Query 018689
Match_columns 352
No_of_seqs 480 out of 1860
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 03:12:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018689.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018689hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14369 zf-RING_3: zinc-finge 99.6 7.4E-17 1.6E-21 106.7 2.9 35 22-56 1-35 (35)
2 KOG4628 Predicted E3 ubiquitin 99.6 5.8E-16 1.2E-20 150.3 5.5 80 168-247 203-283 (348)
3 PF13639 zf-RING_2: Ring finge 99.5 5.5E-15 1.2E-19 102.7 1.4 44 195-238 1-44 (44)
4 COG5243 HRD1 HRD ubiquitin lig 99.3 2.7E-12 5.9E-17 123.9 8.2 70 173-244 268-347 (491)
5 COG5540 RING-finger-containing 99.2 5.4E-12 1.2E-16 119.1 2.6 50 194-243 323-373 (374)
6 PHA02929 N1R/p28-like protein; 99.2 7E-12 1.5E-16 116.9 3.3 71 172-242 150-227 (238)
7 PF12678 zf-rbx1: RING-H2 zinc 99.2 9E-12 1.9E-16 96.1 3.1 45 194-238 19-73 (73)
8 PF13920 zf-C3HC4_3: Zinc fing 98.9 4.3E-10 9.3E-15 80.2 2.2 46 194-242 2-48 (50)
9 cd00162 RING RING-finger (Real 98.9 7.3E-10 1.6E-14 75.4 2.3 44 196-241 1-45 (45)
10 PLN03208 E3 ubiquitin-protein 98.9 9E-10 1.9E-14 99.3 2.8 50 193-245 17-82 (193)
11 PF13923 zf-C3HC4_2: Zinc fing 98.9 1.1E-09 2.3E-14 74.1 2.1 39 197-237 1-39 (39)
12 KOG0317 Predicted E3 ubiquitin 98.9 8.6E-10 1.9E-14 104.0 2.0 49 194-245 239-287 (293)
13 KOG0802 E3 ubiquitin ligase [P 98.8 7.8E-10 1.7E-14 115.2 0.5 50 193-242 290-341 (543)
14 KOG0823 Predicted E3 ubiquitin 98.8 2.3E-09 4.9E-14 98.4 2.2 49 194-245 47-98 (230)
15 PF12861 zf-Apc11: Anaphase-pr 98.8 2.5E-09 5.5E-14 84.1 1.6 50 194-243 21-83 (85)
16 PF15227 zf-C3HC4_4: zinc fing 98.7 4.3E-09 9.2E-14 72.6 2.0 38 197-237 1-42 (42)
17 smart00504 Ubox Modified RING 98.7 8.7E-09 1.9E-13 76.3 3.4 47 195-244 2-48 (63)
18 KOG0320 Predicted E3 ubiquitin 98.7 5.7E-09 1.2E-13 92.2 1.3 50 193-243 130-179 (187)
19 PF14634 zf-RING_5: zinc-RING 98.7 8.2E-09 1.8E-13 71.7 1.7 44 196-239 1-44 (44)
20 PHA02926 zinc finger-like prot 98.7 6.2E-09 1.3E-13 95.1 1.2 52 191-242 167-230 (242)
21 PF00097 zf-C3HC4: Zinc finger 98.6 1.5E-08 3.2E-13 68.9 2.2 39 197-237 1-41 (41)
22 smart00184 RING Ring finger. E 98.6 1.6E-08 3.4E-13 66.3 1.5 38 197-237 1-39 (39)
23 TIGR00599 rad18 DNA repair pro 98.5 5.7E-08 1.2E-12 97.0 2.6 48 194-244 26-73 (397)
24 COG5194 APC11 Component of SCF 98.5 5.2E-08 1.1E-12 75.1 1.6 47 197-243 34-82 (88)
25 KOG1493 Anaphase-promoting com 98.3 6.4E-08 1.4E-12 74.0 -1.3 49 194-242 20-81 (84)
26 PF13445 zf-RING_UBOX: RING-ty 98.3 3.4E-07 7.4E-12 63.4 1.8 38 197-235 1-43 (43)
27 KOG1734 Predicted RING-contain 98.3 1.6E-07 3.5E-12 87.8 -0.1 49 194-242 224-281 (328)
28 COG5574 PEX10 RING-finger-cont 98.2 3.4E-07 7.5E-12 85.6 1.0 48 194-244 215-264 (271)
29 PF04564 U-box: U-box domain; 98.2 5E-07 1.1E-11 69.5 1.6 49 194-245 4-53 (73)
30 smart00744 RINGv The RING-vari 98.2 5E-07 1.1E-11 64.3 1.4 42 196-238 1-49 (49)
31 KOG0287 Postreplication repair 98.2 4.6E-07 9.9E-12 87.2 0.3 49 194-245 23-71 (442)
32 COG5219 Uncharacterized conser 98.2 2.8E-07 6.1E-12 98.0 -1.2 68 175-242 1450-1523(1525)
33 KOG2164 Predicted E3 ubiquitin 98.1 8.5E-07 1.8E-11 89.7 1.9 49 194-245 186-239 (513)
34 KOG0828 Predicted E3 ubiquitin 98.1 5.4E-07 1.2E-11 90.4 0.5 51 193-243 570-635 (636)
35 COG5432 RAD18 RING-finger-cont 98.0 2.1E-06 4.5E-11 81.3 1.2 46 194-242 25-70 (391)
36 TIGR00570 cdk7 CDK-activating 98.0 3.9E-06 8.5E-11 81.0 2.7 50 194-243 3-55 (309)
37 PF11793 FANCL_C: FANCL C-term 98.0 1.7E-06 3.8E-11 66.1 0.1 49 194-242 2-66 (70)
38 KOG2930 SCF ubiquitin ligase, 97.9 3.7E-06 8E-11 68.1 0.7 49 194-242 46-108 (114)
39 KOG2177 Predicted E3 ubiquitin 97.9 3.9E-06 8.4E-11 78.0 0.5 44 193-239 12-55 (386)
40 KOG0804 Cytoplasmic Zn-finger 97.7 1E-05 2.3E-10 80.6 1.2 48 193-242 174-222 (493)
41 PF14835 zf-RING_6: zf-RING of 97.7 2.3E-05 5E-10 58.5 1.9 47 194-245 7-54 (65)
42 KOG0827 Predicted E3 ubiquitin 97.7 1.2E-05 2.6E-10 78.8 0.5 47 195-241 5-55 (465)
43 KOG4265 Predicted E3 ubiquitin 97.6 2.1E-05 4.7E-10 76.6 2.1 47 194-243 290-337 (349)
44 KOG0825 PHD Zn-finger protein 97.6 1.1E-05 2.3E-10 84.9 -1.0 50 194-243 123-172 (1134)
45 KOG0824 Predicted E3 ubiquitin 97.5 4.1E-05 9E-10 73.0 1.5 48 194-244 7-55 (324)
46 KOG0311 Predicted E3 ubiquitin 97.5 1.1E-05 2.3E-10 78.5 -2.7 47 194-243 43-91 (381)
47 KOG1039 Predicted E3 ubiquitin 97.4 5.6E-05 1.2E-09 74.4 1.7 48 194-241 161-220 (344)
48 KOG1645 RING-finger-containing 97.2 0.00017 3.8E-09 71.3 2.0 48 194-241 4-55 (463)
49 KOG4445 Uncharacterized conser 97.2 6.2E-05 1.3E-09 71.8 -1.1 90 151-244 76-188 (368)
50 KOG1785 Tyrosine kinase negati 97.2 0.0001 2.3E-09 72.6 0.4 48 195-245 370-419 (563)
51 KOG0978 E3 ubiquitin ligase in 97.1 0.0001 2.2E-09 78.0 -0.2 48 194-244 643-691 (698)
52 KOG4172 Predicted E3 ubiquitin 97.1 3.3E-05 7.2E-10 55.6 -3.1 47 194-243 7-55 (62)
53 KOG0801 Predicted E3 ubiquitin 97.0 0.00033 7.2E-09 61.4 1.4 42 181-222 164-205 (205)
54 KOG4159 Predicted E3 ubiquitin 96.9 0.00036 7.7E-09 70.1 1.3 47 194-243 84-130 (398)
55 KOG0297 TNF receptor-associate 96.8 0.00055 1.2E-08 68.9 2.2 49 193-244 20-69 (391)
56 KOG1428 Inhibitor of type V ad 96.7 0.00068 1.5E-08 75.5 1.9 70 174-243 3465-3545(3738)
57 KOG1941 Acetylcholine receptor 96.6 0.00036 7.9E-09 68.7 -0.8 46 194-239 365-413 (518)
58 PF11789 zf-Nse: Zinc-finger o 96.6 0.00076 1.7E-08 49.5 1.0 41 194-236 11-53 (57)
59 PF12906 RINGv: RING-variant d 96.4 0.0021 4.6E-08 45.2 2.3 40 197-237 1-47 (47)
60 KOG2660 Locus-specific chromos 96.4 0.00052 1.1E-08 66.4 -1.1 46 194-242 15-61 (331)
61 KOG4692 Predicted E3 ubiquitin 96.0 0.0029 6.3E-08 61.8 1.5 51 192-245 420-470 (489)
62 PF10367 Vps39_2: Vacuolar sor 96.0 0.0037 8.1E-08 50.6 2.0 31 194-225 78-108 (109)
63 PF05883 Baculo_RING: Baculovi 95.9 0.0016 3.4E-08 55.7 -0.6 35 194-228 26-66 (134)
64 PF14570 zf-RING_4: RING/Ubox 95.9 0.0034 7.4E-08 44.4 1.0 44 197-241 1-47 (48)
65 KOG1002 Nucleotide excision re 95.9 0.0033 7.1E-08 64.3 1.2 49 194-245 536-589 (791)
66 KOG2879 Predicted E3 ubiquitin 95.7 0.009 1.9E-07 56.7 3.5 49 193-243 238-288 (298)
67 COG5152 Uncharacterized conser 95.7 0.0024 5.1E-08 57.9 -0.4 45 194-241 196-240 (259)
68 KOG1952 Transcription factor N 95.6 0.0036 7.7E-08 67.2 0.5 51 191-241 188-246 (950)
69 KOG1814 Predicted E3 ubiquitin 95.5 0.004 8.7E-08 62.0 0.5 46 194-239 184-237 (445)
70 KOG3970 Predicted E3 ubiquitin 95.5 0.0067 1.4E-07 56.0 1.7 50 194-244 50-107 (299)
71 PF14447 Prok-RING_4: Prokaryo 95.5 0.011 2.4E-07 42.9 2.5 46 195-245 8-53 (55)
72 KOG3039 Uncharacterized conser 95.4 0.0074 1.6E-07 56.4 1.8 58 193-250 220-278 (303)
73 PHA02862 5L protein; Provision 95.4 0.0054 1.2E-07 53.0 0.6 45 195-243 3-54 (156)
74 KOG0827 Predicted E3 ubiquitin 95.3 0.0011 2.3E-08 65.5 -4.5 52 194-245 196-248 (465)
75 KOG4275 Predicted E3 ubiquitin 95.3 0.0035 7.5E-08 59.9 -1.0 42 194-242 300-342 (350)
76 KOG1813 Predicted E3 ubiquitin 95.2 0.0072 1.6E-07 57.9 0.9 46 194-242 241-286 (313)
77 KOG1571 Predicted E3 ubiquitin 95.2 0.0098 2.1E-07 58.4 1.7 43 194-242 305-347 (355)
78 PHA02825 LAP/PHD finger-like p 94.9 0.012 2.6E-07 51.7 1.3 47 193-243 7-60 (162)
79 PF08746 zf-RING-like: RING-li 94.8 0.01 2.2E-07 41.0 0.6 41 197-237 1-43 (43)
80 PF04641 Rtf2: Rtf2 RING-finge 94.7 0.049 1.1E-06 51.8 5.2 92 151-245 58-164 (260)
81 COG5236 Uncharacterized conser 94.4 0.022 4.7E-07 55.7 2.0 47 192-241 59-107 (493)
82 COG0375 HybF Zn finger protein 93.8 0.042 9.1E-07 46.0 2.3 37 19-58 66-102 (115)
83 KOG0826 Predicted E3 ubiquitin 93.7 0.032 7E-07 54.2 1.7 49 191-242 297-346 (357)
84 PHA03096 p28-like protein; Pro 93.7 0.021 4.5E-07 55.1 0.4 45 195-239 179-231 (284)
85 KOG3268 Predicted E3 ubiquitin 93.7 0.028 6E-07 50.3 1.1 50 194-243 165-229 (234)
86 KOG4185 Predicted E3 ubiquitin 93.4 0.059 1.3E-06 51.9 3.0 47 195-241 4-54 (296)
87 KOG4739 Uncharacterized protei 93.4 0.026 5.7E-07 52.7 0.5 44 195-241 4-47 (233)
88 COG5222 Uncharacterized conser 93.3 0.04 8.7E-07 52.9 1.6 43 194-239 274-318 (427)
89 PF14446 Prok-RING_1: Prokaryo 93.1 0.062 1.3E-06 39.0 1.9 39 194-236 5-44 (54)
90 KOG1940 Zn-finger protein [Gen 93.0 0.038 8.3E-07 53.0 0.9 45 195-239 159-204 (276)
91 PF07800 DUF1644: Protein of u 92.8 0.086 1.9E-06 46.4 2.7 54 194-250 2-99 (162)
92 KOG2932 E3 ubiquitin ligase in 92.3 0.045 9.7E-07 52.9 0.3 43 195-241 91-133 (389)
93 KOG2114 Vacuolar assembly/sort 91.8 0.052 1.1E-06 58.6 0.3 43 195-242 841-883 (933)
94 KOG0298 DEAD box-containing he 91.5 0.07 1.5E-06 60.0 0.8 45 194-240 1153-1197(1394)
95 PF03854 zf-P11: P-11 zinc fin 91.4 0.062 1.3E-06 37.8 0.2 44 196-244 4-48 (50)
96 KOG3002 Zn finger protein [Gen 91.1 0.12 2.6E-06 50.3 1.9 44 193-243 47-92 (299)
97 TIGR00100 hypA hydrogenase nic 89.9 0.25 5.3E-06 41.3 2.5 37 18-57 65-101 (115)
98 COG5175 MOT2 Transcriptional r 89.7 0.11 2.4E-06 50.8 0.3 50 194-243 14-65 (480)
99 PRK00398 rpoP DNA-directed RNA 89.4 0.36 7.9E-06 33.5 2.7 34 22-56 2-35 (46)
100 PF10272 Tmpp129: Putative tra 88.8 0.31 6.7E-06 48.6 2.7 29 215-243 311-352 (358)
101 PRK03681 hypA hydrogenase nick 88.8 0.35 7.6E-06 40.4 2.7 38 18-57 65-102 (114)
102 KOG2817 Predicted E3 ubiquitin 88.6 0.26 5.6E-06 49.3 2.0 46 194-239 334-382 (394)
103 KOG1001 Helicase-like transcri 87.9 0.13 2.8E-06 55.4 -0.6 45 195-243 455-501 (674)
104 PF10571 UPF0547: Uncharacteri 87.4 0.36 7.7E-06 29.8 1.4 23 26-53 3-25 (26)
105 PRK12380 hydrogenase nickel in 87.2 0.53 1.1E-05 39.3 2.8 36 18-56 65-100 (113)
106 KOG2034 Vacuolar sorting prote 86.9 0.2 4.2E-06 54.6 0.0 34 194-228 817-850 (911)
107 KOG0309 Conserved WD40 repeat- 86.7 0.26 5.7E-06 52.8 0.8 40 196-236 1030-1069(1081)
108 KOG1812 Predicted E3 ubiquitin 86.7 0.32 6.9E-06 49.0 1.4 37 194-230 146-183 (384)
109 PRK00564 hypA hydrogenase nick 86.5 0.54 1.2E-05 39.4 2.5 38 18-57 66-103 (117)
110 KOG3053 Uncharacterized conser 86.2 0.17 3.7E-06 47.7 -0.7 48 194-241 20-81 (293)
111 PRK03824 hypA hydrogenase nick 86.1 0.54 1.2E-05 40.4 2.4 38 19-56 66-121 (135)
112 PF01155 HypA: Hydrogenase exp 85.7 0.35 7.6E-06 40.2 1.0 35 20-57 67-101 (113)
113 PF03604 DNA_RNApol_7kD: DNA d 84.4 1 2.2E-05 29.2 2.5 28 24-53 1-28 (32)
114 KOG1609 Protein involved in mR 83.7 0.32 6.9E-06 46.7 -0.2 50 194-243 78-135 (323)
115 PRK00762 hypA hydrogenase nick 82.9 1 2.2E-05 38.2 2.6 39 18-57 65-107 (124)
116 COG5183 SSM4 Protein involved 82.6 0.45 9.7E-06 51.5 0.4 52 191-243 9-67 (1175)
117 COG2093 DNA-directed RNA polym 82.6 0.61 1.3E-05 34.7 1.0 29 25-58 6-35 (64)
118 KOG0802 E3 ubiquitin ligase [P 82.2 0.62 1.3E-05 49.0 1.2 46 193-245 478-523 (543)
119 PF13240 zinc_ribbon_2: zinc-r 81.9 0.71 1.5E-05 27.5 0.9 23 25-52 1-23 (23)
120 KOG1100 Predicted E3 ubiquitin 81.6 0.81 1.8E-05 42.2 1.7 40 196-242 160-200 (207)
121 KOG3800 Predicted E3 ubiquitin 81.1 0.78 1.7E-05 44.1 1.4 46 196-241 2-50 (300)
122 smart00659 RPOLCX RNA polymera 80.5 1.2 2.6E-05 30.9 1.8 33 23-57 2-34 (44)
123 COG5270 PUA domain (predicted 80.4 0.98 2.1E-05 40.8 1.7 31 20-58 11-41 (202)
124 COG1996 RPC10 DNA-directed RNA 80.1 0.98 2.1E-05 32.1 1.3 37 20-57 3-39 (49)
125 PRK06266 transcription initiat 79.9 0.83 1.8E-05 41.1 1.1 36 19-54 113-148 (178)
126 smart00834 CxxC_CXXC_SSSS Puta 79.4 1.3 2.9E-05 29.4 1.7 29 22-50 4-34 (41)
127 PF05290 Baculo_IE-1: Baculovi 79.0 0.75 1.6E-05 39.4 0.5 51 194-244 80-134 (140)
128 KOG4367 Predicted Zn-finger pr 78.7 0.66 1.4E-05 46.9 0.1 33 193-228 3-35 (699)
129 KOG1829 Uncharacterized conser 78.4 0.51 1.1E-05 49.7 -0.9 41 194-237 511-556 (580)
130 KOG0825 PHD Zn-finger protein 78.4 0.82 1.8E-05 49.4 0.7 50 194-243 96-155 (1134)
131 PF07754 DUF1610: Domain of un 77.1 1.5 3.2E-05 26.6 1.2 22 26-49 1-23 (24)
132 KOG4362 Transcriptional regula 76.5 0.57 1.2E-05 50.1 -1.1 46 194-242 21-69 (684)
133 KOG0269 WD40 repeat-containing 76.5 1.4 3E-05 47.5 1.7 41 195-236 780-820 (839)
134 TIGR00373 conserved hypothetic 74.0 1.2 2.7E-05 39.2 0.5 39 19-58 105-143 (158)
135 KOG3113 Uncharacterized conser 73.8 3.9 8.5E-05 38.8 3.7 87 152-245 59-161 (293)
136 PF13248 zf-ribbon_3: zinc-rib 71.9 2.1 4.5E-05 26.1 1.0 23 24-51 3-25 (26)
137 KOG2066 Vacuolar assembly/sort 71.6 2 4.4E-05 46.5 1.5 46 194-240 784-833 (846)
138 smart00531 TFIIE Transcription 71.5 1.4 3E-05 38.3 0.2 36 20-55 96-136 (147)
139 smart00132 LIM Zinc-binding do 70.9 3.2 6.9E-05 26.5 1.8 38 196-242 1-38 (39)
140 PF13901 DUF4206: Domain of un 69.3 3.1 6.6E-05 38.2 2.0 39 194-238 152-196 (202)
141 TIGR02605 CxxC_CxxC_SSSS putat 68.7 4.8 0.0001 28.3 2.5 35 22-56 4-40 (52)
142 KOG3899 Uncharacterized conser 68.3 1.3 2.8E-05 42.8 -0.8 31 215-245 325-368 (381)
143 PF09538 FYDLN_acid: Protein o 68.2 3.2 6.8E-05 34.5 1.6 29 24-55 10-39 (108)
144 KOG3579 Predicted E3 ubiquitin 67.7 3.5 7.6E-05 39.7 2.0 48 194-242 268-328 (352)
145 KOG4718 Non-SMC (structural ma 67.6 1.9 4.2E-05 39.8 0.3 45 194-240 181-225 (235)
146 PF09723 Zn-ribbon_8: Zinc rib 66.5 5.8 0.00013 27.0 2.4 33 22-54 4-38 (42)
147 KOG1812 Predicted E3 ubiquitin 65.9 3 6.4E-05 42.1 1.3 44 194-237 306-351 (384)
148 KOG1815 Predicted E3 ubiquitin 65.3 3.3 7.2E-05 42.4 1.5 35 194-230 70-104 (444)
149 smart00154 ZnF_AN1 AN1-like Zi 63.7 4 8.7E-05 27.5 1.2 25 26-55 1-25 (39)
150 PF02891 zf-MIZ: MIZ/SP-RING z 63.5 2.5 5.5E-05 30.0 0.2 42 195-239 3-49 (50)
151 PF01363 FYVE: FYVE zinc finge 61.8 6.3 0.00014 29.3 2.1 35 194-228 9-44 (69)
152 PF00628 PHD: PHD-finger; Int 61.6 5.7 0.00012 27.5 1.7 43 196-238 1-49 (51)
153 COG5109 Uncharacterized conser 60.7 4.4 9.5E-05 39.6 1.3 45 194-238 336-383 (396)
154 smart00249 PHD PHD zinc finger 60.1 4.2 9.2E-05 26.8 0.8 31 196-226 1-31 (47)
155 COG5220 TFB3 Cdk activating ki 59.4 3.2 6.9E-05 39.1 0.1 46 194-239 10-61 (314)
156 KOG3161 Predicted E3 ubiquitin 59.0 2.3 5.1E-05 45.1 -0.9 43 194-239 11-54 (861)
157 PF00412 LIM: LIM domain; Int 58.7 8.7 0.00019 27.1 2.3 40 197-245 1-40 (58)
158 PF07191 zinc-ribbons_6: zinc- 58.0 2.7 5.7E-05 32.2 -0.5 40 195-242 2-41 (70)
159 KOG2068 MOT2 transcription fac 57.6 8.8 0.00019 37.7 2.8 49 194-242 249-298 (327)
160 KOG2169 Zn-finger transcriptio 55.9 10 0.00022 40.8 3.2 46 194-246 306-360 (636)
161 KOG3005 GIY-YIG type nuclease 54.4 4.5 9.8E-05 38.6 0.3 48 195-242 183-243 (276)
162 KOG3842 Adaptor protein Pellin 54.0 8.2 0.00018 37.8 1.9 50 194-243 341-415 (429)
163 TIGR02300 FYDLN_acid conserved 53.9 8.4 0.00018 32.9 1.7 29 24-55 10-39 (129)
164 KOG3993 Transcription factor ( 53.7 5.7 0.00012 40.3 0.9 24 27-56 286-309 (500)
165 TIGR02098 MJ0042_CXXC MJ0042 f 53.2 5.2 0.00011 26.2 0.3 30 24-53 3-36 (38)
166 PF13719 zinc_ribbon_5: zinc-r 53.2 7.3 0.00016 25.8 1.0 26 195-220 3-36 (37)
167 TIGR00622 ssl1 transcription f 49.7 28 0.0006 29.1 4.2 44 195-238 56-110 (112)
168 PF08772 NOB1_Zn_bind: Nin one 49.1 13 0.00027 28.8 1.9 33 23-59 9-41 (73)
169 PF04710 Pellino: Pellino; In 48.3 5.9 0.00013 39.9 0.0 50 194-243 328-402 (416)
170 COG4391 Uncharacterized protei 47.6 8.8 0.00019 28.6 0.8 15 39-53 45-59 (62)
171 KOG2807 RNA polymerase II tran 47.6 20 0.00044 35.3 3.5 47 194-240 330-376 (378)
172 PRK12496 hypothetical protein; 47.3 13 0.00028 33.0 2.0 27 23-52 127-153 (164)
173 PF07295 DUF1451: Protein of u 46.7 16 0.00035 31.9 2.5 32 20-52 109-141 (146)
174 smart00647 IBR In Between Ring 45.6 12 0.00027 26.7 1.4 35 21-55 16-53 (64)
175 TIGR00155 pqiA_fam integral me 45.2 12 0.00027 37.9 1.7 31 23-53 13-44 (403)
176 PF01485 IBR: IBR domain; Int 44.0 13 0.00029 26.5 1.3 31 22-52 17-50 (64)
177 KOG4577 Transcription factor L 43.6 13 0.00028 36.0 1.5 53 194-255 92-157 (383)
178 KOG0824 Predicted E3 ubiquitin 43.5 13 0.00028 36.2 1.5 48 193-242 104-151 (324)
179 PF06906 DUF1272: Protein of u 42.9 24 0.00051 25.9 2.4 47 195-243 6-53 (57)
180 PF04216 FdhE: Protein involve 42.9 6.8 0.00015 37.7 -0.5 46 194-240 172-220 (290)
181 PF08271 TF_Zn_Ribbon: TFIIB z 42.9 9.8 0.00021 25.8 0.4 33 24-57 1-33 (43)
182 COG1439 Predicted nucleic acid 42.4 17 0.00038 32.7 2.0 25 23-52 139-163 (177)
183 cd00065 FYVE FYVE domain; Zinc 42.1 14 0.0003 26.1 1.1 35 195-229 3-38 (57)
184 PRK06393 rpoE DNA-directed RNA 42.0 14 0.0003 27.8 1.1 18 26-50 8-25 (64)
185 PF05605 zf-Di19: Drought indu 41.2 15 0.00033 26.1 1.2 11 42-52 2-12 (54)
186 PF06844 DUF1244: Protein of u 40.7 9.1 0.0002 28.9 -0.0 12 218-229 11-22 (68)
187 PF14169 YdjO: Cold-inducible 40.4 33 0.00072 25.4 2.9 40 18-57 13-54 (59)
188 PF07975 C1_4: TFIIH C1-like d 40.4 13 0.00028 26.7 0.7 42 197-238 2-50 (51)
189 smart00064 FYVE Protein presen 39.7 13 0.00027 27.5 0.6 36 194-229 10-46 (68)
190 smart00661 RPOL9 RNA polymeras 39.2 17 0.00037 25.2 1.2 31 25-57 2-33 (52)
191 PF13717 zinc_ribbon_4: zinc-r 39.0 15 0.00032 24.2 0.8 26 195-220 3-36 (36)
192 KOG3039 Uncharacterized conser 36.9 17 0.00036 34.6 1.1 32 195-229 44-75 (303)
193 PF04710 Pellino: Pellino; In 36.8 11 0.00025 37.9 0.0 31 209-242 303-339 (416)
194 COG1198 PriA Primosomal protei 36.4 24 0.00053 38.6 2.4 34 19-58 458-491 (730)
195 PF05191 ADK_lid: Adenylate ki 36.4 33 0.00072 22.6 2.2 33 23-55 1-34 (36)
196 PRK13794 hypothetical protein; 35.8 19 0.00041 37.4 1.4 29 22-58 9-37 (479)
197 PRK08351 DNA-directed RNA poly 35.8 21 0.00046 26.6 1.3 19 25-50 5-23 (61)
198 COG3813 Uncharacterized protei 35.7 11 0.00023 29.1 -0.3 29 22-54 25-53 (84)
199 TIGR01206 lysW lysine biosynth 35.3 21 0.00046 25.9 1.2 31 23-53 2-33 (54)
200 KOG1074 Transcriptional repres 35.0 24 0.00053 38.9 2.1 55 188-242 599-679 (958)
201 PF00527 E7: E7 protein, Early 34.6 8.5 0.00018 30.9 -1.1 29 20-48 45-91 (92)
202 PF14255 Cys_rich_CPXG: Cystei 34.5 27 0.00059 25.1 1.6 18 43-60 1-18 (52)
203 PRK15103 paraquat-inducible me 34.1 22 0.00048 36.3 1.6 29 24-52 11-40 (419)
204 PHA02776 E7 protein; Provision 33.7 14 0.00031 30.3 0.1 31 20-50 51-99 (101)
205 COG1579 Zn-ribbon protein, pos 33.5 13 0.00029 35.1 -0.1 29 22-50 196-229 (239)
206 PF02148 zf-UBP: Zn-finger in 33.3 22 0.00047 26.1 1.0 15 20-34 46-60 (63)
207 KOG4185 Predicted E3 ubiquitin 33.3 8.2 0.00018 37.0 -1.6 47 194-240 207-265 (296)
208 KOG4443 Putative transcription 33.0 18 0.00039 38.7 0.7 26 214-239 40-70 (694)
209 KOG1815 Predicted E3 ubiquitin 32.9 18 0.0004 37.0 0.7 37 194-230 226-267 (444)
210 PF10263 SprT-like: SprT-like 32.5 24 0.00051 30.3 1.3 35 20-54 120-155 (157)
211 KOG2879 Predicted E3 ubiquitin 32.2 17 0.00036 35.0 0.3 28 21-51 258-285 (298)
212 TIGR00155 pqiA_fam integral me 32.0 28 0.00061 35.3 1.9 26 23-52 215-240 (403)
213 PF13913 zf-C2HC_2: zinc-finge 31.3 15 0.00033 22.1 -0.1 13 43-55 3-15 (25)
214 KOG1729 FYVE finger containing 31.0 13 0.00028 36.1 -0.7 37 195-231 215-251 (288)
215 PF14353 CpXC: CpXC protein 30.8 28 0.0006 29.1 1.4 18 42-59 1-18 (128)
216 PF03811 Zn_Tnp_IS1: InsA N-te 30.7 22 0.00047 23.6 0.5 11 41-51 4-14 (36)
217 PF10122 Mu-like_Com: Mu-like 30.2 16 0.00034 26.2 -0.2 31 22-52 3-34 (51)
218 PF06750 DiS_P_DiS: Bacterial 29.9 43 0.00094 26.8 2.3 44 194-249 33-76 (92)
219 PF06220 zf-U1: U1 zinc finger 29.6 21 0.00045 23.9 0.3 12 22-33 2-13 (38)
220 COG1675 TFA1 Transcription ini 29.0 15 0.00032 33.2 -0.6 38 20-58 110-147 (176)
221 KOG2231 Predicted E3 ubiquitin 29.0 31 0.00066 37.3 1.6 44 196-242 2-52 (669)
222 PF12773 DZR: Double zinc ribb 28.5 39 0.00084 23.3 1.6 27 22-50 11-37 (50)
223 PF14968 CCDC84: Coiled coil p 28.3 29 0.00063 34.5 1.2 33 18-57 53-85 (336)
224 PRK12495 hypothetical protein; 28.3 33 0.00071 32.0 1.5 32 20-54 39-70 (226)
225 KOG2071 mRNA cleavage and poly 27.5 39 0.00084 35.9 2.0 34 194-227 513-556 (579)
226 PRK00432 30S ribosomal protein 27.4 29 0.00064 24.6 0.8 15 42-56 20-34 (50)
227 PF00130 C1_1: Phorbol esters/ 27.4 39 0.00085 23.4 1.5 33 194-226 11-45 (53)
228 PF13832 zf-HC5HC2H_2: PHD-zin 27.1 27 0.00059 28.2 0.7 32 194-227 55-88 (110)
229 KOG2041 WD40 repeat protein [G 26.9 39 0.00084 36.9 1.9 44 194-241 1131-1184(1189)
230 PRK11827 hypothetical protein; 26.6 28 0.00061 25.8 0.6 20 225-244 2-21 (60)
231 PF14803 Nudix_N_2: Nudix N-te 26.5 24 0.00051 23.1 0.2 25 25-49 2-29 (34)
232 PF02318 FYVE_2: FYVE-type zin 26.3 58 0.0013 27.0 2.6 45 194-239 54-102 (118)
233 PRK04338 N(2),N(2)-dimethylgua 25.9 47 0.001 33.4 2.3 30 22-53 243-272 (382)
234 PF11261 IRF-2BP1_2: Interfero 25.8 31 0.00068 24.8 0.7 28 22-49 2-31 (54)
235 PF06044 DRP: Dam-replacing fa 25.8 19 0.00041 34.1 -0.5 30 23-52 31-63 (254)
236 PF14787 zf-CCHC_5: GAG-polypr 25.0 38 0.00083 22.5 0.9 11 43-53 3-13 (36)
237 PF14311 DUF4379: Domain of un 25.0 46 0.001 23.6 1.5 22 215-237 34-55 (55)
238 TIGR01053 LSD1 zinc finger dom 24.9 46 0.001 21.3 1.3 25 24-49 2-26 (31)
239 PF10276 zf-CHCC: Zinc-finger 24.8 17 0.00037 24.7 -0.7 12 42-53 29-40 (40)
240 PRK11088 rrmA 23S rRNA methylt 24.3 40 0.00087 31.8 1.4 26 195-220 3-28 (272)
241 TIGR00595 priA primosomal prot 24.3 59 0.0013 33.9 2.7 30 21-56 238-267 (505)
242 PF07649 C1_3: C1-like domain; 24.0 25 0.00054 21.9 -0.1 29 196-224 2-30 (30)
243 PF08792 A2L_zn_ribbon: A2L zi 23.7 35 0.00076 22.1 0.6 29 23-52 3-31 (33)
244 cd04718 BAH_plant_2 BAH, or Br 23.7 31 0.00067 30.3 0.4 24 219-242 2-29 (148)
245 TIGR00308 TRM1 tRNA(guanine-26 23.6 59 0.0013 32.7 2.5 32 22-53 232-263 (374)
246 PRK13795 hypothetical protein; 23.5 56 0.0012 35.2 2.4 29 22-58 11-39 (636)
247 PRK05978 hypothetical protein; 23.4 47 0.001 29.1 1.5 32 195-244 34-65 (148)
248 PRK10220 hypothetical protein; 23.4 41 0.00089 28.0 1.1 28 26-55 6-33 (111)
249 PF04423 Rad50_zn_hook: Rad50 22.6 25 0.00055 24.9 -0.3 13 232-244 21-33 (54)
250 KOG4218 Nuclear hormone recept 22.5 30 0.00065 34.4 0.1 46 194-240 15-76 (475)
251 PF13771 zf-HC5HC2H: PHD-like 22.5 24 0.00052 27.4 -0.5 33 194-226 36-68 (90)
252 PRK03564 formate dehydrogenase 22.4 60 0.0013 31.9 2.2 44 194-239 187-234 (309)
253 PF12760 Zn_Tnp_IS1595: Transp 22.4 52 0.0011 22.6 1.3 11 41-51 17-27 (46)
254 PF09889 DUF2116: Uncharacteri 21.9 50 0.0011 24.4 1.2 16 230-245 2-17 (59)
255 PLN02436 cellulose synthase A 21.9 70 0.0015 36.5 2.8 49 194-242 36-89 (1094)
256 PRK14873 primosome assembly pr 21.8 66 0.0014 34.9 2.6 31 21-58 408-438 (665)
257 PF06937 EURL: EURL protein; 21.8 49 0.0011 31.8 1.4 45 195-241 31-78 (285)
258 PF07282 OrfB_Zn_ribbon: Putat 21.8 98 0.0021 22.7 2.8 31 194-224 28-61 (69)
259 PF14569 zf-UDP: Zinc-binding 21.7 59 0.0013 25.5 1.5 48 194-241 9-61 (80)
260 PLN02189 cellulose synthase 21.6 74 0.0016 36.2 2.9 49 194-242 34-87 (1040)
261 COG5257 GCD11 Translation init 21.0 69 0.0015 32.0 2.2 28 20-51 54-81 (415)
262 PF01396 zf-C4_Topoisom: Topoi 21.0 57 0.0012 21.8 1.2 14 43-56 2-15 (39)
263 TIGR02159 PA_CoA_Oxy4 phenylac 20.9 55 0.0012 28.5 1.4 17 42-58 105-121 (146)
264 KOG1597 Transcription initiati 20.9 44 0.00095 32.6 0.9 31 25-55 2-34 (308)
265 COG4068 Uncharacterized protei 20.8 59 0.0013 24.1 1.3 17 230-246 7-23 (64)
266 KOG0956 PHD finger protein AF1 20.5 31 0.00066 37.4 -0.3 65 177-241 100-181 (900)
267 PRK06260 threonine synthase; V 20.4 71 0.0015 32.1 2.3 29 22-53 2-30 (397)
268 TIGR01562 FdhE formate dehydro 20.3 46 0.001 32.6 0.9 45 194-239 184-232 (305)
269 COG1066 Sms Predicted ATP-depe 20.2 89 0.0019 32.1 2.9 34 22-60 6-41 (456)
270 PRK05580 primosome assembly pr 20.2 79 0.0017 34.3 2.7 31 21-57 406-436 (679)
No 1
>PF14369 zf-RING_3: zinc-finger
Probab=99.65 E-value=7.4e-17 Score=106.66 Aligned_cols=35 Identities=66% Similarity=1.462 Sum_probs=31.2
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi 56 (352)
++||||+|+|+|++.+...++++||+|++||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 58999999999999776666777999999999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.60 E-value=5.8e-16 Score=150.31 Aligned_cols=80 Identities=29% Similarity=0.695 Sum_probs=68.3
Q ss_pred CCCCCCHHHHhhCCcceeccccccCCCCccccccccccccCCceEcccCceecccchHHHhhcCC-CCCccCCCCCCCCh
Q 018689 168 GTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN-SCPVCRYELPTDDP 246 (352)
Q Consensus 168 g~~pas~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~-sCP~CR~~l~~~~~ 246 (352)
....+.+..++++|..+++..........|+||+|+|+.++++++|||+|.||..||++||.++. .||+||.++.+...
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 45578899999999999987655333359999999999999999999999999999999998775 59999999876554
Q ss_pred h
Q 018689 247 D 247 (352)
Q Consensus 247 ~ 247 (352)
.
T Consensus 283 ~ 283 (348)
T KOG4628|consen 283 S 283 (348)
T ss_pred C
Confidence 3
No 3
>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=99.49 E-value=5.5e-15 Score=102.71 Aligned_cols=44 Identities=45% Similarity=1.196 Sum_probs=40.6
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCR 238 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR 238 (352)
.+|+||++.|..++.++.|+|+|+||..||.+|++.+.+||+||
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 4
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.33 E-value=2.7e-12 Score=123.88 Aligned_cols=70 Identities=29% Similarity=0.760 Sum_probs=53.1
Q ss_pred CHHHHhhCCcceeccccccCCCCcccccccc-cccc---------CCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 173 SKSAIEALPSIKINEAMMSSDSSQCAVCKDS-FELN---------EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 173 s~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~-~~~~---------~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
.|+.-+.+|++..+ ....++..|.||+++ |+.+ .++++|||||+||.+|++.|++++.+||+||.++.
T Consensus 268 ~kdl~~~~~t~t~e--ql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 268 TKDLNAMYPTATEE--QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred hhHHHhhcchhhhh--hhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 34444445544433 334557899999999 5443 35799999999999999999999999999999965
Q ss_pred CC
Q 018689 243 TD 244 (352)
Q Consensus 243 ~~ 244 (352)
-+
T Consensus 346 fd 347 (491)
T COG5243 346 FD 347 (491)
T ss_pred cc
Confidence 43
No 5
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=5.4e-12 Score=119.08 Aligned_cols=50 Identities=40% Similarity=1.022 Sum_probs=46.8
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~ 243 (352)
.-+|+|||+.|..+++++.|||.|.||..||++|+. -++.||+||.++|+
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 579999999999999999999999999999999997 67899999999985
No 6
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.20 E-value=7e-12 Score=116.94 Aligned_cols=71 Identities=27% Similarity=0.593 Sum_probs=55.3
Q ss_pred CCHHHHhhCCcceeccccc--cCCCCccccccccccccCC-----ceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 172 ASKSAIEALPSIKINEAMM--SSDSSQCAVCKDSFELNEE-----ARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 172 as~~~i~~lp~~~~~~~~~--~~~~~~C~IC~e~~~~~~~-----~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
.++..++.+|.+...-+.. ...+.+|+||++.+..... .+.++|+|.||..||.+|++.+.+||+||..+.
T Consensus 150 ~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 150 NYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred hhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 3888899999886543322 2335899999999865431 244569999999999999999999999999875
No 7
>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=99.20 E-value=9e-12 Score=96.07 Aligned_cols=45 Identities=40% Similarity=1.001 Sum_probs=36.0
Q ss_pred CCcccccccccccc----------CCceEcccCceecccchHHHhhcCCCCCccC
Q 018689 194 SSQCAVCKDSFELN----------EEARQMPCKHIYHPDCIMPWLELHNSCPVCR 238 (352)
Q Consensus 194 ~~~C~IC~e~~~~~----------~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR 238 (352)
...|+||++.|... -.+...+|+|.||..||.+||+.+.+||+||
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 45699999999332 2344557999999999999999999999998
No 8
>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=98.93 E-value=4.3e-10 Score=80.15 Aligned_cols=46 Identities=24% Similarity=0.753 Sum_probs=39.9
Q ss_pred CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
+..|.||++.... +..+||||. |+..|+..|++....||+||+++.
T Consensus 2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4689999998655 889999999 999999999999999999999874
No 9
>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=98.89 E-value=7.3e-10 Score=75.39 Aligned_cols=44 Identities=36% Similarity=1.073 Sum_probs=36.5
Q ss_pred ccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCC
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYEL 241 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l 241 (352)
+|+||++.+. .....++|+|.||..|++.|++. ...||+||..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 5999999982 33555559999999999999987 77899999864
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.88 E-value=9e-10 Score=99.25 Aligned_cols=50 Identities=24% Similarity=0.634 Sum_probs=41.8
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhc----------------CCCCCccCCCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL----------------HNSCPVCRYELPTDD 245 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~----------------~~sCP~CR~~l~~~~ 245 (352)
+..+|+||++.++. +++++|||.||..||.+|+.. +..||+||..+...+
T Consensus 17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 35899999999865 678899999999999999852 347999999996544
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.86 E-value=1.1e-09 Score=74.14 Aligned_cols=39 Identities=36% Similarity=0.923 Sum_probs=33.4
Q ss_pred cccccccccccCCceEcccCceecccchHHHhhcCCCCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~C 237 (352)
|+||++.+.. .++.++|||.||..||.+|++.+.+||+|
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 8999999877 34788999999999999999998999998
No 12
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=8.6e-10 Score=103.97 Aligned_cols=49 Identities=27% Similarity=0.800 Sum_probs=44.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
...|.||++.... +..+||||+||..||..|+..+..||+||.++.+.+
T Consensus 239 ~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 239 TRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK 287 (293)
T ss_pred CCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence 5799999998655 789999999999999999999999999999987654
No 13
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.82 E-value=7.8e-10 Score=115.18 Aligned_cols=50 Identities=30% Similarity=0.935 Sum_probs=45.0
Q ss_pred CCCccccccccccccCC--ceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 193 DSSQCAVCKDSFELNEE--ARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~--~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
....|+||+|.+..+.+ +++|+|+|+||..|++.|+++.++||+||..+.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY 341 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence 36899999999988655 899999999999999999999999999999543
No 14
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.78 E-value=2.3e-09 Score=98.42 Aligned_cols=49 Identities=29% Similarity=0.717 Sum_probs=41.9
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc---CCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL---HNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~~~~ 245 (352)
..+|.|||+.-++ +++..|||.||..||.+||.. .+.||+||..|..+.
T Consensus 47 ~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 47 FFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred ceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 5899999998555 888889999999999999975 446999999987654
No 15
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.76 E-value=2.5e-09 Score=84.11 Aligned_cols=50 Identities=28% Similarity=0.822 Sum_probs=38.8
Q ss_pred CCccccccccccc--------cCC-ceEc-ccCceecccchHHHhhc---CCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFEL--------NEE-ARQM-PCKHIYHPDCIMPWLEL---HNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~--------~~~-~~~l-pC~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~~ 243 (352)
++.|.||+..|.. ++. +.++ .|+|.||..||.+||.. +..||+||+++..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 5789999999862 222 3333 49999999999999975 4689999998753
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.74 E-value=4.3e-09 Score=72.55 Aligned_cols=38 Identities=32% Similarity=0.816 Sum_probs=30.2
Q ss_pred cccccccccccCCceEcccCceecccchHHHhhcC----CCCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----NSCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP~C 237 (352)
|+||++.|.. ++.|+|||.|+..||..|++.. ..||+|
T Consensus 1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999988 8999999999999999999653 369988
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=98.72 E-value=8.7e-09 Score=76.28 Aligned_cols=47 Identities=21% Similarity=0.399 Sum_probs=42.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~ 244 (352)
..|+||++.+.. ++.++|||+|++.||.+|++.+.+||+|+..+...
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 579999999877 68889999999999999998899999999988543
No 18
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=5.7e-09 Score=92.17 Aligned_cols=50 Identities=28% Similarity=0.689 Sum_probs=42.2
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
....|+|||+.+.... +....|||+||+.||+.-|+....||+|+++|..
T Consensus 130 ~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 3589999999997732 2346799999999999999999999999997754
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.67 E-value=8.2e-09 Score=71.68 Aligned_cols=44 Identities=25% Similarity=0.748 Sum_probs=39.0
Q ss_pred ccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
.|.||++.|.......+++|||+|+..||..+......||+||+
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 49999999966667899999999999999999866778999985
No 20
>PHA02926 zinc finger-like protein; Provisional
Probab=98.66 E-value=6.2e-09 Score=95.11 Aligned_cols=52 Identities=25% Similarity=0.701 Sum_probs=38.7
Q ss_pred cCCCCcccccccccccc-----CCceEc-ccCceecccchHHHhhcC------CCCCccCCCCC
Q 018689 191 SSDSSQCAVCKDSFELN-----EEARQM-PCKHIYHPDCIMPWLELH------NSCPVCRYELP 242 (352)
Q Consensus 191 ~~~~~~C~IC~e~~~~~-----~~~~~l-pC~H~FH~~Ci~~Wl~~~------~sCP~CR~~l~ 242 (352)
.+.+.+|+||++.+-.. ....+| +|+|.||..||..|.+.+ .+||+||..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 34468999999986332 122344 599999999999999753 46999999764
No 21
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.64 E-value=1.5e-08 Score=68.90 Aligned_cols=39 Identities=38% Similarity=1.036 Sum_probs=33.7
Q ss_pred cccccccccccCCceEcccCceecccchHHHhh--cCCCCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE--LHNSCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~--~~~sCP~C 237 (352)
|+||++.+... ...++|+|.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999998772 35889999999999999998 46689998
No 22
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.60 E-value=1.6e-08 Score=66.31 Aligned_cols=38 Identities=34% Similarity=1.121 Sum_probs=33.2
Q ss_pred cccccccccccCCceEcccCceecccchHHHhh-cCCCCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~C 237 (352)
|+||++.. .....++|+|.||..|++.|++ ....||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 88999883 4588899999999999999998 66789998
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.49 E-value=5.7e-08 Score=96.96 Aligned_cols=48 Identities=33% Similarity=0.732 Sum_probs=42.7
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~ 244 (352)
...|+||++.|.. +++++|+|.||..||..||.....||+||..+...
T Consensus 26 ~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 26 SLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred ccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 5899999999866 66889999999999999998888999999988653
No 24
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.47 E-value=5.2e-08 Score=75.10 Aligned_cols=47 Identities=28% Similarity=0.723 Sum_probs=34.3
Q ss_pred cccccccccccCCceEc-c-cCceecccchHHHhhcCCCCCccCCCCCC
Q 018689 197 CAVCKDSFELNEEARQM-P-CKHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~l-p-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
|+-|.-.+..+++..+. . |.|.||..||.+||..++.||++|++...
T Consensus 34 C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred CcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 33333333344444333 3 99999999999999999999999998753
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.32 E-value=6.4e-08 Score=74.03 Aligned_cols=49 Identities=29% Similarity=0.887 Sum_probs=38.0
Q ss_pred CCccccccccccc--------cCC-ceEcc-cCceecccchHHHhhc---CCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFEL--------NEE-ARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~--------~~~-~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~~l~ 242 (352)
++.|-||...|.. ++. +.++. |.|.||..||.+||.. +..||+||+++.
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 5699999999853 333 33444 9999999999999954 457999999864
No 26
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.28 E-value=3.4e-07 Score=63.39 Aligned_cols=38 Identities=29% Similarity=0.871 Sum_probs=22.9
Q ss_pred cccccccccc-cCCceEcccCceecccchHHHhhcC----CCCC
Q 018689 197 CAVCKDSFEL-NEEARQMPCKHIYHPDCIMPWLELH----NSCP 235 (352)
Q Consensus 197 C~IC~e~~~~-~~~~~~lpC~H~FH~~Ci~~Wl~~~----~sCP 235 (352)
|+||++ |.. ...+++|+|||+|+++||.+|++.. ..||
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 744 4557889999999999999999753 2576
No 27
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=1.6e-07 Score=87.82 Aligned_cols=49 Identities=29% Similarity=0.836 Sum_probs=41.6
Q ss_pred CCccccccccccccC-------CceEcccCceecccchHHHh--hcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNE-------EARQMPCKHIYHPDCIMPWL--ELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~-------~~~~lpC~H~FH~~Ci~~Wl--~~~~sCP~CR~~l~ 242 (352)
+..|+||-..+.... +.-+|.|+|+||..||+-|. -++.+||.|+..+.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 479999998886544 67889999999999999995 56789999988774
No 28
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=3.4e-07 Score=85.61 Aligned_cols=48 Identities=25% Similarity=0.779 Sum_probs=41.1
Q ss_pred CCccccccccccccCCceEcccCceecccchHH-HhhcCCC-CCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMP-WLELHNS-CPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~-Wl~~~~s-CP~CR~~l~~~ 244 (352)
+..|+||++..+. +..++|||+||..||.. |-.++.- ||+||+.+..+
T Consensus 215 d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk 264 (271)
T COG5574 215 DYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK 264 (271)
T ss_pred ccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence 5789999998666 88999999999999999 9766655 99999987654
No 29
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.22 E-value=5e-07 Score=69.55 Aligned_cols=49 Identities=24% Similarity=0.443 Sum_probs=39.6
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~~ 245 (352)
...|+||.+.|.+ +++++|||.|.+.||..||+. +.+||+|+..+...+
T Consensus 4 ~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~ 53 (73)
T PF04564_consen 4 EFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD 53 (73)
T ss_dssp GGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred ccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence 4789999999988 889999999999999999988 889999999887644
No 30
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.21 E-value=5e-07 Score=64.31 Aligned_cols=42 Identities=24% Similarity=0.838 Sum_probs=33.7
Q ss_pred ccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccC
Q 018689 196 QCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCR 238 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR 238 (352)
.|.||++ ...++...++||. |.+|..|+.+|+.. +.+||+|+
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 4445566788985 89999999999955 44899995
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.15 E-value=4.6e-07 Score=87.24 Aligned_cols=49 Identities=27% Similarity=0.735 Sum_probs=45.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
...|-||.+.|.. +.+.||+|.||.-||..+|..+..||.|+.++...+
T Consensus 23 lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~ 71 (442)
T KOG0287|consen 23 LLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD 71 (442)
T ss_pred HHHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccchhh
Confidence 4789999999988 789999999999999999999999999999987654
No 32
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.15 E-value=2.8e-07 Score=98.02 Aligned_cols=68 Identities=26% Similarity=0.670 Sum_probs=47.6
Q ss_pred HHHhhCCcceeccccccCCCCccccccccccccC---CceEcc-cCceecccchHHHhhc--CCCCCccCCCCC
Q 018689 175 SAIEALPSIKINEAMMSSDSSQCAVCKDSFELNE---EARQMP-CKHIYHPDCIMPWLEL--HNSCPVCRYELP 242 (352)
Q Consensus 175 ~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~---~~~~lp-C~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~ 242 (352)
+..+.|...+......-+..++|+||+..+..-+ .-+..+ |+|.||..|+.+|++. +++||+||.+++
T Consensus 1450 s~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1450 SFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3445555555555444455789999998876211 122333 9999999999999976 568999998875
No 33
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=8.5e-07 Score=89.65 Aligned_cols=49 Identities=29% Similarity=0.765 Sum_probs=40.2
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc-----CCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-----HNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-----~~sCP~CR~~l~~~~ 245 (352)
+..|+||++.... +..+.|||+||..||.++|.. ...||+||..|-.++
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 4799999998665 566669999999999998754 457999999886644
No 34
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=5.4e-07 Score=90.36 Aligned_cols=51 Identities=33% Similarity=1.004 Sum_probs=40.8
Q ss_pred CCCccccccccccccC--------------CceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689 193 DSSQCAVCKDSFELNE--------------EARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT 243 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~--------------~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~ 243 (352)
....|+||+..+..-. .-...||.|+||..|+..|.. .+-.||+||..|+.
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 3578999999875321 134559999999999999998 55699999999874
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.98 E-value=2.1e-06 Score=81.26 Aligned_cols=46 Identities=26% Similarity=0.614 Sum_probs=41.8
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
...|-||.+.|.. ....+|||.||.-||+..|..+..||+||.+..
T Consensus 25 ~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 4789999999887 678889999999999999999999999998753
No 36
>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=97.96 E-value=3.9e-06 Score=80.98 Aligned_cols=50 Identities=24% Similarity=0.436 Sum_probs=37.1
Q ss_pred CCccccccccccccCCc--eEcccCceecccchHHHh-hcCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEA--RQMPCKHIYHPDCIMPWL-ELHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~--~~lpC~H~FH~~Ci~~Wl-~~~~sCP~CR~~l~~ 243 (352)
+..|+||+..--..... .+.+|||.||..||+..+ .....||.|+..+..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 46899999964333333 333799999999999965 445689999987754
No 37
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.96 E-value=1.7e-06 Score=66.10 Aligned_cols=49 Identities=20% Similarity=0.539 Sum_probs=22.9
Q ss_pred CCcccccccccc-ccCCc-eEc---ccCceecccchHHHhhc----C-------CCCCccCCCCC
Q 018689 194 SSQCAVCKDSFE-LNEEA-RQM---PCKHIYHPDCIMPWLEL----H-------NSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~-~~~~~-~~l---pC~H~FH~~Ci~~Wl~~----~-------~sCP~CR~~l~ 242 (352)
+.+|.||+..+. .++.+ ... .|++.||..||.+||.. + ..||.|+.+|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 368999999876 32222 222 49999999999999953 1 14999999874
No 38
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=3.7e-06 Score=68.06 Aligned_cols=49 Identities=33% Similarity=0.742 Sum_probs=37.5
Q ss_pred CCccccccccccc------------cCCc-eEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFEL------------NEEA-RQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~------------~~~~-~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
.+.|+||...+-+ .++. +... |.|.||..||.+||+.++.||+|.++..
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~ 108 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV 108 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence 4689999876521 1223 3333 9999999999999999999999988754
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=3.9e-06 Score=78.03 Aligned_cols=44 Identities=32% Similarity=0.714 Sum_probs=39.0
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
+...|+||++.|... ++++|+|.||..||..|+.....||.||.
T Consensus 12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 468999999999884 89999999999999999885568999993
No 40
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.73 E-value=1e-05 Score=80.61 Aligned_cols=48 Identities=33% Similarity=0.901 Sum_probs=38.8
Q ss_pred CCCccccccccccccC-CceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 193 DSSQCAVCKDSFELNE-EARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
+..+|+||||.+...- .++...|.|.||..|+.+|. ..+||+||.-..
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 4579999999997643 24555699999999999994 457999999765
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.66 E-value=2.3e-05 Score=58.49 Aligned_cols=47 Identities=28% Similarity=0.654 Sum_probs=24.9
Q ss_pred CCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
...|++|.+.++. ++.| .|.|+|+..||..-+.. .||+|+.+.-..|
T Consensus 7 lLrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 7 LLRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp TTS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred hcCCcHHHHHhcC---CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 4689999999876 5444 59999999999986653 4999998765443
No 42
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=1.2e-05 Score=78.84 Aligned_cols=47 Identities=32% Similarity=0.930 Sum_probs=36.9
Q ss_pred CccccccccccccCCceEcc-cCceecccchHHHhhc---CCCCCccCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRYEL 241 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~~l 241 (352)
..|.||.+-+-...++.-+. |||+||..|+.+|++. ...||+|+-.+
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 58999966555555566666 9999999999999976 34799999444
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=2.1e-05 Score=76.61 Aligned_cols=47 Identities=23% Similarity=0.678 Sum_probs=40.9
Q ss_pred CCccccccccccccCCceEcccCce-ecccchHHHhhcCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
..+|.||+.+-++ ..+|||.|. .|..|.+..--+++.||+||+.+..
T Consensus 290 gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 290 GKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred CCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 6799999999666 899999997 7899999876778999999998853
No 44
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.58 E-value=1.1e-05 Score=84.91 Aligned_cols=50 Identities=26% Similarity=0.536 Sum_probs=44.5
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
...|+||+..+.+.......+|+|+||..||..|-+.-++||+||.++..
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 46899999999887777777899999999999999999999999998743
No 45
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=4.1e-05 Score=73.04 Aligned_cols=48 Identities=21% Similarity=0.557 Sum_probs=40.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc-CCCCCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~~ 244 (352)
..+|+||+..... ++.|+|+|.||..||+--... +.+|++||.+|...
T Consensus 7 ~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 7 KKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 4689999998554 688999999999999987655 55799999999653
No 46
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=1.1e-05 Score=78.50 Aligned_cols=47 Identities=30% Similarity=0.656 Sum_probs=38.9
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHhhc-CCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLEL-HNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~-~~sCP~CR~~l~~ 243 (352)
+..|+||++.++. .+..+ |.|.||..||.+-|+. .++||.||+.+..
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 5799999999876 34444 9999999999998865 7799999998743
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=5.6e-05 Score=74.35 Aligned_cols=48 Identities=27% Similarity=0.799 Sum_probs=37.1
Q ss_pred CCccccccccccccC----CceEcc-cCceecccchHHHh--hc-----CCCCCccCCCC
Q 018689 194 SSQCAVCKDSFELNE----EARQMP-CKHIYHPDCIMPWL--EL-----HNSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~----~~~~lp-C~H~FH~~Ci~~Wl--~~-----~~sCP~CR~~l 241 (352)
+..|.||++.+.... .-.+|| |.|.||..||..|- .+ ...||.||...
T Consensus 161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 589999999875532 122345 99999999999997 44 46899999865
No 48
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00017 Score=71.31 Aligned_cols=48 Identities=27% Similarity=0.800 Sum_probs=38.1
Q ss_pred CCccccccccccccC--CceEcccCceecccchHHHhhc--CCCCCccCCCC
Q 018689 194 SSQCAVCKDSFELNE--EARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~--~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l 241 (352)
..+|+||++.++..- ....+.|||.|-..||++||-+ ...||.|..+.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 478999999997543 3555569999999999999942 34799997765
No 49
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.18 E-value=6.2e-05 Score=71.75 Aligned_cols=90 Identities=22% Similarity=0.446 Sum_probs=57.9
Q ss_pred cHHHHHHHHHhcCCCCCCCCCCCHHHHhhCCcceeccccccCCCCccccccccccccCCceEcccCceecccchHHHhhc
Q 018689 151 GLEQLIQQLAENDPNRYGTPPASKSAIEALPSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL 230 (352)
Q Consensus 151 ~le~li~~L~~~~~~~~g~~pas~~~i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~ 230 (352)
.|..|..++...-....+ -|.--..|+....+..... -...+|.|||--|..++...+.+|-|.||..|+.++|..
T Consensus 76 ~~~~i~~~~~~iikq~~g-~pii~~lie~~~e~LT~nn---~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~ 151 (368)
T KOG4445|consen 76 EFREIQRQIQEIIKQNSG-MPIICQLIEHCSEFLTENN---HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTE 151 (368)
T ss_pred HHHHHHHHHHHHHHhcCC-CchhHHHHHHHHHHcccCC---CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHH
Confidence 455666665554333444 2333334433222211111 124689999999999998999999999999999887621
Q ss_pred -----------------------CCCCCccCCCCCCC
Q 018689 231 -----------------------HNSCPVCRYELPTD 244 (352)
Q Consensus 231 -----------------------~~sCP~CR~~l~~~ 244 (352)
...||+||..|..+
T Consensus 152 ~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e 188 (368)
T KOG4445|consen 152 CLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE 188 (368)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence 12599999988544
No 50
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.17 E-value=0.0001 Score=72.63 Aligned_cols=48 Identities=25% Similarity=0.894 Sum_probs=40.1
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPTDD 245 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~~~ 245 (352)
..|.||-|. +..+++-||||..|..|+..|-.. .++||.||.+|.-.+
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 579999887 445888899999999999999733 679999999986544
No 51
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.13 E-value=0.0001 Score=78.04 Aligned_cols=48 Identities=23% Similarity=0.655 Sum_probs=40.1
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhh-cCCCCCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~~ 244 (352)
-..|++|-..+++ +++..|+|+||..||.+-+. ++..||.|...+-.-
T Consensus 643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 4689999988766 66677999999999999995 577899998887543
No 52
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.07 E-value=3.3e-05 Score=55.62 Aligned_cols=47 Identities=26% Similarity=0.622 Sum_probs=35.1
Q ss_pred CCccccccccccccCCceEcccCce-ecccchHHHh-hcCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHI-YHPDCIMPWL-ELHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~-FH~~Ci~~Wl-~~~~sCP~CR~~l~~ 243 (352)
..+|.||+|.-.+ .++..|||+ .|..|-.+.+ ..+..||+||.++..
T Consensus 7 ~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 7 SDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD 55 (62)
T ss_pred ccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence 3789999987544 445569997 6788855544 478999999998753
No 53
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.95 E-value=0.00033 Score=61.38 Aligned_cols=42 Identities=26% Similarity=0.786 Sum_probs=36.1
Q ss_pred CcceeccccccCCCCccccccccccccCCceEcccCceeccc
Q 018689 181 PSIKINEAMMSSDSSQCAVCKDSFELNEEARQMPCKHIYHPD 222 (352)
Q Consensus 181 p~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~ 222 (352)
|.+.+.+..+..+..+|.||+|+++.++.+..|||-.+||+.
T Consensus 164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK~ 205 (205)
T KOG0801|consen 164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHKQ 205 (205)
T ss_pred cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeecC
Confidence 455666666677788999999999999999999999999973
No 54
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00036 Score=70.07 Aligned_cols=47 Identities=30% Similarity=0.708 Sum_probs=42.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
+..|.||+..+.. ++.+||||.||..||++-+.....||+||..+..
T Consensus 84 ef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 84 EFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred hhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCccccccccc
Confidence 5899999888776 7888999999999999988878889999999974
No 55
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.84 E-value=0.00055 Score=68.87 Aligned_cols=49 Identities=31% Similarity=0.729 Sum_probs=42.0
Q ss_pred CCCccccccccccccCCceE-cccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQ-MPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~-lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~ 244 (352)
++..|+||...+.+ +.. ..|+|.||..|+..|+..+..||.|+..+...
T Consensus 20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~ 69 (391)
T KOG0297|consen 20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQA 69 (391)
T ss_pred ccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCcccccccchh
Confidence 35899999999887 444 57999999999999999999999998887543
No 56
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.72 E-value=0.00068 Score=75.46 Aligned_cols=70 Identities=26% Similarity=0.562 Sum_probs=50.8
Q ss_pred HHHHhhCCcceeccccc-cCCCCccccccccccccCCceEcccCceecccchHHHhhcC----------CCCCccCCCCC
Q 018689 174 KSAIEALPSIKINEAMM-SSDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH----------NSCPVCRYELP 242 (352)
Q Consensus 174 ~~~i~~lp~~~~~~~~~-~~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~----------~sCP~CR~~l~ 242 (352)
+..-..||......+.. ...+..|.||+.+--.....+.|.|+|+||..|...-|++. .+||+|+.+|.
T Consensus 3465 kNEE~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3465 KNEEHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred cchhhcccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 33445666665544333 22368999999886666778999999999999998876542 27999999874
Q ss_pred C
Q 018689 243 T 243 (352)
Q Consensus 243 ~ 243 (352)
.
T Consensus 3545 H 3545 (3738)
T KOG1428|consen 3545 H 3545 (3738)
T ss_pred h
Confidence 3
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.63 E-value=0.00036 Score=68.74 Aligned_cols=46 Identities=39% Similarity=0.908 Sum_probs=38.7
Q ss_pred CCcccccccccccc-CCceEcccCceecccchHHHhhcC--CCCCccCC
Q 018689 194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELH--NSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~--~sCP~CR~ 239 (352)
..-|-.|-+.+... +....|||.|+||..|+...|+++ .+||.||+
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 46899999988654 457889999999999999999664 58999994
No 58
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.62 E-value=0.00076 Score=49.50 Aligned_cols=41 Identities=24% Similarity=0.668 Sum_probs=28.1
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc--CCCCCc
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPV 236 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~ 236 (352)
...|+|.+..|+. .++...|+|+|-+..|..||+. ...||+
T Consensus 11 ~~~CPiT~~~~~~--PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFED--PVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-SS--EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhhC--CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4799999999876 3555679999999999999944 447998
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.44 E-value=0.0021 Score=45.22 Aligned_cols=40 Identities=28% Similarity=0.861 Sum_probs=27.5
Q ss_pred cccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~C 237 (352)
|-||++.-.... ..+.||. ...|..|+.+|+.. ..+|++|
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 779999876654 5667863 37899999999964 5679988
No 60
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.44 E-value=0.00052 Score=66.43 Aligned_cols=46 Identities=26% Similarity=0.662 Sum_probs=39.6
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
..+|.+|...|.+ +..+. |-|.||+.||.+.|+..++||.|...|-
T Consensus 15 ~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 15 HITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred ceehhhccceeec---chhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 5799999988877 44455 9999999999999999999999988664
No 61
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.02 E-value=0.0029 Score=61.82 Aligned_cols=51 Identities=24% Similarity=0.406 Sum_probs=43.1
Q ss_pred CCCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 192 ~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
.++..|+||+..- -.++..||+|.=|+.||.+.|...+.|=.|+..+.+..
T Consensus 420 sEd~lCpICyA~p---i~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~~ 470 (489)
T KOG4692|consen 420 SEDNLCPICYAGP---INAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDVI 470 (489)
T ss_pred cccccCcceeccc---chhhccCCCCchHHHHHHHHHhcCCeeeEecceeeehh
Confidence 4568999998763 34778899999999999999999999999999887533
No 62
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.00 E-value=0.0037 Score=50.59 Aligned_cols=31 Identities=32% Similarity=0.734 Sum_probs=27.0
Q ss_pred CCccccccccccccCCceEcccCceecccchH
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIM 225 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~ 225 (352)
...|+||...+.. ......||+|+||..|+.
T Consensus 78 ~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 5789999999876 567788999999999985
No 63
>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=95.93 E-value=0.0016 Score=55.71 Aligned_cols=35 Identities=20% Similarity=0.561 Sum_probs=30.6
Q ss_pred CCccccccccccccCCceEcccC------ceecccchHHHh
Q 018689 194 SSQCAVCKDSFELNEEARQMPCK------HIYHPDCIMPWL 228 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~------H~FH~~Ci~~Wl 228 (352)
..+|.||++.+...+.++.++|+ |+||..|+++|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 46899999999886678888886 899999999994
No 64
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.88 E-value=0.0034 Score=44.39 Aligned_cols=44 Identities=25% Similarity=0.588 Sum_probs=21.9
Q ss_pred cccccccccccCCceEcc--cCceecccchHHHhh-cCCCCCccCCCC
Q 018689 197 CAVCKDSFELNEEARQMP--CKHIYHPDCIMPWLE-LHNSCPVCRYEL 241 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~-~~~sCP~CR~~l 241 (352)
|++|.+++.. .....+| |++.++..|...-++ ....||-||.+.
T Consensus 1 cp~C~e~~d~-~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDE-TDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--C-CCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCccccccc-CCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899999833 2334555 899999999888775 477899999864
No 65
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.86 E-value=0.0033 Score=64.31 Aligned_cols=49 Identities=31% Similarity=0.676 Sum_probs=39.9
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc-----CCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL-----HNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~-----~~sCP~CR~~l~~~~ 245 (352)
...|.+|-+.-++ .+...|.|.||+.||..++.. .-+||+|...|..+.
T Consensus 536 ~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 536 EVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred ceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 5789999987444 778889999999999998743 458999988886554
No 66
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.009 Score=56.70 Aligned_cols=49 Identities=24% Similarity=0.535 Sum_probs=37.5
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPT 243 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~ 243 (352)
.+.+|++|-+.-.. .....+|+|+||.-||..-+.. ..+||.|-..+.+
T Consensus 238 ~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 238 SDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred CCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence 36899999887544 2445569999999999987653 4689999887753
No 67
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.71 E-value=0.0024 Score=57.88 Aligned_cols=45 Identities=22% Similarity=0.547 Sum_probs=39.6
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l 241 (352)
...|.||.++|+. +++..|||.||..|...-++....|-+|-+..
T Consensus 196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 4689999999988 77888999999999988888888999997754
No 68
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.63 E-value=0.0036 Score=67.15 Aligned_cols=51 Identities=24% Similarity=0.683 Sum_probs=38.2
Q ss_pred cCCCCccccccccccccCCceEcc-cCceecccchHHHhhcC-------CCCCccCCCC
Q 018689 191 SSDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELH-------NSCPVCRYEL 241 (352)
Q Consensus 191 ~~~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~-------~sCP~CR~~l 241 (352)
.....+|.||++.+.....+.... |-|+||..||.+|-+.. -.||.|+...
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 344689999999998755444333 88999999999997541 1599998543
No 69
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.54 E-value=0.004 Score=61.98 Aligned_cols=46 Identities=17% Similarity=0.569 Sum_probs=38.1
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcC--------CCCCccCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH--------NSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~--------~sCP~CR~ 239 (352)
...|.||+++..-....+.|||+|+||+.|++.++..+ -.||-|.-
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 57999999998776789999999999999999998543 25876654
No 70
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.52 E-value=0.0067 Score=56.01 Aligned_cols=50 Identities=20% Similarity=0.614 Sum_probs=40.5
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc--------CCCCCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--------HNSCPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--------~~sCP~CR~~l~~~ 244 (352)
...|..|.-.+..++.+ .|-|-|+||.+|+..|-.. ...||.|..+|.+.
T Consensus 50 ~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 46799999998887654 6779999999999999643 23699999998653
No 71
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=95.52 E-value=0.011 Score=42.90 Aligned_cols=46 Identities=28% Similarity=0.681 Sum_probs=35.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
..|..|... +.+-.++||+|+.+..|..- ++-+-||+|-+++..++
T Consensus 8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD 53 (55)
T ss_pred eeEEEcccc---ccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence 456666554 44578899999999999664 56778999999886554
No 72
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.44 E-value=0.0074 Score=56.43 Aligned_cols=58 Identities=19% Similarity=0.276 Sum_probs=48.3
Q ss_pred CCCccccccccccccCCceEc-ccCceecccchHHHhhcCCCCCccCCCCCCCChhHHH
Q 018689 193 DSSQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYEQ 250 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~e~ 250 (352)
....|+||.+.+.....+..| ||||+|+..|+.+.+.....||+|-.++...+...-+
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence 357899999999887766666 4999999999999999999999999998776554433
No 73
>PHA02862 5L protein; Provisional
Probab=95.37 E-value=0.0054 Score=52.97 Aligned_cols=45 Identities=20% Similarity=0.676 Sum_probs=34.5
Q ss_pred CccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCRYELPT 243 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~ 243 (352)
..|-||+++-++ . .-||. ...|..|+.+|+.. +.+|++|+.+...
T Consensus 3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 589999998433 2 35653 57899999999954 5689999998754
No 74
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.0011 Score=65.45 Aligned_cols=52 Identities=31% Similarity=0.708 Sum_probs=45.4
Q ss_pred CCcccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
...|+||.+.++.. +++..+-|||.+|..||.+||.....||.|+.+|+...
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNG 248 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence 46899999999876 66778889999999999999999889999999986543
No 75
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.27 E-value=0.0035 Score=59.89 Aligned_cols=42 Identities=29% Similarity=0.645 Sum_probs=33.1
Q ss_pred CCccccccccccccCCceEcccCcee-cccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIY-HPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~F-H~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
...|+||++.-.+ ...|+|||.. |..|-+. -+.||+||+.|.
T Consensus 300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCcc---eEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence 4689999998655 8999999974 6677554 458999998764
No 76
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.20 E-value=0.0072 Score=57.89 Aligned_cols=46 Identities=20% Similarity=0.478 Sum_probs=40.6
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
...|-||...|.. .++..|+|.||..|...-++....|.+|-+.+.
T Consensus 241 Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 241 PFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred Ccccccccccccc---chhhcCCceeehhhhccccccCCcceecccccc
Confidence 3679999999987 778889999999999998888899999988764
No 77
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.15 E-value=0.0098 Score=58.40 Aligned_cols=43 Identities=33% Similarity=0.712 Sum_probs=33.4
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
...|.||+++... .+.+||||+-| |+.-- +.-.+||+||..+.
T Consensus 305 p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 305 PDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred CCceEEecCCccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 5789999999766 88999999976 66543 23345999998774
No 78
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.87 E-value=0.012 Score=51.68 Aligned_cols=47 Identities=28% Similarity=0.762 Sum_probs=34.6
Q ss_pred CCCccccccccccccCCceEccc--Cc---eecccchHHHhhc--CCCCCccCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPC--KH---IYHPDCIMPWLEL--HNSCPVCRYELPT 243 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC--~H---~FH~~Ci~~Wl~~--~~sCP~CR~~l~~ 243 (352)
.+..|-||.++-.. ..-|| .. ..|..|+..|+.. ..+|++|+++...
T Consensus 7 ~~~~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence 35799999988432 23465 44 5699999999964 4589999987753
No 79
>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=94.79 E-value=0.01 Score=40.98 Aligned_cols=41 Identities=24% Similarity=0.729 Sum_probs=24.3
Q ss_pred cccccccccccCCceEcccCceecccchHHHhhcCC--CCCcc
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHN--SCPVC 237 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~--sCP~C 237 (352)
|.+|.+.+..+.....-.|+=.+|..|+..+++... .||.|
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 778888887765444445999999999999997655 79988
No 80
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.74 E-value=0.049 Score=51.85 Aligned_cols=92 Identities=21% Similarity=0.385 Sum_probs=57.8
Q ss_pred cHHHHHHHHHhcCCCCCCCCCCCHHHHh---hCCcceecccc-----------ccCCCCccccccccccccCCceE-ccc
Q 018689 151 GLEQLIQQLAENDPNRYGTPPASKSAIE---ALPSIKINEAM-----------MSSDSSQCAVCKDSFELNEEARQ-MPC 215 (352)
Q Consensus 151 ~le~li~~L~~~~~~~~g~~pas~~~i~---~lp~~~~~~~~-----------~~~~~~~C~IC~e~~~~~~~~~~-lpC 215 (352)
..+.||+-|..-... +..+..-.-|. .|-.++++... .......|||...+|......+. .+|
T Consensus 58 nKeaile~Ll~~~~~--~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~c 135 (260)
T PF04641_consen 58 NKEAILEFLLDKKKN--KDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPC 135 (260)
T ss_pred cHHHHHHHHHhcCcC--CCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCC
Confidence 578888888865432 11222222333 33334444331 12336899999999965544444 479
Q ss_pred CceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 216 KHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 216 ~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
||+|...+|..- .....||+|-.++...|
T Consensus 136 G~V~s~~alke~-k~~~~Cp~c~~~f~~~D 164 (260)
T PF04641_consen 136 GCVFSEKALKEL-KKSKKCPVCGKPFTEED 164 (260)
T ss_pred CCEeeHHHHHhh-cccccccccCCccccCC
Confidence 999999999986 33557999999875443
No 81
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.42 E-value=0.022 Score=55.74 Aligned_cols=47 Identities=28% Similarity=0.736 Sum_probs=38.8
Q ss_pred CCCCccccccccccccCCceEcccCceecccchHHH--hhcCCCCCccCCCC
Q 018689 192 SDSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPW--LELHNSCPVCRYEL 241 (352)
Q Consensus 192 ~~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~W--l~~~~sCP~CR~~l 241 (352)
.+...|.||-+.+.- ..++||+|..|..|.... |-..+.||+||.+.
T Consensus 59 Een~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 346789999988665 788999999999997665 45688999999875
No 82
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=93.79 E-value=0.042 Score=45.99 Aligned_cols=37 Identities=24% Similarity=0.618 Sum_probs=29.4
Q ss_pred CCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 19 QEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 19 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
-.+...||..|+..|.... .+..||.|+|..+.-+..
T Consensus 66 ~~p~~~~C~~C~~~~~~e~---~~~~CP~C~s~~~~i~~G 102 (115)
T COG0375 66 EEPAECWCLDCGQEVELEE---LDYRCPKCGSINLRIIGG 102 (115)
T ss_pred EeccEEEeccCCCeecchh---heeECCCCCCCceEEecC
Confidence 4567899999999986443 567799999999887654
No 83
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=93.74 E-value=0.032 Score=54.20 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=38.4
Q ss_pred cCCCCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCccCCCCC
Q 018689 191 SSDSSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 191 ~~~~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
..+...|+||+..... ..++. -|-+||..||...+..++.||+=-.++.
T Consensus 297 ~~~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred CCccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 3446899999987544 33444 5999999999999999999999766553
No 84
>PHA03096 p28-like protein; Provisional
Probab=93.73 E-value=0.021 Score=55.15 Aligned_cols=45 Identities=20% Similarity=0.458 Sum_probs=32.2
Q ss_pred Ccccccccccccc----CCceEcc-cCceecccchHHHhhc---CCCCCccCC
Q 018689 195 SQCAVCKDSFELN----EEARQMP-CKHIYHPDCIMPWLEL---HNSCPVCRY 239 (352)
Q Consensus 195 ~~C~IC~e~~~~~----~~~~~lp-C~H~FH~~Ci~~Wl~~---~~sCP~CR~ 239 (352)
..|.||++..... ..-..|+ |.|.||..||..|... ..+||.||.
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 6899999987643 2345566 9999999999999743 234444443
No 85
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.72 E-value=0.028 Score=50.26 Aligned_cols=50 Identities=20% Similarity=0.568 Sum_probs=35.5
Q ss_pred CCcccccccccccc----CCceEcccCceecccchHHHhhcC-----------CCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELH-----------NSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~-----------~sCP~CR~~l~~ 243 (352)
...|-||+..--.+ ...--..|+.-||.-|+..||+.- ..||.|..++..
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 45788887654333 233445699999999999999641 159999888753
No 86
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.44 E-value=0.059 Score=51.87 Aligned_cols=47 Identities=23% Similarity=0.660 Sum_probs=39.1
Q ss_pred CccccccccccccC---CceEcccCceecccchHHHhhc-CCCCCccCCCC
Q 018689 195 SQCAVCKDSFELNE---EARQMPCKHIYHPDCIMPWLEL-HNSCPVCRYEL 241 (352)
Q Consensus 195 ~~C~IC~e~~~~~~---~~~~lpC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l 241 (352)
..|-||-++|...+ .++.|.|||.|+..|+.+.+.. ...||.||...
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 57999999998763 4777889999999999987754 45799999985
No 87
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.39 E-value=0.026 Score=52.68 Aligned_cols=44 Identities=18% Similarity=0.580 Sum_probs=32.8
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l 241 (352)
..|-.|...-. .+...++.|.|+||..|...-. ...||+|++.|
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~i 47 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSI 47 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccCC--cccccccccee
Confidence 35777765443 6677778899999999976532 22899999976
No 88
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.31 E-value=0.04 Score=52.93 Aligned_cols=43 Identities=28% Similarity=0.675 Sum_probs=34.2
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHh-hcCCCCCccCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWL-ELHNSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl-~~~~sCP~CR~ 239 (352)
...|+.|..-+.. +.+.| |+|.||..||..-| .....||.|..
T Consensus 274 ~LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 274 SLKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred cccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 3789999887665 45556 99999999999776 56778999944
No 89
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=93.10 E-value=0.062 Score=38.95 Aligned_cols=39 Identities=28% Similarity=0.675 Sum_probs=32.3
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHhhcCCCCCc
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWLELHNSCPV 236 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~ 236 (352)
...|.+|-+.|+.++.+++-| |+-.||+.|..+ ...|-+
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 468999999999888999999 999999999543 445544
No 90
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=93.00 E-value=0.038 Score=52.96 Aligned_cols=45 Identities=29% Similarity=0.721 Sum_probs=38.3
Q ss_pred Ccccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689 195 SQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 195 ~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
..|+||.+.+... ..+..++|||.-|..|+......+-+||+|.+
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 4599999987665 35778899999999999988877799999988
No 91
>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=92.76 E-value=0.086 Score=46.36 Aligned_cols=54 Identities=20% Similarity=0.445 Sum_probs=36.3
Q ss_pred CCccccccccccccCCceEcccC-------------ceecccchHHHhhc------------------------------
Q 018689 194 SSQCAVCKDSFELNEEARQMPCK-------------HIYHPDCIMPWLEL------------------------------ 230 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~-------------H~FH~~Ci~~Wl~~------------------------------ 230 (352)
+..|+||||.-.. +++|-|. -.-|..|++++-+.
T Consensus 2 d~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (162)
T PF07800_consen 2 DVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ 78 (162)
T ss_pred CccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence 4789999997433 6666552 22478899987532
Q ss_pred -CCCCCccCCCCCCCChhHHH
Q 018689 231 -HNSCPVCRYELPTDDPDYEQ 250 (352)
Q Consensus 231 -~~sCP~CR~~l~~~~~~~e~ 250 (352)
+-.||+||.+|.......+.
T Consensus 79 ~~L~CPLCRG~V~GWtvve~A 99 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVEPA 99 (162)
T ss_pred ccccCccccCceeceEEchHH
Confidence 11499999999766544443
No 92
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=92.28 E-value=0.045 Score=52.89 Aligned_cols=43 Identities=26% Similarity=0.764 Sum_probs=31.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYEL 241 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l 241 (352)
-.|--|-..+.. .-+.+||+|+||.+|... ...+.||.|-..|
T Consensus 91 HfCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred EeecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 356667555444 567889999999999653 3466899997665
No 93
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.84 E-value=0.052 Score=58.56 Aligned_cols=43 Identities=33% Similarity=0.849 Sum_probs=34.4
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
..|..|--.+.. ..+..-|||.||..|+. .....||.|+.++.
T Consensus 841 skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhh
Confidence 589999887765 45666799999999988 44568999998654
No 94
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=91.52 E-value=0.07 Score=59.98 Aligned_cols=45 Identities=24% Similarity=0.554 Sum_probs=38.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~ 240 (352)
...|.||++.+.. ...+..|+|.||..|+..|+..+..||+|+..
T Consensus 1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence 4589999999874 23455699999999999999999999999753
No 95
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=91.40 E-value=0.062 Score=37.82 Aligned_cols=44 Identities=27% Similarity=0.652 Sum_probs=25.6
Q ss_pred ccccccccccccCCceEccc-CceecccchHHHhhcCCCCCccCCCCCCC
Q 018689 196 QCAVCKDSFELNEEARQMPC-KHIYHPDCIMPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC-~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~ 244 (352)
.|.-|.-.. ...+.| .|..|..|+...|.....||+|.++||+.
T Consensus 4 nCKsCWf~~-----k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFAN-----KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S-------SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred cChhhhhcC-----CCeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 455565442 224557 49999999999999999999999999864
No 96
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=91.14 E-value=0.12 Score=50.33 Aligned_cols=44 Identities=27% Similarity=0.714 Sum_probs=35.3
Q ss_pred CCCccccccccccccCCceEccc--CceecccchHHHhhcCCCCCccCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPC--KHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC--~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
+-.+|+||.+.+.. -.+.| ||+-|..|-. +..+.||.||.++..
T Consensus 47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN 92 (299)
T ss_pred hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence 35799999999876 34556 7999999965 457889999999973
No 97
>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=89.87 E-value=0.25 Score=41.35 Aligned_cols=37 Identities=24% Similarity=0.547 Sum_probs=27.5
Q ss_pred CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
...+...||..|...+.+.. ....||.|++..++-+.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPEI---DLYRCPKCHGIMLQVRA 101 (115)
T ss_pred EeeCcEEEcccCCCEEecCC---cCccCcCCcCCCcEEec
Confidence 34567899999998875432 46789999998766543
No 98
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=89.68 E-value=0.11 Score=50.78 Aligned_cols=50 Identities=20% Similarity=0.548 Sum_probs=36.2
Q ss_pred CCccccccccccccCC-ceEcccCceecccchHHHhh-cCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEE-ARQMPCKHIYHPDCIMPWLE-LHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~-~~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l~~ 243 (352)
+..|+.|++.+...++ -.-.|||...|.-|...--+ .+..||.||.....
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence 4569999999987654 44456998888888554332 35689999987643
No 99
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.41 E-value=0.36 Score=33.48 Aligned_cols=34 Identities=24% Similarity=0.554 Sum_probs=27.0
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi 56 (352)
..|-|-.|...+.+.... ..+.||+|++.|+...
T Consensus 2 ~~y~C~~CG~~~~~~~~~-~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDEYG-TGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECCCC-CceECCCCCCeEEEcc
Confidence 469999999998876532 3799999999888543
No 100
>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=88.85 E-value=0.31 Score=48.56 Aligned_cols=29 Identities=24% Similarity=0.857 Sum_probs=21.8
Q ss_pred cCceecccchHHHhhcC-------------CCCCccCCCCCC
Q 018689 215 CKHIYHPDCIMPWLELH-------------NSCPVCRYELPT 243 (352)
Q Consensus 215 C~H~FH~~Ci~~Wl~~~-------------~sCP~CR~~l~~ 243 (352)
|.-++|.+|+-+|+..+ -.||+||+.+..
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 45567789999998432 269999998764
No 101
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=88.79 E-value=0.35 Score=40.37 Aligned_cols=38 Identities=18% Similarity=0.601 Sum_probs=27.0
Q ss_pred CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
...+..+||..|...+.+.. .....||.|++.-++-+.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~--~~~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLT--QRVRRCPQCHGDMLRIVA 102 (114)
T ss_pred EeeCcEEEcccCCCeeecCC--ccCCcCcCcCCCCcEEcc
Confidence 44568899999998875432 123669999988766543
No 102
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.64 E-value=0.26 Score=49.25 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=39.3
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcC---CCCCccCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH---NSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~sCP~CR~ 239 (352)
...|||=.+.-.+...+..|.|||+..++-|.+..+.. ..||.|=.
T Consensus 334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred eeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 57999999998888899999999999999999876543 36999944
No 103
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=87.94 E-value=0.13 Score=55.36 Aligned_cols=45 Identities=24% Similarity=0.614 Sum_probs=36.6
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhc--CCCCCccCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL--HNSCPVCRYELPT 243 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~ 243 (352)
..|.||++ .+.....+|+|.||..|+.+-+.. ...||+||..+..
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence 79999999 345778889999999999988754 2369999987753
No 104
>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=87.37 E-value=0.36 Score=29.76 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=19.2
Q ss_pred eecCCcccccCCCCCCCCcCCCCCCCce
Q 018689 26 CHQCNRTVRVTPSPSSDLVCPSCNGGFI 53 (352)
Q Consensus 26 Ch~C~r~V~~~~~~~~~~~CP~C~~gFv 53 (352)
|-.|...|.+ ....||+|+-.|.
T Consensus 3 CP~C~~~V~~-----~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPE-----SAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchh-----hcCcCCCCCCCCc
Confidence 7889999864 5689999998884
No 105
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=87.19 E-value=0.53 Score=39.26 Aligned_cols=36 Identities=25% Similarity=0.661 Sum_probs=26.3
Q ss_pred CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi 56 (352)
...+..+||..|.....+. .....||.|++.-++-+
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~---~~~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIH---QHDAQCPHCHGERLRVD 100 (113)
T ss_pred EeeCcEEEcccCCCEEecC---CcCccCcCCCCCCcEEc
Confidence 3456889999999876543 24567999998766544
No 106
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.90 E-value=0.2 Score=54.60 Aligned_cols=34 Identities=24% Similarity=0.726 Sum_probs=27.8
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHh
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWL 228 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl 228 (352)
.+.|.+|...+.. ..-.+.||||.||+.||.+-.
T Consensus 817 ~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 817 QDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred ccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence 5799999887755 356678999999999998764
No 107
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=86.69 E-value=0.26 Score=52.76 Aligned_cols=40 Identities=30% Similarity=0.783 Sum_probs=28.9
Q ss_pred ccccccccccccCCceEcccCceecccchHHHhhcCCCCCc
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPV 236 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~ 236 (352)
.|.||.-.+. +.......|+|+.|..|...|++....||.
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 3455443332 233455679999999999999999999984
No 108
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.68 E-value=0.32 Score=49.03 Aligned_cols=37 Identities=22% Similarity=0.624 Sum_probs=28.2
Q ss_pred CCcccccc-ccccccCCceEcccCceecccchHHHhhc
Q 018689 194 SSQCAVCK-DSFELNEEARQMPCKHIYHPDCIMPWLEL 230 (352)
Q Consensus 194 ~~~C~IC~-e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~ 230 (352)
..+|.||+ +.....+....+.|+|.||..|+++.++.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev 183 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV 183 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence 57899999 44444344446669999999999998864
No 109
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.53 E-value=0.54 Score=39.42 Aligned_cols=38 Identities=16% Similarity=0.313 Sum_probs=26.5
Q ss_pred CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
...+..+||..|.....+.. .....||.|++..++-+.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~~--~~~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPNA--LDYGVCEKCHSKNVIITQ 103 (117)
T ss_pred EecCCEEEhhhCCCccccCC--ccCCcCcCCCCCceEEec
Confidence 44678899999997764321 123459999998877543
No 110
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.25 E-value=0.17 Score=47.74 Aligned_cols=48 Identities=31% Similarity=0.677 Sum_probs=35.0
Q ss_pred CCccccccccccccCCc-eEccc-----CceecccchHHHhhcC--------CCCCccCCCC
Q 018689 194 SSQCAVCKDSFELNEEA-RQMPC-----KHIYHPDCIMPWLELH--------NSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~-~~lpC-----~H~FH~~Ci~~Wl~~~--------~sCP~CR~~l 241 (352)
+..|-||+..=++.... -+-|| .|..|..|+..|+..+ -+||.|+.+.
T Consensus 20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 20 ERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 57899998875543322 34466 4899999999999432 2699999875
No 111
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.13 E-value=0.54 Score=40.44 Aligned_cols=38 Identities=24% Similarity=0.532 Sum_probs=26.0
Q ss_pred CCCCceeeecCCcccccCC---------------CC---CCCCcCCCCCCCceEEc
Q 018689 19 QEPQMYFCHQCNRTVRVTP---------------SP---SSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 19 ~~~~~ywCh~C~r~V~~~~---------------~~---~~~~~CP~C~~gFvEEi 56 (352)
..+..|||..|.....+.. .+ .....||.|++.-++-+
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 3458899999998776530 00 23467999998766543
No 112
>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=85.74 E-value=0.35 Score=40.23 Aligned_cols=35 Identities=23% Similarity=0.544 Sum_probs=23.2
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
.+..+||..|.....+.. ....||+|++..++-+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDE---FDFSCPRCGSPDVEIIS 101 (113)
T ss_dssp E--EEEETTTS-EEECHH---CCHH-SSSSSS-EEEEE
T ss_pred cCCcEECCCCCCEEecCC---CCCCCcCCcCCCcEEcc
Confidence 457899999999976543 45889999999776543
No 113
>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=84.43 E-value=1 Score=29.16 Aligned_cols=28 Identities=29% Similarity=0.936 Sum_probs=21.8
Q ss_pred eeeecCCcccccCCCCCCCCcCCCCCCCce
Q 018689 24 YFCHQCNRTVRVTPSPSSDLVCPSCNGGFI 53 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~~~~~~CP~C~~gFv 53 (352)
|-|-.|...|.+.. ...+.||+|+...|
T Consensus 1 Y~C~~Cg~~~~~~~--~~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKP--GDPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BST--SSTSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCC--CCcEECCcCCCeEE
Confidence 78999999998765 46799999998765
No 114
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=83.65 E-value=0.32 Score=46.73 Aligned_cols=50 Identities=20% Similarity=0.579 Sum_probs=37.6
Q ss_pred CCccccccccccccCC-ceEcccC-----ceecccchHHHhh--cCCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELNEE-ARQMPCK-----HIYHPDCIMPWLE--LHNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~-~~~lpC~-----H~FH~~Ci~~Wl~--~~~sCP~CR~~l~~ 243 (352)
...|-||.++...... ..+.||. +..|+.|+..|+. ....|.+|......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 4689999998765322 5567763 6679999999996 45689999886644
No 115
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.90 E-value=1 Score=38.18 Aligned_cols=39 Identities=21% Similarity=0.333 Sum_probs=25.6
Q ss_pred CCCCCceeeecCCcccccCCCCC--C--CCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPS--S--DLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~--~--~~~CP~C~~gFvEEi~ 57 (352)
...+..+|| .|.....+..... - ...||.|++..++-+.
T Consensus 65 ~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 65 EMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred EecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 346688999 9998754431110 1 2569999988876543
No 116
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=82.65 E-value=0.45 Score=51.45 Aligned_cols=52 Identities=29% Similarity=0.805 Sum_probs=38.0
Q ss_pred cCCCCccccccccccccCCceEcccC-----ceecccchHHHhhc--CCCCCccCCCCCC
Q 018689 191 SSDSSQCAVCKDSFELNEEARQMPCK-----HIYHPDCIMPWLEL--HNSCPVCRYELPT 243 (352)
Q Consensus 191 ~~~~~~C~IC~e~~~~~~~~~~lpC~-----H~FH~~Ci~~Wl~~--~~sCP~CR~~l~~ 243 (352)
..++..|.||..+=..++ +..-||+ ...|..|+..|+.- ...|-+|+.++.-
T Consensus 9 N~d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 9 NEDKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred CccchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 345689999998754433 4455775 34899999999964 4579999987743
No 117
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=82.60 E-value=0.61 Score=34.72 Aligned_cols=29 Identities=28% Similarity=0.673 Sum_probs=21.5
Q ss_pred eeecCCcccccCCCCCCCCcCCCCCCC-ceEEccC
Q 018689 25 FCHQCNRTVRVTPSPSSDLVCPSCNGG-FIEELET 58 (352)
Q Consensus 25 wCh~C~r~V~~~~~~~~~~~CP~C~~g-FvEEi~~ 58 (352)
=|++|.|.+. ...-+||.|++. |.||-..
T Consensus 6 AC~~Ck~l~~-----~d~e~CP~Cgs~~~te~W~G 35 (64)
T COG2093 6 ACKNCKRLTP-----EDTEICPVCGSTDLTEEWFG 35 (64)
T ss_pred HHhhccccCC-----CCCccCCCCCCcccchhhcc
Confidence 3999998763 245679999986 8887543
No 118
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.21 E-value=0.62 Score=49.00 Aligned_cols=46 Identities=35% Similarity=0.905 Sum_probs=38.7
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
....|.||+..+ ..+..+|. |..|+.+|+..+..||+|+..+..++
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~ 523 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD 523 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence 357899999998 46677788 99999999999999999988876543
No 119
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.87 E-value=0.71 Score=27.54 Aligned_cols=23 Identities=22% Similarity=0.881 Sum_probs=18.2
Q ss_pred eeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689 25 FCHQCNRTVRVTPSPSSDLVCPSCNGGF 52 (352)
Q Consensus 25 wCh~C~r~V~~~~~~~~~~~CP~C~~gF 52 (352)
||.+|-..|. +...+||+|+..|
T Consensus 1 ~Cp~CG~~~~-----~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIE-----DDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCC-----CcCcchhhhCCcC
Confidence 6899999874 3678999998754
No 120
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.65 E-value=0.81 Score=42.23 Aligned_cols=40 Identities=25% Similarity=0.658 Sum_probs=29.3
Q ss_pred ccccccccccccCCceEcccCc-eecccchHHHhhcCCCCCccCCCCC
Q 018689 196 QCAVCKDSFELNEEARQMPCKH-IYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H-~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
.|-+|.+. ...+..+||.| .+|..|-.. -..||+|+....
T Consensus 160 ~Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 160 SCRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred cceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 38888776 45589999976 577888654 345999987654
No 121
>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=81.08 E-value=0.78 Score=44.13 Aligned_cols=46 Identities=30% Similarity=0.629 Sum_probs=34.0
Q ss_pred ccccccccccccCCceEc--ccCceecccchHHHhhc-CCCCCccCCCC
Q 018689 196 QCAVCKDSFELNEEARQM--PCKHIYHPDCIMPWLEL-HNSCPVCRYEL 241 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~l--pC~H~FH~~Ci~~Wl~~-~~sCP~CR~~l 241 (352)
.|++|....-..-.++.+ +|+|..|..|++.-+.. ...||.|-..+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 599998764433333333 69999999999998755 55899997765
No 122
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.48 E-value=1.2 Score=30.89 Aligned_cols=33 Identities=18% Similarity=0.578 Sum_probs=26.9
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
.|-|-.|...|.+.. ...+.||+|++..|--.-
T Consensus 2 ~Y~C~~Cg~~~~~~~--~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 2 IYICGECGRENEIKS--KDVVRCRECGYRILYKKR 34 (44)
T ss_pred EEECCCCCCEeecCC--CCceECCCCCceEEEEeC
Confidence 489999999998763 578999999998875543
No 123
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=80.38 E-value=0.98 Score=40.83 Aligned_cols=31 Identities=29% Similarity=0.708 Sum_probs=23.1
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
...-|||..|+-.+ ..-.|+-|+++| +++.-
T Consensus 11 k~~iyWCe~cNlPl-------~~~~c~~cg~~~-~~l~L 41 (202)
T COG5270 11 KFPIYWCEKCNLPL-------LGRRCSVCGSKV-EELRL 41 (202)
T ss_pred ccceeehhhCCCcc-------ccccccccCCcc-eEEEe
Confidence 44679999999876 346899999665 55544
No 124
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=80.10 E-value=0.98 Score=32.13 Aligned_cols=37 Identities=22% Similarity=0.582 Sum_probs=27.8
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
....|-|-.|.+.|.+. .....+.||+|++..+-..-
T Consensus 3 ~~~~Y~C~~Cg~~~~~~-~~~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 3 AMMEYKCARCGREVELD-QETRGIRCPYCGSRILVKER 39 (49)
T ss_pred ceEEEEhhhcCCeeehh-hccCceeCCCCCcEEEEecc
Confidence 34679999999999632 23578999999997765443
No 125
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.87 E-value=0.83 Score=41.14 Aligned_cols=36 Identities=19% Similarity=0.575 Sum_probs=27.7
Q ss_pred CCCCceeeecCCcccccCCCCCCCCcCCCCCCCceE
Q 018689 19 QEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIE 54 (352)
Q Consensus 19 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvE 54 (352)
.+...|.|-.|.+.++.---.+.++.||.|++-.+|
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 355789999999887653323568999999998777
No 126
>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=79.39 E-value=1.3 Score=29.35 Aligned_cols=29 Identities=31% Similarity=0.714 Sum_probs=22.3
Q ss_pred CceeeecCCcccccCCCC--CCCCcCCCCCC
Q 018689 22 QMYFCHQCNRTVRVTPSP--SSDLVCPSCNG 50 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~--~~~~~CP~C~~ 50 (352)
-.|.|-.|...+.+.... ...+.||.|++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 469999999977655422 45789999998
No 127
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=78.99 E-value=0.75 Score=39.44 Aligned_cols=51 Identities=20% Similarity=0.468 Sum_probs=35.7
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHh---hcCCCCCccCCCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWL---ELHNSCPVCRYELPTD 244 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl---~~~~sCP~CR~~l~~~ 244 (352)
-.+|-||.|...+..-++-=- ||-..|..|-...+ ..+..||+|+..+...
T Consensus 80 lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 80 LYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred ceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 589999999865532111111 89999998866544 3477899999988654
No 128
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=78.72 E-value=0.66 Score=46.95 Aligned_cols=33 Identities=24% Similarity=0.586 Sum_probs=28.3
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHh
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWL 228 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl 228 (352)
++..|+||..-|++ +++|||+|..|..|...-+
T Consensus 3 eelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~ 35 (699)
T KOG4367|consen 3 EELKCPVCGSFYRE---PIILPCSHNLCQACARNIL 35 (699)
T ss_pred ccccCceehhhccC---ceEeecccHHHHHHHHhhc
Confidence 35789999999887 8999999999999987544
No 129
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=78.42 E-value=0.51 Score=49.74 Aligned_cols=41 Identities=27% Similarity=0.764 Sum_probs=27.3
Q ss_pred CCcccccccc-----ccccCCceEcccCceecccchHHHhhcCCCCCcc
Q 018689 194 SSQCAVCKDS-----FELNEEARQMPCKHIYHPDCIMPWLELHNSCPVC 237 (352)
Q Consensus 194 ~~~C~IC~e~-----~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~C 237 (352)
...|.||... |+.....+...|+++||+.|+.. ...-||.|
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC 556 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRC 556 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence 5788888432 33333344556999999999543 44459999
No 130
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=78.41 E-value=0.82 Score=49.38 Aligned_cols=50 Identities=16% Similarity=0.348 Sum_probs=36.6
Q ss_pred CCcccccccccccc-CCceEcc---cCceecccchHHHhhc------CCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFELN-EEARQMP---CKHIYHPDCIMPWLEL------HNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~~-~~~~~lp---C~H~FH~~Ci~~Wl~~------~~sCP~CR~~l~~ 243 (352)
...|.||.-++... +..-.+| |.|.||..||..|+.+ +-.|++|..-|..
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s 155 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS 155 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence 46788888887662 2334455 9999999999999843 4468999876644
No 131
>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=77.06 E-value=1.5 Score=26.58 Aligned_cols=22 Identities=32% Similarity=1.044 Sum_probs=16.4
Q ss_pred eecCCcccccCCCC-CCCCcCCCCC
Q 018689 26 CHQCNRTVRVTPSP-SSDLVCPSCN 49 (352)
Q Consensus 26 Ch~C~r~V~~~~~~-~~~~~CP~C~ 49 (352)
|..|.+.|. +.. ...+.||.|+
T Consensus 1 C~sC~~~i~--~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIA--PREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCccc--CcccCceEeCCCCC
Confidence 778988763 333 5679999997
No 132
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=76.52 E-value=0.57 Score=50.10 Aligned_cols=46 Identities=20% Similarity=0.657 Sum_probs=37.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcC---CCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH---NSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~---~sCP~CR~~l~ 242 (352)
..+|+||+..+.. ...+.|.|.|+..|+..-|... ..||+|+..+.
T Consensus 21 ~lEc~ic~~~~~~---p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 21 ILECPICLEHVKE---PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hccCCceeEEeec---cchhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 4789999999877 3678899999999988776554 47999996553
No 133
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=76.45 E-value=1.4 Score=47.48 Aligned_cols=41 Identities=20% Similarity=0.417 Sum_probs=30.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCc
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPV 236 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~ 236 (352)
..|.+|-..+.. ..+..--|+|.-|..|+++|+..+.-||.
T Consensus 780 ~~CtVC~~vi~G-~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIRG-VDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred cCceeecceeee-eEeecccccccccHHHHHHHHhcCCCCcc
Confidence 478888766543 11222239999999999999998888876
No 134
>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=74.01 E-value=1.2 Score=39.19 Aligned_cols=39 Identities=13% Similarity=0.443 Sum_probs=28.0
Q ss_pred CCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 19 QEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 19 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
.+..-|.|-.|.+.++..--.+.++.||.|++- ++++++
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~-L~~~dn 143 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAM-LDYLDN 143 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE-eeeccC
Confidence 356789999999887643322568999999987 445543
No 135
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=73.78 E-value=3.9 Score=38.76 Aligned_cols=87 Identities=20% Similarity=0.285 Sum_probs=54.2
Q ss_pred HHHHHHHHHhcCCCCCCCCCCCHHHHhhCCcc---eeccc-----cc-------cCCCCccccccccccccCC-ceEccc
Q 018689 152 LEQLIQQLAENDPNRYGTPPASKSAIEALPSI---KINEA-----MM-------SSDSSQCAVCKDSFELNEE-ARQMPC 215 (352)
Q Consensus 152 le~li~~L~~~~~~~~g~~pas~~~i~~lp~~---~~~~~-----~~-------~~~~~~C~IC~e~~~~~~~-~~~lpC 215 (352)
=+.+|+.|.+-. ..|.+.+-|..|..+ +++.. +. ..-...|+|---+|..... +...+|
T Consensus 59 Ke~vi~~LL~Ks-----~~pksaShIKslKDvveLklt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~~F~~l~~C 133 (293)
T KOG3113|consen 59 KESVIEFLLDKS-----SLPKSASHIKSLKDVVELKLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKYRFCALRCC 133 (293)
T ss_pred HHHHHHHHHhcc-----cCCcchhhhcchhhHhheecccCcccccccCccccccccceeecccccceecceEEEEEEecc
Confidence 467777777542 456666667766543 22221 00 0114689987777655433 445569
Q ss_pred CceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 216 KHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 216 ~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
||+|-..-+.+. ...+|++|...+..++
T Consensus 134 GcV~SerAlKei--kas~C~~C~a~y~~~d 161 (293)
T KOG3113|consen 134 GCVFSERALKEI--KASVCHVCGAAYQEDD 161 (293)
T ss_pred ceeccHHHHHHh--hhccccccCCcccccC
Confidence 999998776653 2568999999887665
No 136
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=71.90 E-value=2.1 Score=26.12 Aligned_cols=23 Identities=26% Similarity=0.895 Sum_probs=17.8
Q ss_pred eeeecCCcccccCCCCCCCCcCCCCCCC
Q 018689 24 YFCHQCNRTVRVTPSPSSDLVCPSCNGG 51 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~~~~~~CP~C~~g 51 (352)
..|.+|...|. .++.+||+|+..
T Consensus 3 ~~Cp~Cg~~~~-----~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID-----PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC-----cccccChhhCCC
Confidence 47999999653 368999999864
No 137
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.58 E-value=2 Score=46.49 Aligned_cols=46 Identities=20% Similarity=0.477 Sum_probs=34.5
Q ss_pred CCcccccccccccc----CCceEcccCceecccchHHHhhcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELN----EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~----~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~ 240 (352)
+..|.-|.+..... +.++++.|+|+||+.|+.--..+.+ |-.|-..
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~~ 833 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESGK 833 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhce
Confidence 46899999887532 3578889999999999987765554 7666443
No 138
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.46 E-value=1.4 Score=38.30 Aligned_cols=36 Identities=19% Similarity=0.557 Sum_probs=26.3
Q ss_pred CCCceeeecCCcccccCC-----CCCCCCcCCCCCCCceEE
Q 018689 20 EPQMYFCHQCNRTVRVTP-----SPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~-----~~~~~~~CP~C~~gFvEE 55 (352)
+...|.|-.|...+.... .++..++||.|+.-.++.
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 567899999998876522 123349999999887664
No 139
>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=70.89 E-value=3.2 Score=26.49 Aligned_cols=38 Identities=26% Similarity=0.643 Sum_probs=25.4
Q ss_pred ccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
.|..|.+.+...+.. ...=+..||..|+ .|..|...|.
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 378888887665222 2224778999885 4888877663
No 140
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.35 E-value=3.1 Score=38.17 Aligned_cols=39 Identities=31% Similarity=0.974 Sum_probs=27.6
Q ss_pred CCcccccccc-----ccccCCceEcc-cCceecccchHHHhhcCCCCCccC
Q 018689 194 SSQCAVCKDS-----FELNEEARQMP-CKHIYHPDCIMPWLELHNSCPVCR 238 (352)
Q Consensus 194 ~~~C~IC~e~-----~~~~~~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR 238 (352)
...|-||... |... .+..-+ |+-+||+.|..+ ..||-|.
T Consensus 152 GfiCe~C~~~~~IfPF~~~-~~~~C~~C~~v~H~~C~~~-----~~CpkC~ 196 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQID-TTVRCPKCKSVFHKSCFRK-----KSCPKCA 196 (202)
T ss_pred CCCCccCCCCCCCCCCCCC-CeeeCCcCccccchhhcCC-----CCCCCcH
Confidence 5789999753 2232 344444 999999999662 6799994
No 141
>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=68.66 E-value=4.8 Score=28.29 Aligned_cols=35 Identities=26% Similarity=0.584 Sum_probs=24.1
Q ss_pred CceeeecCCcccccCCCC--CCCCcCCCCCCCceEEc
Q 018689 22 QMYFCHQCNRTVRVTPSP--SSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~--~~~~~CP~C~~gFvEEi 56 (352)
-.|.|-.|.....++... ...+.||.|++.=++.+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 368999999966554322 34678999999544444
No 142
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=68.28 E-value=1.3 Score=42.80 Aligned_cols=31 Identities=23% Similarity=0.659 Sum_probs=23.2
Q ss_pred cCceecccchHHHhhc-------------CCCCCccCCCCCCCC
Q 018689 215 CKHIYHPDCIMPWLEL-------------HNSCPVCRYELPTDD 245 (352)
Q Consensus 215 C~H~FH~~Ci~~Wl~~-------------~~sCP~CR~~l~~~~ 245 (352)
|.-.+|..|+.+|+.. +-+||+||+.+...|
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 5667788999998732 347999999886543
No 143
>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=68.15 E-value=3.2 Score=34.46 Aligned_cols=29 Identities=28% Similarity=0.683 Sum_probs=21.4
Q ss_pred eeeecCCc-ccccCCCCCCCCcCCCCCCCceEE
Q 018689 24 YFCHQCNR-TVRVTPSPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 24 ywCh~C~r-~V~~~~~~~~~~~CP~C~~gFvEE 55 (352)
.-|..|.. |.-+. -..++||+|+.-|.-+
T Consensus 10 R~Cp~CG~kFYDLn---k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN---KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC---CCCccCCCCCCccCcc
Confidence 45899965 44343 3668899999999877
No 144
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.73 E-value=3.5 Score=39.71 Aligned_cols=48 Identities=21% Similarity=0.467 Sum_probs=35.3
Q ss_pred CCccccccccccccCCceEcc--cCceecccchHHHhhcCC-----------CCCccCCCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP--CKHIYHPDCIMPWLELHN-----------SCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp--C~H~FH~~Ci~~Wl~~~~-----------sCP~CR~~l~ 242 (352)
...|.+|.|.+++..- ++.| =.|.||..|-++-++.+. .||+--..++
T Consensus 268 pLcCTLC~ERLEDTHF-VQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~vP 328 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHF-VQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNVP 328 (352)
T ss_pred ceeehhhhhhhccCce-eecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCccc
Confidence 4799999999988432 2333 379999999999887643 4777766554
No 145
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=67.56 E-value=1.9 Score=39.77 Aligned_cols=45 Identities=27% Similarity=0.589 Sum_probs=35.9
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~ 240 (352)
-..|.+|.+-.-.+ .+.=.|+-.||..|+...+++...||.|..-
T Consensus 181 lk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d~ 225 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGDL 225 (235)
T ss_pred HHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhcc
Confidence 46899998876552 3444588899999999999999999999443
No 146
>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=66.50 E-value=5.8 Score=26.97 Aligned_cols=33 Identities=24% Similarity=0.621 Sum_probs=22.3
Q ss_pred CceeeecCCcccccCCC--CCCCCcCCCCCCCceE
Q 018689 22 QMYFCHQCNRTVRVTPS--PSSDLVCPSCNGGFIE 54 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~--~~~~~~CP~C~~gFvE 54 (352)
-.|-|-.|.....+... ....+.||.|++.=++
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 46899999954433322 2468999999985444
No 147
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.93 E-value=3 Score=42.10 Aligned_cols=44 Identities=32% Similarity=0.612 Sum_probs=33.2
Q ss_pred CCccccccccccccCCceEc--ccCceecccchHHHhhcCCCCCcc
Q 018689 194 SSQCAVCKDSFELNEEARQM--PCKHIYHPDCIMPWLELHNSCPVC 237 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l--pC~H~FH~~Ci~~Wl~~~~sCP~C 237 (352)
-..|++|.-.++.......+ .|+|.|+..|...|......|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 46899998887665543333 389999999999998777777555
No 148
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.28 E-value=3.3 Score=42.43 Aligned_cols=35 Identities=29% Similarity=0.705 Sum_probs=30.1
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL 230 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~ 230 (352)
..+|-||.+.+.. ....+.|+|.|+..|+...|..
T Consensus 70 ~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 70 DVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred cccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 5799999999865 5778889999999999998854
No 149
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=63.69 E-value=4 Score=27.46 Aligned_cols=25 Identities=36% Similarity=0.848 Sum_probs=19.8
Q ss_pred eecCCcccccCCCCCCCCcCCCCCCCceEE
Q 018689 26 CHQCNRTVRVTPSPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 26 Ch~C~r~V~~~~~~~~~~~CP~C~~gFvEE 55 (352)
|+.|.+.+.+. .+.|.+|+.-|=.+
T Consensus 1 C~~C~~~~~l~-----~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT-----GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc-----CeECCccCCccccc
Confidence 78899987654 38899999988654
No 150
>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=63.52 E-value=2.5 Score=29.97 Aligned_cols=42 Identities=24% Similarity=0.549 Sum_probs=20.8
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcC-----CCCCccCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH-----NSCPVCRY 239 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~-----~sCP~CR~ 239 (352)
..|+|....+.. .++-..|.|.-+. =+..||... -.||+|.+
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CF-Dl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCF-DLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--E-EHHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEe--CccCCcCcccceE-CHHHHHHHhhccCCeECcCCcC
Confidence 478998888766 3555669987442 245566432 25999976
No 151
>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=61.82 E-value=6.3 Score=29.25 Aligned_cols=35 Identities=20% Similarity=0.564 Sum_probs=19.1
Q ss_pred CCccccccccccccCCceEcc-cCceecccchHHHh
Q 018689 194 SSQCAVCKDSFELNEEARQMP-CKHIYHPDCIMPWL 228 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp-C~H~FH~~Ci~~Wl 228 (352)
...|.+|...|..-..-..-. ||++|+..|....+
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 578999999997644333344 99999999987665
No 152
>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=61.58 E-value=5.7 Score=27.52 Aligned_cols=43 Identities=30% Similarity=0.654 Sum_probs=27.8
Q ss_pred ccccccccccccCCceEcccCceecccchHHHhhc------CCCCCccC
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL------HNSCPVCR 238 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~------~~sCP~CR 238 (352)
.|.||......+..+.--.|...||..|+..=+.. .-.||.|+
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 38899884333332333349999999998875431 33688875
No 153
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.75 E-value=4.4 Score=39.65 Aligned_cols=45 Identities=18% Similarity=0.363 Sum_probs=36.2
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhc---CCCCCccC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLEL---HNSCPVCR 238 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~---~~sCP~CR 238 (352)
...|||-.+.-.....+..|.|||+.-+.-++..-+. ...||.|=
T Consensus 336 ~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 336 LFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 4789999888888888999999999998888775433 33699993
No 154
>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 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=59.37 E-value=3.2 Score=39.11 Aligned_cols=46 Identities=28% Similarity=0.657 Sum_probs=34.3
Q ss_pred CCccccccccccccCCceEc--c-cCceecccchHHHhhc-CCCCC--ccCC
Q 018689 194 SSQCAVCKDSFELNEEARQM--P-CKHIYHPDCIMPWLEL-HNSCP--VCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l--p-C~H~FH~~Ci~~Wl~~-~~sCP--~CR~ 239 (352)
+..|+||..+.-..-.++.| | |-|..|..|++.-+.. ...|| -|-+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 46899999875444334433 6 9999999999999866 45799 6744
No 156
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.04 E-value=2.3 Score=45.09 Aligned_cols=43 Identities=23% Similarity=0.569 Sum_probs=32.3
Q ss_pred CCcccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCC
Q 018689 194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
-..|.||+..|... -..+.|-|||..|+.|+..- .+.+|| |++
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 46899998887654 34667779999999999864 355788 654
No 157
>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=58.66 E-value=8.7 Score=27.07 Aligned_cols=40 Identities=28% Similarity=0.617 Sum_probs=28.5
Q ss_pred cccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCC
Q 018689 197 CAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDD 245 (352)
Q Consensus 197 C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~ 245 (352)
|..|...+.... ..+..-+..||..|+ +|-.|+..|....
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCcE-EEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 677888877533 222347889999886 5999998886543
No 158
>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=58.04 E-value=2.7 Score=32.19 Aligned_cols=40 Identities=23% Similarity=0.515 Sum_probs=23.2
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
..|++|..+++... +|.++..|-.. +.....||-|..+|.
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 57999998876533 67778888665 455667999988773
No 159
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=57.63 E-value=8.8 Score=37.74 Aligned_cols=49 Identities=20% Similarity=0.494 Sum_probs=35.2
Q ss_pred CCcccccccccccc-CCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELN-EEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~-~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
...|+||.+..... ....-.||++..|..|+..-...+.+||.||+...
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 37899999987332 23333447888888888777777889999996553
No 160
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=55.87 E-value=10 Score=40.83 Aligned_cols=46 Identities=22% Similarity=0.462 Sum_probs=28.8
Q ss_pred CCccccccccccccCCceEcccCceecc--cchHHH-hhc-C-----CCCCccCCCCCCCCh
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHP--DCIMPW-LEL-H-----NSCPVCRYELPTDDP 246 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~--~Ci~~W-l~~-~-----~sCP~CR~~l~~~~~ 246 (352)
...|+|+...+ .+||.+..|+ .|.+.- +.. + -.||+|.+...-+..
T Consensus 306 SL~CPl~~~Rm-------~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l 360 (636)
T KOG2169|consen 306 SLNCPLSKMRM-------SLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGL 360 (636)
T ss_pred EecCCccccee-------ecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccch
Confidence 36899887664 5556555555 676653 322 1 159999887765543
No 161
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=54.41 E-value=4.5 Score=38.65 Aligned_cols=48 Identities=25% Similarity=0.633 Sum_probs=33.3
Q ss_pred CccccccccccccCCc-eEcc---cCceecccchHHHh-hc--------CCCCCccCCCCC
Q 018689 195 SQCAVCKDSFELNEEA-RQMP---CKHIYHPDCIMPWL-EL--------HNSCPVCRYELP 242 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~-~~lp---C~H~FH~~Ci~~Wl-~~--------~~sCP~CR~~l~ 242 (352)
..|-+|.+++...+.. ...+ |.-++|..|+..-+ .. ...||.|++.+.
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 5899999999433322 2222 88899999999843 22 236999998654
No 162
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=53.95 E-value=8.2 Score=37.80 Aligned_cols=50 Identities=22% Similarity=0.612 Sum_probs=34.1
Q ss_pred CCccccccccccc-----cC-----------CceEcccCceecccchHHHhhc---------CCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFEL-----NE-----------EARQMPCKHIYHPDCIMPWLEL---------HNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~~-----~~-----------~~~~lpC~H~FH~~Ci~~Wl~~---------~~sCP~CR~~l~~ 243 (352)
..+|++|+..=.. +. ...--||||+--.+-.+-|.+. |..||.|-..|..
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g 415 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG 415 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence 5799999876211 10 1223479999888888889753 3469999887754
No 163
>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=53.89 E-value=8.4 Score=32.86 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=21.3
Q ss_pred eeeecCCcc-cccCCCCCCCCcCCCCCCCceEE
Q 018689 24 YFCHQCNRT-VRVTPSPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 24 ywCh~C~r~-V~~~~~~~~~~~CP~C~~gFvEE 55 (352)
.-|..|... .-+ +...++||+|+.-|..+
T Consensus 10 r~Cp~cg~kFYDL---nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL---NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc---CCCCccCCCcCCccCcc
Confidence 569999654 333 34779999999988666
No 164
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=53.73 E-value=5.7 Score=40.30 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=20.1
Q ss_pred ecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689 27 HQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 27 h~C~r~V~~~~~~~~~~~CP~C~~gFvEEi 56 (352)
|.|.|.|++ ++.||.|+.-|-.=-
T Consensus 286 HrC~RIV~v------EYrCPEC~KVFsCPA 309 (500)
T KOG3993|consen 286 HRCPRIVHV------EYRCPECDKVFSCPA 309 (500)
T ss_pred ccCCeeEEe------eecCCcccccccCch
Confidence 889999975 689999999996543
No 165
>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=53.22 E-value=5.2 Score=26.24 Aligned_cols=30 Identities=23% Similarity=0.579 Sum_probs=22.1
Q ss_pred eeeecCCcccccCCCC----CCCCcCCCCCCCce
Q 018689 24 YFCHQCNRTVRVTPSP----SSDLVCPSCNGGFI 53 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~----~~~~~CP~C~~gFv 53 (352)
+-|-+|...+++.... ...+.||.|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4588999988876421 23589999998774
No 166
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.15 E-value=7.3 Score=25.75 Aligned_cols=26 Identities=23% Similarity=0.837 Sum_probs=16.1
Q ss_pred CccccccccccccCC-------ceEcc-cCceec
Q 018689 195 SQCAVCKDSFELNEE-------ARQMP-CKHIYH 220 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~-------~~~lp-C~H~FH 220 (352)
.+|+-|...|...+. .+.-+ |+|+|.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 368888888876542 22223 778775
No 167
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.74 E-value=28 Score=29.11 Aligned_cols=44 Identities=25% Similarity=0.495 Sum_probs=31.8
Q ss_pred CccccccccccccC----------Cce-EcccCceecccchHHHhhcCCCCCccC
Q 018689 195 SQCAVCKDSFELNE----------EAR-QMPCKHIYHPDCIMPWLELHNSCPVCR 238 (352)
Q Consensus 195 ~~C~IC~e~~~~~~----------~~~-~lpC~H~FH~~Ci~~Wl~~~~sCP~CR 238 (352)
..|--|+..|.... ..- .-.|++.|+.+|=.-+-+.-+.||-|.
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 46888988876421 112 234999999999877777777899995
No 168
>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=49.14 E-value=13 Score=28.76 Aligned_cols=33 Identities=18% Similarity=0.624 Sum_probs=16.1
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCceEEccCC
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELETP 59 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~~ 59 (352)
-++||.|-..... ..-.+||.|+..=|..+...
T Consensus 9 vlrC~aCf~~t~~----~~k~FCp~CGn~TL~rvsvs 41 (73)
T PF08772_consen 9 VLRCHACFKITKD----MTKQFCPKCGNATLKRVSVS 41 (73)
T ss_dssp EEE-SSS--EES-----SS--S-SSS--S--EEEE-B
T ss_pred eEEccccccCcCC----CCceeCcccCCCcceEEEEE
Confidence 4799999998642 35699999999988877653
No 169
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=48.29 E-value=5.9 Score=39.89 Aligned_cols=50 Identities=24% Similarity=0.639 Sum_probs=0.0
Q ss_pred CCcccccccccc-------------ccC---CceEcccCceecccchHHHhhc---------CCCCCccCCCCCC
Q 018689 194 SSQCAVCKDSFE-------------LNE---EARQMPCKHIYHPDCIMPWLEL---------HNSCPVCRYELPT 243 (352)
Q Consensus 194 ~~~C~IC~e~~~-------------~~~---~~~~lpC~H~FH~~Ci~~Wl~~---------~~sCP~CR~~l~~ 243 (352)
..+|++|+..-. .+. ...--||||+--.+..+-|-+. +..||.|-..|..
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 579999997621 010 1334489999999999999643 3469999888753
No 170
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.62 E-value=8.8 Score=28.56 Aligned_cols=15 Identities=27% Similarity=0.844 Sum_probs=12.5
Q ss_pred CCCCCcCCCCCCCce
Q 018689 39 PSSDLVCPSCNGGFI 53 (352)
Q Consensus 39 ~~~~~~CP~C~~gFv 53 (352)
+..+++||+|+--|.
T Consensus 45 ~~gev~CPYC~t~y~ 59 (62)
T COG4391 45 DEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCcEecCccccEEE
Confidence 468999999998774
No 171
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=47.61 E-value=20 Score=35.29 Aligned_cols=47 Identities=26% Similarity=0.522 Sum_probs=34.0
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~ 240 (352)
...|-.|.++.......+.-.|+|.||.+|=.--=+.-..||-|...
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~ 376 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEHK 376 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCCC
Confidence 34699998877776666666699999999954433444569999753
No 172
>PRK12496 hypothetical protein; Provisional
Probab=47.34 E-value=13 Score=32.97 Aligned_cols=27 Identities=22% Similarity=0.509 Sum_probs=19.6
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGF 52 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gF 52 (352)
.|+|.-|.+..... ...-+||.|++..
T Consensus 127 ~~~C~gC~~~~~~~---~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPED---YPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCC---CCCCcCCCCCChh
Confidence 38899999986422 2446899999854
No 173
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=46.73 E-value=16 Score=31.88 Aligned_cols=32 Identities=31% Similarity=0.757 Sum_probs=26.1
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCC-Cc
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNG-GF 52 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~-gF 52 (352)
...+|-|-+|...+.+.. +..-+.||.|++ .|
T Consensus 109 g~G~l~C~~Cg~~~~~~~-~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTH-PERLPPCPKCGHTEF 141 (146)
T ss_pred cCceEecccCCCEEEecC-CCcCCCCCCCCCCee
Confidence 357899999999998864 456789999996 44
No 174
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=45.56 E-value=12 Score=26.72 Aligned_cols=35 Identities=26% Similarity=0.690 Sum_probs=25.9
Q ss_pred CCceeee--cCCcccccCC-CCCCCCcCCCCCCCceEE
Q 018689 21 PQMYFCH--QCNRTVRVTP-SPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 21 ~~~ywCh--~C~r~V~~~~-~~~~~~~CP~C~~gFvEE 55 (352)
...-||- .|...|.... .....+.||.|+-.|--.
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 3566999 9999887642 235679999999887543
No 175
>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=45.16 E-value=12 Score=37.91 Aligned_cols=31 Identities=23% Similarity=0.605 Sum_probs=23.2
Q ss_pred ceeeecCCcccccCCCC-CCCCcCCCCCCCce
Q 018689 23 MYFCHQCNRTVRVTPSP-SSDLVCPSCNGGFI 53 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~-~~~~~CP~C~~gFv 53 (352)
.-=||+|+.-+++.+.. .....||+|+.-..
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 34599999988876533 45678999998763
No 176
>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=44.02 E-value=13 Score=26.50 Aligned_cols=31 Identities=26% Similarity=0.687 Sum_probs=16.5
Q ss_pred Cceeeec--CCcccccCCCCCC-CCcCCCCCCCc
Q 018689 22 QMYFCHQ--CNRTVRVTPSPSS-DLVCPSCNGGF 52 (352)
Q Consensus 22 ~~ywCh~--C~r~V~~~~~~~~-~~~CP~C~~gF 52 (352)
..-||-. |...+........ .+.|+.|+..|
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 3349988 9999987654333 28999998766
No 177
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=43.62 E-value=13 Score=36.01 Aligned_cols=53 Identities=26% Similarity=0.718 Sum_probs=37.8
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCCh-------------hHHHhhcCC
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDP-------------DYEQRRNGN 255 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~~-------------~~e~~~~~~ 255 (352)
...|..|.+.+-+.+.++ -.=.|+||..|+. |-+|+..|.+.+. +||+.+...
T Consensus 92 GTKCsaC~~GIpPtqVVR-kAqd~VYHl~CF~--------C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~ 157 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVR-KAQDFVYHLHCFA--------CFICKRQLATGDEFYLMEDARLVCKDDYETAKQKH 157 (383)
T ss_pred CCcchhhcCCCChHHHHH-Hhhcceeehhhhh--------hHhhhcccccCCeeEEeccceeehhhhHHHHHhcc
Confidence 467999988876644333 3368999999974 8999988876553 677765554
No 178
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.53 E-value=13 Score=36.22 Aligned_cols=48 Identities=25% Similarity=0.575 Sum_probs=38.1
Q ss_pred CCCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCC
Q 018689 193 DSSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELP 242 (352)
Q Consensus 193 ~~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~ 242 (352)
+...|-||...+.... +.-.|.|.|+..|...|....+-||.|+....
T Consensus 104 ~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~ 151 (324)
T KOG0824|consen 104 DHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKIS 151 (324)
T ss_pred CccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCcC
Confidence 3578999988876522 11229999999999999999999999988664
No 179
>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=42.93 E-value=24 Score=25.87 Aligned_cols=47 Identities=26% Similarity=0.552 Sum_probs=33.0
Q ss_pred CccccccccccccC-CceEcccCceecccchHHHhhcCCCCCccCCCCCC
Q 018689 195 SQCAVCKDSFELNE-EARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPT 243 (352)
Q Consensus 195 ~~C~IC~e~~~~~~-~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~ 243 (352)
..|-.|-.++..+. ++.+..=...|+.+|.+..| +..||.|-.+|..
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~ 53 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVR 53 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCcccc
Confidence 45777877777655 34443312459999999866 7789999888753
No 180
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=42.93 E-value=6.8 Score=37.73 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=20.6
Q ss_pred CCccccccccccccCCceEc---ccCceecccchHHHhhcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELNEEARQM---PCKHIYHPDCIMPWLELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l---pC~H~FH~~Ci~~Wl~~~~sCP~CR~~ 240 (352)
...|+||-..-.... ++.- .=.|.+|.-|-..|--.+..||.|-..
T Consensus 172 ~g~CPvCGs~P~~s~-l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSV-LRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp -SS-TTT---EEEEE-EE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CCcCCCCCCcCceEE-EecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 479999977632210 0000 024678888999998888899999554
No 181
>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=42.90 E-value=9.8 Score=25.81 Aligned_cols=33 Identities=33% Similarity=0.646 Sum_probs=20.4
Q ss_pred eeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 24 YFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
|.|-.|....-+.-....+++|+.| +--|||..
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~C-G~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNC-GLVLEENI 33 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT--BBEE-TT
T ss_pred CCCcCCcCCceEEcCCCCeEECCCC-CCEeeccc
Confidence 6788888865223334688999999 34444443
No 182
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=42.37 E-value=17 Score=32.71 Aligned_cols=25 Identities=28% Similarity=0.725 Sum_probs=20.3
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGF 52 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gF 52 (352)
.|-||.|-+.+. ...-+||.|++.-
T Consensus 139 ~~rC~GC~~~f~-----~~~~~Cp~CG~~~ 163 (177)
T COG1439 139 RLRCHGCKRIFP-----EPKDFCPICGSPL 163 (177)
T ss_pred eEEEecCceecC-----CCCCcCCCCCCce
Confidence 588999999875 2467999999983
No 183
>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=42.07 E-value=14 Score=26.14 Aligned_cols=35 Identities=23% Similarity=0.578 Sum_probs=25.2
Q ss_pred CccccccccccccCCceEc-ccCceecccchHHHhh
Q 018689 195 SQCAVCKDSFELNEEARQM-PCKHIYHPDCIMPWLE 229 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~l-pC~H~FH~~Ci~~Wl~ 229 (352)
..|.+|...|..-...... .||++|+..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 5799999888764433333 3999999999876543
No 184
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=42.00 E-value=14 Score=27.80 Aligned_cols=18 Identities=28% Similarity=0.881 Sum_probs=14.4
Q ss_pred eecCCcccccCCCCCCCCcCCCCCC
Q 018689 26 CHQCNRTVRVTPSPSSDLVCPSCNG 50 (352)
Q Consensus 26 Ch~C~r~V~~~~~~~~~~~CP~C~~ 50 (352)
|..|.+-| .+-.||.|++
T Consensus 8 C~~C~~i~-------~~~~Cp~Cgs 25 (64)
T PRK06393 8 CKKCKRLT-------PEKTCPVHGD 25 (64)
T ss_pred HhhCCccc-------CCCcCCCCCC
Confidence 88898865 2349999998
No 185
>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=41.17 E-value=15 Score=26.07 Aligned_cols=11 Identities=45% Similarity=1.334 Sum_probs=6.7
Q ss_pred CCcCCCCCCCc
Q 018689 42 DLVCPSCNGGF 52 (352)
Q Consensus 42 ~~~CP~C~~gF 52 (352)
.+.||+|+.+|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 35677776644
No 186
>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=40.68 E-value=9.1 Score=28.90 Aligned_cols=12 Identities=17% Similarity=0.764 Sum_probs=8.7
Q ss_pred eecccchHHHhh
Q 018689 218 IYHPDCIMPWLE 229 (352)
Q Consensus 218 ~FH~~Ci~~Wl~ 229 (352)
-||+.|+.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 399999999985
No 187
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=40.37 E-value=33 Score=25.39 Aligned_cols=40 Identities=25% Similarity=0.556 Sum_probs=30.7
Q ss_pred CCCCCceeeec--CCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQ--CNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~--C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
.-++.-+-|-. |+-=+|-...-....+||.|++..+++.-
T Consensus 13 ~e~t~VW~Ct~e~C~gWmR~nFs~~~~p~CPlC~s~M~~~~r 54 (59)
T PF14169_consen 13 EEETKVWECTSEDCNGWMRDNFSFEEEPVCPLCKSPMVSGTR 54 (59)
T ss_pred ceeeeeEEeCCCCCCcccccccccCCCccCCCcCCcccccee
Confidence 34566777887 88888766555677999999999888754
No 188
>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=40.36 E-value=13 Score=26.70 Aligned_cols=42 Identities=29% Similarity=0.634 Sum_probs=19.3
Q ss_pred cccccccccccC------CceEcc-cCceecccchHHHhhcCCCCCccC
Q 018689 197 CAVCKDSFELNE------EARQMP-CKHIYHPDCIMPWLELHNSCPVCR 238 (352)
Q Consensus 197 C~IC~e~~~~~~------~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR 238 (352)
|--|+..|.... ....-| |++.|+.+|=.--=+.-..||-|-
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 445666665531 223334 899999999432224445799883
No 189
>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 smart00661 RPOL9 RNA polymerase subunit 9.
Probab=39.25 E-value=17 Score=25.20 Aligned_cols=31 Identities=26% Similarity=0.722 Sum_probs=19.9
Q ss_pred eeecCCcccccCCCCC-CCCcCCCCCCCceEEcc
Q 018689 25 FCHQCNRTVRVTPSPS-SDLVCPSCNGGFIEELE 57 (352)
Q Consensus 25 wCh~C~r~V~~~~~~~-~~~~CP~C~~gFvEEi~ 57 (352)
||-.|...+-...... ..++||.|+ |++.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 7889988765432211 368899998 455444
No 191
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.05 E-value=15 Score=24.23 Aligned_cols=26 Identities=27% Similarity=0.839 Sum_probs=16.0
Q ss_pred CccccccccccccCC--------ceEcccCceec
Q 018689 195 SQCAVCKDSFELNEE--------ARQMPCKHIYH 220 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~--------~~~lpC~H~FH 220 (352)
.+|+-|...|...++ ++.-.|+|+|+
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 368888888876543 22223777774
No 192
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.93 E-value=17 Score=34.59 Aligned_cols=32 Identities=9% Similarity=0.259 Sum_probs=28.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhh
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLE 229 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~ 229 (352)
..|+.|+..+.. +++.|=||+|++.||.+.+.
T Consensus 44 dcCsLtLqPc~d---Pvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 44 DCCSLTLQPCRD---PVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ceeeeecccccC---CccCCCCeeeeHHHHHHHHH
Confidence 579999998877 78888999999999999863
No 193
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=36.84 E-value=11 Score=37.91 Aligned_cols=31 Identities=26% Similarity=0.563 Sum_probs=0.0
Q ss_pred CceEcccCceecccchHHHhh------cCCCCCccCCCCC
Q 018689 209 EARQMPCKHIYHPDCIMPWLE------LHNSCPVCRYELP 242 (352)
Q Consensus 209 ~~~~lpC~H~FH~~Ci~~Wl~------~~~sCP~CR~~l~ 242 (352)
..+-|.|||++-. ..|-. ...+||+||..-+
T Consensus 303 P~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g~ 339 (416)
T PF04710_consen 303 PWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVGP 339 (416)
T ss_dssp ----------------------------------------
T ss_pred ceeeccccceeee---cccccccccccccccCCCccccCC
Confidence 3556679998764 35743 2457999998544
No 194
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.39 E-value=24 Score=38.59 Aligned_cols=34 Identities=18% Similarity=0.485 Sum_probs=24.9
Q ss_pred CCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 19 QEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 19 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
.......||.|...-. ....||.|++.=|.....
T Consensus 458 ~~~~~L~CH~Cg~~~~------~p~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 458 KATGQLRCHYCGYQEP------IPQSCPECGSEHLRAVGP 491 (730)
T ss_pred cCCCeeEeCCCCCCCC------CCCCCCCCCCCeeEEecc
Confidence 3457889999999843 347899999986655543
No 195
>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=36.37 E-value=33 Score=22.64 Aligned_cols=33 Identities=24% Similarity=0.707 Sum_probs=25.6
Q ss_pred ceeeecCCcccccCCC-CCCCCcCCCCCCCceEE
Q 018689 23 MYFCHQCNRTVRVTPS-PSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~-~~~~~~CP~C~~gFvEE 55 (352)
+.-|-.|.+...+... +..+-+|..|++.+|..
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEEETTTTEEEETTTB--SSTTBCTTTTEBEBEE
T ss_pred CcCcCCCCCccccccCCCCCCCccCCCCCeeEeC
Confidence 3568899999887654 36789999999988764
No 196
>PRK13794 hypothetical protein; Provisional
Probab=35.84 E-value=19 Score=37.45 Aligned_cols=29 Identities=24% Similarity=0.654 Sum_probs=21.2
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
..|||-.|+.+|- .-.|..|+.. ..++..
T Consensus 9 ~~~wc~~cn~p~~-------~~~c~~cg~~-~~~~~~ 37 (479)
T PRK13794 9 HLKWCDNCNVPVL-------GKKCAICGSE-TREVKV 37 (479)
T ss_pred EEEEcCCCCCeec-------CCchhHhCCC-eeEEec
Confidence 5799999999972 2459999996 334443
No 197
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=35.76 E-value=21 Score=26.56 Aligned_cols=19 Identities=26% Similarity=0.875 Sum_probs=14.2
Q ss_pred eeecCCcccccCCCCCCCCcCCCCCC
Q 018689 25 FCHQCNRTVRVTPSPSSDLVCPSCNG 50 (352)
Q Consensus 25 wCh~C~r~V~~~~~~~~~~~CP~C~~ 50 (352)
=|-+|.+-+ .+-.||.|++
T Consensus 5 AC~~C~~i~-------~~~~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYIT-------TEDRCPVCGS 23 (61)
T ss_pred hhhhCCccc-------CCCcCCCCcC
Confidence 388898865 2337999997
No 198
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.74 E-value=11 Score=29.10 Aligned_cols=29 Identities=21% Similarity=0.619 Sum_probs=17.5
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCceE
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIE 54 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvE 54 (352)
-+|-|--|.--+... -+-+||.|+++||-
T Consensus 25 CtfEcTFCadCae~~----l~g~CPnCGGelv~ 53 (84)
T COG3813 25 CTFECTFCADCAENR----LHGLCPNCGGELVA 53 (84)
T ss_pred EEEeeehhHhHHHHh----hcCcCCCCCchhhc
Confidence 355555554332211 25689999999985
No 199
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=35.31 E-value=21 Score=25.87 Aligned_cols=31 Identities=13% Similarity=0.542 Sum_probs=23.2
Q ss_pred ceeeecCCcccccCCCC-CCCCcCCCCCCCce
Q 018689 23 MYFCHQCNRTVRVTPSP-SSDLVCPSCNGGFI 53 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~-~~~~~CP~C~~gFv 53 (352)
.|-|-.|...|.+.... ...+.||.|+..|-
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 35799999999875433 35689999998763
No 200
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=35.05 E-value=24 Score=38.86 Aligned_cols=55 Identities=20% Similarity=0.499 Sum_probs=32.1
Q ss_pred ccccCCCCccccccccccc------------cCCceEcc-cCceecccc----------hHHHhhcCCCCC---ccCCCC
Q 018689 188 AMMSSDSSQCAVCKDSFEL------------NEEARQMP-CKHIYHPDC----------IMPWLELHNSCP---VCRYEL 241 (352)
Q Consensus 188 ~~~~~~~~~C~IC~e~~~~------------~~~~~~lp-C~H~FH~~C----------i~~Wl~~~~sCP---~CR~~l 241 (352)
+....+..+|.||+..+.- ++.+.+.. ||-.|-.+= +++-++...+|| +|.++.
T Consensus 599 ~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 599 ENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKF 678 (958)
T ss_pred ccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccc
Confidence 3345567899999887642 33444444 665543221 222334456899 998876
Q ss_pred C
Q 018689 242 P 242 (352)
Q Consensus 242 ~ 242 (352)
.
T Consensus 679 t 679 (958)
T KOG1074|consen 679 T 679 (958)
T ss_pred c
Confidence 4
No 201
>PF00527 E7: E7 protein, Early protein; InterPro: IPR000148 This family includes the E7 oncoprotein from various papillomaviruses []. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2F8B_A 2EWL_A 2B9D_A.
Probab=34.56 E-value=8.5 Score=30.91 Aligned_cols=29 Identities=38% Similarity=0.909 Sum_probs=16.2
Q ss_pred CCCce----eeecCCcccccCCCC--------------CCCCcCCCC
Q 018689 20 EPQMY----FCHQCNRTVRVTPSP--------------SSDLVCPSC 48 (352)
Q Consensus 20 ~~~~y----wCh~C~r~V~~~~~~--------------~~~~~CP~C 48 (352)
....| .|+.|++.||+.-.. +-.++||.|
T Consensus 45 ~~~~Y~V~t~C~~C~~~lrl~V~as~~~Ir~lq~LLl~~L~lvCp~C 91 (92)
T PF00527_consen 45 ERQPYRVVTCCGRCGKRLRLVVVASHEGIRTLQQLLLGDLSLVCPPC 91 (92)
T ss_dssp -SCEEEEEEEBTTT--EEEEEEEC-HHHHHHHHHHHHCT-EE--CCC
T ss_pred CCCCeEEEeECCCCCCEEEEEEEeChhhHHHHHHHhhcCceEeCCCC
Confidence 34566 499999999975421 336889988
No 202
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=34.46 E-value=27 Score=25.09 Aligned_cols=18 Identities=17% Similarity=0.492 Sum_probs=14.8
Q ss_pred CcCCCCCCCceEEccCCC
Q 018689 43 LVCPSCNGGFIEELETPN 60 (352)
Q Consensus 43 ~~CP~C~~gFvEEi~~~~ 60 (352)
+.||+|+..|.=.|+...
T Consensus 1 i~CPyCge~~~~~iD~s~ 18 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSA 18 (52)
T ss_pred CCCCCCCCeeEEEEecCC
Confidence 579999999888888654
No 203
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=34.07 E-value=22 Score=36.28 Aligned_cols=29 Identities=24% Similarity=0.654 Sum_probs=22.0
Q ss_pred eeeecCCcccccCCCC-CCCCcCCCCCCCc
Q 018689 24 YFCHQCNRTVRVTPSP-SSDLVCPSCNGGF 52 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~-~~~~~CP~C~~gF 52 (352)
-=||.|+.-+++.+.+ .....||+|+...
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 3499999988876543 3457799999876
No 204
>PHA02776 E7 protein; Provisional
Probab=33.72 E-value=14 Score=30.29 Aligned_cols=31 Identities=32% Similarity=0.704 Sum_probs=22.4
Q ss_pred CCCcee----eecCCcccccCCCC--------------CCCCcCCCCCC
Q 018689 20 EPQMYF----CHQCNRTVRVTPSP--------------SSDLVCPSCNG 50 (352)
Q Consensus 20 ~~~~yw----Ch~C~r~V~~~~~~--------------~~~~~CP~C~~ 50 (352)
+...|+ |+.|.+.||+.-.. .-.++||.|..
T Consensus 51 ~~~~Y~Ivt~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~ 99 (101)
T PHA02776 51 IKQAFQIVTCCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAP 99 (101)
T ss_pred cCCCeEEEeECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCC
Confidence 556675 99999999975421 23589999964
No 205
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=33.49 E-value=13 Score=35.07 Aligned_cols=29 Identities=17% Similarity=0.471 Sum_probs=20.3
Q ss_pred CceeeecCCcccccCCC-----CCCCCcCCCCCC
Q 018689 22 QMYFCHQCNRTVRVTPS-----PSSDLVCPSCNG 50 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~-----~~~~~~CP~C~~ 50 (352)
.-.-|.-|...+..... .++-++||+|+.
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 44569999987654321 356799999975
No 206
>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=33.31 E-value=22 Score=26.12 Aligned_cols=15 Identities=20% Similarity=0.512 Sum_probs=12.2
Q ss_pred CCCceeeecCCcccc
Q 018689 20 EPQMYFCHQCNRTVR 34 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~ 34 (352)
.+.+.|||.|+..|-
T Consensus 46 ~~~~i~C~~C~~~v~ 60 (63)
T PF02148_consen 46 STGSIWCYACDDYVY 60 (63)
T ss_dssp TTTCEEETTTTEEEE
T ss_pred CCCeEEEcCCCcEEe
Confidence 456689999999984
No 207
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.30 E-value=8.2 Score=36.99 Aligned_cols=47 Identities=21% Similarity=0.504 Sum_probs=37.3
Q ss_pred CCcccccccccccc---CCceEcc--------cCceecccchHHHhhcC-CCCCccCCC
Q 018689 194 SSQCAVCKDSFELN---EEARQMP--------CKHIYHPDCIMPWLELH-NSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~---~~~~~lp--------C~H~FH~~Ci~~Wl~~~-~sCP~CR~~ 240 (352)
...|.||...|... ...+++. |+|..+..|+..-+... ..||.|+..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 36799999999843 3456666 99999999999987554 589999874
No 208
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=33.02 E-value=18 Score=38.73 Aligned_cols=26 Identities=38% Similarity=1.066 Sum_probs=19.8
Q ss_pred ccCceecccchHHHhhcC-----CCCCccCC
Q 018689 214 PCKHIYHPDCIMPWLELH-----NSCPVCRY 239 (352)
Q Consensus 214 pC~H~FH~~Ci~~Wl~~~-----~sCP~CR~ 239 (352)
.|+-.||..|+..|+... -.||-||.
T Consensus 40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 389999999999998532 24777765
No 209
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.92 E-value=18 Score=37.04 Aligned_cols=37 Identities=22% Similarity=0.521 Sum_probs=28.1
Q ss_pred CCccccccccccccCC-----ceEcccCceecccchHHHhhc
Q 018689 194 SSQCAVCKDSFELNEE-----ARQMPCKHIYHPDCIMPWLEL 230 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~-----~~~lpC~H~FH~~Ci~~Wl~~ 230 (352)
...|+.|...++.... ....+|+|.||..|+..|...
T Consensus 226 tk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 226 TKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred CccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 3569999999887652 223359999999999888654
No 210
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=32.48 E-value=24 Score=30.27 Aligned_cols=35 Identities=20% Similarity=0.580 Sum_probs=24.6
Q ss_pred CCCceeeecCCcccccCCC-CCCCCcCCCCCCCceE
Q 018689 20 EPQMYFCHQCNRTVRVTPS-PSSDLVCPSCNGGFIE 54 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~-~~~~~~CP~C~~gFvE 54 (352)
..-.|.|-.|...+..... ......|+.|++-|+.
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 4567899999988754332 2345789999977763
No 211
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.22 E-value=17 Score=35.02 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=21.2
Q ss_pred CCceeeecCCcccccCCCCCCCCcCCCCCCC
Q 018689 21 PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGG 51 (352)
Q Consensus 21 ~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~g 51 (352)
-..-|||-|-++-+.+. ....||.|++.
T Consensus 258 C~HiyCY~Ci~ts~~~~---asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 258 CGHIYCYYCIATSRLWD---ASFTCPLCGEN 285 (298)
T ss_pred ccceeehhhhhhhhcch---hhcccCccCCC
Confidence 34569999999865543 56999999974
No 212
>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=31.98 E-value=28 Score=35.34 Aligned_cols=26 Identities=31% Similarity=0.878 Sum_probs=19.5
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGF 52 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gF 52 (352)
..=||+|+..+. ......||+|+.-.
T Consensus 215 ~~~C~~Cd~~~~----~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTIL----PAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCccC----CCCCcCCcCCCCcc
Confidence 445999999763 23567899999876
No 213
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.31 E-value=15 Score=22.13 Aligned_cols=13 Identities=31% Similarity=0.859 Sum_probs=10.2
Q ss_pred CcCCCCCCCceEE
Q 018689 43 LVCPSCNGGFIEE 55 (352)
Q Consensus 43 ~~CP~C~~gFvEE 55 (352)
+.||.|+-.|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 6799999888643
No 214
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=31.00 E-value=13 Score=36.13 Aligned_cols=37 Identities=19% Similarity=0.540 Sum_probs=27.0
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELH 231 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~ 231 (352)
..|.+|+++|..+......-|--+||..|+..|+...
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred eecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 3888898888765555555555588888888887654
No 215
>PF14353 CpXC: CpXC protein
Probab=30.84 E-value=28 Score=29.12 Aligned_cols=18 Identities=33% Similarity=0.713 Sum_probs=15.2
Q ss_pred CCcCCCCCCCceEEccCC
Q 018689 42 DLVCPSCNGGFIEELETP 59 (352)
Q Consensus 42 ~~~CP~C~~gFvEEi~~~ 59 (352)
+++||+|+.-|.-++...
T Consensus 1 ~itCP~C~~~~~~~v~~~ 18 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTS 18 (128)
T ss_pred CcCCCCCCCeeEEEEEeE
Confidence 479999999999988753
No 216
>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=30.72 E-value=22 Score=23.60 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=8.9
Q ss_pred CCCcCCCCCCC
Q 018689 41 SDLVCPSCNGG 51 (352)
Q Consensus 41 ~~~~CP~C~~g 51 (352)
.+|.||+|++.
T Consensus 4 i~v~CP~C~s~ 14 (36)
T PF03811_consen 4 IDVHCPRCQST 14 (36)
T ss_pred EeeeCCCCCCC
Confidence 46899999974
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=30.25 E-value=16 Score=26.24 Aligned_cols=31 Identities=19% Similarity=0.475 Sum_probs=21.9
Q ss_pred CceeeecCCcccccCCC-CCCCCcCCCCCCCc
Q 018689 22 QMYFCHQCNRTVRVTPS-PSSDLVCPSCNGGF 52 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~-~~~~~~CP~C~~gF 52 (352)
+.+-|-.|++-+-.... ..-+|.||.|..=+
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 45789999998754322 24589999998643
No 218
>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=29.88 E-value=43 Score=26.76 Aligned_cols=44 Identities=25% Similarity=0.522 Sum_probs=32.5
Q ss_pred CCccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCCChhHH
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTDDPDYE 249 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~e 249 (352)
...|.-|...+..-+.+- |..||..+..|..|+++++..-.-.|
T Consensus 33 rS~C~~C~~~L~~~~lIP------------i~S~l~lrGrCr~C~~~I~~~y~l~E 76 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP------------ILSYLLLRGRCRYCGAPIPPRYPLIE 76 (92)
T ss_pred CCcCcCCCCcCcccccch------------HHHHHHhCCCCcccCCCCChHHHHHH
Confidence 478999988876633322 67899999999999999976544433
No 219
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=29.62 E-value=21 Score=23.88 Aligned_cols=12 Identities=25% Similarity=1.002 Sum_probs=5.5
Q ss_pred CceeeecCCccc
Q 018689 22 QMYFCHQCNRTV 33 (352)
Q Consensus 22 ~~ywCh~C~r~V 33 (352)
++|||--|+..|
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 579999999987
No 220
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.04 E-value=15 Score=33.17 Aligned_cols=38 Identities=24% Similarity=0.649 Sum_probs=27.1
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
+..-|-|-.|...++.-.-....++||.|++.. +|++.
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L-~~~d~ 147 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDL-EEYDS 147 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHhCCCCCCCCchh-hhccc
Confidence 346788999988887644335679999999864 44443
No 221
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.95 E-value=31 Score=37.32 Aligned_cols=44 Identities=32% Similarity=0.668 Sum_probs=32.2
Q ss_pred ccccccccccccCCceEcccCc-eecccchHHHh--hc----CCCCCccCCCCC
Q 018689 196 QCAVCKDSFELNEEARQMPCKH-IYHPDCIMPWL--EL----HNSCPVCRYELP 242 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H-~FH~~Ci~~Wl--~~----~~sCP~CR~~l~ 242 (352)
.|+||-..+.. ...-.|+| ..+..|..... .. ++.||+||..+.
T Consensus 2 ~c~ic~~s~~~---~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDF---VGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCccc---cccccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 58999887654 44445999 89999988764 22 456899998764
No 222
>PF12773 DZR: Double zinc ribbon
Probab=28.47 E-value=39 Score=23.29 Aligned_cols=27 Identities=30% Similarity=0.901 Sum_probs=16.1
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCC
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNG 50 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~ 50 (352)
..-||..|-..+. ......++||.|+.
T Consensus 11 ~~~fC~~CG~~l~--~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP--PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh--hccCCCCCCcCCcC
Confidence 4556777777664 11234567777776
No 223
>PF14968 CCDC84: Coiled coil protein 84
Probab=28.30 E-value=29 Score=34.47 Aligned_cols=33 Identities=33% Similarity=0.721 Sum_probs=22.0
Q ss_pred CCCCCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 18 QQEPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 18 ~~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
.....+||||=|+..|.-.. +.++| ++.||=|-
T Consensus 53 ~~~~~~fWC~fC~~ev~~~~---s~~~~----~~ai~HLa 85 (336)
T PF14968_consen 53 PEHRNRFWCVFCDCEVREHD---SSFAC----GGAIEHLA 85 (336)
T ss_pred ccccceeEeeCccchhhhcc---chhhh----ccHHhhcC
Confidence 46889999999999986432 23443 45555554
No 224
>PRK12495 hypothetical protein; Provisional
Probab=28.26 E-value=33 Score=32.04 Aligned_cols=32 Identities=19% Similarity=0.504 Sum_probs=24.8
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCCceE
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIE 54 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvE 54 (352)
.+..|+|-.|...|-.. ...++||.|+.-+-+
T Consensus 39 tmsa~hC~~CG~PIpa~---pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH---DGQEFCPTCQQPVTE 70 (226)
T ss_pred ccchhhcccccCcccCC---CCeeECCCCCCcccc
Confidence 34669999999998632 488999999966554
No 225
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.50 E-value=39 Score=35.86 Aligned_cols=34 Identities=26% Similarity=0.719 Sum_probs=24.2
Q ss_pred CCcccccccccccc----C------CceEcccCceecccchHHH
Q 018689 194 SSQCAVCKDSFELN----E------EARQMPCKHIYHPDCIMPW 227 (352)
Q Consensus 194 ~~~C~IC~e~~~~~----~------~~~~lpC~H~FH~~Ci~~W 227 (352)
...|+||.|.|+.- + ..+.+-=|-+||..|+..-
T Consensus 513 ~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~ 556 (579)
T KOG2071|consen 513 QASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEK 556 (579)
T ss_pred ccCCcccccccceeecchhhheeecceeeeccCceeeccccchH
Confidence 57899999999641 1 1333335889999998764
No 226
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.43 E-value=29 Score=24.60 Aligned_cols=15 Identities=40% Similarity=1.092 Sum_probs=11.1
Q ss_pred CCcCCCCCCCceEEc
Q 018689 42 DLVCPSCNGGFIEEL 56 (352)
Q Consensus 42 ~~~CP~C~~gFvEEi 56 (352)
-..||.|+++|+..-
T Consensus 20 ~~fCP~Cg~~~m~~~ 34 (50)
T PRK00432 20 NKFCPRCGSGFMAEH 34 (50)
T ss_pred cCcCcCCCcchhecc
Confidence 359999998866543
No 227
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=27.38 E-value=39 Score=23.43 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=23.3
Q ss_pred CCccccccccc--cccCCceEcccCceecccchHH
Q 018689 194 SSQCAVCKDSF--ELNEEARQMPCKHIYHPDCIMP 226 (352)
Q Consensus 194 ~~~C~IC~e~~--~~~~~~~~lpC~H~FH~~Ci~~ 226 (352)
...|.+|.+.+ ......+-.-|+-++|+.|+..
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 46899999988 3334455556999999999875
No 228
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=27.14 E-value=27 Score=28.22 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=21.9
Q ss_pred CCccccccccccccCCceEcc--cCceecccchHHH
Q 018689 194 SSQCAVCKDSFELNEEARQMP--CKHIYHPDCIMPW 227 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp--C~H~FH~~Ci~~W 227 (352)
...|.||.... +..+.-.. |...||..|....
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 47899999873 22222222 8889999998664
No 229
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=26.91 E-value=39 Score=36.95 Aligned_cols=44 Identities=32% Similarity=0.637 Sum_probs=27.2
Q ss_pred CCccccccccccc----c----C-CceEcc-cCceecccchHHHhhcCCCCCccCCCC
Q 018689 194 SSQCAVCKDSFEL----N----E-EARQMP-CKHIYHPDCIMPWLELHNSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~----~----~-~~~~lp-C~H~FH~~Ci~~Wl~~~~sCP~CR~~l 241 (352)
+.+|+-|...|-. + + ..-..| |+|.-|..=|.+ ++.||+|...+
T Consensus 1131 ~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a~~~EIs~----y~~CPLCHs~~ 1184 (1189)
T KOG2041|consen 1131 DLQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRAHQHEISK----YNCCPLCHSME 1184 (1189)
T ss_pred CCCChhhcCcCceeeccCCccccceEEEccccccccccccccc----cccCccccChh
Confidence 4567777666532 1 1 122234 889888776654 78999997644
No 230
>PRK11827 hypothetical protein; Provisional
Probab=26.56 E-value=28 Score=25.81 Aligned_cols=20 Identities=30% Similarity=0.328 Sum_probs=15.6
Q ss_pred HHHhhcCCCCCccCCCCCCC
Q 018689 225 MPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 225 ~~Wl~~~~sCP~CR~~l~~~ 244 (352)
++||...-.||+|+.++..+
T Consensus 2 d~~LLeILaCP~ckg~L~~~ 21 (60)
T PRK11827 2 DHRLLEIIACPVCNGKLWYN 21 (60)
T ss_pred ChHHHhheECCCCCCcCeEc
Confidence 56777777899999988643
No 231
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.54 E-value=24 Score=23.10 Aligned_cols=25 Identities=36% Similarity=0.901 Sum_probs=9.7
Q ss_pred eeecCCcccccCCCC---CCCCcCCCCC
Q 018689 25 FCHQCNRTVRVTPSP---SSDLVCPSCN 49 (352)
Q Consensus 25 wCh~C~r~V~~~~~~---~~~~~CP~C~ 49 (352)
||-+|-..+...... ..-.+||.|+
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 566666665543221 2236677664
No 232
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.35 E-value=58 Score=27.03 Aligned_cols=45 Identities=27% Similarity=0.540 Sum_probs=28.7
Q ss_pred CCccccccccccc--cCCceEcccCceecccchHHHhhcCC--CCCccCC
Q 018689 194 SSQCAVCKDSFEL--NEEARQMPCKHIYHPDCIMPWLELHN--SCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~--~~~~~~lpC~H~FH~~Ci~~Wl~~~~--sCP~CR~ 239 (352)
...|.+|...|.. +.......|+|.+|..|-.. ..... .|-+|.+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 5799999988743 33455556999999999654 11112 4888854
No 233
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=25.95 E-value=47 Score=33.42 Aligned_cols=30 Identities=30% Similarity=0.692 Sum_probs=20.6
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCce
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFI 53 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFv 53 (352)
-.|+|+.|..+-.... ...-.||+|++.|+
T Consensus 243 ~~~~C~~c~~~~~~~~--~~~~~C~~c~~~~~ 272 (382)
T PRK04338 243 YVYYCPKCLYREEVEG--LPPEECPVCGGKFG 272 (382)
T ss_pred eEEECCCCCcEEEecC--CCCCCCCCCCCcce
Confidence 4689999988754322 23457999988544
No 234
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=25.83 E-value=31 Score=24.77 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=19.3
Q ss_pred CceeeecCCcccccCC--CCCCCCcCCCCC
Q 018689 22 QMYFCHQCNRTVRVTP--SPSSDLVCPSCN 49 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~--~~~~~~~CP~C~ 49 (352)
.+-|||-|+-.--.|. ..-++.+|--|=
T Consensus 2 ~Rq~CyLCdlPr~PWami~df~EpVCRgCv 31 (54)
T PF11261_consen 2 RRQQCYLCDLPRMPWAMIWDFSEPVCRGCV 31 (54)
T ss_pred CceeEEeccCCCCchHHHhhccchhhhhhc
Confidence 5679999998754333 225778888774
No 235
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=25.77 E-value=19 Score=34.07 Aligned_cols=30 Identities=27% Similarity=0.830 Sum_probs=11.3
Q ss_pred ceeeecCCcc-cccCC--CCCCCCcCCCCCCCc
Q 018689 23 MYFCHQCNRT-VRVTP--SPSSDLVCPSCNGGF 52 (352)
Q Consensus 23 ~ywCh~C~r~-V~~~~--~~~~~~~CP~C~~gF 52 (352)
-+||-.|... ++--. .+..|+.||.|+..|
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 4689999877 33222 235789999998776
No 236
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=25.00 E-value=38 Score=22.53 Aligned_cols=11 Identities=45% Similarity=1.165 Sum_probs=7.6
Q ss_pred CcCCCCCCCce
Q 018689 43 LVCPSCNGGFI 53 (352)
Q Consensus 43 ~~CP~C~~gFv 53 (352)
-.||.|+.||-
T Consensus 3 ~~CprC~kg~H 13 (36)
T PF14787_consen 3 GLCPRCGKGFH 13 (36)
T ss_dssp -C-TTTSSSCS
T ss_pred ccCcccCCCcc
Confidence 47999999884
No 237
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.97 E-value=46 Score=23.63 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=12.8
Q ss_pred cCceecccchHHHhhcCCCCCcc
Q 018689 215 CKHIYHPDCIMPWLELHNSCPVC 237 (352)
Q Consensus 215 C~H~FH~~Ci~~Wl~~~~sCP~C 237 (352)
|+|.|-..=-.. ......||.|
T Consensus 34 Cgh~w~~~v~~R-~~~~~~CP~C 55 (55)
T PF14311_consen 34 CGHEWKASVNDR-TRRGKGCPYC 55 (55)
T ss_pred CCCeeEccHhhh-ccCCCCCCCC
Confidence 677665532222 2456679988
No 238
>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=24.88 E-value=46 Score=21.29 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=19.0
Q ss_pred eeeecCCcccccCCCCCCCCcCCCCC
Q 018689 24 YFCHQCNRTVRVTPSPSSDLVCPSCN 49 (352)
Q Consensus 24 ywCh~C~r~V~~~~~~~~~~~CP~C~ 49 (352)
-+|+.|+..+.. +.....+.|..|+
T Consensus 2 ~~C~~C~t~L~y-P~gA~~vrCs~C~ 26 (31)
T TIGR01053 2 VVCGGCRTLLMY-PRGASSVRCALCQ 26 (31)
T ss_pred cCcCCCCcEeec-CCCCCeEECCCCC
Confidence 379999998764 3346789999996
No 239
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=24.81 E-value=17 Score=24.70 Aligned_cols=12 Identities=33% Similarity=1.101 Sum_probs=10.2
Q ss_pred CCcCCCCCCCce
Q 018689 42 DLVCPSCNGGFI 53 (352)
Q Consensus 42 ~~~CP~C~~gFv 53 (352)
.+.||+|+--||
T Consensus 29 ~~~CpYCg~~yv 40 (40)
T PF10276_consen 29 PVVCPYCGTRYV 40 (40)
T ss_dssp EEEETTTTEEEE
T ss_pred eEECCCCCCEEC
Confidence 489999998875
No 240
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=24.30 E-value=40 Score=31.79 Aligned_cols=26 Identities=27% Similarity=0.659 Sum_probs=19.7
Q ss_pred CccccccccccccCCceEcccCceec
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYH 220 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH 220 (352)
..||||...+...+.....+.+|.|-
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~fd 28 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQFD 28 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCCc
Confidence 57999999997765555555688883
No 241
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.27 E-value=59 Score=33.95 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=19.6
Q ss_pred CCceeeecCCcccccCCCCCCCCcCCCCCCCceEEc
Q 018689 21 PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEEL 56 (352)
Q Consensus 21 ~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi 56 (352)
....-||.|..... -...||.|++.-+...
T Consensus 238 ~~~l~Ch~Cg~~~~------~~~~Cp~C~s~~l~~~ 267 (505)
T TIGR00595 238 EGKLRCHYCGYQEP------IPKTCPQCGSEDLVYK 267 (505)
T ss_pred CCeEEcCCCcCcCC------CCCCCCCCCCCeeEee
Confidence 34567888876643 2368999998765544
No 242
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=24.02 E-value=25 Score=21.87 Aligned_cols=29 Identities=21% Similarity=0.470 Sum_probs=9.5
Q ss_pred ccccccccccccCCceEcccCceecccch
Q 018689 196 QCAVCKDSFELNEEARQMPCKHIYHPDCI 224 (352)
Q Consensus 196 ~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci 224 (352)
.|.+|.+.......-.-..|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 47788777654233444458888888774
No 243
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.75 E-value=35 Score=22.11 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=21.1
Q ss_pred ceeeecCCcccccCCCCCCCCcCCCCCCCc
Q 018689 23 MYFCHQCNRTVRVTPSPSSDLVCPSCNGGF 52 (352)
Q Consensus 23 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~gF 52 (352)
.+-|..|...+-+. ...+..+|+.|+.-|
T Consensus 3 ~~~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 35688898887553 345789999998755
No 244
>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=23.65 E-value=31 Score=30.26 Aligned_cols=24 Identities=33% Similarity=0.700 Sum_probs=18.8
Q ss_pred ecccchHHHhhcCC----CCCccCCCCC
Q 018689 219 YHPDCIMPWLELHN----SCPVCRYELP 242 (352)
Q Consensus 219 FH~~Ci~~Wl~~~~----sCP~CR~~l~ 242 (352)
||..||++=|..-. .||.|+..-.
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 89999999886533 6999987644
No 245
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=23.62 E-value=59 Score=32.69 Aligned_cols=32 Identities=22% Similarity=0.541 Sum_probs=19.3
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCce
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFI 53 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFv 53 (352)
-.|+|+.|-..-.+.......-.||+|++.|+
T Consensus 232 ~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~~ 263 (374)
T TIGR00308 232 YTYHCSRCLHNKPVNGISQRKGRCKECGGEYH 263 (374)
T ss_pred eEEECCCcccccccccccCCCCCCCCCCCcce
Confidence 36899999543222111123457999998553
No 246
>PRK13795 hypothetical protein; Provisional
Probab=23.52 E-value=56 Score=35.24 Aligned_cols=29 Identities=21% Similarity=0.563 Sum_probs=21.8
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
..|||..|+-+|- .-.|..|+... .++.-
T Consensus 11 ~~~wc~~cn~p~~-------~~~c~~c~~~~-~~~~~ 39 (636)
T PRK13795 11 HIYWCEKCNVPLL-------GKKCGICGKEG-FKVRL 39 (636)
T ss_pred eEEEcccCCCeec-------cccccccCCCc-eEeec
Confidence 5799999999972 35699999864 45543
No 247
>PRK05978 hypothetical protein; Provisional
Probab=23.38 E-value=47 Score=29.11 Aligned_cols=32 Identities=16% Similarity=0.691 Sum_probs=24.2
Q ss_pred CccccccccccccCCceEcccCceecccchHHHhhcCCCCCccCCCCCCC
Q 018689 195 SQCAVCKDSFELNEEARQMPCKHIYHPDCIMPWLELHNSCPVCRYELPTD 244 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~Wl~~~~sCP~CR~~l~~~ 244 (352)
..|+-|-+ ||.|+ .+|+.+..||.|-.++...
T Consensus 34 grCP~CG~-------------G~LF~-----g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGE-------------GKLFR-----AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCC-------------Ccccc-----cccccCCCccccCCccccC
Confidence 57887754 46675 6889999999998887543
No 248
>PRK10220 hypothetical protein; Provisional
Probab=23.37 E-value=41 Score=27.95 Aligned_cols=28 Identities=21% Similarity=0.681 Sum_probs=17.1
Q ss_pred eecCCcccccCCCCCCCCcCCCCCCCceEE
Q 018689 26 CHQCNRTVRVTPSPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 26 Ch~C~r~V~~~~~~~~~~~CP~C~~gFvEE 55 (352)
|-+|+....- .....++||.|...+-.+
T Consensus 6 CP~C~seytY--~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTY--EDNGMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceE--cCCCeEECCcccCcCCcc
Confidence 6677766432 234557777777766544
No 249
>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=22.58 E-value=25 Score=24.93 Aligned_cols=13 Identities=31% Similarity=0.910 Sum_probs=6.6
Q ss_pred CCCCccCCCCCCC
Q 018689 232 NSCPVCRYELPTD 244 (352)
Q Consensus 232 ~sCP~CR~~l~~~ 244 (352)
..||+|..+|...
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 3899999988643
No 250
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=22.50 E-value=30 Score=34.42 Aligned_cols=46 Identities=24% Similarity=0.581 Sum_probs=26.2
Q ss_pred CCccccccccccccCCceEcc---cCceec--------ccchHHHh-----hcCCCCCccCCC
Q 018689 194 SSQCAVCKDSFELNEEARQMP---CKHIYH--------PDCIMPWL-----ELHNSCPVCRYE 240 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lp---C~H~FH--------~~Ci~~Wl-----~~~~sCP~CR~~ 240 (352)
++.|+||-+.+.- -....|. |+-.|. ..|+..-- ...+.||.||+.
T Consensus 15 ~ElCPVCGDkVSG-YHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 15 GELCPVCGDKVSG-YHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccccCcccc-ceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 5789999887542 2233443 554442 33544321 124579999984
No 251
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.49 E-value=24 Score=27.36 Aligned_cols=33 Identities=18% Similarity=0.434 Sum_probs=21.5
Q ss_pred CCccccccccccccCCceEcccCceecccchHH
Q 018689 194 SSQCAVCKDSFELNEEARQMPCKHIYHPDCIMP 226 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~lpC~H~FH~~Ci~~ 226 (352)
...|.+|.......-....-.|.-.||..|...
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 468999987633211222223899999999765
No 252
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.37 E-value=60 Score=31.89 Aligned_cols=44 Identities=18% Similarity=0.376 Sum_probs=29.2
Q ss_pred CCccccccccccccCCceEc--c--cCceecccchHHHhhcCCCCCccCC
Q 018689 194 SSQCAVCKDSFELNEEARQM--P--CKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l--p--C~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
...|+||-..-... ++.+ . =.|.+|.-|-..|-..+..||.|-.
T Consensus 187 ~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 57999997663211 1111 1 1356777888999888889999964
No 253
>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=22.37 E-value=52 Score=22.57 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=9.2
Q ss_pred CCCcCCCCCCC
Q 018689 41 SDLVCPSCNGG 51 (352)
Q Consensus 41 ~~~~CP~C~~g 51 (352)
..++||+|++-
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 45889999986
No 254
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.92 E-value=50 Score=24.39 Aligned_cols=16 Identities=44% Similarity=1.095 Sum_probs=13.0
Q ss_pred cCCCCCccCCCCCCCC
Q 018689 230 LHNSCPVCRYELPTDD 245 (352)
Q Consensus 230 ~~~sCP~CR~~l~~~~ 245 (352)
.|..||+|-.+++.+.
T Consensus 2 ~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCcCCcCCCcCCcch
Confidence 4788999999998754
No 255
>PLN02436 cellulose synthase A
Probab=21.90 E-value=70 Score=36.50 Aligned_cols=49 Identities=24% Similarity=0.489 Sum_probs=33.5
Q ss_pred CCcccccccccccc---CCceEcc-cCceecccchHHHh-hcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELN---EEARQMP-CKHIYHPDCIMPWL-ELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~---~~~~~lp-C~H~FH~~Ci~~Wl-~~~~sCP~CR~~l~ 242 (352)
...|.||-+++... +.-+... |+--.|+.|.+-=. +.+++||.|+....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 46899999997443 3223333 88889999984322 23668999988764
No 256
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.85 E-value=66 Score=34.93 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=20.2
Q ss_pred CCceeeecCCcccccCCCCCCCCcCCCCCCCceEEccC
Q 018689 21 PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELET 58 (352)
Q Consensus 21 ~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~~ 58 (352)
....-||.|.... ....||.|++.-+..+..
T Consensus 408 ~~~l~Ch~CG~~~-------~p~~Cp~Cgs~~l~~~g~ 438 (665)
T PRK14873 408 GGTPRCRWCGRAA-------PDWRCPRCGSDRLRAVVV 438 (665)
T ss_pred CCeeECCCCcCCC-------cCccCCCCcCCcceeeec
Confidence 3466788887642 135888888876665544
No 257
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=21.80 E-value=49 Score=31.79 Aligned_cols=45 Identities=27% Similarity=0.457 Sum_probs=26.5
Q ss_pred CccccccccccccCCceEc-ccC-ceecccchHHH-hhcCCCCCccCCCC
Q 018689 195 SQCAVCKDSFELNEEARQM-PCK-HIYHPDCIMPW-LELHNSCPVCRYEL 241 (352)
Q Consensus 195 ~~C~IC~e~~~~~~~~~~l-pC~-H~FH~~Ci~~W-l~~~~sCP~CR~~l 241 (352)
..|.||++-...+-...-| -=. =.=|++|+.+| |..+..|| |..+
T Consensus 31 sfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p--rsk~ 78 (285)
T PF06937_consen 31 SFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP--RSKL 78 (285)
T ss_pred eecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCC--cccc
Confidence 5677777665443222212 111 24689999999 56677899 4444
No 258
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.77 E-value=98 Score=22.71 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=20.9
Q ss_pred CCccccccccccc--cCCceEcc-cCceecccch
Q 018689 194 SSQCAVCKDSFEL--NEEARQMP-CKHIYHPDCI 224 (352)
Q Consensus 194 ~~~C~IC~e~~~~--~~~~~~lp-C~H~FH~~Ci 224 (352)
...|+.|-...+. .......+ ||+.+|.+-.
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCEECcHHH
Confidence 4689999887766 33444455 8887777643
No 259
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.74 E-value=59 Score=25.46 Aligned_cols=48 Identities=21% Similarity=0.445 Sum_probs=19.2
Q ss_pred CCccccccccccccCC--c--eEcccCceecccchHHHhh-cCCCCCccCCCC
Q 018689 194 SSQCAVCKDSFELNEE--A--RQMPCKHIYHPDCIMPWLE-LHNSCPVCRYEL 241 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~--~--~~lpC~H~FH~~Ci~~Wl~-~~~sCP~CR~~l 241 (352)
...|.||-+.+..... + ...-|+--.|+.|..-=.+ .++.||.|+...
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 4789999999865432 2 2223777788888764433 367899998655
No 260
>PLN02189 cellulose synthase
Probab=21.61 E-value=74 Score=36.20 Aligned_cols=49 Identities=20% Similarity=0.412 Sum_probs=33.9
Q ss_pred CCcccccccccccc---CCceEcc-cCceecccchHHHh-hcCCCCCccCCCCC
Q 018689 194 SSQCAVCKDSFELN---EEARQMP-CKHIYHPDCIMPWL-ELHNSCPVCRYELP 242 (352)
Q Consensus 194 ~~~C~IC~e~~~~~---~~~~~lp-C~H~FH~~Ci~~Wl-~~~~sCP~CR~~l~ 242 (352)
...|.||-+++... +.-+... |+--.|+.|.+-=. +.+++||.|+....
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 46899999998643 2233333 88889999984322 23668999988764
No 261
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=20.97 E-value=69 Score=32.02 Aligned_cols=28 Identities=25% Similarity=0.793 Sum_probs=21.3
Q ss_pred CCCceeeecCCcccccCCCCCCCCcCCCCCCC
Q 018689 20 EPQMYFCHQCNRTVRVTPSPSSDLVCPSCNGG 51 (352)
Q Consensus 20 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~g 51 (352)
+..-|-|+.|.+.-.. .....||.|+..
T Consensus 54 d~~i~kC~~c~~~~~y----~~~~~C~~cg~~ 81 (415)
T COG5257 54 DAKIYKCPECYRPECY----TTEPKCPNCGAE 81 (415)
T ss_pred cCceEeCCCCCCCccc----ccCCCCCCCCCC
Confidence 4578999999986221 367899999874
No 262
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=20.96 E-value=57 Score=21.76 Aligned_cols=14 Identities=29% Similarity=0.764 Sum_probs=9.9
Q ss_pred CcCCCCCCCceEEc
Q 018689 43 LVCPSCNGGFIEEL 56 (352)
Q Consensus 43 ~~CP~C~~gFvEEi 56 (352)
..||.|++..|+..
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 57999996555544
No 263
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.86 E-value=55 Score=28.51 Aligned_cols=17 Identities=18% Similarity=0.450 Sum_probs=15.0
Q ss_pred CCcCCCCCCCceEEccC
Q 018689 42 DLVCPSCNGGFIEELET 58 (352)
Q Consensus 42 ~~~CP~C~~gFvEEi~~ 58 (352)
.+.||+|+|.-.+++..
T Consensus 105 ~~~cp~c~s~~t~~~s~ 121 (146)
T TIGR02159 105 SVQCPRCGSADTTITSI 121 (146)
T ss_pred CCcCCCCCCCCcEeecC
Confidence 59999999999998864
No 264
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.85 E-value=44 Score=32.58 Aligned_cols=31 Identities=23% Similarity=0.567 Sum_probs=21.0
Q ss_pred eeecCCcccc-cC-CCCCCCCcCCCCCCCceEE
Q 018689 25 FCHQCNRTVR-VT-PSPSSDLVCPSCNGGFIEE 55 (352)
Q Consensus 25 wCh~C~r~V~-~~-~~~~~~~~CP~C~~gFvEE 55 (352)
||+.|.+.=- +. .....+.+|+.|+--|=+.
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r 34 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDR 34 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeeccc
Confidence 8999988643 21 1237899999998654433
No 265
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=20.76 E-value=59 Score=24.07 Aligned_cols=17 Identities=35% Similarity=0.843 Sum_probs=14.2
Q ss_pred cCCCCCccCCCCCCCCh
Q 018689 230 LHNSCPVCRYELPTDDP 246 (352)
Q Consensus 230 ~~~sCP~CR~~l~~~~~ 246 (352)
-|..|++|-+.++.++.
T Consensus 7 PH~HC~VCg~aIp~de~ 23 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CCccccccCCcCCCccc
Confidence 36789999999998864
No 266
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=20.53 E-value=31 Score=37.36 Aligned_cols=65 Identities=17% Similarity=0.472 Sum_probs=0.0
Q ss_pred HhhCCcceeccccccCCCCccccccccccccC-------CceEcccCceecccchHH----------HhhcCCCCCccCC
Q 018689 177 IEALPSIKINEAMMSSDSSQCAVCKDSFELNE-------EARQMPCKHIYHPDCIMP----------WLELHNSCPVCRY 239 (352)
Q Consensus 177 i~~lp~~~~~~~~~~~~~~~C~IC~e~~~~~~-------~~~~lpC~H~FH~~Ci~~----------Wl~~~~sCP~CR~ 239 (352)
+..|..+.+.......-..+|.||-|+=++.+ .+-+-.|+..||..|... .+..-+.|-+|++
T Consensus 100 V~TMEPIiLq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~ 179 (900)
T KOG0956|consen 100 VHTMEPIILQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKY 179 (900)
T ss_pred cccccceeeccCchhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHH
Q ss_pred CC
Q 018689 240 EL 241 (352)
Q Consensus 240 ~l 241 (352)
.+
T Consensus 180 Hf 181 (900)
T KOG0956|consen 180 HF 181 (900)
T ss_pred HH
No 267
>PRK06260 threonine synthase; Validated
Probab=20.40 E-value=71 Score=32.10 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=20.7
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCCCCce
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFI 53 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFv 53 (352)
..|.|..|.++..... ....||.|++-|-
T Consensus 2 ~~~~C~~cg~~~~~~~---~~~~Cp~cg~~l~ 30 (397)
T PRK06260 2 YWLKCIECGKEYDPDE---IIYTCPECGGLLE 30 (397)
T ss_pred CEEEECCCCCCCCCCC---ccccCCCCCCeEE
Confidence 3589999999865332 3578999986443
No 268
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.29 E-value=46 Score=32.61 Aligned_cols=45 Identities=18% Similarity=0.386 Sum_probs=28.4
Q ss_pred CCccccccccccccCCceEc--c--cCceecccchHHHhhcCCCCCccCC
Q 018689 194 SSQCAVCKDSFELNEEARQM--P--CKHIYHPDCIMPWLELHNSCPVCRY 239 (352)
Q Consensus 194 ~~~C~IC~e~~~~~~~~~~l--p--C~H~FH~~Ci~~Wl~~~~sCP~CR~ 239 (352)
...|+||-..-.... ++.. . =.|.+|.-|-..|-..+..||.|-.
T Consensus 184 ~~~CPvCGs~P~~s~-~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACGSPPVASM-VRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCcCCCCCChhhhhh-hcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 358999976532110 0000 0 1255677788899878889999965
No 269
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.18 E-value=89 Score=32.13 Aligned_cols=34 Identities=21% Similarity=0.553 Sum_probs=26.5
Q ss_pred CceeeecCCcccccCCCCCCCCcCCCCC--CCceEEccCCC
Q 018689 22 QMYFCHQCNRTVRVTPSPSSDLVCPSCN--GGFIEELETPN 60 (352)
Q Consensus 22 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~--~gFvEEi~~~~ 60 (352)
..|-|..|--.-.-| .-.||.|+ +-|+||.....
T Consensus 6 t~f~C~~CG~~s~KW-----~GkCp~Cg~Wns~vE~~~~~~ 41 (456)
T COG1066 6 TAFVCQECGYVSPKW-----LGKCPACGAWNTLVEEVLAAS 41 (456)
T ss_pred cEEEcccCCCCCccc-----cccCCCCCCccceEEeecccc
Confidence 679999998764333 37899999 79999996543
No 270
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.18 E-value=79 Score=34.34 Aligned_cols=31 Identities=19% Similarity=0.488 Sum_probs=20.2
Q ss_pred CCceeeecCCcccccCCCCCCCCcCCCCCCCceEEcc
Q 018689 21 PQMYFCHQCNRTVRVTPSPSSDLVCPSCNGGFIEELE 57 (352)
Q Consensus 21 ~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~gFvEEi~ 57 (352)
.....||.|..... -.-.||.|++..+....
T Consensus 406 ~~~l~Ch~Cg~~~~------~~~~Cp~Cg~~~l~~~g 436 (679)
T PRK05580 406 QRRLRCHHCGYQEP------IPKACPECGSTDLVPVG 436 (679)
T ss_pred CCeEECCCCcCCCC------CCCCCCCCcCCeeEEee
Confidence 45567888877642 23579999887655543
Done!