+++.++++++.+.. ....+..++.+++|++++++
T Consensus 81 ~~~~~~s~ss~~~s~~~s~~~~~~~~~s~~s~s~rr 116 (117)
T PF06547_consen 81 RIGSSSSSSSSSSSRSGSRSRSSSSRSSRFSRSSRR 116 (117)
T ss_pred CCCCCccccccccccccccccchhhhhhhhcccccc
Confidence 98888876653322 11222356667888888765
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.63 E-value=2.2e-16 Score=157.92 Aligned_cols=78 Identities=31% Similarity=0.727 Sum_probs=68.5
Q ss_pred CCCCCCHHHHHcCCceeecccCcccC-ccccccccccccCCCceeecccceeChhhhHHHhhcCC-CCCCCCccCCCCCC
Q 039088 184 ENPPASKAAIENMPSILIDSSYVELE-SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN-SCPVCRHELPADNN 261 (409)
Q Consensus 184 ~~ppas~~~i~~lp~~~~~~~~~~~~-~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~~~ 261 (409)
....+.+..++++|..+++....... ..|+||||+|+.|+++++|||+|.||..||++||.++. .||+||+++.+...
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG 282 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence 45678999999999999998765433 49999999999999999999999999999999998875 59999998877654
No 3
>PF14369 zf-RING_3: zinc-finger
Probab=99.57 E-value=1.2e-15 Score=104.56 Aligned_cols=34 Identities=59% Similarity=1.347 Sum_probs=29.4
Q ss_pred CceecccCCcceeecc-CCCCccCCCCCCCceeec
Q 039088 8 SSYWCYRCSRFVRVFS-RDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~-~~~~~~CP~C~~GFiEEi 41 (409)
++||||+|+|+|++.+ ..++++||+|++||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 5899999999999864 445666999999999997
No 4
>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=99.45 E-value=2.1e-14 Score=102.90 Aligned_cols=44 Identities=48% Similarity=1.195 Sum_probs=40.6
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
++|+||++.|..++.++.|+|+|+||.+||.+||+.+.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 37999999999999999999999999999999999999999997
No 5
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=1.3e-11 Score=123.10 Aligned_cols=72 Identities=26% Similarity=0.689 Sum_probs=56.8
Q ss_pred CCHHHHHcCCceeecccCcccCccccccccc-cccC---------CCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 188 ASKAAIENMPSILIDSSYVELESHCAVCKEA-FELG---------SEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 188 as~~~i~~lp~~~~~~~~~~~~~~C~ICle~-f~~g---------~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
+.|+.-+-+|+++.++. ...|..|.||+|+ |..+ .++++|||||++|.+|++.|++++++||+||.++.
T Consensus 267 ~~kdl~~~~~t~t~eql-~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 267 ATKDLNAMYPTATEEQL-TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred HhhHHHhhcchhhhhhh-cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 45555566676665543 4567899999999 5544 35799999999999999999999999999999965
Q ss_pred CCC
Q 039088 258 ADN 260 (409)
Q Consensus 258 ~~~ 260 (409)
-+.
T Consensus 346 fd~ 348 (491)
T COG5243 346 FDQ 348 (491)
T ss_pred ccc
Confidence 543
No 6
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.19 E-value=7.3e-12 Score=122.04 Aligned_cols=50 Identities=38% Similarity=0.971 Sum_probs=46.3
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhh-cCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLS-LRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~ 258 (409)
.-+|+||++.|..+++.+.|||+|.||..||.+|+. -++.||+||.+||.
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 378999999999999999999999999999999998 56699999999975
No 7
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.18 E-value=1.1e-11 Score=119.16 Aligned_cols=72 Identities=26% Similarity=0.582 Sum_probs=55.7
Q ss_pred CCCHHHHHcCCceeecccCc---ccCccccccccccccCCC-----ceeecccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 187 PASKAAIENMPSILIDSSYV---ELESHCAVCKEAFELGSE-----AREMPCKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 187 pas~~~i~~lp~~~~~~~~~---~~~~~C~ICle~f~~g~~-----~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
..+++.++.+|.+...-... ..+.+|+||++.+..... ...++|+|.||..||.+|++.+.+||+||..+..
T Consensus 149 ~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 149 KNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred chhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 34788889999886553322 345799999998775431 2345699999999999999999999999998753
No 8
>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=99.17 E-value=1.6e-11 Score=97.65 Aligned_cols=45 Identities=42% Similarity=1.020 Sum_probs=36.0
Q ss_pred CccccccccccccC----------CCceeecccceeChhhhHHHhhcCCCCCCCC
Q 039088 209 ESHCAVCKEAFELG----------SEAREMPCKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 209 ~~~C~ICle~f~~g----------~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
++.|+||++.|... -.+...+|+|.||..||.+||+.+++||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 45699999999322 2345557999999999999999999999997
No 9
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=5e-10 Score=106.07 Aligned_cols=54 Identities=26% Similarity=0.648 Sum_probs=44.4
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCC---CCCCCCccCCCCCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN---SCPVCRHELPADNNSN 263 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~~~~~~ 263 (409)
....+|.||||.-+ +++++.|+|.||+.||.+||..+. .|||||..|..++...
T Consensus 45 ~~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP 101 (230)
T KOG0823|consen 45 GGFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP 101 (230)
T ss_pred CCceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence 34589999998755 678888999999999999997744 7899999987776443
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.86 E-value=1.3e-09 Score=101.46 Aligned_cols=51 Identities=22% Similarity=0.638 Sum_probs=42.2
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhc----------------CCCCCCCCccCCCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL----------------RNSCPVCRHELPADNN 261 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~----------------~~sCPvCR~~l~~~~~ 261 (409)
.+.+|+||++.++ .+++++|+|.||+.||.+|+.. +..||+||..+...+.
T Consensus 17 ~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 17 GDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred CccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 4578999999876 5677899999999999999853 2479999999976543
No 11
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.83 E-value=1.4e-09 Score=105.80 Aligned_cols=51 Identities=33% Similarity=0.862 Sum_probs=44.5
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
.....|.+|||... .+..+||||+||+.||..|+..+..||+||.++...+
T Consensus 237 ~a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 237 EATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK 287 (293)
T ss_pred CCCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence 34578999998765 6788999999999999999999999999999886654
No 12
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.82 E-value=2.1e-09 Score=75.00 Aligned_cols=44 Identities=36% Similarity=1.051 Sum_probs=36.5
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhc-CCCCCCCCccC
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL-RNSCPVCRHEL 256 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~-~~sCPvCR~~l 256 (409)
.|+||++.+. +....++|+|.||..|+..|++. +..||+|+..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4999999883 34455559999999999999988 67899999864
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.82 E-value=2.1e-09 Score=79.03 Aligned_cols=46 Identities=26% Similarity=0.824 Sum_probs=39.8
Q ss_pred CccccccccccccCCCceeecccce-eChhhhHHHhhcCCCCCCCCccCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHI-YHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~-FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
+..|.||++... .+..+||+|. |+..|+..|++.+..||+||+++.
T Consensus 2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 368999999865 5889999999 999999999999999999999874
No 14
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.76 E-value=3.8e-09 Score=73.78 Aligned_cols=39 Identities=31% Similarity=0.864 Sum_probs=33.2
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvC 252 (409)
|+||++.+.. .++.++|+|.||..||.+|++.+..||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999998874 44788999999999999999998899998
No 15
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=3.8e-09 Score=113.04 Aligned_cols=53 Identities=30% Similarity=0.872 Sum_probs=46.4
Q ss_pred cCccccccccccccCCC--ceeecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGSE--AREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~--~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
.+..|+||+|.+..+.. +++|+|+|+||..|+..|++++++||+||..+....
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~ 344 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDYV 344 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhccc
Confidence 46899999999987655 899999999999999999999999999999554443
No 16
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.65 E-value=1.3e-08 Score=83.05 Aligned_cols=50 Identities=34% Similarity=0.857 Sum_probs=38.3
Q ss_pred cCcccccccccccc--------CC--CceeecccceeChhhhHHHhhc---CCCCCCCCccCC
Q 039088 208 LESHCAVCKEAFEL--------GS--EAREMPCKHIYHSDCILPWLSL---RNSCPVCRHELP 257 (409)
Q Consensus 208 ~~~~C~ICle~f~~--------g~--~~~~lPC~H~FH~~CI~~WL~~---~~sCPvCR~~l~ 257 (409)
.++.|.||...|+. |+ .++.-.|+|.||..||.+||.. +..||+||++..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 46889999998872 22 1222349999999999999986 458999999764
No 17
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.59 E-value=3.9e-08 Score=74.85 Aligned_cols=47 Identities=21% Similarity=0.388 Sum_probs=41.3
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
..|+||++.++. ++.++|+|+|+..||.+|++.+.+||+|+..+...
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 479999998873 67889999999999999999988999999988543
No 18
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.59 E-value=3e-08 Score=70.76 Aligned_cols=38 Identities=29% Similarity=0.892 Sum_probs=30.8
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhhcCC----CCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN----SCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~----sCPvC 252 (409)
|+||++.|+ +++.|+|+|.|+..||..|++... .||+|
T Consensus 1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999998 789999999999999999997643 69988
No 19
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.58 E-value=2e-08 Score=91.89 Aligned_cols=50 Identities=26% Similarity=0.663 Sum_probs=42.2
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
...|+|||+.+.... +..+.|||+||+.||+.-|+....||+|++.|...
T Consensus 131 ~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 378999999998532 24467999999999999999999999999987654
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.56 E-value=3.4e-08 Score=70.89 Aligned_cols=44 Identities=30% Similarity=0.790 Sum_probs=38.8
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
+|.||++.|........|+|+|+||..||..+......||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 59999999966667899999999999999999856679999985
No 21
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.53 E-value=4.9e-08 Score=65.70 Aligned_cols=38 Identities=37% Similarity=1.042 Sum_probs=33.2
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhh-cCCCCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLS-LRNSCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~-~~~sCPvC 252 (409)
|+||++. ......++|+|.||..|+..|++ .+..||+|
T Consensus 1 C~iC~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE---LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC---CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 8899887 34788899999999999999998 56689998
No 22
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.51 E-value=6e-08 Score=68.02 Aligned_cols=39 Identities=38% Similarity=1.008 Sum_probs=33.1
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhh--cCCCCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLS--LRNSCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~--~~~sCPvC 252 (409)
|+||++.+.. ....++|+|.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998874 335889999999999999998 44589998
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.49 E-value=5.5e-08 Score=91.98 Aligned_cols=50 Identities=30% Similarity=0.740 Sum_probs=37.7
Q ss_pred cCccccccccccccCC-----Cceee-cccceeChhhhHHHhhcC------CCCCCCCccCC
Q 039088 208 LESHCAVCKEAFELGS-----EAREM-PCKHIYHSDCILPWLSLR------NSCPVCRHELP 257 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~-----~~~~l-PC~H~FH~~CI~~WL~~~------~sCPvCR~~l~ 257 (409)
.+.+|+||+|..-... .-.+| +|+|.||..||..|.+.+ .+||+||..+.
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 4589999999753221 12344 599999999999999753 36999999764
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.43 E-value=1.3e-07 Score=97.22 Aligned_cols=50 Identities=32% Similarity=0.684 Sum_probs=43.1
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
.....|+||++.|. .+++++|+|.||..||..||..+..||+|+..+...
T Consensus 24 e~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 34579999999887 456789999999999999999888999999987654
No 25
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.34 E-value=2.4e-07 Score=74.27 Aligned_cols=49 Identities=31% Similarity=0.791 Sum_probs=36.3
Q ss_pred cccccccccc-----------ccCCCc-eee-cccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 210 SHCAVCKEAF-----------ELGSEA-REM-PCKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 210 ~~C~ICle~f-----------~~g~~~-~~l-PC~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
+.|+||...| ..+++. ... -|+|.||..||..||..+..||+||++..-
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 5677776554 233332 222 399999999999999999999999997643
No 26
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.19 E-value=7.9e-07 Score=65.55 Aligned_cols=42 Identities=21% Similarity=0.795 Sum_probs=34.3
Q ss_pred cccccccccccCCCceeeccc-----ceeChhhhHHHhhcCC--CCCCCC
Q 039088 211 HCAVCKEAFELGSEAREMPCK-----HIYHSDCILPWLSLRN--SCPVCR 253 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~-----H~FH~~CI~~WL~~~~--sCPvCR 253 (409)
.|.||++ ....+...++||. |.+|..|+.+||..+. +||+|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4899999 4555667789975 8999999999996654 899995
No 27
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=6.1e-07 Score=71.37 Aligned_cols=49 Identities=33% Similarity=0.910 Sum_probs=36.4
Q ss_pred Ccccccccccccc--------CC-Cceeec-ccceeChhhhHHHhhcC---CCCCCCCccCC
Q 039088 209 ESHCAVCKEAFEL--------GS-EAREMP-CKHIYHSDCILPWLSLR---NSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~--------g~-~~~~lP-C~H~FH~~CI~~WL~~~---~sCPvCR~~l~ 257 (409)
++.|-||.-.|.. |+ -+.++- |.|.||..||.+||... ..||+||++..
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 4589999888852 22 233333 99999999999999663 47999998753
No 28
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.12 E-value=6.4e-07 Score=86.72 Aligned_cols=53 Identities=26% Similarity=0.813 Sum_probs=43.1
Q ss_pred cCccccccccccccCC-------CceeecccceeChhhhHHHh--hcCCCCCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGS-------EAREMPCKHIYHSDCILPWL--SLRNSCPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~-------~~~~lPC~H~FH~~CI~~WL--~~~~sCPvCR~~l~~~~ 260 (409)
++..|+||-..+.... +.-+|.|+|+||..||+-|- -++++||.|+..+....
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence 4578999988775444 67889999999999999996 44679999999875553
No 29
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.2e-06 Score=84.76 Aligned_cols=50 Identities=28% Similarity=0.757 Sum_probs=41.6
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHH-HhhcCCC-CCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILP-WLSLRNS-CPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~-WL~~~~s-CPvCR~~l~~~~ 260 (409)
.+..|+||++..+ .+..++|+|+||..||.. |-+.+.. ||+||+.+...+
T Consensus 214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 3578999988766 678899999999999999 9877765 999999775543
No 30
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=1.2e-06 Score=90.73 Aligned_cols=50 Identities=38% Similarity=0.977 Sum_probs=39.7
Q ss_pred CccccccccccccCC--------------CceeecccceeChhhhHHHhhcC-CCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGS--------------EAREMPCKHIYHSDCILPWLSLR-NSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~--------------~~~~lPC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~ 258 (409)
..+|+||+..+..-. .-..+||.|+||..|+..|...- -.||+||..|+.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 468999998875322 12345999999999999999954 499999999874
No 31
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.05 E-value=2.2e-06 Score=61.58 Aligned_cols=38 Identities=32% Similarity=0.898 Sum_probs=22.8
Q ss_pred cccccccccc-CCCceeecccceeChhhhHHHhhcCC----CCC
Q 039088 212 CAVCKEAFEL-GSEAREMPCKHIYHSDCILPWLSLRN----SCP 250 (409)
Q Consensus 212 C~ICle~f~~-g~~~~~lPC~H~FH~~CI~~WL~~~~----sCP 250 (409)
|+||+| |.. ...++.|+|+|+|+.+||.++++... .||
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 754 34578899999999999999998542 676
No 32
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=2.3e-06 Score=89.25 Aligned_cols=49 Identities=29% Similarity=0.766 Sum_probs=39.7
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcC-----CCCCCCCccCCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLR-----NSCPVCRHELPADN 260 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~-----~sCPvCR~~l~~~~ 260 (409)
+..|+|||+... .+..+.|||+||..||...+... ..||+|+..|...+
T Consensus 186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 578999998765 45666699999999999988553 48999999886643
No 33
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.00 E-value=1.7e-06 Score=86.10 Aligned_cols=48 Identities=31% Similarity=0.734 Sum_probs=43.3
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
..|-||.|-|. .+.++||+|.||.-||+..|..+..||+|+.++....
T Consensus 24 LRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~ 71 (442)
T KOG0287|consen 24 LRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD 71 (442)
T ss_pred HHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccchhh
Confidence 68999999888 6889999999999999999999999999999875543
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=97.97 E-value=4.2e-06 Score=66.46 Aligned_cols=48 Identities=25% Similarity=0.494 Sum_probs=38.4
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhc-CCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL-RNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~ 259 (409)
...|+||.+-+. .++++||+|.|...||..||+. +.+||+|+..|...
T Consensus 4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 4 EFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred ccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence 468999999888 7889999999999999999999 77999999888654
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.94 E-value=3.4e-06 Score=82.49 Aligned_cols=47 Identities=30% Similarity=0.605 Sum_probs=41.6
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
-..|-||.+.|. ...+++|+|.||.-||...|..+..||+||.+...
T Consensus 25 ~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 25 MLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred HHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence 368999999887 57788899999999999999999999999986543
No 36
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.91 E-value=3.9e-06 Score=70.46 Aligned_cols=27 Identities=44% Similarity=1.045 Sum_probs=25.7
Q ss_pred ccceeChhhhHHHhhcCCCCCCCCccC
Q 039088 230 CKHIYHSDCILPWLSLRNSCPVCRHEL 256 (409)
Q Consensus 230 C~H~FH~~CI~~WL~~~~sCPvCR~~l 256 (409)
|.|.||..||..||++++.||+|.++.
T Consensus 81 CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 81 CNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred cchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 999999999999999999999998765
No 37
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.89 E-value=2.5e-06 Score=93.67 Aligned_cols=50 Identities=26% Similarity=0.873 Sum_probs=37.3
Q ss_pred cCccccccccccccCC---Cceeec-ccceeChhhhHHHhhcC--CCCCCCCccCC
Q 039088 208 LESHCAVCKEAFELGS---EAREMP-CKHIYHSDCILPWLSLR--NSCPVCRHELP 257 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~---~~~~lP-C~H~FH~~CI~~WL~~~--~sCPvCR~~l~ 257 (409)
.-.+|+||...+..-+ .-+..+ |+|.||..|+.+|++.. ++||+||.+++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3478999987654211 122333 99999999999999874 58999998775
No 38
>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=97.80 E-value=1.3e-05 Score=79.81 Aligned_cols=52 Identities=23% Similarity=0.455 Sum_probs=37.7
Q ss_pred CccccccccccccCCCc--eeecccceeChhhhHHHhhc-CCCCCCCCccCCCCC
Q 039088 209 ESHCAVCKEAFELGSEA--REMPCKHIYHSDCILPWLSL-RNSCPVCRHELPADN 260 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~--~~lPC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~ 260 (409)
+..|+||+..--..... .+.+|+|.||..||...+.. ...||+|+..|....
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 36799999963333332 33379999999999996644 558999998775543
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=6.8e-06 Score=77.64 Aligned_cols=43 Identities=35% Similarity=0.702 Sum_probs=38.2
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
....|+||++.|... +.+||+|.||..||..++...-.||.||
T Consensus 12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 457999999999954 8999999999999999988555899999
No 40
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.7e-05 Score=79.77 Aligned_cols=47 Identities=26% Similarity=0.737 Sum_probs=41.0
Q ss_pred CccccccccccccCCCceeecccce-eChhhhHHHhhcCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHI-YHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
..+|.||+.+-. .+.+|||.|. .|..|.+..--+++.||+||+.+..
T Consensus 290 gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 290 GKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred CCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 478999998766 7899999998 8999999887788999999998744
No 41
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.68 E-value=1.1e-05 Score=63.85 Aligned_cols=48 Identities=23% Similarity=0.596 Sum_probs=22.6
Q ss_pred ccccccccccc-cCCCc-eee---cccceeChhhhHHHhhc----CC-------CCCCCCccCC
Q 039088 210 SHCAVCKEAFE-LGSEA-REM---PCKHIYHSDCILPWLSL----RN-------SCPVCRHELP 257 (409)
Q Consensus 210 ~~C~ICle~f~-~g~~~-~~l---PC~H~FH~~CI~~WL~~----~~-------sCPvCR~~l~ 257 (409)
.+|.||...+. .++.+ ... .|++.||..||.+||.. +. +||.|+.+|.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 58999998765 33222 222 39999999999999964 11 4999999874
No 42
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.68 E-value=1.7e-05 Score=81.68 Aligned_cols=47 Identities=32% Similarity=0.841 Sum_probs=37.9
Q ss_pred CccccccccccccCC-CceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 209 ESHCAVCKEAFELGS-EAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~g~-~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
...|+||||.+...- .++...|.|.||..|+.+| ...+|||||+-..
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence 478999999887533 3455569999999999999 4568999999665
No 43
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=6.9e-06 Score=82.34 Aligned_cols=59 Identities=27% Similarity=0.656 Sum_probs=45.0
Q ss_pred eeecccCcccCccccccccccccCCCceeec-ccceeChhhhHHHhhc-CCCCCCCCccCCCCC
Q 039088 199 ILIDSSYVELESHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLSL-RNSCPVCRHELPADN 260 (409)
Q Consensus 199 ~~~~~~~~~~~~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~ 260 (409)
+.++......+..|+|||+.++. .+..+ |.|.||.+||.+-|+. .++||.||+.+....
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr 93 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR 93 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence 44444455567899999998873 34444 9999999999999976 569999999876553
No 44
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.57 E-value=3.1e-05 Score=76.19 Aligned_cols=92 Identities=23% Similarity=0.509 Sum_probs=63.5
Q ss_pred hhHHHHHHHHHHhhhcCCCCCCCCCCCHHHHHcCCceeecccCcccCccccccccccccCCCceeecccceeChhhhHHH
Q 039088 163 SGFERLLEQLSQIDMNGIGGFENPPASKAAIENMPSILIDSSYVELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPW 242 (409)
Q Consensus 163 ~~le~LleqL~q~~~~~~~~~~~ppas~~~i~~lp~~~~~~~~~~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~W 242 (409)
..|.+|..++..+...+++ -|+--+.|+..........+ ...+|.|||--|..++...+++|-|.||..|+..+
T Consensus 75 ~~~~~i~~~~~~iikq~~g----~pii~~lie~~~e~LT~nn~--p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRy 148 (368)
T KOG4445|consen 75 PEFREIQRQIQEIIKQNSG----MPIICQLIEHCSEFLTENNH--PNGQCVICLYGFASSPAFTVTACDHYMHFACLARY 148 (368)
T ss_pred HHHHHHHHHHHHHHHhcCC----CchhHHHHHHHHHHcccCCC--CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHH
Confidence 4577787877665544432 34444555544333333222 23689999999999999999999999999999887
Q ss_pred hhc-----------------------CCCCCCCCccCCCCC
Q 039088 243 LSL-----------------------RNSCPVCRHELPADN 260 (409)
Q Consensus 243 L~~-----------------------~~sCPvCR~~l~~~~ 260 (409)
|.. +..|||||..|..+.
T Consensus 149 l~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 149 LTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 631 226999999876553
No 45
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.53 E-value=2e-05 Score=85.46 Aligned_cols=50 Identities=26% Similarity=0.566 Sum_probs=44.2
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
...|+||+..+..+......+|.|+||..||..|-+.-++||+||.++..
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 46899999999877777777899999999999999999999999997643
No 46
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.53 E-value=3.4e-05 Score=76.04 Aligned_cols=48 Identities=21% Similarity=0.483 Sum_probs=39.9
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCC-CCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN-SCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~ 259 (409)
+.+|+||+...- ..+.|+|+|.||.-||+--++... +|++||.+++..
T Consensus 7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 468999987644 668999999999999988776644 799999998765
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.35 E-value=0.0001 Score=57.22 Aligned_cols=46 Identities=28% Similarity=0.678 Sum_probs=23.8
Q ss_pred ccccccccccccCCCce-eecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 210 SHCAVCKEAFELGSEAR-EMPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~-~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
..|++|.+.++ +++ ...|.|+||..||..-+.. .||+|+.+.-..+
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 67999999877 444 4459999999999986553 5999998765443
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=7.3e-05 Score=75.85 Aligned_cols=51 Identities=25% Similarity=0.784 Sum_probs=38.0
Q ss_pred ccccccccccccCCCceeec-ccceeChhhhHHHhhcC---CCCCCCCccCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLSLR---NSCPVCRHELPADN 260 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~~~---~sCPvCR~~l~~~~ 260 (409)
..|.||-+-+.....+.-+. |||+||..|+..|++.- ..||+|+-.++...
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~ 59 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERH 59 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccccee
Confidence 57999966555444555555 99999999999999873 37999995554443
No 49
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.00022 Score=72.48 Aligned_cols=53 Identities=30% Similarity=0.710 Sum_probs=38.9
Q ss_pred cCccccccccccccCC----Cceeec-ccceeChhhhHHHh--hc-----CCCCCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGS----EAREMP-CKHIYHSDCILPWL--SL-----RNSCPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~----~~~~lP-C~H~FH~~CI~~WL--~~-----~~sCPvCR~~l~~~~ 260 (409)
.+..|.||++...... .-.+|| |.|.||..||+.|- ++ ...||.||....-..
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~ 224 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN 224 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence 3579999999765322 123445 99999999999997 44 468999998764443
No 50
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00018 Score=54.01 Aligned_cols=46 Identities=26% Similarity=0.643 Sum_probs=34.6
Q ss_pred CccccccccccccCCCceeecccce-eChhhhHHHhh-cCCCCCCCCccCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHI-YHSDCILPWLS-LRNSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~-FH~~CI~~WL~-~~~sCPvCR~~l~ 257 (409)
+++|.||+|.-. ..+.-.|+|. .|.+|-...++ .+..||+||+++.
T Consensus 7 ~dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 378999977533 3344459998 78899877666 7889999999763
No 51
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.92 E-value=0.00043 Score=70.83 Aligned_cols=47 Identities=26% Similarity=0.854 Sum_probs=37.0
Q ss_pred ccccccccccccCC--CceeecccceeChhhhHHHhhc--CCCCCCCCccC
Q 039088 210 SHCAVCKEAFELGS--EAREMPCKHIYHSDCILPWLSL--RNSCPVCRHEL 256 (409)
Q Consensus 210 ~~C~ICle~f~~g~--~~~~lPC~H~FH~~CI~~WL~~--~~sCPvCR~~l 256 (409)
..|+|||+.++..- .+..+.|+|.|-..||.+||-+ ...||.|..+-
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 57999999987543 3455669999999999999953 33799997643
No 52
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.79 E-value=0.00063 Score=70.39 Aligned_cols=50 Identities=32% Similarity=0.666 Sum_probs=43.1
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
..+.+|.||+..+. .++.+||+|.||..||..-|.....||.||.++...
T Consensus 82 ~sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~ 131 (398)
T KOG4159|consen 82 RSEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVEL 131 (398)
T ss_pred cchhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCcccccccccc
Confidence 34689999988776 677789999999999999888888999999998753
No 53
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=96.78 E-value=0.00055 Score=69.87 Aligned_cols=48 Identities=27% Similarity=0.849 Sum_probs=39.7
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhc--CCCCCCCCccCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL--RNSCPVCRHELPADN 260 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~--~~sCPvCR~~l~~~~ 260 (409)
..|-||-|. ...+++-||+|..|..|+..|-.. .++||.||.+|...+
T Consensus 370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte 419 (563)
T KOG1785|consen 370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE 419 (563)
T ss_pred HHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence 579999764 347888899999999999999744 569999999986554
No 54
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.70 E-value=0.00061 Score=61.88 Aligned_cols=40 Identities=28% Similarity=0.706 Sum_probs=31.2
Q ss_pred CceeecccCcc-cCccccccccccccCCCceeecccceeCh
Q 039088 197 PSILIDSSYVE-LESHCAVCKEAFELGSEAREMPCKHIYHS 236 (409)
Q Consensus 197 p~~~~~~~~~~-~~~~C~ICle~f~~g~~~~~lPC~H~FH~ 236 (409)
|.+.+...-+. ...+|.||||+++.++.+..|||-.+||+
T Consensus 164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 34444443333 34799999999999999999999999997
No 55
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.63 E-value=0.00056 Score=74.73 Aligned_cols=47 Identities=23% Similarity=0.723 Sum_probs=38.8
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhc-CCCCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL-RNSCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~ 259 (409)
..|++|-..++ .+++.-|+|+||..||.+-+.. +..||.|...+-..
T Consensus 644 LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 644 LKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred eeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 68999987776 5666679999999999999966 55999998877544
No 56
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.54 E-value=0.0016 Score=67.50 Aligned_cols=52 Identities=29% Similarity=0.692 Sum_probs=43.0
Q ss_pred cccCccccccccccccCCCcee-ecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 206 VELESHCAVCKEAFELGSEARE-MPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 206 ~~~~~~C~ICle~f~~g~~~~~-lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
...+..|+||...+.. +.. ..|+|.||..||.+|+..+..||.|+..+....
T Consensus 18 ~~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE 70 (391)
T ss_pred CcccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence 3456889999998874 333 579999999999999999999999998775554
No 57
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.34 E-value=0.0019 Score=49.10 Aligned_cols=41 Identities=24% Similarity=0.694 Sum_probs=28.5
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcC--CCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLR--NSCPV 251 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~--~sCPv 251 (409)
...|+|.+..|+ +.++...|+|+|-+..|..||+.+ ..||+
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 468999999988 355556799999999999999443 37998
No 58
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.0028 Score=60.46 Aligned_cols=51 Identities=24% Similarity=0.687 Sum_probs=41.4
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhc--------CCCCCCCCccCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL--------RNSCPVCRHELPAD 259 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~--------~~sCPvCR~~l~~~ 259 (409)
....|..|.-.++.++.++ |-|-|+||++|+..|-.. ...||.|..+|...
T Consensus 49 Y~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 49 YNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 3468999999999887654 669999999999999754 23799999988654
No 59
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.22 E-value=0.0012 Score=67.28 Aligned_cols=49 Identities=35% Similarity=0.786 Sum_probs=39.7
Q ss_pred cCccccccccccccCC-CceeecccceeChhhhHHHhhcCC--CCCCCCccC
Q 039088 208 LESHCAVCKEAFELGS-EAREMPCKHIYHSDCILPWLSLRN--SCPVCRHEL 256 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~-~~~~lPC~H~FH~~CI~~WL~~~~--sCPvCR~~l 256 (409)
.+.-|-.|-+.+...+ ..-.|||.|+||..|+...|..+. +||.||+-.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr 415 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR 415 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence 3567999999886554 567789999999999999997654 899999533
No 60
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.13 E-value=0.003 Score=72.72 Aligned_cols=67 Identities=25% Similarity=0.564 Sum_probs=48.1
Q ss_pred HHHcCCceeecccC--cccCccccccccccccCCCceeecccceeChhhhHHHhhcCC----------CCCCCCccCCC
Q 039088 192 AIENMPSILIDSSY--VELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN----------SCPVCRHELPA 258 (409)
Q Consensus 192 ~i~~lp~~~~~~~~--~~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~----------sCPvCR~~l~~ 258 (409)
.-.-||-+..++.. .+.++.|.||.-+--.....+.|-|+|+||..|.+.-|+.+- +||+|+.+|..
T Consensus 3467 EE~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3467 EEHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred hhhcccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 33445555444332 345689999987766566788899999999999988775532 69999988743
No 61
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.08 E-value=0.0037 Score=45.60 Aligned_cols=40 Identities=30% Similarity=0.791 Sum_probs=27.2
Q ss_pred ccccccccccCCCceeecc--cc---eeChhhhHHHhhc--CCCCCCC
Q 039088 212 CAVCKEAFELGSEAREMPC--KH---IYHSDCILPWLSL--RNSCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC--~H---~FH~~CI~~WL~~--~~sCPvC 252 (409)
|-||++.-.... ..+.|| +- ..|..|+..|+.. ..+|++|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 779999766544 566775 43 7899999999975 4579988
No 62
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.01 E-value=0.0042 Score=65.57 Aligned_cols=50 Identities=30% Similarity=0.657 Sum_probs=40.3
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhc-----CCCCCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL-----RNSCPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~-----~~sCPvCR~~l~~~~ 260 (409)
.+.+|-+|.+.-+ ......|.|.||..||..++.. +-+||+|...|..+.
T Consensus 535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 3478999988655 5677789999999999988754 238999999887763
No 63
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.98 E-value=0.0026 Score=59.61 Aligned_cols=44 Identities=25% Similarity=0.595 Sum_probs=39.4
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHEL 256 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l 256 (409)
..|.||.++|+ .++.+.|+|.||..|...-++....|-+|.+..
T Consensus 197 F~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 197 FLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred eeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 68999999998 567788999999999999999999999997754
No 64
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.72 E-value=0.0024 Score=63.94 Aligned_cols=49 Identities=20% Similarity=0.524 Sum_probs=39.3
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
.....|.+|..-|-+ ...+.-|-|.||+.||.+.|...++||+|...|-
T Consensus 13 n~~itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeec--chhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 344789999887763 3334449999999999999999999999987653
No 65
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.66 E-value=0.0072 Score=61.12 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=41.8
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
++..|+|| |...-.++..||+|.=|..||.+.|...+.|=.|+..+...
T Consensus 421 Ed~lCpIC---yA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 421 EDNLCPIC---YAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV 469 (489)
T ss_pred ccccCcce---ecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence 46789999 44445778889999999999999999999999999987653
No 66
>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=95.55 E-value=0.0039 Score=55.22 Aligned_cols=34 Identities=15% Similarity=0.463 Sum_probs=29.7
Q ss_pred ccccccccccccCCCceeeccc------ceeChhhhHHHh
Q 039088 210 SHCAVCKEAFELGSEAREMPCK------HIYHSDCILPWL 243 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~------H~FH~~CI~~WL 243 (409)
.+|.||++.+...+.++.++|+ |+||.+|+.+|-
T Consensus 27 ~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 27 VECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred eeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 6899999999886677888885 889999999994
No 67
>PHA02862 5L protein; Provisional
Probab=95.45 E-value=0.008 Score=53.83 Aligned_cols=47 Identities=17% Similarity=0.651 Sum_probs=35.0
Q ss_pred CccccccccccccCCCceeeccc-----ceeChhhhHHHhhcC--CCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCK-----HIYHSDCILPWLSLR--NSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~-----H~FH~~CI~~WL~~~--~sCPvCR~~l~~~ 259 (409)
...|-||+++-++ . .-||. ..-|..|+..|++.. .+|++|+.+..-.
T Consensus 2 ~diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 2 SDICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CCEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 3679999987442 2 35654 468999999999653 4899999987543
No 68
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.38 E-value=0.013 Score=57.53 Aligned_cols=50 Identities=26% Similarity=0.543 Sum_probs=37.2
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcC--CCCCCCCccCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLR--NSCPVCRHELPA 258 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~--~sCPvCR~~l~~ 258 (409)
..+.+|++|-+.-.. .-...+|+|+||..||..=+... -+||.|-.++..
T Consensus 237 t~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred cCCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence 456899999886442 23344599999999999876543 599999877653
No 69
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=95.18 E-value=0.0094 Score=49.56 Aligned_cols=32 Identities=31% Similarity=0.680 Sum_probs=27.3
Q ss_pred cCccccccccccccCCCceeecccceeChhhhH
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCIL 240 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~ 240 (409)
.+..|+||...+.. ......||+|+||..|+.
T Consensus 77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 35789999998876 667888999999999985
No 70
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.08 E-value=0.012 Score=59.69 Aligned_cols=43 Identities=33% Similarity=0.715 Sum_probs=32.3
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
.+.|.||+++.+ .+..+||||+-| |+.-- +.-.+||+||+.+.
T Consensus 305 p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 305 PDLCVVCLDEPK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred CCceEEecCCcc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 478999999877 488999999966 55432 22346999998763
No 71
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.05 E-value=0.016 Score=52.75 Aligned_cols=49 Identities=24% Similarity=0.748 Sum_probs=35.6
Q ss_pred ccCccccccccccccCCCceeecc--cc---eeChhhhHHHhhcCC--CCCCCCccCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPC--KH---IYHSDCILPWLSLRN--SCPVCRHELPAD 259 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC--~H---~FH~~CI~~WL~~~~--sCPvCR~~l~~~ 259 (409)
..+..|-||.++.. . ..-|| +. .-|..|+..|+..+. +|++|+++..-.
T Consensus 6 ~~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 34578999988743 2 23475 44 469999999997644 899999977544
No 72
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.03 E-value=0.0015 Score=66.54 Aligned_cols=51 Identities=29% Similarity=0.711 Sum_probs=44.2
Q ss_pred CccccccccccccC-CCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELG-SEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g-~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
...|+||.+.|+.. +.+..+-|+|.||.+||.+||.....||.|+.+|+..
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN 247 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence 36899999988865 5667778999999999999999999999999988654
No 73
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.0063 Score=62.62 Aligned_cols=47 Identities=19% Similarity=0.523 Sum_probs=38.0
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhcCC--------CCCCCCc
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN--------SCPVCRH 254 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~--------sCPvCR~ 254 (409)
...+|.||.++..-....+.|||.|+||+.|+...+..+- .||-|.-
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 3478999999877657889999999999999999985522 5877654
No 74
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.71 E-value=0.033 Score=54.01 Aligned_cols=53 Identities=15% Similarity=0.319 Sum_probs=45.1
Q ss_pred CccccccccccccCCCceee-cccceeChhhhHHHhhcCCCCCCCCccCCCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREM-PCKHIYHSDCILPWLSLRNSCPVCRHELPADNN 261 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~l-PC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~ 261 (409)
...|+||.+.+........| ||+|+|+.+|+.+.+.....||+|-.++...+.
T Consensus 221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdi 274 (303)
T KOG3039|consen 221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDI 274 (303)
T ss_pred ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccce
Confidence 36899999999877665555 599999999999999999999999888866653
No 75
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.59 E-value=0.014 Score=57.89 Aligned_cols=45 Identities=22% Similarity=0.525 Sum_probs=39.7
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
..|-||...|. ..+++.|+|.||..|...-++....|++|-+...
T Consensus 242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred ccccccccccc---cchhhcCCceeehhhhccccccCCcceecccccc
Confidence 56999999998 5677889999999999999999899999987653
No 76
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=94.33 E-value=0.021 Score=63.39 Aligned_cols=46 Identities=26% Similarity=0.801 Sum_probs=36.2
Q ss_pred CccccccccccccCCCceeec-ccceeChhhhHHHhhcCC-------CCCCCCc
Q 039088 209 ESHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLSLRN-------SCPVCRH 254 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~~~~-------sCPvCR~ 254 (409)
..+|.||++.+...+.+.... |-|+||..||.+|-+... .||.|..
T Consensus 191 ~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 191 KYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred ceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 479999999988766544433 899999999999986521 5999984
No 77
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=94.30 E-value=0.021 Score=40.93 Aligned_cols=41 Identities=32% Similarity=0.817 Sum_probs=24.0
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhhcCC--CCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN--SCPVC 252 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~--sCPvC 252 (409)
|.+|.+....|..-..-.|.-.+|..|+..+++.+. .||.|
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 778888776554433334888999999999998866 79988
No 78
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.05 E-value=0.031 Score=55.51 Aligned_cols=42 Identities=26% Similarity=0.681 Sum_probs=33.0
Q ss_pred ccccccccccccCCCceeec-ccceeChhhhHHHhh-cCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLS-LRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~-~~~sCPvCR~ 254 (409)
..|+.|..-+. .+.++| |+|.||..||..-|. ....||.|..
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 68999987665 445556 999999999987765 4569999955
No 79
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.81 E-value=0.045 Score=40.30 Aligned_cols=44 Identities=25% Similarity=0.577 Sum_probs=22.0
Q ss_pred ccccccccccCCCceeec--ccceeChhhhHHHhh-cCCCCCCCCccC
Q 039088 212 CAVCKEAFELGSEAREMP--CKHIYHSDCILPWLS-LRNSCPVCRHEL 256 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lP--C~H~FH~~CI~~WL~-~~~sCPvCR~~l 256 (409)
|++|.+++... ....+| |++..+..|...-++ ....||-||++.
T Consensus 1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CC-CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccC-CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 78999998432 234445 899999999888876 467999999864
No 80
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=93.76 E-value=0.093 Score=53.85 Aligned_cols=30 Identities=27% Similarity=0.847 Sum_probs=23.3
Q ss_pred ccceeChhhhHHHhhcC-------------CCCCCCCccCCCC
Q 039088 230 CKHIYHSDCILPWLSLR-------------NSCPVCRHELPAD 259 (409)
Q Consensus 230 C~H~FH~~CI~~WL~~~-------------~sCPvCR~~l~~~ 259 (409)
|.-.+|.+|+-+|+..+ -.||+||+.+..-
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil 353 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL 353 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence 67778999999998442 2699999987543
No 81
>PF04641 Rtf2: Rtf2 RING-finger
Probab=93.60 E-value=0.11 Score=51.01 Aligned_cols=54 Identities=19% Similarity=0.405 Sum_probs=40.9
Q ss_pred ccCccccccccccccCCCce-eecccceeChhhhHHHhhcCCCCCCCCccCCCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAR-EMPCKHIYHSDCILPWLSLRNSCPVCRHELPADNN 261 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~-~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~ 261 (409)
.....|+|+..+|......+ ..||||+|...+|..- .....||+|-.++...+.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~Di 165 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDI 165 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCE
Confidence 34579999999985444444 4479999999999986 335589999998875543
No 82
>PHA03096 p28-like protein; Provisional
Probab=93.52 E-value=0.03 Score=55.73 Aligned_cols=45 Identities=22% Similarity=0.421 Sum_probs=31.6
Q ss_pred ccccccccccccC----CCceeec-ccceeChhhhHHHhhcCC---CCCCCCc
Q 039088 210 SHCAVCKEAFELG----SEAREMP-CKHIYHSDCILPWLSLRN---SCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g----~~~~~lP-C~H~FH~~CI~~WL~~~~---sCPvCR~ 254 (409)
..|.||++..... ..-..|+ |.|.||..||..|-.... +||.|+.
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 6899999976542 2334566 999999999999985432 4444443
No 83
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.47 E-value=0.028 Score=54.29 Aligned_cols=47 Identities=19% Similarity=0.534 Sum_probs=35.9
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCC-CCCCCCccCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN-SCPVCRHELPADN 260 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~~ 260 (409)
.+|..|...-. ++....+.|.|+||..|...- +. .||+|++.|....
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~---~~~~C~lCkk~ir~i~ 51 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS---SPDVCPLCKKSIRIIQ 51 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccC---Cccccccccceeeeee
Confidence 46888876433 677788889999999998753 33 9999999875543
No 84
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.95 E-value=0.068 Score=52.84 Aligned_cols=47 Identities=26% Similarity=0.665 Sum_probs=39.2
Q ss_pred ccccccccccccCC---CceeecccceeChhhhHHHhhcCC-CCCCCCccC
Q 039088 210 SHCAVCKEAFELGS---EAREMPCKHIYHSDCILPWLSLRN-SCPVCRHEL 256 (409)
Q Consensus 210 ~~C~ICle~f~~g~---~~~~lPC~H~FH~~CI~~WL~~~~-sCPvCR~~l 256 (409)
..|-||-++|...+ .++.|.|+|.++..|+.+.+.... .||.||...
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 57999999998764 466677999999999998876644 899999975
No 85
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.82 E-value=0.054 Score=54.84 Aligned_cols=46 Identities=26% Similarity=0.700 Sum_probs=37.6
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHH--hhcCCCCCCCCccC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPW--LSLRNSCPVCRHEL 256 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~W--L~~~~sCPvCR~~l 256 (409)
+...|.||-+.+. ....+||+|..|-.|.... |..++.||+||.+.
T Consensus 60 en~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 60 ENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 3468999988766 6788999999999998654 55678999999875
No 86
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.33 E-value=0.03 Score=55.50 Aligned_cols=42 Identities=29% Similarity=0.703 Sum_probs=32.5
Q ss_pred CccccccccccccCCCceeecccce-eChhhhHHHhhcCCCCCCCCccCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHI-YHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~-FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
+..|+||++.-. ....|+|||. -|..|-+. -+.||+||+.|.
T Consensus 300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKR----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCc---ceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence 578999988654 6788999997 57777654 348999998764
No 87
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=92.22 E-value=0.11 Score=39.33 Aligned_cols=47 Identities=28% Similarity=0.711 Sum_probs=35.0
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADN 260 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~ 260 (409)
...|..|.. .+..-.++||+|+.+..|..-+ .-+-||+|.+++...+
T Consensus 7 ~~~~~~~~~---~~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGF---VGTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD 53 (55)
T ss_pred ceeEEEccc---cccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence 355666644 3446788999999999997743 6678999999886554
No 88
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.90 E-value=0.064 Score=59.71 Aligned_cols=44 Identities=32% Similarity=0.803 Sum_probs=34.0
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
..|..|--.++. ..+..-|+|.||.+|+. .....||-|+.++..
T Consensus 841 skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~~ 884 (933)
T KOG2114|consen 841 SKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELRG 884 (933)
T ss_pred eeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhhh
Confidence 589999776664 45566699999999998 445689999885543
No 89
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=91.78 E-value=0.099 Score=45.34 Aligned_cols=34 Identities=24% Similarity=0.579 Sum_probs=27.2
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeecc
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEIE 42 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi~ 42 (409)
....||..|...+.+. .-++.||.|+|..+.=+.
T Consensus 68 p~~~~C~~C~~~~~~e--~~~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 68 PAECWCLDCGQEVELE--ELDYRCPKCGSINLRIIG 101 (115)
T ss_pred ccEEEeccCCCeecch--hheeECCCCCCCceEEec
Confidence 3568999999999654 457889999999987554
No 90
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=91.70 E-value=0.12 Score=52.12 Aligned_cols=48 Identities=17% Similarity=0.369 Sum_probs=36.8
Q ss_pred cCccccccccccccCCCceeec-ccceeChhhhHHHhhcCCCCCCCCccCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLSLRNSCPVCRHELPA 258 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~~~~sCPvCR~~l~~ 258 (409)
....|+||+..... ...+. -|-+||..||...+..++.|||=..++..
T Consensus 299 ~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v 347 (357)
T KOG0826|consen 299 DREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASV 347 (357)
T ss_pred ccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcchH
Confidence 34789999887552 23333 59999999999999999999997665543
No 91
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=91.69 E-value=0.087 Score=52.20 Aligned_cols=45 Identities=31% Similarity=0.751 Sum_probs=38.4
Q ss_pred ccccccccccccC-CCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELG-SEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g-~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|+||.+.+-.. ..+..++|+|.-|..|.......+-+||+|.+
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 4599999965544 46788899999999999999888899999988
No 92
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=90.21 E-value=0.12 Score=51.82 Aligned_cols=42 Identities=26% Similarity=0.763 Sum_probs=29.2
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccC
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHEL 256 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l 256 (409)
-|--|-..+. -.-+.+||+|+||.+|... ..-+.||.|-..|
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 4555644433 3567789999999999864 3355899996544
No 93
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.00 E-value=0.19 Score=37.90 Aligned_cols=39 Identities=31% Similarity=0.691 Sum_probs=32.2
Q ss_pred CccccccccccccCCCceeec-ccceeChhhhHHHhhcCCCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLSLRNSCPV 251 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~~~~sCPv 251 (409)
...|.+|-+.|+.++.+++.| |+-.||..|..+ ...|-+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~ 44 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN 44 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence 367999999999889999998 999999999653 445544
No 94
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.36 E-value=0.2 Score=46.54 Aligned_cols=50 Identities=24% Similarity=0.686 Sum_probs=34.1
Q ss_pred ccccccccccccCC----CceeecccceeChhhhHHHhhc----CC-------CCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELGS----EAREMPCKHIYHSDCILPWLSL----RN-------SCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g~----~~~~lPC~H~FH~~CI~~WL~~----~~-------sCPvCR~~l~~~ 259 (409)
..|-||.----.|. ..-...|+.-||.-|+..||+. ++ .||.|-.++..+
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 57999975322222 2223459999999999999954 22 599998877543
No 95
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.11 E-value=0.14 Score=50.11 Aligned_cols=53 Identities=32% Similarity=0.653 Sum_probs=36.3
Q ss_pred cccCccccccccccccCCC-ceeecc-----cceeChhhhHHHhhcCC--------CCCCCCccCCC
Q 039088 206 VELESHCAVCKEAFELGSE-AREMPC-----KHIYHSDCILPWLSLRN--------SCPVCRHELPA 258 (409)
Q Consensus 206 ~~~~~~C~ICle~f~~g~~-~~~lPC-----~H~FH~~CI~~WL~~~~--------sCPvCR~~l~~ 258 (409)
.+.+..|-||+..=++... .-+-|| .|..|..||..|+..++ +||-|+.+...
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii 83 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII 83 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence 3445789999775443222 234465 58899999999995433 69999987533
No 96
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=89.10 E-value=0.26 Score=57.25 Aligned_cols=43 Identities=23% Similarity=0.622 Sum_probs=36.7
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|.||++.+.. .-.+.-|+|.+|..|+..|+..+..||+|+.
T Consensus 1154 ~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1154 FVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred cchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence 589999998873 2334559999999999999999999999984
No 97
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=89.03 E-value=0.2 Score=38.73 Aligned_cols=27 Identities=33% Similarity=0.758 Sum_probs=22.2
Q ss_pred cccCCcceeeccCCCCccCCCCCCC-ceeecc
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDGG-FVEEIE 42 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~G-FiEEi~ 42 (409)
|+.|.|.+ ..+.-+||.|++. |.||-.
T Consensus 7 C~~Ck~l~----~~d~e~CP~Cgs~~~te~W~ 34 (64)
T COG2093 7 CKNCKRLT----PEDTEICPVCGSTDLTEEWF 34 (64)
T ss_pred HhhccccC----CCCCccCCCCCCcccchhhc
Confidence 99999988 3456789999998 888753
No 98
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=88.70 E-value=0.14 Score=56.68 Aligned_cols=50 Identities=20% Similarity=0.511 Sum_probs=40.4
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCC--CCCCCCccCCCCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN--SCPVCRHELPADNNSN 263 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~--sCPvCR~~l~~~~~~~ 263 (409)
..|.||++ .+.....+|+|.||..|+.+-+.... .||+||..+......+
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 68999999 35778888999999999999886643 6999999876654433
No 99
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.51 E-value=0.65 Score=33.41 Aligned_cols=34 Identities=29% Similarity=0.512 Sum_probs=27.2
Q ss_pred CceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 8 SSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
..|-|-.|...+.+......+.||+|++-++-..
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 4689999999988774444899999999888543
No 100
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.77 E-value=0.37 Score=52.06 Aligned_cols=48 Identities=31% Similarity=0.819 Sum_probs=40.1
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCCCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADNNS 262 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~~ 262 (409)
....|.||+++. ..+..+|. |..|+.+|+..+..||+|+..+..+...
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~ 525 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFL 525 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccccc
Confidence 347899999887 56777888 9999999999999999999887666443
No 101
>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=86.51 E-value=0.25 Score=36.31 Aligned_cols=44 Identities=30% Similarity=0.690 Sum_probs=25.6
Q ss_pred cccccccccccCCCceeecc-cceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 211 HCAVCKEAFELGSEAREMPC-KHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC-~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
.|--|+-+.+ ....| .|..|..|+...|.....||+|.++||+.
T Consensus 4 nCKsCWf~~k-----~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFANK-----GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S--S-----SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred cChhhhhcCC-----CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 4666664432 23347 59999999999999999999999999864
No 102
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=85.15 E-value=0.71 Score=39.84 Aligned_cols=34 Identities=26% Similarity=0.916 Sum_probs=24.7
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
....||..|...+.+. ......||.|++.-++=+
T Consensus 68 p~~~~C~~Cg~~~~~~-~~~~~~CP~Cgs~~~~i~ 101 (114)
T PRK03681 68 EAECWCETCQQYVTLL-TQRVRRCPQCHGDMLRIV 101 (114)
T ss_pred CcEEEcccCCCeeecC-CccCCcCcCcCCCCcEEc
Confidence 4689999999887553 222366999998876644
No 103
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=84.91 E-value=0.46 Score=48.23 Aligned_cols=53 Identities=25% Similarity=0.533 Sum_probs=36.5
Q ss_pred cCccccccccccccCCC-ceeecccceeChhhhHHHhh-cCCCCCCCCccCCCCC
Q 039088 208 LESHCAVCKEAFELGSE-AREMPCKHIYHSDCILPWLS-LRNSCPVCRHELPADN 260 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~-~~~lPC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~~~ 260 (409)
+++-|+.|+|++...++ -.-.||+-..|.-|...--+ .+..||.||+....++
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den 67 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN 67 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence 44669999999887664 34456888777777544322 3458999998765544
No 104
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=84.40 E-value=0.8 Score=39.57 Aligned_cols=33 Identities=27% Similarity=0.474 Sum_probs=25.3
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
....||..|...+.+. .....||.|++..++=+
T Consensus 68 p~~~~C~~Cg~~~~~~--~~~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 68 PVECECEDCSEEVSPE--IDLYRCPKCHGIMLQVR 100 (115)
T ss_pred CcEEEcccCCCEEecC--CcCccCcCCcCCCcEEe
Confidence 4678999999887553 34678999999876544
No 105
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=84.27 E-value=0.61 Score=34.54 Aligned_cols=35 Identities=26% Similarity=0.571 Sum_probs=28.0
Q ss_pred CCCceecccCCcceeeccCCCCccCCCCCCCceee
Q 039088 6 SSSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 6 ~~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEE 40 (409)
....|-|-.|.+.|.+......+.||+|++--|=.
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEEEe
Confidence 34679999999999754467899999999876644
No 106
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=84.14 E-value=0.6 Score=29.55 Aligned_cols=23 Identities=26% Similarity=0.722 Sum_probs=17.8
Q ss_pred cccCCcceeeccCCCCccCCCCC
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCD 34 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~ 34 (409)
|..|.+.|........+.||.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 78999988554235689999997
No 107
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.12 E-value=0.59 Score=44.56 Aligned_cols=39 Identities=28% Similarity=0.717 Sum_probs=28.7
Q ss_pred ccccccccccCCCceeecccce-eChhhhHHHhhcCCCCCCCCccCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHI-YHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~-FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
|-+|.+. ...+..+||.|. +|..|-.. -.+||+|+....
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 8888554 457899999876 88888654 446999987543
No 108
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=83.90 E-value=0.53 Score=46.35 Aligned_cols=51 Identities=24% Similarity=0.594 Sum_probs=37.6
Q ss_pred CccccccccccccCCC-ceeeccc-----ceeChhhhHHHhhc--CCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSE-AREMPCK-----HIYHSDCILPWLSL--RNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~-~~~lPC~-----H~FH~~CI~~WL~~--~~sCPvCR~~l~~~ 259 (409)
+..|-||.++...... ..+.||. +..|..|+..|+.. ...|.+|.......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 4689999997654322 5677764 55799999999974 45899998866544
No 109
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=83.43 E-value=0.59 Score=51.80 Aligned_cols=40 Identities=33% Similarity=0.852 Sum_probs=28.8
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhcCCCCCC
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPV 251 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPv 251 (409)
.|+||--.+. +.......|+|+.|..|...|++....||.
T Consensus 1030 ~C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 3444433222 334455569999999999999999999984
No 110
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.29 E-value=0.34 Score=52.68 Aligned_cols=42 Identities=24% Similarity=0.623 Sum_probs=32.2
Q ss_pred ccccccccccccCC-CceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGS-EAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~-~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|.||+..|.... ..+.|-|+|..|..|+... -+.+|| |++
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 57999988776433 5667779999999999865 355898 655
No 111
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.28 E-value=0.46 Score=53.43 Aligned_cols=36 Identities=25% Similarity=0.708 Sum_probs=28.6
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHh
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWL 243 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL 243 (409)
+..+.|.+|...+-. ..-.+.||+|.||++||.+-.
T Consensus 815 ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred cCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence 456889999887654 356677899999999998764
No 112
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.14 E-value=0.9 Score=39.40 Aligned_cols=34 Identities=21% Similarity=0.277 Sum_probs=24.2
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
....||..|.....+. ......||.|++..++=+
T Consensus 69 p~~~~C~~Cg~~~~~~-~~~~~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 69 KVELECKDCSHVFKPN-ALDYGVCEKCHSKNVIIT 102 (117)
T ss_pred CCEEEhhhCCCccccC-CccCCcCcCCCCCceEEe
Confidence 4679999999777443 222345999999887644
No 113
>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=82.53 E-value=0.81 Score=45.54 Aligned_cols=50 Identities=28% Similarity=0.534 Sum_probs=36.4
Q ss_pred cccccccccccCCCcee--ecccceeChhhhHHHhhcCC-CCCCCCccCCCCC
Q 039088 211 HCAVCKEAFELGSEARE--MPCKHIYHSDCILPWLSLRN-SCPVCRHELPADN 260 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~--lPC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~~ 260 (409)
.|++|+-..-..-.++. -+|+|..|..|++..+.... .||.|-..|-...
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcc
Confidence 59999875433333333 36999999999999987765 8999987765443
No 114
>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=82.48 E-value=1.1 Score=41.00 Aligned_cols=32 Identities=25% Similarity=0.578 Sum_probs=21.1
Q ss_pred CccccccccccccCCCceeecc------------cc-eeChhhhHHHh
Q 039088 209 ESHCAVCKEAFELGSEAREMPC------------KH-IYHSDCILPWL 243 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC------------~H-~FH~~CI~~WL 243 (409)
+..|+||||-- ..++.|-| .- .-|..|+++.-
T Consensus 2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 46899998853 34555544 22 24788999874
No 115
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=82.31 E-value=1.1 Score=38.60 Aligned_cols=33 Identities=27% Similarity=0.811 Sum_probs=24.7
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
...+||..|.....+. .....||.|++.-++=+
T Consensus 68 p~~~~C~~Cg~~~~~~--~~~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 68 PAQAWCWDCSQVVEIH--QHDAQCPHCHGERLRVD 100 (113)
T ss_pred CcEEEcccCCCEEecC--CcCccCcCCCCCCcEEc
Confidence 4689999999877553 34567999998766544
No 116
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=81.98 E-value=0.83 Score=51.03 Aligned_cols=50 Identities=22% Similarity=0.646 Sum_probs=36.7
Q ss_pred cCccccccccccccCCCceeecccc-----eeChhhhHHHhhcC--CCCCCCCccCCC
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKH-----IYHSDCILPWLSLR--NSCPVCRHELPA 258 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H-----~FH~~CI~~WL~~~--~sCPvCR~~l~~ 258 (409)
++..|-||..+=..+ .+.--||+. ..|.+|+..|+.-. ..|-+|+.++.-
T Consensus 11 d~~~CRICr~e~~~d-~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 11 DKRSCRICRTEDIRD-DPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred cchhceeecCCCCCC-CcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 347899999874443 344557765 38999999999653 479999987643
No 117
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=81.76 E-value=0.99 Score=45.39 Aligned_cols=41 Identities=29% Similarity=0.703 Sum_probs=33.3
Q ss_pred ccccccccccccCCCceeecc--cceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 210 SHCAVCKEAFELGSEAREMPC--KHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC--~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
.+|+||.+.+.. -++.| +|+-|..|-. +.++.||.||.++.
T Consensus 49 leCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 689999998773 34456 7999999976 46889999999886
No 118
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=80.88 E-value=1.1 Score=39.98 Aligned_cols=50 Identities=24% Similarity=0.505 Sum_probs=36.2
Q ss_pred CccccccccccccCCCceeec---ccceeChhhhHHHhh---cCCCCCCCCccCCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMP---CKHIYHSDCILPWLS---LRNSCPVCRHELPADN 260 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP---C~H~FH~~CI~~WL~---~~~sCPvCR~~l~~~~ 260 (409)
-.+|.||.|.-.+.. -.-| |+-..|..|-...++ .+..||+|+..+....
T Consensus 80 lYeCnIC~etS~ee~--FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 80 LYECNICKETSAEER--FLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred ceeccCcccccchhh--cCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 379999999765322 2223 898889888766654 4679999999886654
No 119
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.70 E-value=1.2 Score=46.31 Aligned_cols=51 Identities=20% Similarity=0.550 Sum_probs=33.9
Q ss_pred CccccccccccccC-CCceeecccceeChhhhHHHhhcCC------CCC--CCCccCCCC
Q 039088 209 ESHCAVCKEAFELG-SEAREMPCKHIYHSDCILPWLSLRN------SCP--VCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g-~~~~~lPC~H~FH~~CI~~WL~~~~------sCP--vCR~~l~~~ 259 (409)
...|.||..++... +....+-|+|.||.+|+...++.+. .|| -|...|+.+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~ 205 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE 205 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH
Confidence 46899999444333 3344556999999999999887542 464 355554443
No 120
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.63 E-value=1.5 Score=45.48 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=41.1
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcCC---CCCCCCc
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN---SCPVCRH 254 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~---sCPvCR~ 254 (409)
..-..|+|=.+.-.+...+..|.|||+..++-|.+..+... .||.|-.
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 44578999999888888999999999999999999876644 7999944
No 121
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=79.87 E-value=0.95 Score=38.91 Aligned_cols=33 Identities=27% Similarity=0.408 Sum_probs=22.3
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
....||..|.....+. .....||.|++..++=+
T Consensus 68 p~~~~C~~Cg~~~~~~--~~~~~CP~Cgs~~~~i~ 100 (113)
T PF01155_consen 68 PARARCRDCGHEFEPD--EFDFSCPRCGSPDVEII 100 (113)
T ss_dssp --EEEETTTS-EEECH--HCCHH-SSSSSS-EEEE
T ss_pred CCcEECCCCCCEEecC--CCCCCCcCCcCCCcEEc
Confidence 3578999999998765 34588999999977544
No 122
>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=79.70 E-value=1 Score=28.93 Aligned_cols=23 Identities=30% Similarity=0.722 Sum_probs=18.9
Q ss_pred cccCCcceeeccCCCCccCCCCCCCce
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDGGFV 38 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~GFi 38 (409)
|-.|...| +....+||+|+=-|.
T Consensus 3 CP~C~~~V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEV----PESAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCc----hhhcCcCCCCCCCCc
Confidence 78899999 345789999998774
No 123
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.69 E-value=1.4 Score=39.14 Aligned_cols=34 Identities=18% Similarity=0.376 Sum_probs=23.9
Q ss_pred CCceecccCCcceeecc-------------------CCCCccCCCCCCCceee
Q 039088 7 SSSYWCYRCSRFVRVFS-------------------RDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~-------------------~~~~~~CP~C~~GFiEE 40 (409)
...|||..|.....+.. ....+.||.|++.-++=
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i 120 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEI 120 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEE
Confidence 36899999997765430 02457799999876653
No 124
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=78.76 E-value=1.7 Score=29.31 Aligned_cols=27 Identities=30% Similarity=0.748 Sum_probs=21.3
Q ss_pred eecccCCcceeeccCCCCccCCCCCCCc
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
|-|-.|...|.+. ..+.+.||.|+.--
T Consensus 1 Y~C~~Cg~~~~~~-~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELK-PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BS-TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcC-CCCcEECCcCCCeE
Confidence 7899999999887 56789999998654
No 125
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.66 E-value=1.2 Score=27.74 Aligned_cols=23 Identities=30% Similarity=0.882 Sum_probs=18.2
Q ss_pred ecccCCcceeeccCCCCccCCCCCCCc
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
+|..|-..| .....+||.|+..|
T Consensus 1 ~Cp~CG~~~----~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEI----EDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCC----CCcCcchhhhCCcC
Confidence 689999988 34678999998643
No 126
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=75.99 E-value=2.4 Score=30.62 Aligned_cols=31 Identities=29% Similarity=0.598 Sum_probs=26.2
Q ss_pred ceecccCCcceeeccCCCCccCCCCCCCceee
Q 039088 9 SYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 9 ~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEE 40 (409)
.|-|-.|...|.+. ..+.+.||.|+.--|=.
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~rIlyK 32 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGYRILYK 32 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCceEEEE
Confidence 48999999999887 56889999999876643
No 127
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=74.18 E-value=1.4 Score=46.09 Aligned_cols=34 Identities=29% Similarity=0.586 Sum_probs=28.7
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhh
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLS 244 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~ 244 (409)
++..|+||-.-|+ ++++|||+|..|..|...-+.
T Consensus 3 eelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFYR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhcc---CceEeecccHHHHHHHHhhcc
Confidence 4578999999887 789999999999999875443
No 128
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.14 E-value=2 Score=37.56 Aligned_cols=34 Identities=21% Similarity=0.335 Sum_probs=22.8
Q ss_pred CCceecccCCcceeecc-CC----CCccCCCCCCCceeec
Q 039088 7 SSSYWCYRCSRFVRVFS-RD----DVVSCPDCDGGFVEEI 41 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~-~~----~~~~CP~C~~GFiEEi 41 (409)
....|| .|.....+.. .. ....||.|++.-++=+
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 467999 9998764420 10 1257999998887644
No 129
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=72.52 E-value=3.1 Score=28.55 Aligned_cols=28 Identities=32% Similarity=0.910 Sum_probs=21.5
Q ss_pred CceecccCCcceeecc---CCCCccCCCCCC
Q 039088 8 SSYWCYRCSRFVRVFS---RDDVVSCPDCDG 35 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~---~~~~~~CP~C~~ 35 (409)
-.|-|..|...+.+.. ....+.||.|++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4689999999766542 245788999998
No 130
>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=71.02 E-value=2 Score=41.85 Aligned_cols=48 Identities=29% Similarity=0.644 Sum_probs=36.7
Q ss_pred CccccccccccccCCCceee--c-ccceeChhhhHHHhhcCC-CCC--CCCccC
Q 039088 209 ESHCAVCKEAFELGSEAREM--P-CKHIYHSDCILPWLSLRN-SCP--VCRHEL 256 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~l--P-C~H~FH~~CI~~WL~~~~-sCP--vCR~~l 256 (409)
+..|+||..+--..-.++.| | |-|..|..|++.-+.... .|| -|-+-|
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 46899999875444444444 5 999999999999997765 899 786644
No 131
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=70.47 E-value=2.5 Score=39.62 Aligned_cols=32 Identities=31% Similarity=0.702 Sum_probs=23.6
Q ss_pred CceecccCCcceeeccCCCCccCCCCCCCceeecccCCC
Q 039088 8 SSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEIENTPR 46 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi~~~~~ 46 (409)
.-|||-.|+-.+ -.-.|+-|+++| ||+.-.+|
T Consensus 13 ~iyWCe~cNlPl------~~~~c~~cg~~~-~~l~LTpP 44 (202)
T COG5270 13 PIYWCEKCNLPL------LGRRCSVCGSKV-EELRLTPP 44 (202)
T ss_pred ceeehhhCCCcc------ccccccccCCcc-eEEEeCCC
Confidence 569999999877 246899999665 56654444
No 132
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=69.88 E-value=2.2 Score=47.72 Aligned_cols=48 Identities=10% Similarity=0.217 Sum_probs=34.4
Q ss_pred ccccccccccccC-CCceeec---ccceeChhhhHHHhhc------CCCCCCCCccCC
Q 039088 210 SHCAVCKEAFELG-SEAREMP---CKHIYHSDCILPWLSL------RNSCPVCRHELP 257 (409)
Q Consensus 210 ~~C~ICle~f~~g-~~~~~lP---C~H~FH~~CI~~WL~~------~~sCPvCR~~l~ 257 (409)
..|.||.-++... +..-.+| |.|.||..||..|+.+ +-.|+.|..-|.
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~ 154 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG 154 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence 5677777766652 2344555 9999999999999854 336888887653
No 133
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=69.82 E-value=1.2 Score=49.09 Aligned_cols=48 Identities=19% Similarity=0.593 Sum_probs=37.6
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCC---CCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN---SCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~~ 259 (409)
..+|.||+..+... ..+.|-|.|+..|+..-+...+ .||+|+..+...
T Consensus 21 ~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 36899999988743 5667999999999988775544 799999665443
No 134
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.31 E-value=2 Score=42.95 Aligned_cols=31 Identities=19% Similarity=0.671 Sum_probs=24.0
Q ss_pred ccceeChhhhHHHhh-------------cCCCCCCCCccCCCCC
Q 039088 230 CKHIYHSDCILPWLS-------------LRNSCPVCRHELPADN 260 (409)
Q Consensus 230 C~H~FH~~CI~~WL~-------------~~~sCPvCR~~l~~~~ 260 (409)
|...+|..|+..|+. .+-+||+||+.+...+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 778889999999863 3447999999876543
No 135
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.87 E-value=2.6 Score=26.81 Aligned_cols=23 Identities=26% Similarity=0.785 Sum_probs=17.7
Q ss_pred eecccCCcceeeccCCCCccCCCCCCC
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCDGG 36 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~~G 36 (409)
..|..|...| ..++-+||.|+..
T Consensus 3 ~~Cp~Cg~~~----~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEI----DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcC----CcccccChhhCCC
Confidence 4689999966 3468899999864
No 136
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=68.46 E-value=3.3 Score=46.17 Aligned_cols=41 Identities=22% Similarity=0.535 Sum_probs=29.8
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPV 251 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPv 251 (409)
..|.+|-..+. |..+..--|+|.-|..|+.+|+..+..||.
T Consensus 780 ~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred cCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 46888866543 122222239999999999999999988876
No 137
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=68.05 E-value=2.2 Score=40.75 Aligned_cols=43 Identities=30% Similarity=0.699 Sum_probs=34.5
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|.+|.+-.-. .++.-.|+-.||..|+...+.....||.|..
T Consensus 182 k~Cn~Ch~LvIq--g~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 182 KNCNLCHCLVIQ--GIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHhHhHHHhhe--eeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 689999886542 3344458999999999999999999999943
No 138
>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 KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=65.93 E-value=2 Score=46.82 Aligned_cols=42 Identities=26% Similarity=0.714 Sum_probs=27.2
Q ss_pred Cccccccccc-----cccCCCceeecccceeChhhhHHHhhcCCCCCCCC
Q 039088 209 ESHCAVCKEA-----FELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 209 ~~~C~ICle~-----f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
...|.||... |+.....+...|+++||..|+.. ....||-|-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~ 557 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCE 557 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence 3678888432 33223344445999999999764 344599993
No 140
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.59 E-value=4.8 Score=42.51 Aligned_cols=36 Identities=22% Similarity=0.589 Sum_probs=30.7
Q ss_pred cCccccccccccccCCCceeecccceeChhhhHHHhhc
Q 039088 208 LESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL 245 (409)
Q Consensus 208 ~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~ 245 (409)
...+|-||.+.+.. ....+.|+|.|+..|+...|..
T Consensus 69 ~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 69 GDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred ccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 45789999998875 5777889999999999999865
No 141
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.46 E-value=3.5 Score=42.86 Aligned_cols=44 Identities=25% Similarity=0.507 Sum_probs=33.3
Q ss_pred CccccccccccccCCC--ceeecccceeChhhhHHHhhcCCCCCCC
Q 039088 209 ESHCAVCKEAFELGSE--AREMPCKHIYHSDCILPWLSLRNSCPVC 252 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~--~~~lPC~H~FH~~CI~~WL~~~~sCPvC 252 (409)
-.+|++|.-.++.... ..+..|+|.||..|...|......|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 3689999887765543 3333499999999999998887777555
No 142
>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=63.35 E-value=4.9 Score=26.49 Aligned_cols=38 Identities=24% Similarity=0.615 Sum_probs=25.1
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
.|..|.+.+...+.. ...=+..||..|. .|..|...|.
T Consensus 1 ~C~~C~~~i~~~~~~-~~~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELV-LRALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEE-EEeCCccccccCC--------CCcccCCcCc
Confidence 378888877654222 2224678998886 4888887663
No 143
>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=62.84 E-value=5 Score=29.55 Aligned_cols=42 Identities=24% Similarity=0.619 Sum_probs=20.1
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcC---C--CCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLR---N--SCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~---~--sCPvCR~ 254 (409)
..|+|....+.. .++...|.|.-+.+ +..||+.. . .||+|.+
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence 468888777663 55556699985433 34555432 2 6999976
No 144
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=62.11 E-value=5.1 Score=37.24 Aligned_cols=35 Identities=17% Similarity=0.393 Sum_probs=26.7
Q ss_pred CCCCceecccCCcceeec-cCCCCccCCCCCCCcee
Q 039088 5 VSSSSYWCYRCSRFVRVF-SRDDVVSCPDCDGGFVE 39 (409)
Q Consensus 5 ~~~~~ywCh~C~r~V~~~-~~~~~~~CP~C~~GFiE 39 (409)
....-|.|-.|...+... ....+..||.|++-.+|
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 345679999998877542 25578999999988776
No 145
>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=58.64 E-value=17 Score=27.78 Aligned_cols=48 Identities=27% Similarity=0.544 Sum_probs=35.0
Q ss_pred ccccccccccccCC-CceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELGS-EAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g~-~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
..|-.|-.++.... .+.+..=...||.+|....| +..||.|-.+|...
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~R 54 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRR 54 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccC
Confidence 46778888777655 45553334469999999876 78999998887654
No 146
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.97 E-value=6.5 Score=26.66 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=22.1
Q ss_pred eecccCCcceeeccCCCCccCCCCCCCc
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
+-|..|....-+...++..+|+.|+.-|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 4588999997663467899999998755
No 147
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=57.06 E-value=8.5 Score=27.78 Aligned_cols=30 Identities=23% Similarity=0.621 Sum_probs=20.9
Q ss_pred ecccCCcceeeccCC--CCccCCCCCCCceeecc
Q 039088 11 WCYRCSRFVRVFSRD--DVVSCPDCDGGFVEEIE 42 (409)
Q Consensus 11 wCh~C~r~V~~~~~~--~~~~CP~C~~GFiEEi~ 42 (409)
||-.|...+.+.... ..++||.|+ |++.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 799999987554221 368999998 565553
No 148
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=57.03 E-value=12 Score=27.14 Aligned_cols=34 Identities=26% Similarity=0.758 Sum_probs=23.6
Q ss_pred CceecccCCcceeecc---CCCCccCCCCCCCceeec
Q 039088 8 SSYWCYRCSRFVRVFS---RDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~---~~~~~~CP~C~~GFiEEi 41 (409)
-.|.|-.|.....++. ....+.||.|++.=++.+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 3689999999655442 224678999999555554
No 149
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=55.95 E-value=7.1 Score=36.93 Aligned_cols=40 Identities=30% Similarity=0.939 Sum_probs=27.8
Q ss_pred Cccccccccc-----cccCCCceeec-ccceeChhhhHHHhhcCCCCCCCCc
Q 039088 209 ESHCAVCKEA-----FELGSEAREMP-CKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 209 ~~~C~ICle~-----f~~g~~~~~lP-C~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
...|-||.+. |+. +.+...+ |+-+||..|.. +..||-|-.
T Consensus 152 GfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 3678888753 333 2344444 99999999976 267999943
No 150
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=54.35 E-value=5.2 Score=39.59 Aligned_cols=47 Identities=23% Similarity=0.575 Sum_probs=32.9
Q ss_pred ccccccccccccCCC-ceeec---ccceeChhhhHHHhh-c--------CCCCCCCCccC
Q 039088 210 SHCAVCKEAFELGSE-AREMP---CKHIYHSDCILPWLS-L--------RNSCPVCRHEL 256 (409)
Q Consensus 210 ~~C~ICle~f~~g~~-~~~lP---C~H~FH~~CI~~WL~-~--------~~sCPvCR~~l 256 (409)
.+|-+|.+++...+. ....+ |.-.+|..|+..-+. . ...||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 589999999943332 22222 888999999998432 2 23699999854
No 151
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=53.93 E-value=8.4 Score=30.88 Aligned_cols=31 Identities=16% Similarity=0.482 Sum_probs=15.3
Q ss_pred eecccCCcceeeccCCCCccCCCCCCCceeeccc
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEIEN 43 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi~~ 43 (409)
++||.|-..... ..-.+||.|+..=|..+.-
T Consensus 10 lrC~aCf~~t~~---~~k~FCp~CGn~TL~rvsv 40 (73)
T PF08772_consen 10 LRCHACFKITKD---MTKQFCPKCGNATLKRVSV 40 (73)
T ss_dssp EE-SSS--EES----SS--S-SSS--S--EEEE-
T ss_pred EEccccccCcCC---CCceeCcccCCCcceEEEE
Confidence 579999988743 3579999999999888853
No 152
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.93 E-value=6.3 Score=39.39 Aligned_cols=38 Identities=18% Similarity=0.331 Sum_probs=28.9
Q ss_pred CccccccccccccCCCceeec--ccceeChhhhHHHhhcCC
Q 039088 209 ESHCAVCKEAFELGSEAREMP--CKHIYHSDCILPWLSLRN 247 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP--C~H~FH~~CI~~WL~~~~ 247 (409)
...|.+|.|.+++.. -+..| =.|.||..|-+.-++.+.
T Consensus 268 pLcCTLC~ERLEDTH-FVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTH-FVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred ceeehhhhhhhccCc-eeecCCCcccceecccCHHHHHhhc
Confidence 378999999998533 33333 389999999999998754
No 153
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.65 E-value=5.4 Score=44.72 Aligned_cols=45 Identities=22% Similarity=0.492 Sum_probs=32.7
Q ss_pred CccccccccccccC----CCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 209 ESHCAVCKEAFELG----SEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 209 ~~~C~ICle~f~~g----~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
+..|.-|.+..... +.++.+-|+|+||..|+.--..+.+ |-.|-.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~ 832 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESG 832 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhc
Confidence 45899998865422 4677888999999999987665554 666533
No 154
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=53.28 E-value=6.8 Score=41.15 Aligned_cols=22 Identities=45% Similarity=0.922 Sum_probs=18.8
Q ss_pred ccCCcceeeccCCCCccCCCCCCCcee
Q 039088 13 YRCSRFVRVFSRDDVVSCPDCDGGFVE 39 (409)
Q Consensus 13 h~C~r~V~~~~~~~~~~CP~C~~GFiE 39 (409)
|.|.|.|++ |+.||.|+.-|--
T Consensus 286 HrC~RIV~v-----EYrCPEC~KVFsC 307 (500)
T KOG3993|consen 286 HRCPRIVHV-----EYRCPECDKVFSC 307 (500)
T ss_pred ccCCeeEEe-----eecCCcccccccC
Confidence 899999977 4999999998843
No 155
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=52.95 E-value=8.5 Score=38.98 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=20.7
Q ss_pred CCCCCceecccCCcceeeccCCCCccCCCCCCCc
Q 039088 4 IVSSSSYWCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 4 ~~~~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
.++.+.-+||.|.-.- .+++||+|+--+
T Consensus 2 ~pts~~~~C~ic~vq~------~~YtCPRCn~~Y 29 (383)
T KOG4317|consen 2 MPTSSFLACGICGVQK------REYTCPRCNLLY 29 (383)
T ss_pred CCCCceeecccccccc------ccccCCCCCccc
Confidence 3455778999998644 359999998544
No 156
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.82 E-value=16 Score=25.79 Aligned_cols=33 Identities=36% Similarity=0.760 Sum_probs=22.2
Q ss_pred CceecccCCcceeec-c--CCCCccCCCCCCCceee
Q 039088 8 SSYWCYRCSRFVRVF-S--RDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~-~--~~~~~~CP~C~~GFiEE 40 (409)
-.|-|-.|.....+. + ....+.||.|++.=++.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGSTEVRR 39 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEE
Confidence 468899999543322 2 24689999999854443
No 157
>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=52.66 E-value=6.5 Score=28.22 Aligned_cols=43 Identities=30% Similarity=0.656 Sum_probs=27.5
Q ss_pred cccccccccccCCCceeecccceeChhhhHHHhhc------CCCCCCCC
Q 039088 211 HCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL------RNSCPVCR 253 (409)
Q Consensus 211 ~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~------~~sCPvCR 253 (409)
.|.||...-..+..+.--.|...||..|+..=+.. .-.||.|+
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 38899883333222222349999999999876542 23687774
No 158
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.99 E-value=19 Score=35.52 Aligned_cols=51 Identities=14% Similarity=0.217 Sum_probs=35.0
Q ss_pred ccccccccccccCCC-ceeecccceeChhhhHHHhhcCCCCCCCCccCCCCCCC
Q 039088 210 SHCAVCKEAFELGSE-AREMPCKHIYHSDCILPWLSLRNSCPVCRHELPADNNS 262 (409)
Q Consensus 210 ~~C~ICle~f~~g~~-~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~~ 262 (409)
..|+|=--+|..... ....+|+|+|-..-+.+- ...+|++|.+.+..++..
T Consensus 112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvI 163 (293)
T KOG3113|consen 112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVI 163 (293)
T ss_pred eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeE
Confidence 678886555543322 344569999998877653 256899999988766543
No 159
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=51.55 E-value=7 Score=35.57 Aligned_cols=37 Identities=11% Similarity=0.296 Sum_probs=26.3
Q ss_pred CCCCceecccCCcceeec-cCCCCccCCCCCCCceeecc
Q 039088 5 VSSSSYWCYRCSRFVRVF-SRDDVVSCPDCDGGFVEEIE 42 (409)
Q Consensus 5 ~~~~~ywCh~C~r~V~~~-~~~~~~~CP~C~~GFiEEi~ 42 (409)
....-|.|-.|...+... ....+..||.|++- +|+++
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~-L~~~d 142 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAM-LDYLD 142 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE-eeecc
Confidence 345678999999876532 24568999999987 44443
No 160
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=50.63 E-value=11 Score=41.93 Aligned_cols=88 Identities=27% Similarity=0.458 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHHhhhcCCCCCCCCCCCHHHHH----cCCceeecccCcccCccccccccccccCCCceeecccceeChhh
Q 039088 163 SGFERLLEQLSQIDMNGIGGFENPPASKAAIE----NMPSILIDSSYVELESHCAVCKEAFELGSEAREMPCKHIYHSDC 238 (409)
Q Consensus 163 ~~le~LleqL~q~~~~~~~~~~~ppas~~~i~----~lp~~~~~~~~~~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~C 238 (409)
-..+.||+.+.++.... .....+...++ ..+...+.......-..|+|+...+.. .++-+.|+|+ .|
T Consensus 260 ~t~~~llq~~~~~~~~~----~~~~~s~~~~~~~l~~~~d~~i~tt~~~vSL~CPl~~~Rm~~--P~r~~~CkHl---Qc 330 (636)
T KOG2169|consen 260 LTSKDLLQRLKQNGKIN----RNLSQSDALIKKKLTAGPDSEIATTSLRVSLNCPLSKMRMSL--PARGHTCKHL---QC 330 (636)
T ss_pred cCHHHHHHHHhccCCcc----CchhHhHHHhhcccccCCcccceeccceeEecCCcccceeec--CCcccccccc---ee
Confidence 35677888776654211 11123333322 223323333333344789998665442 2333335554 55
Q ss_pred hHH-Hhhc----CC--CCCCCCccCCCC
Q 039088 239 ILP-WLSL----RN--SCPVCRHELPAD 259 (409)
Q Consensus 239 I~~-WL~~----~~--sCPvCR~~l~~~ 259 (409)
.+. |+.. +. .||||.+...-+
T Consensus 331 FD~~~~lq~n~~~pTW~CPVC~~~~~~e 358 (636)
T KOG2169|consen 331 FDALSYLQMNEQKPTWRCPVCQKAAPFE 358 (636)
T ss_pred cchhhhHHhccCCCeeeCccCCcccccc
Confidence 543 3322 11 699998765433
No 161
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=49.58 E-value=16 Score=37.25 Aligned_cols=50 Identities=24% Similarity=0.486 Sum_probs=36.6
Q ss_pred ccccccccccccC-CCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELG-SEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g-~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
..|+||-+..... ....-.||++..|..|+..-...+.+||.||+.....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 6899998876332 2333445888888888888888888999999655433
No 162
>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=48.72 E-value=11 Score=28.19 Aligned_cols=42 Identities=29% Similarity=0.664 Sum_probs=20.7
Q ss_pred ccccccccccCC------Cceeec-ccceeChhhhHHHhhcCCCCCCCC
Q 039088 212 CAVCKEAFELGS------EAREMP-CKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 212 C~ICle~f~~g~------~~~~lP-C~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
|.-|+..|.... ....-| |++.|+.+|=.--=+.-..||-|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 556676666542 223344 999999999543323344799883
No 163
>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=48.59 E-value=4.1 Score=32.44 Aligned_cols=40 Identities=23% Similarity=0.528 Sum_probs=22.3
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELP 257 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~ 257 (409)
..|++|..+++... +|.+|..|-.. ++....||-|..+|.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHHH
Confidence 47999988876432 67777777664 445567999988773
No 164
>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=46.26 E-value=15 Score=26.71 Aligned_cols=39 Identities=21% Similarity=0.489 Sum_probs=27.1
Q ss_pred ccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 212 CAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 212 C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
|..|.+.+...+ .....-+..||..|.. |-.|...|...
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~H~~Cf~--------C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFWHPECFK--------CSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEEETTTSB--------ETTTTCBTTTS
T ss_pred CCCCCCCccCcE-EEEEeCCcEEEccccc--------cCCCCCccCCC
Confidence 677888777433 2223478889998874 88998887554
No 165
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=45.56 E-value=11 Score=33.67 Aligned_cols=36 Identities=22% Similarity=0.585 Sum_probs=25.4
Q ss_pred CCCCceecccCCcceeecc------CCCCccCCCCCCCceee
Q 039088 5 VSSSSYWCYRCSRFVRVFS------RDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 5 ~~~~~ywCh~C~r~V~~~~------~~~~~~CP~C~~GFiEE 40 (409)
.....|.|-.|...+.... +...+.||.|++-.++.
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 3456899999998876421 22339999999877663
No 166
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=45.23 E-value=18 Score=36.89 Aligned_cols=45 Identities=24% Similarity=0.567 Sum_probs=31.9
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|-.|.++.......+.-.|+|.||.+|=.--=+.-..||-|.+
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 459999777665444444459999999996554344457999974
No 167
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.15 E-value=10 Score=38.27 Aligned_cols=49 Identities=22% Similarity=0.527 Sum_probs=38.3
Q ss_pred cccCccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccC
Q 039088 206 VELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHEL 256 (409)
Q Consensus 206 ~~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l 256 (409)
......|-||...+.... +.--|.|.|+..|...|....+-||.|+...
T Consensus 102 ~~~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 102 QQDHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred cCCccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCc
Confidence 344578999988776432 2223999999999999999999999998754
No 168
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=45.00 E-value=14 Score=25.11 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=21.4
Q ss_pred eecccCCcceeecc-----CCCCccCCCCCCCce
Q 039088 10 YWCYRCSRFVRVFS-----RDDVVSCPDCDGGFV 38 (409)
Q Consensus 10 ywCh~C~r~V~~~~-----~~~~~~CP~C~~GFi 38 (409)
+-|-.|...+++.. ....+.||.|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 55889999887752 123589999998774
No 169
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=44.94 E-value=12 Score=39.13 Aligned_cols=27 Identities=22% Similarity=0.664 Sum_probs=21.3
Q ss_pred ecccCCcceeecc--CCCCccCCCCCCCc
Q 039088 11 WCYRCSRFVRVFS--RDDVVSCPDCDGGF 37 (409)
Q Consensus 11 wCh~C~r~V~~~~--~~~~~~CP~C~~GF 37 (409)
=||.|+..+++.+ ..+...||+|+.-.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 3999999887653 45678999999865
No 170
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=44.80 E-value=22 Score=39.99 Aligned_cols=44 Identities=32% Similarity=0.656 Sum_probs=28.5
Q ss_pred Ccccccccccccc----CC-----Cceeec-ccceeChhhhHHHhhcCCCCCCCCccC
Q 039088 209 ESHCAVCKEAFEL----GS-----EAREMP-CKHIYHSDCILPWLSLRNSCPVCRHEL 256 (409)
Q Consensus 209 ~~~C~ICle~f~~----g~-----~~~~lP-C~H~FH~~CI~~WL~~~~sCPvCR~~l 256 (409)
+.+|+-|.-.|-. |. ..-..| |+|.-|..=|. .++.||+|...+
T Consensus 1131 ~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a~~~EIs----~y~~CPLCHs~~ 1184 (1189)
T KOG2041|consen 1131 DLQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRAHQHEIS----KYNCCPLCHSME 1184 (1189)
T ss_pred CCCChhhcCcCceeeccCCccccceEEEcccccccccccccc----ccccCccccChh
Confidence 4678777776631 11 122234 99998887765 378999997644
No 171
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=44.27 E-value=12 Score=29.26 Aligned_cols=19 Identities=26% Similarity=0.681 Sum_probs=15.2
Q ss_pred cccCCcceeeccCCCCccCCCCCCC
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDGG 36 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~G 36 (409)
|..|.+.+ . +-.||.|++.
T Consensus 8 C~~C~~i~--~----~~~Cp~Cgs~ 26 (64)
T PRK06393 8 CKKCKRLT--P----EKTCPVHGDE 26 (64)
T ss_pred HhhCCccc--C----CCcCCCCCCC
Confidence 88999887 2 3499999994
No 172
>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=43.34 E-value=15 Score=28.07 Aligned_cols=36 Identities=22% Similarity=0.526 Sum_probs=19.1
Q ss_pred CccccccccccccCCCceeec-ccceeChhhhHHHhh
Q 039088 209 ESHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLS 244 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~ 244 (409)
...|.+|...|..-..-..-. ||++|+..|....+.
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEc
Confidence 368999999997644333333 999999999876653
No 173
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=42.41 E-value=18 Score=36.73 Aligned_cols=47 Identities=19% Similarity=0.306 Sum_probs=37.2
Q ss_pred ccCccccccccccccCCCceeecccceeChhhhHHHhhcC---CCCCCCC
Q 039088 207 ELESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLR---NSCPVCR 253 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~---~sCPvCR 253 (409)
..-..|+|-.+.-.....+..|.|+|+.-..-+...-+.. -.||.|-
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 3457899988888777888999999999998888765432 2799993
No 174
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.40 E-value=8 Score=34.62 Aligned_cols=51 Identities=20% Similarity=0.430 Sum_probs=33.7
Q ss_pred CcccCcccccccc-ccccCCCceeecccceeChhhhHHHhhc-CC---CCCCCCcc
Q 039088 205 YVELESHCAVCKE-AFELGSEAREMPCKHIYHSDCILPWLSL-RN---SCPVCRHE 255 (409)
Q Consensus 205 ~~~~~~~C~ICle-~f~~g~~~~~lPC~H~FH~~CI~~WL~~-~~---sCPvCR~~ 255 (409)
....+..|-||+. .|.+|-......|.-.||..|--.--.. +. .|-+|+..
T Consensus 61 Gv~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 61 GVGDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred ccCcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 3455689999998 5666555455557777777776554333 22 69999874
No 175
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=41.04 E-value=21 Score=25.10 Aligned_cols=31 Identities=26% Similarity=0.494 Sum_probs=19.4
Q ss_pred eecccCCcce-eeccCCCCccCCCCCCCceeec
Q 039088 10 YWCYRCSRFV-RVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 10 ywCh~C~r~V-~~~~~~~~~~CP~C~~GFiEEi 41 (409)
|.|-.|.... -......+++|+.| |--|||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~C-G~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNC-GLVLEEN 32 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT--BBEE-T
T ss_pred CCCcCCcCCceEEcCCCCeEECCCC-CCEeecc
Confidence 6688888764 22235689999999 3344443
No 176
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=40.75 E-value=20 Score=26.53 Aligned_cols=34 Identities=29% Similarity=0.600 Sum_probs=25.7
Q ss_pred Cceecc--cCCcceeecc--CCCCccCCCCCCCceeec
Q 039088 8 SSYWCY--RCSRFVRVFS--RDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 8 ~~ywCh--~C~r~V~~~~--~~~~~~CP~C~~GFiEEi 41 (409)
..=||. .|...|.... ....+.||.|+--|--.-
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C 54 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRC 54 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCC
Confidence 455899 9999887642 456899999998886544
No 177
>PLN02189 cellulose synthase
Probab=40.22 E-value=30 Score=40.44 Aligned_cols=50 Identities=16% Similarity=0.314 Sum_probs=34.1
Q ss_pred ccccccccccccC---CCceeec-ccceeChhhhHHHhh-cCCCCCCCCccCCCC
Q 039088 210 SHCAVCKEAFELG---SEAREMP-CKHIYHSDCILPWLS-LRNSCPVCRHELPAD 259 (409)
Q Consensus 210 ~~C~ICle~f~~g---~~~~~lP-C~H~FH~~CI~~WL~-~~~sCPvCR~~l~~~ 259 (409)
..|.||-|++... +.-+... |+--.|..|..-=-+ .++.||.|+......
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~ 89 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRL 89 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhc
Confidence 5899999987633 3223333 777799999843332 356999999877633
No 178
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=40.01 E-value=16 Score=25.55 Aligned_cols=26 Identities=27% Similarity=0.538 Sum_probs=20.8
Q ss_pred cccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
|+.|++.+.+. -+.|.+|+.-|=.+-
T Consensus 1 C~~C~~~~~l~----~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKKVGLT----GFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCccccc----CeECCccCCcccccc
Confidence 88999987553 488999999997754
No 179
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=39.85 E-value=16 Score=28.34 Aligned_cols=19 Identities=26% Similarity=0.670 Sum_probs=14.6
Q ss_pred ecccCCcceeeccCCCCccCCCCCC
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
=|-.|.+.+ . +-.||.|++
T Consensus 5 AC~~C~~i~--~----~~~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYIT--T----EDRCPVCGS 23 (61)
T ss_pred hhhhCCccc--C----CCcCCCCcC
Confidence 388899877 2 237999998
No 180
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.72 E-value=34 Score=29.69 Aligned_cols=44 Identities=23% Similarity=0.505 Sum_probs=32.2
Q ss_pred ccccccccccccCC----------Cceeec-ccceeChhhhHHHhhcCCCCCCCC
Q 039088 210 SHCAVCKEAFELGS----------EAREMP-CKHIYHSDCILPWLSLRNSCPVCR 253 (409)
Q Consensus 210 ~~C~ICle~f~~g~----------~~~~lP-C~H~FH~~CI~~WL~~~~sCPvCR 253 (409)
..|--|+..|.... ..-.-+ |++.|+.+|=.-+-+.-..||-|-
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 46999988876431 112233 999999999888877777899995
No 181
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=38.40 E-value=23 Score=27.25 Aligned_cols=29 Identities=17% Similarity=0.383 Sum_probs=19.7
Q ss_pred CCceecccCCcceeeccCCCCccCCCCCC
Q 039088 7 SSSYWCYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 7 ~~~ywCh~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
...+.|-.|.+.|..........||.|+.
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 34557888888875442346788888865
No 182
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=37.83 E-value=27 Score=30.03 Aligned_cols=32 Identities=28% Similarity=0.663 Sum_probs=24.1
Q ss_pred CCceecccCCc-ceeeccCCCCccCCCCCCCceee
Q 039088 7 SSSYWCYRCSR-FVRVFSRDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 7 ~~~ywCh~C~r-~V~~~~~~~~~~CP~C~~GFiEE 40 (409)
++-.-|..|.. |+-+. ..-++||.|+.-|--+
T Consensus 7 GtKR~Cp~CG~kFYDLn--k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLN--KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCC--CCCccCCCCCCccCcc
Confidence 45566999975 45554 3668899999999877
No 183
>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 PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=37.39 E-value=19 Score=26.59 Aligned_cols=28 Identities=29% Similarity=0.809 Sum_probs=15.7
Q ss_pred eeccc--CCcceeeccCCCC--ccCCCCCCCc
Q 039088 10 YWCYR--CSRFVRVFSRDDV--VSCPDCDGGF 37 (409)
Q Consensus 10 ywCh~--C~r~V~~~~~~~~--~~CP~C~~GF 37 (409)
-||-. |...+........ +.|+.|+--|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 39988 9999877643344 8999998766
No 185
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=37.25 E-value=23 Score=24.36 Aligned_cols=31 Identities=23% Similarity=0.560 Sum_probs=23.9
Q ss_pred ceecccCCcceeec--cCCCCccCCCCCCCcee
Q 039088 9 SYWCYRCSRFVRVF--SRDDVVSCPDCDGGFVE 39 (409)
Q Consensus 9 ~ywCh~C~r~V~~~--~~~~~~~CP~C~~GFiE 39 (409)
+.-|-.|.+...+. ++..+-+|..|++.+|.
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred CcCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 45689999998874 35678999999997765
No 186
>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=36.54 E-value=8 Score=38.39 Aligned_cols=45 Identities=24% Similarity=0.418 Sum_probs=21.1
Q ss_pred ccccccccccccCCCceee--cccceeChhhhHHHhhcCCCCCCCCc
Q 039088 210 SHCAVCKEAFELGSEAREM--PCKHIYHSDCILPWLSLRNSCPVCRH 254 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~l--PC~H~FH~~CI~~WL~~~~sCPvCR~ 254 (409)
..|+||=..-..+.....- -=.|.+|.-|-..|-..+..||.|-.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 6899997753221100000 12677888899999888889999954
No 187
>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=35.62 E-value=19 Score=26.48 Aligned_cols=12 Identities=42% Similarity=1.110 Sum_probs=7.2
Q ss_pred CccCCCCCCCce
Q 039088 27 VVSCPDCDGGFV 38 (409)
Q Consensus 27 ~~~CP~C~~GFi 38 (409)
.+.||+|+.+|=
T Consensus 2 ~f~CP~C~~~~~ 13 (54)
T PF05605_consen 2 SFTCPYCGKGFS 13 (54)
T ss_pred CcCCCCCCCccC
Confidence 456777766543
No 188
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=35.48 E-value=12 Score=37.62 Aligned_cols=38 Identities=24% Similarity=0.615 Sum_probs=27.3
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhcCC
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN 247 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~ 247 (409)
.+|.+|+++|+.+......-|.-+||..|+..|++...
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTGA 252 (288)
T ss_pred eecHHHHHHHhcccccchhhcccccccccccccccccc
Confidence 47888888887655555555666888888888876544
No 189
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=35.23 E-value=22 Score=37.48 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=21.2
Q ss_pred eecccCCcceeecc--CCCCccCCCCCCCc
Q 039088 10 YWCYRCSRFVRVFS--RDDVVSCPDCDGGF 37 (409)
Q Consensus 10 ywCh~C~r~V~~~~--~~~~~~CP~C~~GF 37 (409)
-=||.|+..++..+ ......||+|+.-.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 34999999987653 34567899999865
No 190
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=34.75 E-value=28 Score=22.92 Aligned_cols=25 Identities=24% Similarity=0.586 Sum_probs=15.3
Q ss_pred ecccCCcceeeccCCCCccCCCCCC
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
||-.|-....+....-..+||.|+.
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 7889988877665567889999974
No 191
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=34.40 E-value=31 Score=30.63 Aligned_cols=32 Identities=13% Similarity=0.091 Sum_probs=24.3
Q ss_pred CCceecccCCcc-eeeccCCCCccCCCCCCCceee
Q 039088 7 SSSYWCYRCSRF-VRVFSRDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 7 ~~~ywCh~C~r~-V~~~~~~~~~~CP~C~~GFiEE 40 (409)
.+-.-|..|... +-+. ..-++||.|+.-|-.+
T Consensus 7 GtKr~Cp~cg~kFYDLn--k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLN--RRPAVSPYTGEQFPPE 39 (129)
T ss_pred CccccCCCcCccccccC--CCCccCCCcCCccCcc
Confidence 456679999764 5454 4789999999988666
No 192
>PLN02436 cellulose synthase A
Probab=34.06 E-value=48 Score=38.96 Aligned_cols=49 Identities=20% Similarity=0.463 Sum_probs=33.4
Q ss_pred cccccccccccc---CCCceeec-ccceeChhhhHHHhh-cCCCCCCCCccCCC
Q 039088 210 SHCAVCKEAFEL---GSEAREMP-CKHIYHSDCILPWLS-LRNSCPVCRHELPA 258 (409)
Q Consensus 210 ~~C~ICle~f~~---g~~~~~lP-C~H~FH~~CI~~WL~-~~~sCPvCR~~l~~ 258 (409)
..|-||-|++.. |+.-+... |+--.|..|..-=.+ .++.||.|+.....
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKR 90 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhh
Confidence 589999998743 33323333 777799999843332 35699999987753
No 193
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=33.53 E-value=39 Score=28.02 Aligned_cols=39 Identities=31% Similarity=0.645 Sum_probs=30.9
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~ 259 (409)
...|.-|...+..-+.+- |..||..+..|..|+++++..
T Consensus 33 rS~C~~C~~~L~~~~lIP------------i~S~l~lrGrCr~C~~~I~~~ 71 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP------------ILSYLLLRGRCRYCGAPIPPR 71 (92)
T ss_pred CCcCcCCCCcCcccccch------------HHHHHHhCCCCcccCCCCChH
Confidence 368999988877544433 788999999999999988653
No 194
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=33.27 E-value=19 Score=24.86 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=8.6
Q ss_pred CccCCCCCCC
Q 039088 27 VVSCPDCDGG 36 (409)
Q Consensus 27 ~~~CP~C~~G 36 (409)
++.||+|++-
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 6899999974
No 195
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.07 E-value=9.2 Score=37.74 Aligned_cols=46 Identities=20% Similarity=0.494 Sum_probs=37.5
Q ss_pred ccccccccccccC---CCceeec--------ccceeChhhhHHHhhcCC-CCCCCCcc
Q 039088 210 SHCAVCKEAFELG---SEAREMP--------CKHIYHSDCILPWLSLRN-SCPVCRHE 255 (409)
Q Consensus 210 ~~C~ICle~f~~g---~~~~~lP--------C~H~FH~~CI~~WL~~~~-sCPvCR~~ 255 (409)
..|.||...|... ...+.+. |+|..+..|+..-+.... .||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 6799999998832 3456666 999999999999987765 89999874
No 196
>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=32.55 E-value=21 Score=28.14 Aligned_cols=13 Identities=15% Similarity=0.618 Sum_probs=9.1
Q ss_pred eeChhhhHHHhhc
Q 039088 233 IYHSDCILPWLSL 245 (409)
Q Consensus 233 ~FH~~CI~~WL~~ 245 (409)
-||..|+.+|+..
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999853
No 197
>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=32.22 E-value=27 Score=25.51 Aligned_cols=35 Identities=26% Similarity=0.570 Sum_probs=24.9
Q ss_pred ccccccccccccCCCceeec-ccceeChhhhHHHhh
Q 039088 210 SHCAVCKEAFELGSEAREMP-CKHIYHSDCILPWLS 244 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lP-C~H~FH~~CI~~WL~ 244 (409)
..|.+|...|.....-.... |+++|+..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 57999998887644333333 999999999876543
No 198
>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=32.03 E-value=28 Score=27.71 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=12.4
Q ss_pred CceecccCCcceeeccCCCCccCCCCCC
Q 039088 8 SSYWCYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
..|.|-.|...+... ..||.|+.
T Consensus 16 ~~~~C~~C~~~~~~~-----a~CPdC~~ 38 (70)
T PF07191_consen 16 GHYHCEACQKDYKKE-----AFCPDCGQ 38 (70)
T ss_dssp TEEEETTT--EEEEE-----EE-TTT-S
T ss_pred CEEECccccccceec-----ccCCCccc
Confidence 467777777766443 66777764
No 199
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=31.91 E-value=24 Score=37.03 Aligned_cols=24 Identities=21% Similarity=0.564 Sum_probs=18.3
Q ss_pred ecccCCcceeeccCCCCccCCCCCCCc
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
=||.|+..+. ......||+|+.-.
T Consensus 217 ~C~~Cd~~~~---~~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTIL---PAQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCccC---CCCCcCCcCCCCcc
Confidence 4999999763 34568899999765
No 200
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=31.67 E-value=36 Score=22.78 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=19.8
Q ss_pred ecccCCcceeeccCCCCccCCCCC
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCD 34 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~ 34 (409)
+|+.|+..+...+....+.|..|+
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQ 26 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCC
Confidence 699999988766566789999996
No 201
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.58 E-value=28 Score=27.06 Aligned_cols=15 Identities=27% Similarity=0.718 Sum_probs=12.2
Q ss_pred CCCCccCCCCCCCce
Q 039088 24 RDDVVSCPDCDGGFV 38 (409)
Q Consensus 24 ~~~~~~CP~C~~GFi 38 (409)
...+++||+|+--|.
T Consensus 45 ~~gev~CPYC~t~y~ 59 (62)
T COG4391 45 DEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCcEecCccccEEE
Confidence 568999999987663
No 202
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.56 E-value=24 Score=34.71 Aligned_cols=33 Identities=12% Similarity=0.343 Sum_probs=28.2
Q ss_pred ccccccccccccCCCceeecccceeChhhhHHHhhc
Q 039088 210 SHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSL 245 (409)
Q Consensus 210 ~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~ 245 (409)
+.|+.||..+. .+++.|=+|+|+..||...+..
T Consensus 44 dcCsLtLqPc~---dPvit~~GylfdrEaILe~ila 76 (303)
T KOG3039|consen 44 DCCSLTLQPCR---DPVITPDGYLFDREAILEYILA 76 (303)
T ss_pred ceeeeeccccc---CCccCCCCeeeeHHHHHHHHHH
Confidence 67999998877 6788889999999999998743
No 203
>PLN02400 cellulose synthase
Probab=30.88 E-value=48 Score=38.99 Aligned_cols=50 Identities=14% Similarity=0.327 Sum_probs=32.7
Q ss_pred CccccccccccccCCC----ceeecccceeChhhhHHHh-hcCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGSE----AREMPCKHIYHSDCILPWL-SLRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~----~~~lPC~H~FH~~CI~~WL-~~~~sCPvCR~~l~~ 258 (409)
...|-||-|++..... +...-|+--.|..|..-=- +.++.||.|+.....
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcccc
Confidence 3589999998764331 2222377778999974211 235689999987753
No 204
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=30.73 E-value=46 Score=33.96 Aligned_cols=51 Identities=25% Similarity=0.699 Sum_probs=35.0
Q ss_pred Cccccccccccc-----cCC-----------CceeecccceeChhhhHHHhhc---------CCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFE-----LGS-----------EAREMPCKHIYHSDCILPWLSL---------RNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~-----~g~-----------~~~~lPC~H~FH~~CI~~WL~~---------~~sCPvCR~~l~~~ 259 (409)
+.+|++|+..=. .|. ...-.||+|+--..-..-|-+. |..||.|-+.|..+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 478999987411 111 1223479999888888889754 44799998877554
No 205
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=30.52 E-value=28 Score=31.60 Aligned_cols=27 Identities=30% Similarity=0.623 Sum_probs=20.8
Q ss_pred eChhhhHHHhhcCC----CCCCCCccCCCCC
Q 039088 234 YHSDCILPWLSLRN----SCPVCRHELPADN 260 (409)
Q Consensus 234 FH~~CI~~WL~~~~----sCPvCR~~l~~~~ 260 (409)
||..||++=|..-. .||.|...-....
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~ 32 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQS 32 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCCCCc
Confidence 89999999987643 7999987654443
No 206
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.44 E-value=20 Score=37.92 Aligned_cols=37 Identities=22% Similarity=0.477 Sum_probs=27.1
Q ss_pred ccccccccccccCCC-----ceeecccceeChhhhHHHhhcC
Q 039088 210 SHCAVCKEAFELGSE-----AREMPCKHIYHSDCILPWLSLR 246 (409)
Q Consensus 210 ~~C~ICle~f~~g~~-----~~~lPC~H~FH~~CI~~WL~~~ 246 (409)
..|+.|....+.... ....+|+|.||+.|+..|-...
T Consensus 227 k~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 227 KECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred ccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 349999888776552 2223599999999999987654
No 207
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.26 E-value=19 Score=22.65 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=11.3
Q ss_pred CccCCCCCCCceee
Q 039088 27 VVSCPDCDGGFVEE 40 (409)
Q Consensus 27 ~~~CP~C~~GFiEE 40 (409)
-+.||.|+-.|.++
T Consensus 2 l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 2 LVPCPICGRKFNPD 15 (25)
T ss_pred CCcCCCCCCEECHH
Confidence 36899999999764
No 208
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.24 E-value=26 Score=39.54 Aligned_cols=31 Identities=19% Similarity=0.581 Sum_probs=22.9
Q ss_pred CCCceecccCCcceeeccCCCCccCCCCCCCceeec
Q 039088 6 SSSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEI 41 (409)
Q Consensus 6 ~~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi 41 (409)
.+....||.|...-.+ -..||.|++-=|..+
T Consensus 459 ~~~~L~CH~Cg~~~~~-----p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 459 ATGQLRCHYCGYQEPI-----PQSCPECGSEHLRAV 489 (730)
T ss_pred CCCeeEeCCCCCCCCC-----CCCCCCCCCCeeEEe
Confidence 3567889999998533 378999999855444
No 209
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.65 E-value=33 Score=22.37 Aligned_cols=22 Identities=32% Similarity=0.970 Sum_probs=16.4
Q ss_pred eecccCCcceeeccCCCCccCCCCC
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCD 34 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~ 34 (409)
|||-.|.+.+... . -+.|-.|.
T Consensus 1 ~~C~~C~~~~~~~--~-~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGF--Y-FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCC--E-eEEeCCCC
Confidence 7899999988322 2 78888887
No 210
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=28.86 E-value=72 Score=26.00 Aligned_cols=51 Identities=16% Similarity=0.356 Sum_probs=19.5
Q ss_pred CccccccccccccCCC----ceeecccceeChhhhHHHhhc-CCCCCCCCccCCCC
Q 039088 209 ESHCAVCKEAFELGSE----AREMPCKHIYHSDCILPWLSL-RNSCPVCRHELPAD 259 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~----~~~lPC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~ 259 (409)
...|-||-+++..... +...-|+--.|..|..-=.+. ++.||-|+......
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccc
Confidence 4689999998765432 222237777888888654443 66899999776543
No 211
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.01 E-value=50 Score=21.14 Aligned_cols=23 Identities=22% Similarity=0.512 Sum_probs=18.1
Q ss_pred cccCCcceeeccCCCCccCCCCC
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCD 34 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~ 34 (409)
|..|+..+........+.|..|+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~ 23 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCH 23 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccC
Confidence 78898887655466789999997
No 212
>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=27.41 E-value=20 Score=26.43 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=5.8
Q ss_pred CCCCCCccCCC
Q 039088 248 SCPVCRHELPA 258 (409)
Q Consensus 248 sCPvCR~~l~~ 258 (409)
.||+|..+|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999988754
No 213
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.22 E-value=75 Score=37.43 Aligned_cols=50 Identities=16% Similarity=0.311 Sum_probs=33.1
Q ss_pred CccccccccccccCC---Cceee-cccceeChhhhHHHh-hcCCCCCCCCccCCC
Q 039088 209 ESHCAVCKEAFELGS---EAREM-PCKHIYHSDCILPWL-SLRNSCPVCRHELPA 258 (409)
Q Consensus 209 ~~~C~ICle~f~~g~---~~~~l-PC~H~FH~~CI~~WL-~~~~sCPvCR~~l~~ 258 (409)
...|-||-|++.... .-+.. -|+--.|..|..-=- +.++.||.|+.....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKR 71 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 358999999876443 22222 277779999984222 336699999987753
No 214
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=27.22 E-value=38 Score=23.21 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=18.2
Q ss_pred ecccCCcceeecc-----CCCCccCCCCCCCc
Q 039088 11 WCYRCSRFVRVFS-----RDDVVSCPDCDGGF 37 (409)
Q Consensus 11 wCh~C~r~V~~~~-----~~~~~~CP~C~~GF 37 (409)
-|.+|.....+.. ....+.||.|+--|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4788888776541 33568888887654
No 215
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=27.21 E-value=34 Score=36.02 Aligned_cols=24 Identities=25% Similarity=0.556 Sum_probs=17.8
Q ss_pred eecccCCcceeeccCCCCccCCCCCCCc
Q 039088 10 YWCYRCSRFVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 10 ywCh~C~r~V~~~~~~~~~~CP~C~~GF 37 (409)
--||.|+..+ ......||+|+.-.
T Consensus 222 ~~C~~Cd~l~----~~~~a~CpRC~~~L 245 (419)
T PRK15103 222 RSCSCCTAIL----PADQPVCPRCHTKG 245 (419)
T ss_pred CcCCCCCCCC----CCCCCCCCCCCCcC
Confidence 3499999975 23456899999764
No 216
>PRK10220 hypothetical protein; Provisional
Probab=27.19 E-value=40 Score=29.16 Aligned_cols=28 Identities=18% Similarity=0.580 Sum_probs=21.2
Q ss_pred cccCCcceeeccCCCCccCCCCCCCceee
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDGGFVEE 40 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~GFiEE 40 (409)
|-+|+-...-. ....++||.|...+-.+
T Consensus 6 CP~C~seytY~-d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYE-DNGMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEc-CCCeEECCcccCcCCcc
Confidence 88888876544 55679999998888655
No 217
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=26.66 E-value=25 Score=26.34 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=20.6
Q ss_pred CceecccCCcceeec-c-CCCCccCCCCCCCc
Q 039088 8 SSYWCYRCSRFVRVF-S-RDDVVSCPDCDGGF 37 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~-~-~~~~~~CP~C~~GF 37 (409)
..+-|-.|++.+-.. . ..-+++||+|.-=+
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 456799999986431 1 23489999998633
No 218
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=26.11 E-value=26 Score=22.68 Aligned_cols=23 Identities=26% Similarity=0.810 Sum_probs=11.2
Q ss_pred cccCCcceeecc--CCCCccCCCCC
Q 039088 12 CYRCSRFVRVFS--RDDVVSCPDCD 34 (409)
Q Consensus 12 Ch~C~r~V~~~~--~~~~~~CP~C~ 34 (409)
|..|...+.... .....+||+|.
T Consensus 4 C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 4 CPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp -TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CccCCCcceEeEecCCCCeECcCCc
Confidence 667777654321 33567888886
No 219
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=25.57 E-value=22 Score=42.99 Aligned_cols=48 Identities=29% Similarity=0.503 Sum_probs=37.8
Q ss_pred CccccccccccccCCCceeecccceeChhhhHHHhhcCC----CCCCCCccC
Q 039088 209 ESHCAVCKEAFELGSEAREMPCKHIYHSDCILPWLSLRN----SCPVCRHEL 256 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lPC~H~FH~~CI~~WL~~~~----sCPvCR~~l 256 (409)
...|-||+........+...-|.-.||..|+++-+.... .||-|+.+-
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 478999998877544444455999999999999987644 799998765
No 220
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.29 E-value=32 Score=25.40 Aligned_cols=15 Identities=40% Similarity=0.904 Sum_probs=11.4
Q ss_pred CccCCCCCCCceeec
Q 039088 27 VVSCPDCDGGFVEEI 41 (409)
Q Consensus 27 ~~~CP~C~~GFiEEi 41 (409)
-..||.|+++|+.+.
T Consensus 20 ~~fCP~Cg~~~m~~~ 34 (50)
T PRK00432 20 NKFCPRCGSGFMAEH 34 (50)
T ss_pred cCcCcCCCcchhecc
Confidence 358999999876654
No 221
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=25.14 E-value=37 Score=28.73 Aligned_cols=27 Identities=26% Similarity=0.701 Sum_probs=18.8
Q ss_pred ecccCCcceeeccCCCCccCCCCCCCcee
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCDGGFVE 39 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~~GFiE 39 (409)
=|..|...+... .-.+-.||.|+ +|++
T Consensus 5 AC~~C~~I~~~~-qf~~~gCpnC~-~~l~ 31 (98)
T cd07973 5 ACLLCSLIKTED-QFERDGCPNCE-GYLD 31 (98)
T ss_pred hhccCCcccccc-cccCCCCCCCc-chhc
Confidence 388999887432 12346899998 7775
No 222
>PHA00616 hypothetical protein
Probab=25.02 E-value=19 Score=26.14 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=11.0
Q ss_pred ccCCCCCCCceee
Q 039088 28 VSCPDCDGGFVEE 40 (409)
Q Consensus 28 ~~CP~C~~GFiEE 40 (409)
+.||.|+..|+.-
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 5799999999864
No 223
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=24.86 E-value=53 Score=28.53 Aligned_cols=23 Identities=22% Similarity=0.429 Sum_probs=16.6
Q ss_pred HHhhcCCCCCCCCccCCCCCCCC
Q 039088 241 PWLSLRNSCPVCRHELPADNNSN 263 (409)
Q Consensus 241 ~WL~~~~sCPvCR~~l~~~~~~~ 263 (409)
+-|.+...|+.|+++|.-++..+
T Consensus 80 KmLGr~D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 80 KMLGRVDACMHCKEPLTLDPSLE 102 (114)
T ss_pred hhhchhhccCcCCCcCccCchhh
Confidence 34555668999999998776543
No 224
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=24.52 E-value=35 Score=37.81 Aligned_cols=25 Identities=36% Similarity=0.983 Sum_probs=19.8
Q ss_pred ccceeChhhhHHHhhcC-----CCCCCCCc
Q 039088 230 CKHIYHSDCILPWLSLR-----NSCPVCRH 254 (409)
Q Consensus 230 C~H~FH~~CI~~WL~~~-----~sCPvCR~ 254 (409)
|+-.||..|+..|+... ..||-||.
T Consensus 41 c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 41 CGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 89999999999998542 25877765
No 225
>PF14353 CpXC: CpXC protein
Probab=24.26 E-value=40 Score=29.10 Aligned_cols=17 Identities=29% Similarity=0.700 Sum_probs=14.8
Q ss_pred CccCCCCCCCceeeccc
Q 039088 27 VVSCPDCDGGFVEEIEN 43 (409)
Q Consensus 27 ~~~CP~C~~GFiEEi~~ 43 (409)
++.||.|+.-|--|+..
T Consensus 1 ~itCP~C~~~~~~~v~~ 17 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWT 17 (128)
T ss_pred CcCCCCCCCeeEEEEEe
Confidence 47899999999999864
No 226
>PF12773 DZR: Double zinc ribbon
Probab=24.12 E-value=49 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.566 Sum_probs=16.1
Q ss_pred ceecccCCcceeeccCCCCccCCCCCC
Q 039088 9 SYWCYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 9 ~ywCh~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
.=||..|-..+... ....++||.|+.
T Consensus 12 ~~fC~~CG~~l~~~-~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPP-DQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhc-cCCCCCCcCCcC
Confidence 44677777776411 234577887776
No 227
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=23.64 E-value=28 Score=26.44 Aligned_cols=17 Identities=41% Similarity=1.114 Sum_probs=13.3
Q ss_pred CCCCCceecccCCccee
Q 039088 4 IVSSSSYWCYRCSRFVR 20 (409)
Q Consensus 4 ~~~~~~ywCh~C~r~V~ 20 (409)
...+.+-|||.|+.+|.
T Consensus 44 ~~~~~~i~C~~C~~~v~ 60 (63)
T PF02148_consen 44 SLSTGSIWCYACDDYVY 60 (63)
T ss_dssp ETTTTCEEETTTTEEEE
T ss_pred ECCCCeEEEcCCCcEEe
Confidence 34566789999999984
No 228
>PF14968 CCDC84: Coiled coil protein 84
Probab=23.44 E-value=35 Score=35.00 Aligned_cols=32 Identities=31% Similarity=0.777 Sum_probs=22.3
Q ss_pred CCCCceecccCCcceeeccCCCCccCCCCCCCceeecc
Q 039088 5 VSSSSYWCYRCSRFVRVFSRDDVVSCPDCDGGFVEEIE 42 (409)
Q Consensus 5 ~~~~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFiEEi~ 42 (409)
....+||||-|...|.-. .+.++| +|.||-|.
T Consensus 54 ~~~~~fWC~fC~~ev~~~--~s~~~~----~~ai~HLa 85 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREH--DSSFAC----GGAIEHLA 85 (336)
T ss_pred cccceeEeeCccchhhhc--cchhhh----ccHHhhcC
Confidence 467899999999998543 233444 67777664
No 229
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.28 E-value=33 Score=34.84 Aligned_cols=12 Identities=42% Similarity=0.811 Sum_probs=9.4
Q ss_pred CCCccCCCCCCC
Q 039088 25 DDVVSCPDCDGG 36 (409)
Q Consensus 25 ~~~~~CP~C~~G 36 (409)
+++-+||.|..-
T Consensus 121 ~~dK~Cp~C~d~ 132 (389)
T KOG2932|consen 121 DSDKICPLCDDR 132 (389)
T ss_pred CccccCcCcccH
Confidence 357799999875
No 230
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.16 E-value=45 Score=22.77 Aligned_cols=24 Identities=21% Similarity=0.654 Sum_probs=10.9
Q ss_pred ecccCCcceeecc----CCCCccCCCCC
Q 039088 11 WCYRCSRFVRVFS----RDDVVSCPDCD 34 (409)
Q Consensus 11 wCh~C~r~V~~~~----~~~~~~CP~C~ 34 (409)
||-+|--.+.... .....+||.|+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 5777777654421 22457777775
No 231
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.01 E-value=39 Score=23.50 Aligned_cols=12 Identities=42% Similarity=0.866 Sum_probs=7.8
Q ss_pred ccCCCCCCCcee
Q 039088 28 VSCPDCDGGFVE 39 (409)
Q Consensus 28 ~~CP~C~~GFiE 39 (409)
-.||.|+.||-=
T Consensus 3 ~~CprC~kg~Hw 14 (36)
T PF14787_consen 3 GLCPRCGKGFHW 14 (36)
T ss_dssp -C-TTTSSSCS-
T ss_pred ccCcccCCCcch
Confidence 369999999853
No 232
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=22.50 E-value=55 Score=22.42 Aligned_cols=26 Identities=35% Similarity=0.714 Sum_probs=17.0
Q ss_pred cccCCcceeecc-----CCCCccCCCCCCCc
Q 039088 12 CYRCSRFVRVFS-----RDDVVSCPDCDGGF 37 (409)
Q Consensus 12 Ch~C~r~V~~~~-----~~~~~~CP~C~~GF 37 (409)
|-.|....++.. ....+.||.|+--|
T Consensus 5 CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred CCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 677777766542 23577888887655
No 233
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=22.46 E-value=29 Score=37.05 Aligned_cols=47 Identities=26% Similarity=0.578 Sum_probs=30.3
Q ss_pred Ccccccccccc-ccCCCceeec-ccceeChhhhHHHhhc--------CCCCCCCCcc
Q 039088 209 ESHCAVCKEAF-ELGSEAREMP-CKHIYHSDCILPWLSL--------RNSCPVCRHE 255 (409)
Q Consensus 209 ~~~C~ICle~f-~~g~~~~~lP-C~H~FH~~CI~~WL~~--------~~sCPvCR~~ 255 (409)
..+|++|.... .....+...- |+-.||..|..+..+. .-.|=+|...
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred cceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 45699998643 2333333332 8999999998876533 1159999764
No 234
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=22.31 E-value=40 Score=37.73 Aligned_cols=47 Identities=23% Similarity=0.523 Sum_probs=30.1
Q ss_pred ccccccccccccCC--Cceee-----cccceeChhhhHHH--h--------hcCCCCCCCCccC
Q 039088 210 SHCAVCKEAFELGS--EAREM-----PCKHIYHSDCILPW--L--------SLRNSCPVCRHEL 256 (409)
Q Consensus 210 ~~C~ICle~f~~g~--~~~~l-----PC~H~FH~~CI~~W--L--------~~~~sCPvCR~~l 256 (409)
..|.||.|+=...+ .-..| -|+..||..|...- | ..-+.|-.|++-+
T Consensus 118 KtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hf 181 (900)
T KOG0956|consen 118 KTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHF 181 (900)
T ss_pred ceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHH
Confidence 57999988633222 11222 38889999998754 1 2234799998754
No 235
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=22.22 E-value=71 Score=22.74 Aligned_cols=23 Identities=22% Similarity=0.600 Sum_probs=14.2
Q ss_pred ecccCCcceeeccCCCCccCCCCC
Q 039088 11 WCYRCSRFVRVFSRDDVVSCPDCD 34 (409)
Q Consensus 11 wCh~C~r~V~~~~~~~~~~CP~C~ 34 (409)
.|..|.-..- ...+..++||.|+
T Consensus 19 ~Cp~C~~PL~-~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLM-RDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeE-EecCCCEECCCCC
Confidence 4778854421 2245678888885
No 236
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=21.61 E-value=70 Score=33.23 Aligned_cols=30 Identities=30% Similarity=0.559 Sum_probs=20.6
Q ss_pred CceecccCCcceeeccCCCCccCCCCCCCce
Q 039088 8 SSYWCYRCSRFVRVFSRDDVVSCPDCDGGFV 38 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~~~~~~~CP~C~~GFi 38 (409)
--|.|+.|..+.... ....-.||.|++.|+
T Consensus 243 ~~~~C~~c~~~~~~~-~~~~~~C~~c~~~~~ 272 (382)
T PRK04338 243 YVYYCPKCLYREEVE-GLPPEECPVCGGKFG 272 (382)
T ss_pred eEEECCCCCcEEEec-CCCCCCCCCCCCcce
Confidence 458899999875332 223457999988554
No 237
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=21.49 E-value=49 Score=22.01 Aligned_cols=23 Identities=22% Similarity=0.649 Sum_probs=10.6
Q ss_pred cccCCcceeeccCCCCccCCCCCC
Q 039088 12 CYRCSRFVRVFSRDDVVSCPDCDG 35 (409)
Q Consensus 12 Ch~C~r~V~~~~~~~~~~CP~C~~ 35 (409)
|-.|.-..... ...-++||.|..
T Consensus 5 Cp~C~se~~y~-D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTYE-DGELLVCPECGH 27 (30)
T ss_dssp -TTT-----EE--SSSEEETTTTE
T ss_pred CCCCCCcceec-cCCEEeCCcccc
Confidence 56666665444 456678888863
No 238
>PRK13794 hypothetical protein; Provisional
Probab=21.02 E-value=58 Score=34.89 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=18.6
Q ss_pred CceecccCCcceeeccCCCCccCCCCCCC
Q 039088 8 SSYWCYRCSRFVRVFSRDDVVSCPDCDGG 36 (409)
Q Consensus 8 ~~ywCh~C~r~V~~~~~~~~~~CP~C~~G 36 (409)
+-|||-.|+-.| . .-.|..|+..
T Consensus 9 ~~~wc~~cn~p~--~----~~~c~~cg~~ 31 (479)
T PRK13794 9 HLKWCDNCNVPV--L----GKKCAICGSE 31 (479)
T ss_pred EEEEcCCCCCee--c----CCchhHhCCC
Confidence 579999999988 2 2359999986
No 239
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.00 E-value=23 Score=25.30 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=9.0
Q ss_pred CCccCCCCCCC
Q 039088 26 DVVSCPDCDGG 36 (409)
Q Consensus 26 ~~~~CP~C~~G 36 (409)
+-++||+|++-
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 45889999986
No 240
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=20.85 E-value=56 Score=27.25 Aligned_cols=32 Identities=19% Similarity=0.525 Sum_probs=21.7
Q ss_pred CccccccccccccCCCceeec--ccceeChhhhHHH
Q 039088 209 ESHCAVCKEAFELGSEAREMP--CKHIYHSDCILPW 242 (409)
Q Consensus 209 ~~~C~ICle~f~~g~~~~~lP--C~H~FH~~CI~~W 242 (409)
...|.||.... |..+.-.- |...||..|....
T Consensus 55 ~~~C~iC~~~~--G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 55 KLKCSICGKSG--GACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CCcCcCCCCCC--ceeEEcCCCCCCcCCCHHHHHHC
Confidence 36899998862 22222222 8889999998653
No 241
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=20.22 E-value=68 Score=35.23 Aligned_cols=36 Identities=31% Similarity=0.668 Sum_probs=24.4
Q ss_pred ccCccccccccccccC-----C-----CceeecccceeChhhhHHH
Q 039088 207 ELESHCAVCKEAFELG-----S-----EAREMPCKHIYHSDCILPW 242 (409)
Q Consensus 207 ~~~~~C~ICle~f~~g-----~-----~~~~lPC~H~FH~~CI~~W 242 (409)
+....|+||.|.|+.- + .++.+-=+-+||..|+..-
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 3447899999998621 1 2333335889999998764
No 242
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.10 E-value=65 Score=27.68 Aligned_cols=18 Identities=33% Similarity=0.783 Sum_probs=12.8
Q ss_pred ceeeccCCCCccCCCCCCCc
Q 039088 18 FVRVFSRDDVVSCPDCDGGF 37 (409)
Q Consensus 18 ~V~~~~~~~~~~CP~C~~GF 37 (409)
+|.+. .....||.|+..|
T Consensus 42 yV~ie--~G~t~CP~Cg~~~ 59 (115)
T COG1885 42 YVEIE--VGSTSCPKCGEPF 59 (115)
T ss_pred eEEEe--cccccCCCCCCcc
Confidence 35444 3578999999876
Done!