Query 045745
Match_columns 351
No_of_seqs 363 out of 1727
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:07:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045745.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045745hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06547 DUF1117: Protein of u 99.7 3.9E-19 8.4E-24 144.9 2.7 77 255-335 1-90 (117)
2 PF14369 zf-RING_3: zinc-finge 99.6 2.8E-16 6.1E-21 105.0 3.3 35 10-44 1-35 (35)
3 KOG4628 Predicted E3 ubiquitin 99.6 2.6E-16 5.6E-21 153.6 4.1 79 171-249 203-283 (348)
4 PF13639 zf-RING_2: Ring finge 99.5 5.8E-15 1.2E-19 103.2 2.2 43 198-240 2-44 (44)
5 PHA02929 N1R/p28-like protein; 99.2 3.8E-12 8.2E-17 119.4 3.6 73 173-245 148-228 (238)
6 COG5243 HRD1 HRD ubiquitin lig 99.2 4.1E-12 9E-17 123.5 3.1 73 175-248 267-349 (491)
7 PF12678 zf-rbx1: RING-H2 zinc 99.2 5.5E-12 1.2E-16 97.9 3.0 45 196-240 19-73 (73)
8 COG5540 RING-finger-containing 99.2 5.5E-12 1.2E-16 120.0 3.0 50 196-245 323-373 (374)
9 PF13920 zf-C3HC4_3: Zinc fing 98.9 5.9E-10 1.3E-14 79.9 3.2 46 196-244 2-48 (50)
10 PLN03208 E3 ubiquitin-protein 98.9 6.9E-10 1.5E-14 100.7 3.5 51 194-247 16-82 (193)
11 cd00162 RING RING-finger (Real 98.9 8.3E-10 1.8E-14 75.3 3.0 44 198-243 1-45 (45)
12 PF13923 zf-C3HC4_2: Zinc fing 98.9 1E-09 2.2E-14 74.7 2.8 39 199-239 1-39 (39)
13 KOG0823 Predicted E3 ubiquitin 98.8 1.9E-09 4.2E-14 99.6 2.8 51 194-247 45-98 (230)
14 KOG0802 E3 ubiquitin ligase [P 98.8 1.3E-09 2.8E-14 113.8 1.6 51 195-245 290-342 (543)
15 KOG0317 Predicted E3 ubiquitin 98.8 6.3E-09 1.4E-13 98.9 4.2 49 195-246 238-286 (293)
16 PF15227 zf-C3HC4_4: zinc fing 98.7 7.3E-09 1.6E-13 72.0 2.8 38 199-239 1-42 (42)
17 PF12861 zf-Apc11: Anaphase-pr 98.7 7.4E-09 1.6E-13 82.2 2.6 51 194-244 19-82 (85)
18 smart00504 Ubox Modified RING 98.7 1.3E-08 2.7E-13 75.7 3.7 48 197-247 2-49 (63)
19 PF00097 zf-C3HC4: Zinc finger 98.6 2E-08 4.4E-13 68.6 2.8 39 199-239 1-41 (41)
20 KOG0320 Predicted E3 ubiquitin 98.6 1.4E-08 3.1E-13 90.5 2.5 50 196-246 131-180 (187)
21 PF14634 zf-RING_5: zinc-RING 98.6 1.8E-08 4E-13 70.4 2.3 44 198-241 1-44 (44)
22 smart00184 RING Ring finger. E 98.6 2.3E-08 4.9E-13 65.7 2.6 38 199-239 1-39 (39)
23 PHA02926 zinc finger-like prot 98.6 2.3E-08 5.1E-13 92.1 2.5 53 193-245 167-231 (242)
24 TIGR00599 rad18 DNA repair pro 98.5 4.9E-08 1.1E-12 97.9 3.4 51 193-246 23-73 (397)
25 COG5194 APC11 Component of SCF 98.4 1.9E-07 4E-12 72.9 2.3 48 197-244 21-81 (88)
26 smart00744 RINGv The RING-vari 98.3 2.7E-07 5.8E-12 66.3 2.1 42 198-240 1-49 (49)
27 PF13445 zf-RING_UBOX: RING-ty 98.3 5.5E-07 1.2E-11 62.9 2.4 38 199-237 1-43 (43)
28 KOG1734 Predicted RING-contain 98.2 3.6E-07 7.7E-12 86.3 1.6 52 195-246 223-283 (328)
29 KOG1493 Anaphase-promoting com 98.2 2.5E-07 5.5E-12 71.6 -0.2 50 195-244 19-81 (84)
30 PF04564 U-box: U-box domain; 98.2 1.3E-06 2.8E-11 67.6 3.5 50 196-248 4-54 (73)
31 COG5219 Uncharacterized conser 98.1 6.2E-07 1.3E-11 96.1 0.8 53 193-245 1466-1524(1525)
32 COG5574 PEX10 RING-finger-cont 98.1 1.4E-06 3E-11 82.2 1.7 50 195-247 214-265 (271)
33 KOG2164 Predicted E3 ubiquitin 98.0 2.2E-06 4.7E-11 87.3 2.4 48 196-246 186-238 (513)
34 KOG0287 Postreplication repair 98.0 1.7E-06 3.8E-11 83.9 1.2 48 197-247 24-71 (442)
35 COG5432 RAD18 RING-finger-cont 98.0 2.4E-06 5.2E-11 81.5 1.9 47 196-245 25-71 (391)
36 KOG0828 Predicted E3 ubiquitin 98.0 2.2E-06 4.7E-11 86.7 1.3 51 195-245 570-635 (636)
37 KOG2177 Predicted E3 ubiquitin 97.9 3.4E-06 7.3E-11 78.0 1.5 46 193-241 10-55 (386)
38 PF11793 FANCL_C: FANCL C-term 97.9 2.2E-06 4.8E-11 66.0 0.2 50 196-245 2-67 (70)
39 TIGR00570 cdk7 CDK-activating 97.9 8.3E-06 1.8E-10 79.2 3.4 51 196-246 3-56 (309)
40 KOG2930 SCF ubiquitin ligase, 97.8 6.3E-06 1.4E-10 67.4 1.2 27 217-243 81-107 (114)
41 KOG0804 Cytoplasmic Zn-finger 97.8 1E-05 2.3E-10 81.1 2.1 81 196-278 175-259 (493)
42 KOG4265 Predicted E3 ubiquitin 97.7 1.8E-05 3.8E-10 77.7 2.3 47 196-245 290-337 (349)
43 KOG0311 Predicted E3 ubiquitin 97.7 4.3E-06 9.4E-11 81.7 -2.4 59 186-246 33-92 (381)
44 KOG0824 Predicted E3 ubiquitin 97.5 3.1E-05 6.7E-10 74.4 1.5 48 197-247 8-56 (324)
45 KOG0825 PHD Zn-finger protein 97.5 2.5E-05 5.5E-10 82.7 -0.1 50 195-244 122-171 (1134)
46 KOG0827 Predicted E3 ubiquitin 97.4 4.7E-05 1E-09 75.3 1.3 50 197-246 5-58 (465)
47 PF14835 zf-RING_6: zf-RING of 97.4 5.8E-05 1.3E-09 56.9 1.2 44 197-244 8-51 (65)
48 KOG1039 Predicted E3 ubiquitin 97.4 7.3E-05 1.6E-09 74.0 1.9 49 195-243 160-220 (344)
49 KOG4445 Uncharacterized conser 97.4 8E-05 1.7E-09 71.6 1.8 92 150-247 75-189 (368)
50 KOG4159 Predicted E3 ubiquitin 97.1 0.00025 5.4E-09 71.5 2.3 50 194-246 82-131 (398)
51 KOG1645 RING-finger-containing 97.1 0.00028 6.1E-09 70.3 2.4 48 196-243 4-55 (463)
52 KOG4172 Predicted E3 ubiquitin 97.0 0.00015 3.3E-09 52.9 -0.2 46 197-245 8-55 (62)
53 KOG0801 Predicted E3 ubiquitin 97.0 0.00023 5.1E-09 62.9 0.9 40 184-223 164-204 (205)
54 KOG0297 TNF receptor-associate 96.9 0.00058 1.3E-08 68.9 2.7 54 193-249 18-72 (391)
55 KOG1785 Tyrosine kinase negati 96.7 0.0005 1.1E-08 68.5 0.4 48 197-247 370-419 (563)
56 PF12906 RINGv: RING-variant d 96.7 0.0012 2.7E-08 46.9 2.2 40 199-239 1-47 (47)
57 KOG1941 Acetylcholine receptor 96.5 0.00065 1.4E-08 67.5 0.3 47 195-241 364-413 (518)
58 PF11789 zf-Nse: Zinc-finger o 96.5 0.0012 2.6E-08 48.8 1.6 41 196-238 11-53 (57)
59 KOG0978 E3 ubiquitin ligase in 96.4 0.00092 2E-08 71.3 0.6 46 197-245 644-690 (698)
60 KOG2660 Locus-specific chromos 96.4 0.00066 1.4E-08 66.2 -0.5 50 195-246 14-63 (331)
61 PF05883 Baculo_RING: Baculovi 96.3 0.0012 2.6E-08 56.9 0.5 37 196-232 26-68 (134)
62 COG5152 Uncharacterized conser 95.9 0.0023 4.9E-08 58.5 0.3 45 197-244 197-241 (259)
63 PF10367 Vps39_2: Vacuolar sor 95.8 0.0039 8.5E-08 50.6 1.3 33 194-227 76-108 (109)
64 PHA02862 5L protein; Provision 95.8 0.0042 9.1E-08 54.1 1.5 46 197-246 3-55 (156)
65 PF08746 zf-RING-like: RING-li 95.7 0.0061 1.3E-07 42.5 1.7 41 199-239 1-43 (43)
66 PHA02825 LAP/PHD finger-like p 95.7 0.0073 1.6E-07 53.5 2.5 49 194-246 6-61 (162)
67 KOG1428 Inhibitor of type V ad 95.5 0.0074 1.6E-07 68.1 2.3 52 194-245 3484-3545(3738)
68 KOG1002 Nucleotide excision re 95.5 0.0057 1.2E-07 63.0 1.2 51 194-247 534-589 (791)
69 PF14570 zf-RING_4: RING/Ubox 95.4 0.012 2.6E-07 42.1 2.3 44 199-243 1-47 (48)
70 KOG3039 Uncharacterized conser 95.4 0.02 4.3E-07 54.1 4.3 68 180-247 195-273 (303)
71 KOG3970 Predicted E3 ubiquitin 95.2 0.011 2.4E-07 55.1 2.2 49 197-246 51-107 (299)
72 KOG2879 Predicted E3 ubiquitin 95.1 0.019 4E-07 55.0 3.4 53 192-246 235-289 (298)
73 KOG1571 Predicted E3 ubiquitin 95.1 0.012 2.5E-07 58.3 1.9 44 196-245 305-348 (355)
74 KOG0827 Predicted E3 ubiquitin 95.0 0.0019 4.1E-08 64.2 -3.8 50 197-246 197-247 (465)
75 KOG1814 Predicted E3 ubiquitin 94.6 0.012 2.7E-07 59.0 0.8 47 195-241 183-237 (445)
76 KOG1813 Predicted E3 ubiquitin 94.6 0.013 2.9E-07 56.5 0.9 46 197-245 242-287 (313)
77 COG5222 Uncharacterized conser 94.4 0.027 5.8E-07 54.6 2.6 45 197-244 275-322 (427)
78 KOG1952 Transcription factor N 94.1 0.023 4.9E-07 61.6 1.6 47 195-241 190-244 (950)
79 KOG4692 Predicted E3 ubiquitin 93.8 0.029 6.2E-07 55.5 1.5 50 194-246 420-469 (489)
80 PF04641 Rtf2: Rtf2 RING-finge 93.6 0.13 2.8E-06 49.1 5.6 52 194-246 111-163 (260)
81 KOG4185 Predicted E3 ubiquitin 93.6 0.05 1.1E-06 52.5 2.7 47 197-243 4-54 (296)
82 PHA03096 p28-like protein; Pro 93.5 0.033 7.2E-07 54.0 1.3 45 197-241 179-231 (284)
83 COG0375 HybF Zn finger protein 93.3 0.06 1.3E-06 45.4 2.5 35 10-47 69-103 (115)
84 PF14446 Prok-RING_1: Prokaryo 92.9 0.069 1.5E-06 39.1 1.9 33 196-228 5-38 (54)
85 KOG0826 Predicted E3 ubiquitin 92.9 0.053 1.1E-06 53.2 1.7 49 195-246 299-348 (357)
86 KOG4275 Predicted E3 ubiquitin 92.6 0.021 4.6E-07 55.1 -1.4 43 196-245 300-343 (350)
87 COG5236 Uncharacterized conser 92.4 0.082 1.8E-06 52.3 2.3 47 194-243 59-107 (493)
88 PF14447 Prok-RING_4: Prokaryo 92.1 0.097 2.1E-06 38.5 1.8 45 197-246 8-52 (55)
89 KOG1940 Zn-finger protein [Gen 91.9 0.086 1.9E-06 50.9 1.8 44 198-241 160-204 (276)
90 KOG4739 Uncharacterized protei 91.8 0.057 1.2E-06 50.8 0.5 45 197-245 4-49 (233)
91 KOG2114 Vacuolar assembly/sort 91.8 0.063 1.4E-06 58.3 0.8 44 197-245 841-884 (933)
92 KOG0298 DEAD box-containing he 91.6 0.11 2.5E-06 58.7 2.5 43 197-241 1154-1196(1394)
93 KOG3268 Predicted E3 ubiquitin 90.8 0.14 3.1E-06 46.3 1.9 49 197-245 166-229 (234)
94 KOG2932 E3 ubiquitin ligase in 90.7 0.086 1.9E-06 51.4 0.5 43 198-244 92-134 (389)
95 PF10272 Tmpp129: Putative tra 90.3 0.24 5.3E-06 49.6 3.3 29 217-245 311-352 (358)
96 COG5175 MOT2 Transcriptional r 90.0 0.16 3.5E-06 50.1 1.7 51 196-246 14-66 (480)
97 TIGR00100 hypA hydrogenase nic 89.1 0.38 8.3E-06 40.4 3.1 34 10-46 69-102 (115)
98 PF07754 DUF1610: Domain of un 88.6 0.27 5.8E-06 30.2 1.3 23 14-37 1-23 (24)
99 KOG2034 Vacuolar sorting prote 88.5 0.17 3.6E-06 55.4 0.7 37 193-230 814-850 (911)
100 PRK03681 hypA hydrogenase nick 87.9 0.49 1.1E-05 39.7 3.0 34 10-45 69-102 (114)
101 KOG3002 Zn finger protein [Gen 87.9 0.33 7.1E-06 47.5 2.2 42 197-245 49-92 (299)
102 KOG1609 Protein involved in mR 87.5 0.26 5.6E-06 47.4 1.2 51 196-246 78-136 (323)
103 PF07800 DUF1644: Protein of u 87.2 0.51 1.1E-05 42.0 2.8 51 196-249 2-96 (162)
104 PRK00398 rpoP DNA-directed RNA 87.0 0.7 1.5E-05 32.3 2.9 34 10-44 2-35 (46)
105 KOG1001 Helicase-like transcri 86.8 0.18 3.9E-06 54.5 -0.3 48 197-248 455-504 (674)
106 PF03854 zf-P11: P-11 zinc fin 86.4 0.32 7E-06 34.7 0.9 33 214-246 15-48 (50)
107 PRK12380 hydrogenase nickel in 86.3 0.69 1.5E-05 38.8 3.1 33 10-45 69-101 (113)
108 PRK00564 hypA hydrogenase nick 86.0 0.66 1.4E-05 39.2 2.8 35 10-46 70-104 (117)
109 PF01155 HypA: Hydrogenase exp 85.9 0.55 1.2E-05 39.3 2.2 33 10-45 69-101 (113)
110 KOG0802 E3 ubiquitin ligase [P 85.4 0.41 8.9E-06 50.5 1.5 47 195-248 478-524 (543)
111 KOG3053 Uncharacterized conser 84.4 0.36 7.7E-06 46.1 0.5 51 193-243 17-81 (293)
112 COG2093 DNA-directed RNA polym 84.4 0.45 9.7E-06 35.9 0.9 29 13-46 6-35 (64)
113 PRK03824 hypA hydrogenase nick 84.0 0.97 2.1E-05 39.1 3.0 36 10-45 69-122 (135)
114 COG5183 SSM4 Protein involved 83.7 0.55 1.2E-05 51.1 1.5 52 194-246 10-68 (1175)
115 KOG2817 Predicted E3 ubiquitin 82.3 1.1 2.5E-05 45.0 3.1 47 193-239 331-380 (394)
116 KOG4367 Predicted Zn-finger pr 81.9 0.6 1.3E-05 47.6 0.9 36 194-232 2-37 (699)
117 smart00834 CxxC_CXXC_SSSS Puta 81.6 1.2 2.7E-05 29.7 2.2 29 10-38 4-34 (41)
118 KOG1100 Predicted E3 ubiquitin 80.2 0.82 1.8E-05 42.4 1.2 40 199-245 161-201 (207)
119 KOG1812 Predicted E3 ubiquitin 80.0 1.3 2.8E-05 44.9 2.6 38 196-233 146-184 (384)
120 PRK00762 hypA hydrogenase nick 79.0 1.5 3.2E-05 37.4 2.3 36 10-46 69-108 (124)
121 PF10571 UPF0547: Uncharacteri 78.8 1.1 2.5E-05 27.9 1.1 23 14-41 3-25 (26)
122 PRK06266 transcription initiat 78.6 1.2 2.6E-05 40.3 1.7 35 8-42 114-148 (178)
123 KOG0309 Conserved WD40 repeat- 78.5 1.1 2.5E-05 48.5 1.7 26 213-238 1044-1069(1081)
124 smart00659 RPOLCX RNA polymera 76.8 2.5 5.3E-05 29.6 2.5 31 11-43 2-32 (44)
125 COG5270 PUA domain (predicted 75.7 1.6 3.4E-05 39.9 1.6 26 10-42 13-38 (202)
126 KOG3800 Predicted E3 ubiquitin 75.6 1.9 4E-05 41.9 2.2 47 198-244 2-51 (300)
127 KOG0825 PHD Zn-finger protein 74.0 1.5 3.2E-05 47.8 1.1 52 197-248 97-158 (1134)
128 PF03604 DNA_RNApol_7kD: DNA d 73.5 3.6 7.9E-05 26.9 2.5 28 12-41 1-28 (32)
129 COG1996 RPC10 DNA-directed RNA 72.8 2.7 5.8E-05 30.3 1.8 33 9-42 4-36 (49)
130 TIGR00373 conserved hypothetic 72.3 1.8 3.9E-05 38.4 1.1 38 8-46 106-143 (158)
131 TIGR02605 CxxC_CxxC_SSSS putat 72.1 4.4 9.6E-05 28.7 2.9 35 10-44 4-40 (52)
132 KOG0269 WD40 repeat-containing 71.8 2.6 5.7E-05 45.8 2.3 39 197-238 780-820 (839)
133 PF05290 Baculo_IE-1: Baculovi 71.7 2.6 5.5E-05 36.6 1.9 49 196-247 80-135 (140)
134 smart00132 LIM Zinc-binding do 69.4 3.8 8.2E-05 26.3 1.9 38 198-244 1-38 (39)
135 PF13240 zinc_ribbon_2: zinc-r 68.8 2.3 4.9E-05 25.7 0.7 23 13-40 1-23 (23)
136 KOG1812 Predicted E3 ubiquitin 68.5 2.6 5.6E-05 42.7 1.4 43 197-239 307-351 (384)
137 smart00531 TFIIE Transcription 64.4 3.3 7.2E-05 36.1 1.2 36 8-43 96-136 (147)
138 PF09723 Zn-ribbon_8: Zinc rib 63.9 8.5 0.00018 26.4 2.9 35 10-44 4-40 (42)
139 KOG1815 Predicted E3 ubiquitin 63.9 5 0.00011 41.3 2.5 36 195-232 69-104 (444)
140 KOG4718 Non-SMC (structural ma 63.6 3.3 7.2E-05 38.6 1.0 43 197-241 182-224 (235)
141 KOG3899 Uncharacterized conser 63.4 2.8 6E-05 40.9 0.5 30 217-246 325-367 (381)
142 smart00154 ZnF_AN1 AN1-like Zi 62.7 4.5 9.8E-05 27.5 1.3 27 14-45 1-27 (39)
143 KOG4362 Transcriptional regula 62.6 2 4.3E-05 46.3 -0.7 48 196-246 21-71 (684)
144 KOG1829 Uncharacterized conser 61.0 2.4 5.3E-05 45.0 -0.4 39 197-239 512-556 (580)
145 KOG3161 Predicted E3 ubiquitin 61.0 3.1 6.7E-05 44.5 0.3 42 197-241 12-54 (861)
146 PF06906 DUF1272: Protein of u 60.6 2.7 5.9E-05 31.0 -0.1 28 11-42 26-53 (57)
147 PF07191 zinc-ribbons_6: zinc- 57.3 2.7 5.8E-05 32.5 -0.6 43 197-247 2-44 (70)
148 KOG3005 GIY-YIG type nuclease 56.9 4.9 0.00011 38.7 0.9 47 197-243 183-242 (276)
149 KOG3579 Predicted E3 ubiquitin 56.6 5.9 0.00013 38.5 1.4 37 197-234 269-307 (352)
150 PF13901 DUF4206: Domain of un 56.5 6.3 0.00014 36.3 1.6 39 196-240 152-196 (202)
151 COG5220 TFB3 Cdk activating ki 56.4 5 0.00011 38.2 0.9 46 196-241 10-61 (314)
152 PF08772 NOB1_Zn_bind: Nin one 56.1 8.9 0.00019 29.9 2.1 33 11-47 9-41 (73)
153 PF13248 zf-ribbon_3: zinc-rib 54.9 5.9 0.00013 24.3 0.8 23 12-39 3-25 (26)
154 PF07975 C1_4: TFIIH C1-like d 52.8 9.9 0.00021 27.6 1.7 41 199-239 2-49 (51)
155 TIGR02098 MJ0042_CXXC MJ0042 f 52.7 6.9 0.00015 25.9 0.9 30 12-41 3-36 (38)
156 PF02891 zf-MIZ: MIZ/SP-RING z 52.4 4 8.7E-05 29.2 -0.3 42 197-241 3-49 (50)
157 KOG2066 Vacuolar assembly/sort 52.1 5.6 0.00012 43.5 0.5 45 196-241 784-832 (846)
158 PF00412 LIM: LIM domain; Int 51.7 14 0.0003 26.1 2.4 39 199-246 1-39 (58)
159 smart00661 RPOL9 RNA polymeras 51.7 13 0.00027 26.1 2.2 31 13-45 2-33 (52)
160 COG5109 Uncharacterized conser 51.2 14 0.0003 36.6 3.0 48 192-239 332-382 (396)
161 smart00249 PHD PHD zinc finger 50.3 7.3 0.00016 25.8 0.7 30 198-228 1-31 (47)
162 PF08271 TF_Zn_Ribbon: TFIIB z 50.0 9.6 0.00021 26.1 1.3 32 12-44 1-32 (43)
163 KOG2068 MOT2 transcription fac 49.6 12 0.00026 37.1 2.4 49 197-245 250-299 (327)
164 PF06906 DUF1272: Protein of u 49.2 24 0.00052 26.1 3.3 47 197-245 6-53 (57)
165 KOG0824 Predicted E3 ubiquitin 49.1 8 0.00017 37.9 1.0 52 191-244 100-151 (324)
166 PF00628 PHD: PHD-finger; Int 47.6 11 0.00024 26.2 1.3 42 198-240 1-49 (51)
167 KOG3842 Adaptor protein Pellin 45.2 21 0.00045 35.4 3.2 51 196-246 341-416 (429)
168 smart00647 IBR In Between Ring 44.4 17 0.00038 26.1 2.0 35 10-44 17-54 (64)
169 KOG1729 FYVE finger containing 44.3 5.9 0.00013 38.7 -0.7 38 197-234 215-252 (288)
170 PF05191 ADK_lid: Adenylate ki 43.9 25 0.00055 23.5 2.5 33 11-43 1-34 (36)
171 COG4391 Uncharacterized protei 43.2 15 0.00033 27.6 1.5 20 21-40 39-58 (62)
172 PF05605 zf-Di19: Drought indu 42.9 13 0.00028 26.6 1.1 11 30-40 2-12 (54)
173 PF06750 DiS_P_DiS: Bacterial 42.2 24 0.00053 28.4 2.7 41 196-248 33-73 (92)
174 PRK14890 putative Zn-ribbon RN 41.8 23 0.00049 26.5 2.2 29 10-39 6-34 (59)
175 PF08792 A2L_zn_ribbon: A2L zi 40.8 16 0.00035 24.0 1.2 27 12-40 4-31 (33)
176 PF09538 FYDLN_acid: Protein o 40.6 18 0.00038 30.3 1.7 31 10-43 8-39 (108)
177 PF06844 DUF1244: Protein of u 40.2 14 0.00031 28.2 1.0 12 220-231 11-22 (68)
178 COG3813 Uncharacterized protei 40.1 8.8 0.00019 29.9 -0.2 29 11-43 26-54 (84)
179 COG4847 Uncharacterized protei 39.4 16 0.00035 29.9 1.2 33 197-230 7-39 (103)
180 TIGR00622 ssl1 transcription f 38.9 38 0.00083 28.5 3.4 44 197-240 56-110 (112)
181 KOG1815 Predicted E3 ubiquitin 38.5 13 0.00028 38.2 0.7 37 197-233 227-268 (444)
182 PRK06393 rpoE DNA-directed RNA 38.1 18 0.00038 27.6 1.2 19 14-39 8-26 (64)
183 KOG2807 RNA polymerase II tran 37.2 29 0.00063 34.5 2.8 45 196-241 330-375 (378)
184 PF01363 FYVE: FYVE zinc finge 36.8 18 0.0004 26.8 1.1 35 196-230 9-44 (69)
185 PRK10220 hypothetical protein; 36.4 28 0.0006 29.2 2.2 28 14-43 6-33 (111)
186 PF13717 zinc_ribbon_4: zinc-r 35.8 17 0.00038 24.1 0.8 28 13-40 4-35 (36)
187 TIGR00155 pqiA_fam integral me 35.4 23 0.0005 36.1 1.9 29 13-41 15-44 (403)
188 KOG4185 Predicted E3 ubiquitin 34.0 8.4 0.00018 37.0 -1.4 47 196-242 207-265 (296)
189 PRK08351 DNA-directed RNA poly 33.8 23 0.0005 26.6 1.2 19 13-38 5-23 (61)
190 PF04216 FdhE: Protein involve 33.3 9.9 0.00022 36.7 -1.1 45 196-241 172-219 (290)
191 PF04423 Rad50_zn_hook: Rad50 32.1 13 0.00029 26.7 -0.3 14 235-248 22-35 (54)
192 PF01485 IBR: IBR domain; Int 31.9 28 0.0006 24.9 1.4 29 12-40 19-50 (64)
193 COG1885 Uncharacterized protei 31.3 30 0.00065 28.8 1.6 19 20-41 42-60 (115)
194 PRK04338 N(2),N(2)-dimethylgua 30.9 39 0.00085 34.2 2.7 30 10-41 243-272 (382)
195 PRK12495 hypothetical protein; 30.8 28 0.00061 32.7 1.5 32 8-42 39-70 (226)
196 TIGR01206 lysW lysine biosynth 30.6 39 0.00084 24.8 1.9 30 12-41 3-33 (54)
197 cd00065 FYVE FYVE domain; Zinc 30.4 31 0.00067 24.4 1.4 35 197-231 3-38 (57)
198 PF00527 E7: E7 protein, Early 29.9 17 0.00037 29.4 -0.1 24 13-36 54-91 (92)
199 PHA02776 E7 protein; Provision 29.8 25 0.00055 29.1 0.9 26 13-38 60-99 (101)
200 PF06220 zf-U1: U1 zinc finger 29.8 21 0.00046 24.1 0.4 12 10-21 2-13 (38)
201 PF03811 Zn_Tnp_IS1: InsA N-te 29.0 25 0.00055 23.5 0.7 11 29-39 4-14 (36)
202 PF13719 zinc_ribbon_5: zinc-r 28.7 26 0.00057 23.3 0.7 27 14-40 5-35 (37)
203 PF07282 OrfB_Zn_ribbon: Putat 28.5 73 0.0016 23.6 3.2 32 195-226 27-61 (69)
204 PF02148 zf-UBP: Zn-finger in 28.4 33 0.00072 25.3 1.3 15 9-23 47-61 (63)
205 PRK15103 paraquat-inducible me 28.2 38 0.00082 34.8 2.1 29 12-40 11-40 (419)
206 PF02318 FYVE_2: FYVE-type zin 28.0 41 0.00089 28.1 1.9 46 195-241 53-102 (118)
207 KOG2041 WD40 repeat protein [G 27.2 33 0.00071 37.7 1.5 46 195-244 1130-1185(1189)
208 PRK13794 hypothetical protein; 27.1 33 0.00071 35.8 1.4 29 10-45 9-38 (479)
209 PF03107 C1_2: C1 domain; Int 26.8 35 0.00075 21.6 1.0 22 12-37 1-22 (30)
210 TIGR02300 FYDLN_acid conserved 26.8 46 0.001 28.7 2.0 31 10-43 8-39 (129)
211 KOG3993 Transcription factor ( 25.9 34 0.00075 35.2 1.3 22 15-42 286-307 (500)
212 PF13832 zf-HC5HC2H_2: PHD-zin 25.9 31 0.00067 28.0 0.8 34 196-229 55-88 (110)
213 PRK03922 hypothetical protein; 25.3 45 0.00097 28.0 1.6 19 19-40 41-59 (113)
214 PF14353 CpXC: CpXC protein 25.1 42 0.00091 28.2 1.5 18 30-47 1-18 (128)
215 PLN02189 cellulose synthase 24.8 56 0.0012 37.3 2.8 48 197-244 35-87 (1040)
216 TIGR01053 LSD1 zinc finger dom 24.8 65 0.0014 20.8 2.0 24 13-37 3-26 (31)
217 KOG2169 Zn-finger transcriptio 24.7 57 0.0012 35.4 2.7 50 194-247 304-359 (636)
218 PF14803 Nudix_N_2: Nudix N-te 24.6 31 0.00066 22.8 0.4 25 13-37 2-29 (34)
219 PF13913 zf-C2HC_2: zinc-finge 24.5 26 0.00056 21.3 0.1 13 30-42 2-14 (25)
220 TIGR00155 pqiA_fam integral me 24.3 41 0.00089 34.3 1.5 24 13-40 217-240 (403)
221 smart00064 FYVE Protein presen 24.2 34 0.00074 25.3 0.7 35 197-231 11-46 (68)
222 KOG4317 Predicted Zn-finger pr 24.0 47 0.001 32.9 1.8 28 7-41 3-30 (383)
223 PF14255 Cys_rich_CPXG: Cystei 23.9 53 0.0011 23.9 1.6 18 31-48 1-18 (52)
224 COG3813 Uncharacterized protei 23.8 67 0.0015 25.1 2.2 47 199-247 8-55 (84)
225 PF14569 zf-UDP: Zinc-binding 23.6 82 0.0018 24.9 2.7 49 196-244 9-62 (80)
226 KOG3039 Uncharacterized conser 22.5 63 0.0014 31.1 2.2 32 197-231 44-75 (303)
227 PF04475 DUF555: Protein of un 22.4 54 0.0012 27.1 1.5 19 19-40 39-57 (102)
228 COG1867 TRM1 N2,N2-dimethylgua 22.2 58 0.0012 33.1 2.0 29 10-40 239-267 (380)
229 KOG1597 Transcription initiati 22.1 39 0.00085 33.1 0.8 32 13-44 2-35 (308)
230 COG1675 TFA1 Transcription ini 22.0 24 0.00051 32.1 -0.6 33 10-42 112-144 (176)
231 PF06943 zf-LSD1: LSD1 zinc fi 22.0 92 0.002 19.3 2.2 23 14-37 1-23 (25)
232 PF00130 C1_1: Phorbol esters/ 21.9 74 0.0016 22.2 2.1 34 195-228 10-45 (53)
233 PRK00464 nrdR transcriptional 21.3 54 0.0012 29.1 1.5 17 31-47 1-17 (154)
234 TIGR00627 tfb4 transcription f 20.8 1.3E+02 0.0027 29.4 4.0 9 234-242 270-278 (279)
235 PF12760 Zn_Tnp_IS1595: Transp 20.6 53 0.0011 22.7 1.0 11 29-39 17-27 (46)
236 cd07973 Spt4 Transcription elo 20.5 53 0.0012 27.0 1.2 28 13-43 5-32 (98)
237 PLN02248 cellulose synthase-li 20.5 86 0.0019 36.1 3.1 37 211-247 144-180 (1135)
238 PRK05978 hypothetical protein; 20.4 55 0.0012 28.9 1.3 23 219-246 43-65 (148)
239 KOG3799 Rab3 effector RIM1 and 20.2 28 0.0006 30.4 -0.6 51 192-242 61-116 (169)
240 PRK11088 rrmA 23S rRNA methylt 20.2 53 0.0011 31.1 1.3 26 197-222 3-28 (272)
241 PF10276 zf-CHCC: Zinc-finger 20.2 43 0.00093 23.0 0.5 12 30-41 29-40 (40)
242 PRK00432 30S ribosomal protein 20.1 48 0.0011 23.7 0.8 14 31-44 21-34 (50)
243 KOG2071 mRNA cleavage and poly 20.0 72 0.0016 34.1 2.3 35 195-229 512-556 (579)
No 1
>PF06547 DUF1117: Protein of unknown function (DUF1117); InterPro: IPR010543 This entry represents the C terminus of a number of hypothetical plant proteins.
Probab=99.75 E-value=3.9e-19 Score=144.88 Aligned_cols=77 Identities=49% Similarity=0.841 Sum_probs=65.4
Q ss_pred hcccccccCCCCcccccccccccccccccccCcccccccccC---CCC-CCCcccC-------CCCC--Ccchhhhhccc
Q 045745 255 SMALSIWWLPGGGFAVGRYEGRRVVAGAAERGLSIEFADNMD---NQT-SSSRVFP-------QRRV--GGFFRVFRGFG 321 (351)
Q Consensus 255 ~~~~~~~~~p~~~~a~gr~~g~~~~~g~~e~~~p~~~~~e~d---~~~-~~~r~~~-------~~~~--~~~~r~~~~~~ 321 (351)
+++++||+||+++|||||++|+++ ++|+++||+|| ||| |++ +.||+|+ .+++ ++++|+|||+|
T Consensus 1 avGLTIWRLPGGGFAVGRF~GgrR---~gErelPvVyT-EmDGgfn~~~g~PRRisW~~r~~r~~~~~gg~~~R~frn~f 76 (117)
T PF06547_consen 1 AVGLTIWRLPGGGFAVGRFSGGRR---AGERELPVVYT-EMDGGFNNGGGAPRRISWSSRGGRSRERRGGGFRRVFRNLF 76 (117)
T ss_pred CcceEEEEcCCCceEEeeecCCCc---CCcccCCEEEE-EecCCccCCCCCceeeeecccCCcccccccchHHHHHHHHH
Confidence 468999999999999999999999 99999999999 999 555 8999998 3344 44999999998
Q ss_pred cccccccCCCCCCC
Q 045745 322 SIFRRFRGNSSRSS 335 (351)
Q Consensus 322 ~~~~~~~~~~~~~s 335 (351)
++|+.++..+++++
T Consensus 77 s~f~~~~~~~s~ss 90 (117)
T PF06547_consen 77 SCFGRIGSSSSSSS 90 (117)
T ss_pred HHhcCCCCCccccc
Confidence 88887776665544
No 2
>PF14369 zf-RING_3: zinc-finger
Probab=99.61 E-value=2.8e-16 Score=104.97 Aligned_cols=35 Identities=46% Similarity=1.170 Sum_probs=30.7
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEee
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi 44 (351)
++||||+|+|+|++....+++++||+|++||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 47999999999999865556677999999999997
No 3
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.61 E-value=2.6e-16 Score=153.58 Aligned_cols=79 Identities=29% Similarity=0.730 Sum_probs=69.0
Q ss_pred CCCCCCHHHHhcCCceeeecCCCCCc-ccccccccccccCCcceeeccCceechhhHHHHhhcCC-CCCCCCCCCCcchh
Q 045745 171 ENLPASKASIESMPSIEISSGHVSSE-CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN-SCPVCRQELPAAAA 248 (351)
Q Consensus 171 ~~~pas~~~i~~lp~~~~~~~~~~~~-~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~-sCP~CR~~l~~~~~ 248 (351)
....+.+..+.++|..+++....... ..|+||+|+|+.||.++.|||+|.||..||++||.++. .||+||..+..+..
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 56678999999999999987665443 48999999999999999999999999999999998775 59999998887754
Q ss_pred h
Q 045745 249 A 249 (351)
Q Consensus 249 ~ 249 (351)
.
T Consensus 283 ~ 283 (348)
T KOG4628|consen 283 S 283 (348)
T ss_pred C
Confidence 3
No 4
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.51 E-value=5.8e-15 Score=103.22 Aligned_cols=43 Identities=51% Similarity=1.257 Sum_probs=40.5
Q ss_pred cccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCR 240 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR 240 (351)
+|+||+++|..++.++.++|+|.||.+||..||+.+.+||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 6999999999889999999999999999999999999999997
No 5
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.24 E-value=3.8e-12 Score=119.37 Aligned_cols=73 Identities=27% Similarity=0.529 Sum_probs=56.7
Q ss_pred CCCCHHHHhcCCceeeecCC---CCCcccccccccccccCCc-----ceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 173 LPASKASIESMPSIEISSGH---VSSECHCAVCKEAFELGNE-----AREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 173 ~pas~~~i~~lp~~~~~~~~---~~~~~~C~ICle~~~~g~~-----~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
...++..++++|++...-.. ...+.+|+||++.+...+. +..++|+|.||..||..|++.+.+||+||..+.
T Consensus 148 ~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 148 GKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred cchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 33488899999988654332 2346799999999875431 234569999999999999999999999999876
Q ss_pred c
Q 045745 245 A 245 (351)
Q Consensus 245 ~ 245 (351)
.
T Consensus 228 ~ 228 (238)
T PHA02929 228 S 228 (238)
T ss_pred E
Confidence 4
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.22 E-value=4.1e-12 Score=123.53 Aligned_cols=73 Identities=26% Similarity=0.655 Sum_probs=56.0
Q ss_pred CCHHHHhcCCceeeecCCCCCcccccccccc-cccC---------CcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 175 ASKASIESMPSIEISSGHVSSECHCAVCKEA-FELG---------NEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 175 as~~~i~~lp~~~~~~~~~~~~~~C~ICle~-~~~g---------~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
+.|+.-+-+|+++..+- ..++..|.||+|+ |+.+ ..++.|||+|+||-.|++.|++++++||+||.++.
T Consensus 267 ~~kdl~~~~~t~t~eql-~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 267 ATKDLNAMYPTATEEQL-TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred HhhHHHhhcchhhhhhh-cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 44555555665554332 4467899999999 5544 25799999999999999999999999999999976
Q ss_pred cchh
Q 045745 245 AAAA 248 (351)
Q Consensus 245 ~~~~ 248 (351)
.+..
T Consensus 346 fd~~ 349 (491)
T COG5243 346 FDQS 349 (491)
T ss_pred cccC
Confidence 6543
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=99.22 E-value=5.5e-12 Score=97.88 Aligned_cols=45 Identities=44% Similarity=0.998 Sum_probs=35.6
Q ss_pred cccccccccccccC----------CcceeeccCceechhhHHHHhhcCCCCCCCC
Q 045745 196 ECHCAVCKEAFELG----------NEAREMPCKHIYHEDCILPWLKMRNSCPVCR 240 (351)
Q Consensus 196 ~~~C~ICle~~~~g----------~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR 240 (351)
+..|+||++.|... -.+...+|+|.||..||.+||+.+++||+||
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 34699999999321 2344557999999999999999999999997
No 8
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.21 E-value=5.5e-12 Score=119.97 Aligned_cols=50 Identities=38% Similarity=0.984 Sum_probs=46.4
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhh-cCCCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLK-MRNSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~-~~~sCP~CR~~l~~ 245 (351)
..+|+||++.|..+|.++.|||+|.||..||++|+. -++.||+||.+||.
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 378999999999999999999999999999999997 56789999999975
No 9
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.94 E-value=5.9e-10 Score=79.94 Aligned_cols=46 Identities=33% Similarity=0.814 Sum_probs=40.1
Q ss_pred cccccccccccccCCcceeeccCce-echhhHHHHhhcCCCCCCCCCCCC
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHI-YHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
+..|.||++.... +..+||+|. |+..|+..|++....||+||.+|.
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 4689999999764 789999999 999999999999999999999875
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.91 E-value=6.9e-10 Score=100.65 Aligned_cols=51 Identities=24% Similarity=0.677 Sum_probs=42.1
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhc----------------CCCCCCCCCCCCcch
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM----------------RNSCPVCRQELPAAA 247 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~----------------~~sCP~CR~~l~~~~ 247 (351)
..+.+|+||++.++. +++++|+|.||+.||..|+.. ...||+||.+|....
T Consensus 16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 356789999999874 678899999999999999852 247999999986543
No 11
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.91 E-value=8.3e-10 Score=75.31 Aligned_cols=44 Identities=39% Similarity=1.092 Sum_probs=36.6
Q ss_pred cccccccccccCCcceeeccCceechhhHHHHhhc-CCCCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-RNSCPVCRQEL 243 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCP~CR~~l 243 (351)
+|+||++.+. +.+..++|+|.||..||..|++. +..||+|+..+
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 4999999983 34455559999999999999987 67899999764
No 12
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.89 E-value=1e-09 Score=74.75 Aligned_cols=39 Identities=31% Similarity=0.887 Sum_probs=33.5
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCC
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~C 239 (351)
|+||++.+.. .++.++|+|.||..||.+|++.+.+||+|
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 8999999885 44788999999999999999998899998
No 13
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.81 E-value=1.9e-09 Score=99.61 Aligned_cols=51 Identities=25% Similarity=0.700 Sum_probs=43.2
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhcCC---CCCCCCCCCCcch
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN---SCPVCRQELPAAA 247 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~---sCP~CR~~l~~~~ 247 (351)
....+|.||||.-++ ++++.|+|.||+.||.+||..+. .|||||..|..++
T Consensus 45 ~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 345789999998765 78899999999999999997543 6999999987765
No 14
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=1.3e-09 Score=113.81 Aligned_cols=51 Identities=33% Similarity=0.981 Sum_probs=45.6
Q ss_pred CcccccccccccccCCc--ceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 195 SECHCAVCKEAFELGNE--AREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~--~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
.+..|+||+|++..+.. +++|||+|+||..||..|+++.++||+||..+..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD 342 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence 46789999999998765 8999999999999999999999999999995533
No 15
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.75 E-value=6.3e-09 Score=98.90 Aligned_cols=49 Identities=31% Similarity=0.841 Sum_probs=43.6
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
....|.+|||.... +.-+||||+||+.||..|+..+..||+||.++...
T Consensus 238 a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 238 ATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence 34789999999865 78899999999999999999999999999988654
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.72 E-value=7.3e-09 Score=71.99 Aligned_cols=38 Identities=32% Similarity=0.837 Sum_probs=30.3
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhhcC----CCCCCC
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMR----NSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~----~sCP~C 239 (351)
|+||++.|+. ++.|+|+|.|+..||..|++.. ..||+|
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 8999999997 8999999999999999999654 369988
No 17
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.70 E-value=7.4e-09 Score=82.23 Aligned_cols=51 Identities=33% Similarity=0.931 Sum_probs=39.2
Q ss_pred CCcccccccccccc--------cCCc-ceee-ccCceechhhHHHHhhc---CCCCCCCCCCCC
Q 045745 194 SSECHCAVCKEAFE--------LGNE-AREM-PCKHIYHEDCILPWLKM---RNSCPVCRQELP 244 (351)
Q Consensus 194 ~~~~~C~ICle~~~--------~g~~-~~~l-pC~H~FH~~CI~~WL~~---~~sCP~CR~~l~ 244 (351)
..+..|.||+..|+ +|+. +.++ .|+|.||..||.+||.. +..||+||++..
T Consensus 19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 34678999999997 2332 2233 49999999999999975 458999999764
No 18
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.70 E-value=1.3e-08 Score=75.68 Aligned_cols=48 Identities=23% Similarity=0.393 Sum_probs=42.4
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
..|+||++.++. ++.++|+|+|+..||..|++.+.+||+|+.++...+
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 479999999986 678899999999999999998889999999885443
No 19
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.63 E-value=2e-08 Score=68.64 Aligned_cols=39 Identities=38% Similarity=1.020 Sum_probs=33.6
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhh--cCCCCCCC
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLK--MRNSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~--~~~sCP~C 239 (351)
|+||++.++.. ...++|+|.||..||..|++ ....||+|
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 89999998852 35889999999999999998 45579998
No 20
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=1.4e-08 Score=90.47 Aligned_cols=50 Identities=26% Similarity=0.679 Sum_probs=42.5
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
...|+|||+.+++. .+....|||+||+.||..-|+....||+|+++|...
T Consensus 131 ~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 131 TYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 36899999999863 234577999999999999999999999999987654
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.62 E-value=1.8e-08 Score=70.41 Aligned_cols=44 Identities=32% Similarity=0.820 Sum_probs=38.8
Q ss_pred cccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
+|.||++.|.....+..++|+|+|+..||..+......||+||+
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 49999999965567899999999999999999866778999984
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=98.61 E-value=2.3e-08 Score=65.73 Aligned_cols=38 Identities=39% Similarity=1.144 Sum_probs=33.2
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhh-cCCCCCCC
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLK-MRNSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~-~~~sCP~C 239 (351)
|+||++.. ..+..++|+|.||..||..|++ .+..||+|
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 78999983 3578899999999999999998 66689998
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.58 E-value=2.3e-08 Score=92.10 Aligned_cols=53 Identities=32% Similarity=0.749 Sum_probs=39.1
Q ss_pred CCCcccccccccccccCC-----cceee-ccCceechhhHHHHhhcC------CCCCCCCCCCCc
Q 045745 193 VSSECHCAVCKEAFELGN-----EAREM-PCKHIYHEDCILPWLKMR------NSCPVCRQELPA 245 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~-----~~~~l-pC~H~FH~~CI~~WL~~~------~sCP~CR~~l~~ 245 (351)
.+.+.+|+||+|..-... .-..| +|+|.||..||..|.+.+ .+||+||..+..
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 345689999999863321 12344 599999999999999753 359999997653
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.53 E-value=4.9e-08 Score=97.91 Aligned_cols=51 Identities=27% Similarity=0.701 Sum_probs=44.3
Q ss_pred CCCcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 193 VSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
+.....|+||++.|.. +++++|+|.||..||..||..+..||+||..+...
T Consensus 23 Le~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 4456799999999975 56889999999999999999888999999987654
No 25
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.37 E-value=1.9e-07 Score=72.89 Aligned_cols=48 Identities=33% Similarity=0.841 Sum_probs=36.1
Q ss_pred cccccccccc-----------ccCCccee-ec-cCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 197 CHCAVCKEAF-----------ELGNEARE-MP-CKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 197 ~~C~ICle~~-----------~~g~~~~~-lp-C~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
+.|+||...| ..+++... .- |+|.||..||.+||..++.||++|++..
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence 4577776654 34444332 22 9999999999999999999999998754
No 26
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.32 E-value=2.7e-07 Score=66.27 Aligned_cols=42 Identities=21% Similarity=0.816 Sum_probs=33.8
Q ss_pred cccccccccccCCcceeeccC-----ceechhhHHHHhhcC--CCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCK-----HIYHEDCILPWLKMR--NSCPVCR 240 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~-----H~FH~~CI~~WL~~~--~sCP~CR 240 (351)
.|.||++ .+.++...++||. |.+|..||.+||..+ .+||+|+
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 4444567789975 899999999999644 4899995
No 27
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.26 E-value=5.5e-07 Score=62.94 Aligned_cols=38 Identities=37% Similarity=0.920 Sum_probs=22.9
Q ss_pred cccccccccc-CCcceeeccCceechhhHHHHhhcC----CCCC
Q 045745 199 CAVCKEAFEL-GNEAREMPCKHIYHEDCILPWLKMR----NSCP 237 (351)
Q Consensus 199 C~ICle~~~~-g~~~~~lpC~H~FH~~CI~~WL~~~----~sCP 237 (351)
|+||+| |.. ...++.|+|+|.|+.+||.+|++.. ..||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 754 4467899999999999999999843 2576
No 28
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=3.6e-07 Score=86.25 Aligned_cols=52 Identities=29% Similarity=0.852 Sum_probs=41.9
Q ss_pred CcccccccccccccCC-------cceeeccCceechhhHHHHh--hcCCCCCCCCCCCCcc
Q 045745 195 SECHCAVCKEAFELGN-------EAREMPCKHIYHEDCILPWL--KMRNSCPVCRQELPAA 246 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~-------~~~~lpC~H~FH~~CI~~WL--~~~~sCP~CR~~l~~~ 246 (351)
++..|+||-..+.... +.-+|.|+|+||..||+-|- ..+++||.|+..+...
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence 4568999988876443 56778999999999999995 4677999998877543
No 29
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=2.5e-07 Score=71.59 Aligned_cols=50 Identities=34% Similarity=0.891 Sum_probs=37.4
Q ss_pred Cccccccccccccc--------CC-cceeec-cCceechhhHHHHhhcC---CCCCCCCCCCC
Q 045745 195 SECHCAVCKEAFEL--------GN-EAREMP-CKHIYHEDCILPWLKMR---NSCPVCRQELP 244 (351)
Q Consensus 195 ~~~~C~ICle~~~~--------g~-~~~~lp-C~H~FH~~CI~~WL~~~---~sCP~CR~~l~ 244 (351)
.+.+|-||.-.|.. || -+.++- |.|.||..||.+||... ..||+||+...
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 34589999998862 33 233444 99999999999999643 36999998753
No 30
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.19 E-value=1.3e-06 Score=67.64 Aligned_cols=50 Identities=26% Similarity=0.462 Sum_probs=40.1
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhc-CCCCCCCCCCCCcchh
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-RNSCPVCRQELPAAAA 248 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCP~CR~~l~~~~~ 248 (351)
+..|+||.+.|.. ++++||+|.|.+.||..||+. +.+||+|+..|.....
T Consensus 4 ~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l 54 (73)
T PF04564_consen 4 EFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL 54 (73)
T ss_dssp GGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred ccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence 4689999999996 789999999999999999998 7899999998877654
No 31
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.14 E-value=6.2e-07 Score=96.09 Aligned_cols=53 Identities=28% Similarity=0.863 Sum_probs=39.9
Q ss_pred CCCcccccccccccccCC---cceeec-cCceechhhHHHHhhc--CCCCCCCCCCCCc
Q 045745 193 VSSECHCAVCKEAFELGN---EAREMP-CKHIYHEDCILPWLKM--RNSCPVCRQELPA 245 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~---~~~~lp-C~H~FH~~CI~~WL~~--~~sCP~CR~~l~~ 245 (351)
.+...+|+||+..+..-+ .-+..+ |+|.||..||.+|++. +++||+||.+++.
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 445579999999876211 123344 9999999999999985 4579999988763
No 32
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=1.4e-06 Score=82.25 Aligned_cols=50 Identities=30% Similarity=0.796 Sum_probs=42.1
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHH-HhhcCC-CCCCCCCCCCcch
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILP-WLKMRN-SCPVCRQELPAAA 247 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~-WL~~~~-sCP~CR~~l~~~~ 247 (351)
.+..|.||++..+. +.-++|+|+||..||.. |=+.+. .||+||+.+...+
T Consensus 214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred cccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 46789999999876 78899999999999999 976665 5999999876543
No 33
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=2.2e-06 Score=87.32 Aligned_cols=48 Identities=29% Similarity=0.777 Sum_probs=39.8
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhc-----CCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-----RNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-----~~sCP~CR~~l~~~ 246 (351)
+..|+|||+.... +..+.|||+||..||...+.. ...||+||..|...
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k 238 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLK 238 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence 5789999998775 566679999999999998854 34799999988763
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.01 E-value=1.7e-06 Score=83.95 Aligned_cols=48 Identities=27% Similarity=0.737 Sum_probs=44.2
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
..|.||.|-|.. +.++||+|.||.-||+.+|..+..||.|+.++....
T Consensus 24 LRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~ 71 (442)
T KOG0287|consen 24 LRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD 71 (442)
T ss_pred HHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccchhh
Confidence 579999999997 789999999999999999999999999999886654
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.00 E-value=2.4e-06 Score=81.54 Aligned_cols=47 Identities=28% Similarity=0.638 Sum_probs=42.3
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
-..|-||.+.|.. +..++|+|.||.-||...|..+..||+||.+...
T Consensus 25 ~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 25 MLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred HHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence 3689999999997 6788999999999999999999999999997543
No 36
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=2.2e-06 Score=86.71 Aligned_cols=51 Identities=35% Similarity=0.973 Sum_probs=39.6
Q ss_pred CcccccccccccccC---Cc-----------ceeeccCceechhhHHHHhhc-CCCCCCCCCCCCc
Q 045745 195 SECHCAVCKEAFELG---NE-----------AREMPCKHIYHEDCILPWLKM-RNSCPVCRQELPA 245 (351)
Q Consensus 195 ~~~~C~ICle~~~~g---~~-----------~~~lpC~H~FH~~CI~~WL~~-~~sCP~CR~~l~~ 245 (351)
....|+||+..++.- .. -...||.|+||..|+..|... +-.||+||.+|+.
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 346899999987531 11 134599999999999999985 4489999999874
No 37
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.93 E-value=3.4e-06 Score=78.03 Aligned_cols=46 Identities=33% Similarity=0.727 Sum_probs=39.8
Q ss_pred CCCcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 193 VSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
...+..|+||++.|.. ++.+||+|.||..||..|+.....||.||.
T Consensus 10 ~~~~~~C~iC~~~~~~---p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFRE---PVLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHhhc---CccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 3456799999999997 389999999999999999985558999993
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.93 E-value=2.2e-06 Score=65.97 Aligned_cols=50 Identities=24% Similarity=0.582 Sum_probs=23.1
Q ss_pred cccccccccccc-cCCcc-eee---ccCceechhhHHHHhhc----C-------CCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFE-LGNEA-REM---PCKHIYHEDCILPWLKM----R-------NSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~-~g~~~-~~l---pC~H~FH~~CI~~WL~~----~-------~sCP~CR~~l~~ 245 (351)
+.+|.||++.+. .++.+ ... .|++.||..||..||.. + ..||.|+.+|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 357999999866 33332 233 39999999999999952 1 149999988753
No 39
>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=97.89 E-value=8.3e-06 Score=79.21 Aligned_cols=51 Identities=24% Similarity=0.437 Sum_probs=37.5
Q ss_pred cccccccccccccCCcc--eeeccCceechhhHHHHh-hcCCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNEA--REMPCKHIYHEDCILPWL-KMRNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~--~~lpC~H~FH~~CI~~WL-~~~~sCP~CR~~l~~~ 246 (351)
+..|+||+.+--..... .+-+|+|.||..||...+ .....||+|+..+...
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence 35799999964433333 233799999999999965 4456899999877554
No 40
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=6.3e-06 Score=67.44 Aligned_cols=27 Identities=48% Similarity=1.089 Sum_probs=25.2
Q ss_pred cCceechhhHHHHhhcCCCCCCCCCCC
Q 045745 217 CKHIYHEDCILPWLKMRNSCPVCRQEL 243 (351)
Q Consensus 217 C~H~FH~~CI~~WL~~~~sCP~CR~~l 243 (351)
|.|.||..||.+||+.++.||+|.++.
T Consensus 81 CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 81 CNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred cchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 999999999999999999999997653
No 41
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.77 E-value=1e-05 Score=81.15 Aligned_cols=81 Identities=26% Similarity=0.627 Sum_probs=51.8
Q ss_pred cccccccccccccCC-cceeeccCceechhhHHHHhhcCCCCCCCCCCCCcchhhhh--hhhhcccccc-cCCCCccccc
Q 045745 196 ECHCAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAAAAAA--EESSMALSIW-WLPGGGFAVG 271 (351)
Q Consensus 196 ~~~C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~~~~~--~e~~~~~~~~-~~p~~~~a~g 271 (351)
-.+|+||||-+...- -++...|.|.||..|+.+| ...+||+||.-......... .+-...-..| -+--|....|
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~p~~ve~~~c~~c~~~~~LwicliCg~vgcg 252 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQSPSVVESSLCLACGCTEDLWICLICGNVGCG 252 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcCcchhhhhhhhhhcccccEEEEEEccceecc
Confidence 358999999998643 2355669999999999999 45689999996652111000 0111112233 2455666778
Q ss_pred ccccccc
Q 045745 272 RYEGRRV 278 (351)
Q Consensus 272 r~~g~~~ 278 (351)
|+..+++
T Consensus 253 rY~eghA 259 (493)
T KOG0804|consen 253 RYKEGHA 259 (493)
T ss_pred cccchhH
Confidence 8876644
No 42
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.70 E-value=1.8e-05 Score=77.68 Aligned_cols=47 Identities=26% Similarity=0.668 Sum_probs=41.3
Q ss_pred cccccccccccccCCcceeeccCce-echhhHHHHhhcCCCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHI-YHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..+|.||+.+-.. +.+|||.|. .|..|.+..--+++.||+||++|..
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 4789999999876 789999998 8999998876789999999998754
No 43
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=4.3e-06 Score=81.69 Aligned_cols=59 Identities=25% Similarity=0.572 Sum_probs=45.4
Q ss_pred eeeecCCCCCcccccccccccccCCcceeeccCceechhhHHHHhhc-CCCCCCCCCCCCcc
Q 045745 186 IEISSGHVSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-RNSCPVCRQELPAA 246 (351)
Q Consensus 186 ~~~~~~~~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-~~sCP~CR~~l~~~ 246 (351)
+.++-..+..+..|+|||+.++. ...+.-|.|.||.+||.+-|+. .++||.||+.+...
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 44555556677899999999985 2333349999999999999974 56899999977543
No 44
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=3.1e-05 Score=74.44 Aligned_cols=48 Identities=23% Similarity=0.468 Sum_probs=40.7
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCC-CCCCCCCCCCcch
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN-SCPVCRQELPAAA 247 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~-sCP~CR~~l~~~~ 247 (351)
.+|+||+..... ++.|+|+|.||..||+--.+... +|++||.+|++.-
T Consensus 8 ~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 8 KECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred CcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 589999998765 68899999999999998776544 6999999997653
No 45
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.47 E-value=2.5e-05 Score=82.72 Aligned_cols=50 Identities=28% Similarity=0.584 Sum_probs=43.9
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
....|++|+..+..+......+|.|+||..||..|-+.-++||+||.++.
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 34689999999987766667789999999999999999999999999764
No 46
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=4.7e-05 Score=75.34 Aligned_cols=50 Identities=26% Similarity=0.799 Sum_probs=37.0
Q ss_pred ccccccccccccCCcceeec-cCceechhhHHHHhhcC---CCCCCCCCCCCcc
Q 045745 197 CHCAVCKEAFELGNEAREMP-CKHIYHEDCILPWLKMR---NSCPVCRQELPAA 246 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL~~~---~sCP~CR~~l~~~ 246 (351)
..|.||-+-+-...++.-+. |+|+||..|+..|++.- ..||+|+-.++..
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r 58 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQER 58 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccce
Confidence 47999955554444555555 99999999999999743 4799999555443
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.41 E-value=5.8e-05 Score=56.94 Aligned_cols=44 Identities=25% Similarity=0.639 Sum_probs=22.8
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
..|++|.+.|+. .+....|.|+|+..||..-+. ..||+|+.+..
T Consensus 8 LrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAW 51 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TTTGGGGTT--TB-SSS--B-S
T ss_pred cCCcHHHHHhcC--CceeccCccHHHHHHhHHhcC--CCCCCcCChHH
Confidence 579999999985 233445999999999988655 34999988653
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=7.3e-05 Score=73.98 Aligned_cols=49 Identities=33% Similarity=0.768 Sum_probs=37.2
Q ss_pred CcccccccccccccCC----cceeec-cCceechhhHHHHh--hc-----CCCCCCCCCCC
Q 045745 195 SECHCAVCKEAFELGN----EAREMP-CKHIYHEDCILPWL--KM-----RNSCPVCRQEL 243 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~----~~~~lp-C~H~FH~~CI~~WL--~~-----~~sCP~CR~~l 243 (351)
.+.+|.||+|...... .-.+|| |.|.||..||..|- ++ ..+||.||...
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 4578999999876422 012345 99999999999998 44 46899999865
No 49
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.36 E-value=8e-05 Score=71.56 Aligned_cols=92 Identities=21% Similarity=0.428 Sum_probs=59.7
Q ss_pred hhHHHHHHHhhHhhhhhcCCCCCCCCCHHHHhcCCceeeecCCCCCcccccccccccccCCcceeeccCceechhhHHHH
Q 045745 150 SGFHLLLHQLSQIDLTALSRPENLPASKASIESMPSIEISSGHVSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPW 229 (351)
Q Consensus 150 ~~le~ll~qL~~~~~~~~~~~~~~pas~~~i~~lp~~~~~~~~~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~W 229 (351)
+.|..|..++..+--.+ .+ -|.--..|+.-..+.... .....+|.|||--|..++...+++|-|.||..|+.++
T Consensus 75 ~~~~~i~~~~~~iikq~---~g-~pii~~lie~~~e~LT~n--n~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRy 148 (368)
T KOG4445|consen 75 PEFREIQRQIQEIIKQN---SG-MPIICQLIEHCSEFLTEN--NHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARY 148 (368)
T ss_pred HHHHHHHHHHHHHHHhc---CC-CchhHHHHHHHHHHcccC--CCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHH
Confidence 44667777665433221 12 334444554433332221 1233579999999999998999999999999999876
Q ss_pred hhc-----------------------CCCCCCCCCCCCcch
Q 045745 230 LKM-----------------------RNSCPVCRQELPAAA 247 (351)
Q Consensus 230 L~~-----------------------~~sCP~CR~~l~~~~ 247 (351)
|.. ...||+||..|..+.
T Consensus 149 l~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 149 LTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 621 225999999886553
No 50
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.00025 Score=71.51 Aligned_cols=50 Identities=34% Similarity=0.713 Sum_probs=44.0
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
.++.+|.||+..|.. ++.+||+|.||..||++-|.....||.||.++..-
T Consensus 82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~ 131 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVEL 131 (398)
T ss_pred cchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCcccccccccc
Confidence 567899999999886 77889999999999999888777899999998753
No 51
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.07 E-value=0.00028 Score=70.35 Aligned_cols=48 Identities=27% Similarity=0.866 Sum_probs=36.4
Q ss_pred ccccccccccccc-CCc-ceeeccCceechhhHHHHhhc--CCCCCCCCCCC
Q 045745 196 ECHCAVCKEAFEL-GNE-AREMPCKHIYHEDCILPWLKM--RNSCPVCRQEL 243 (351)
Q Consensus 196 ~~~C~ICle~~~~-g~~-~~~lpC~H~FH~~CI~~WL~~--~~sCP~CR~~l 243 (351)
..+|+||++.++. ++. ...+.|+|.|..+||++||.+ ...||.|..+-
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 3589999999874 333 344559999999999999952 22599997653
No 52
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00015 Score=52.92 Aligned_cols=46 Identities=26% Similarity=0.577 Sum_probs=35.9
Q ss_pred ccccccccccccCCcceeeccCce-echhhHHHHhh-cCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHI-YHEDCILPWLK-MRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~-FH~~CI~~WL~-~~~sCP~CR~~l~~ 245 (351)
.+|.||+|.-.. .+...|+|. .|.+|-.+-++ .+..||+||++|..
T Consensus 8 dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 8 DECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD 55 (62)
T ss_pred cceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence 689999997543 244569998 78999777665 78899999998753
No 53
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.00023 Score=62.89 Aligned_cols=40 Identities=28% Similarity=0.735 Sum_probs=32.4
Q ss_pred CceeeecCCCCC-cccccccccccccCCcceeeccCceech
Q 045745 184 PSIEISSGHVSS-ECHCAVCKEAFELGNEAREMPCKHIYHE 223 (351)
Q Consensus 184 p~~~~~~~~~~~-~~~C~ICle~~~~g~~~~~lpC~H~FH~ 223 (351)
|++.+.+..+.. .-+|.||||+++.|+.+..|||-.+||+
T Consensus 164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 455555554443 4789999999999999999999999997
No 54
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.88 E-value=0.00058 Score=68.94 Aligned_cols=54 Identities=30% Similarity=0.673 Sum_probs=45.0
Q ss_pred CCCcccccccccccccCCccee-eccCceechhhHHHHhhcCCCCCCCCCCCCcchhh
Q 045745 193 VSSECHCAVCKEAFELGNEARE-MPCKHIYHEDCILPWLKMRNSCPVCRQELPAAAAA 249 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~~~-lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~~~ 249 (351)
+..+..|++|...+.. +.. ..|+|.||..||..|+..+..||.|+..+......
T Consensus 18 ~~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred CcccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 4556899999999986 334 58999999999999999999999999887655443
No 55
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=96.67 E-value=0.0005 Score=68.48 Aligned_cols=48 Identities=27% Similarity=0.787 Sum_probs=40.0
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhc--CCCCCCCCCCCCcch
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM--RNSCPVCRQELPAAA 247 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCP~CR~~l~~~~ 247 (351)
.-|-||-|.=+ .+++-||+|..|..|+..|-.. .++||.||.+|....
T Consensus 370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte 419 (563)
T KOG1785|consen 370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE 419 (563)
T ss_pred HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence 46999988644 4889999999999999999743 568999999997654
No 56
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.66 E-value=0.0012 Score=46.85 Aligned_cols=40 Identities=30% Similarity=0.821 Sum_probs=27.8
Q ss_pred ccccccccccCCcceeecc--Cc---eechhhHHHHhh--cCCCCCCC
Q 045745 199 CAVCKEAFELGNEAREMPC--KH---IYHEDCILPWLK--MRNSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC--~H---~FH~~CI~~WL~--~~~sCP~C 239 (351)
|-||++.-+..+ ..+.|| +- ..|..||..|+. ...+|++|
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 789999877644 567785 43 889999999996 44579988
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.54 E-value=0.00065 Score=67.50 Aligned_cols=47 Identities=38% Similarity=0.913 Sum_probs=38.8
Q ss_pred CcccccccccccccCC-cceeeccCceechhhHHHHhhcCC--CCCCCCC
Q 045745 195 SECHCAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRN--SCPVCRQ 241 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~--sCP~CR~ 241 (351)
.+.-|..|-+.+-..+ ...-|||.|+||..|+...|..+. +||.||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 3567999999986544 566789999999999999997654 7999994
No 58
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.53 E-value=0.0012 Score=48.84 Aligned_cols=41 Identities=24% Similarity=0.736 Sum_probs=28.8
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcC--CCCCC
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMR--NSCPV 238 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~--~sCP~ 238 (351)
...|+|.+..|+ +.++...|+|.|-++.|..||+.+ ..||+
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 368999999998 456667899999999999999443 36998
No 59
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.00092 Score=71.30 Aligned_cols=46 Identities=26% Similarity=0.712 Sum_probs=38.3
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhh-cCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLK-MRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~-~~~sCP~CR~~l~~ 245 (351)
..|++|-.-++. +++.-|+|.||..||.+-+. ++..||.|-..+..
T Consensus 644 LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 589999988775 56667999999999999996 55689999876643
No 60
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.43 E-value=0.00066 Score=66.17 Aligned_cols=50 Identities=20% Similarity=0.556 Sum_probs=40.8
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
...+|.+|.--|... ..+.-|-|.||+.||.+.|...++||.|...|-..
T Consensus 14 ~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred cceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 447899999988852 33445999999999999999999999998866433
No 61
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=96.32 E-value=0.0012 Score=56.94 Aligned_cols=37 Identities=14% Similarity=0.445 Sum_probs=31.1
Q ss_pred cccccccccccccCCcceeeccC------ceechhhHHHHhhc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCK------HIYHEDCILPWLKM 232 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~------H~FH~~CI~~WL~~ 232 (351)
..+|.||++.+...+-++.++|+ |.||.+|+.+|-+.
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence 36899999999886668888886 99999999999433
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.92 E-value=0.0023 Score=58.51 Aligned_cols=45 Identities=22% Similarity=0.564 Sum_probs=39.8
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
..|.||.++|+. +++..|+|.||..|..+=++....|-+|.+...
T Consensus 197 F~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 197 FLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred eeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 479999999996 788889999999999998888899999976543
No 63
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=95.81 E-value=0.0039 Score=50.58 Aligned_cols=33 Identities=27% Similarity=0.664 Sum_probs=27.9
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHH
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCIL 227 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~ 227 (351)
..+..|+||...+.. ......||+|+||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 345689999999987 567888999999999975
No 64
>PHA02862 5L protein; Provisional
Probab=95.80 E-value=0.0042 Score=54.13 Aligned_cols=46 Identities=17% Similarity=0.645 Sum_probs=34.8
Q ss_pred ccccccccccccCCcceeeccC-----ceechhhHHHHhhc--CCCCCCCCCCCCcc
Q 045745 197 CHCAVCKEAFELGNEAREMPCK-----HIYHEDCILPWLKM--RNSCPVCRQELPAA 246 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~-----H~FH~~CI~~WL~~--~~sCP~CR~~l~~~ 246 (351)
..|-||+++-++ . .-||. ...|++||.+|+.. +.+|++|+.+....
T Consensus 3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 579999998543 2 35654 67899999999964 44799999987543
No 65
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=95.71 E-value=0.0061 Score=42.50 Aligned_cols=41 Identities=32% Similarity=0.867 Sum_probs=25.4
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhhcCC--CCCCC
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN--SCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~--sCP~C 239 (351)
|.+|.+....|..-....|.=.+|..|+..++..+. .||.|
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 789999988875555555999999999999998666 79988
No 66
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.67 E-value=0.0073 Score=53.48 Aligned_cols=49 Identities=24% Similarity=0.706 Sum_probs=35.6
Q ss_pred CCcccccccccccccCCcceeec--cCc---eechhhHHHHhhcC--CCCCCCCCCCCcc
Q 045745 194 SSECHCAVCKEAFELGNEAREMP--CKH---IYHEDCILPWLKMR--NSCPVCRQELPAA 246 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lp--C~H---~FH~~CI~~WL~~~--~sCP~CR~~l~~~ 246 (351)
..+..|-||+++-. +. .-| |+. ..|.+|+.+|+... .+|++|+.+....
T Consensus 6 ~~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 34568999998843 22 346 444 56999999999643 4799999877544
No 67
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.49 E-value=0.0074 Score=68.10 Aligned_cols=52 Identities=27% Similarity=0.642 Sum_probs=41.1
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhc-----CC-----CCCCCCCCCCc
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-----RN-----SCPVCRQELPA 245 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-----~~-----sCP~CR~~l~~ 245 (351)
..++.|-||.-+--....++.|.|+|+||..|.+.-|+. +- +||+|+.+|..
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 345789999987666667899999999999999865543 21 69999998854
No 68
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.46 E-value=0.0057 Score=63.03 Aligned_cols=51 Identities=27% Similarity=0.635 Sum_probs=40.7
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhc-----CCCCCCCCCCCCcch
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM-----RNSCPVCRQELPAAA 247 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~-----~~sCP~CR~~l~~~~ 247 (351)
.++.+|-+|.+.-++ ..+..|.|.||..||..++.. +-+||+|...|.-+.
T Consensus 534 k~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 534 KGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred cCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 345789999998664 678889999999999888742 348999988876553
No 69
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.41 E-value=0.012 Score=42.12 Aligned_cols=44 Identities=25% Similarity=0.601 Sum_probs=22.4
Q ss_pred ccccccccccCCcceeec--cCceechhhHHHHhh-cCCCCCCCCCCC
Q 045745 199 CAVCKEAFELGNEAREMP--CKHIYHEDCILPWLK-MRNSCPVCRQEL 243 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lp--C~H~FH~~CI~~WL~-~~~sCP~CR~~l 243 (351)
|++|.+++...+ ...+| |++..+..|...-++ ....||-||.+.
T Consensus 1 cp~C~e~~d~~d-~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETD-KDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCC-TT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCC-CccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 789999994432 34455 899999999988886 477999999863
No 70
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.35 E-value=0.02 Score=54.11 Aligned_cols=68 Identities=13% Similarity=0.327 Sum_probs=52.3
Q ss_pred HhcCCceeeecCCC----------CCcccccccccccccCCcceee-ccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 180 IESMPSIEISSGHV----------SSECHCAVCKEAFELGNEAREM-PCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 180 i~~lp~~~~~~~~~----------~~~~~C~ICle~~~~g~~~~~l-pC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
++.|-.++|+.... +....|+||.+.+........| ||+|+|+.+|+.+.+.....||+|-.++...+
T Consensus 195 lkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 195 LKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD 273 (303)
T ss_pred hhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence 45555666654332 1236799999999987665555 59999999999999999999999988886654
No 71
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.24 E-value=0.011 Score=55.08 Aligned_cols=49 Identities=24% Similarity=0.668 Sum_probs=40.6
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhc--------CCCCCCCCCCCCcc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM--------RNSCPVCRQELPAA 246 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~--------~~sCP~CR~~l~~~ 246 (351)
.-|..|.-.++.||. ..|-|-|.||.+|+..|-.. .-.||.|-.+|...
T Consensus 51 pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 469999999999875 57889999999999999743 22599999988654
No 72
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.13 E-value=0.019 Score=55.01 Aligned_cols=53 Identities=26% Similarity=0.509 Sum_probs=39.3
Q ss_pred CCCCcccccccccccccCCcceeeccCceechhhHHHHhhc--CCCCCCCCCCCCcc
Q 045745 192 HVSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM--RNSCPVCRQELPAA 246 (351)
Q Consensus 192 ~~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~--~~sCP~CR~~l~~~ 246 (351)
...++.+|++|-+.=.. .-...+|+|+||..||..=+.. ..+||.|-.++..-
T Consensus 235 ~~t~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~l 289 (298)
T KOG2879|consen 235 TGTSDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPL 289 (298)
T ss_pred cccCCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCcch
Confidence 34567899999987553 2234459999999999997754 35899998776543
No 73
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.06 E-value=0.012 Score=58.31 Aligned_cols=44 Identities=34% Similarity=0.643 Sum_probs=33.2
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..-|.||+++.+. +..+||+|.-| |..--. .-.+||+||..|..
T Consensus 305 p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 305 PDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIRL 348 (355)
T ss_pred CCceEEecCCccc---eeeecCCcEEE--chHHHh-hCCCCchhHHHHHH
Confidence 3679999999886 89999999977 655432 22359999987643
No 74
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.95 E-value=0.0019 Score=64.22 Aligned_cols=50 Identities=30% Similarity=0.721 Sum_probs=44.1
Q ss_pred ccccccccccccC-CcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 197 CHCAVCKEAFELG-NEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 197 ~~C~ICle~~~~g-~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
..|+||.+.++.. +....+-|+|.+|.+||.+||.....||.|+.+|+..
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN 247 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence 5799999999865 5677778999999999999999988999999998754
No 75
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.61 E-value=0.012 Score=59.00 Aligned_cols=47 Identities=21% Similarity=0.565 Sum_probs=38.0
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhcCC--------CCCCCCC
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN--------SCPVCRQ 241 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~--------sCP~CR~ 241 (351)
....|.||.++..-..-.+.+||.|+||+.|+..++..+. .||-|.-
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 4468999999987657788999999999999999985321 4877654
No 76
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.56 E-value=0.013 Score=56.50 Aligned_cols=46 Identities=26% Similarity=0.563 Sum_probs=40.4
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..|-||.+.|.. +++..|+|.||..|...-++....|.+|-+.+..
T Consensus 242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc---chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 359999999996 6888999999999999999999999999876643
No 77
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.43 E-value=0.027 Score=54.58 Aligned_cols=45 Identities=24% Similarity=0.656 Sum_probs=35.2
Q ss_pred ccccccccccccCCcceeec-cCceechhhHHHHhh-cCCCCCCCCC-CCC
Q 045745 197 CHCAVCKEAFELGNEAREMP-CKHIYHEDCILPWLK-MRNSCPVCRQ-ELP 244 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL~-~~~sCP~CR~-~l~ 244 (351)
..|+.|...+.. +..+| |+|.||..||..-|. ....||.|.. .|.
T Consensus 275 LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvl 322 (427)
T COG5222 275 LKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVL 322 (427)
T ss_pred ccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCcccccch
Confidence 679999998874 44456 899999999998875 5668999944 443
No 78
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=94.13 E-value=0.023 Score=61.57 Aligned_cols=47 Identities=26% Similarity=0.813 Sum_probs=35.0
Q ss_pred CcccccccccccccCCcceee-ccCceechhhHHHHhhcC-C------CCCCCCC
Q 045745 195 SECHCAVCKEAFELGNEAREM-PCKHIYHEDCILPWLKMR-N------SCPVCRQ 241 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~l-pC~H~FH~~CI~~WL~~~-~------sCP~CR~ 241 (351)
...+|.||++.+...+.+-.. .|-|+||..||..|-+.. . .||.|..
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 447999999999875543222 278999999999997531 1 4999974
No 79
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.79 E-value=0.029 Score=55.50 Aligned_cols=50 Identities=24% Similarity=0.443 Sum_probs=42.1
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
.++..|+||+..=. .++..||+|.=|+.||.+.|...+.|=.|+..+...
T Consensus 420 sEd~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 420 SEDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV 469 (489)
T ss_pred cccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence 35678999987533 368889999999999999999999999999877643
No 80
>PF04641 Rtf2: Rtf2 RING-finger
Probab=93.57 E-value=0.13 Score=49.11 Aligned_cols=52 Identities=21% Similarity=0.506 Sum_probs=39.9
Q ss_pred CCcccccccccccccCCc-ceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 194 SSECHCAVCKEAFELGNE-AREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~-~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
.....|+|...+|..... +...||||+|...+|..- +....||+|-.++...
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEE 163 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccC
Confidence 445789999999954433 444589999999999996 3355799999887644
No 81
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.56 E-value=0.05 Score=52.49 Aligned_cols=47 Identities=26% Similarity=0.646 Sum_probs=39.2
Q ss_pred ccccccccccccCC---cceeeccCceechhhHHHHhhcC-CCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGN---EAREMPCKHIYHEDCILPWLKMR-NSCPVCRQEL 243 (351)
Q Consensus 197 ~~C~ICle~~~~g~---~~~~lpC~H~FH~~CI~~WL~~~-~sCP~CR~~l 243 (351)
..|-||-++|..++ .++.|-|+|.|+..|+.+-+... ..||.||...
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 47999999998763 56778899999999999877644 4799999985
No 82
>PHA03096 p28-like protein; Provisional
Probab=93.49 E-value=0.033 Score=54.04 Aligned_cols=45 Identities=22% Similarity=0.413 Sum_probs=31.4
Q ss_pred ccccccccccccCC----cceeec-cCceechhhHHHHhhcC---CCCCCCCC
Q 045745 197 CHCAVCKEAFELGN----EAREMP-CKHIYHEDCILPWLKMR---NSCPVCRQ 241 (351)
Q Consensus 197 ~~C~ICle~~~~g~----~~~~lp-C~H~FH~~CI~~WL~~~---~sCP~CR~ 241 (351)
..|.||+|...... .-..|+ |.|.||..||..|-... .+||.||.
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 58999999765421 234566 99999999999998532 24555543
No 83
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=93.34 E-value=0.06 Score=45.43 Aligned_cols=35 Identities=26% Similarity=0.565 Sum_probs=29.5
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeeccC
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIETE 47 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~~~ 47 (351)
...||..|++.+..... +..||.|+|..+.-+...
T Consensus 69 ~~~~C~~C~~~~~~e~~---~~~CP~C~s~~~~i~~G~ 103 (115)
T COG0375 69 AECWCLDCGQEVELEEL---DYRCPKCGSINLRIIGGD 103 (115)
T ss_pred cEEEeccCCCeecchhh---eeECCCCCCCceEEecCC
Confidence 46899999999988864 788999999999887543
No 84
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=92.87 E-value=0.069 Score=39.12 Aligned_cols=33 Identities=36% Similarity=0.884 Sum_probs=29.2
Q ss_pred cccccccccccccCCcceeec-cCceechhhHHH
Q 045745 196 ECHCAVCKEAFELGNEAREMP-CKHIYHEDCILP 228 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~ 228 (351)
...|.+|-+.|+.++.+++.| |+-.||.+|..+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 357999999999888899998 999999999654
No 85
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=92.86 E-value=0.053 Score=53.16 Aligned_cols=49 Identities=16% Similarity=0.367 Sum_probs=38.5
Q ss_pred CcccccccccccccCCcceeec-cCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 195 SECHCAVCKEAFELGNEAREMP-CKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
....|+||+..... ..++. -|-+||..||...+..++.||+=-.++..+
T Consensus 299 ~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~ 348 (357)
T KOG0826|consen 299 DREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVD 348 (357)
T ss_pred ccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcchHH
Confidence 34689999998664 33444 589999999999999999999976665443
No 86
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.61 E-value=0.021 Score=55.08 Aligned_cols=43 Identities=30% Similarity=0.614 Sum_probs=33.6
Q ss_pred cccccccccccccCCcceeeccCce-echhhHHHHhhcCCCCCCCCCCCCc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHI-YHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
+.-|+||++.-.+ ...|+|+|. -|..|-.. -+.||+||+.|..
T Consensus 300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr----m~eCPICRqyi~r 343 (350)
T KOG4275|consen 300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR----MNECPICRQYIVR 343 (350)
T ss_pred HHHHHHHhcCCcc---eEEeecCcEEeehhhccc----cccCchHHHHHHH
Confidence 5679999998664 789999997 46777544 3589999987643
No 87
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.40 E-value=0.082 Score=52.27 Aligned_cols=47 Identities=28% Similarity=0.746 Sum_probs=39.3
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHH--hhcCCCCCCCCCCC
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPW--LKMRNSCPVCRQEL 243 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~W--L~~~~sCP~CR~~l 243 (351)
++...|.||-+.+.- +..+||+|..|..|..+. |.....||+||.+.
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 445679999998775 688999999999998765 56788999999864
No 88
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=92.11 E-value=0.097 Score=38.45 Aligned_cols=45 Identities=22% Similarity=0.599 Sum_probs=33.0
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
..|..|...= ..-.++||+|+.+..|..- ++-+-||+|-.++...
T Consensus 8 ~~~~~~~~~~---~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 8 QPCVFCGFVG---TKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFD 52 (55)
T ss_pred eeEEEccccc---cccccccccceeeccccCh--hhccCCCCCCCcccCC
Confidence 4566665543 3357899999999999665 3667899998887654
No 89
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=91.93 E-value=0.086 Score=50.91 Aligned_cols=44 Identities=30% Similarity=0.770 Sum_probs=37.8
Q ss_pred cccccccccccC-CcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 198 HCAVCKEAFELG-NEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 198 ~C~ICle~~~~g-~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
-|+||.+.+-.. ..+..++|+|.-|..|+......+-+||+|.+
T Consensus 160 ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 160 NCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 499999976554 36788999999999999998877789999987
No 90
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.80 E-value=0.057 Score=50.82 Aligned_cols=45 Identities=22% Similarity=0.632 Sum_probs=34.2
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCC-CCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN-SCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~-sCP~CR~~l~~ 245 (351)
.+|-.|..-=. ++.-..+.|.|+||..|...- +. .||+|+..|..
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~---~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS---SPDVCPLCKKSIRI 49 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccC---Cccccccccceeee
Confidence 46887876544 666777889999999997653 33 89999998643
No 91
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.79 E-value=0.063 Score=58.33 Aligned_cols=44 Identities=30% Similarity=0.810 Sum_probs=34.9
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..|..|--.++. .++..-|+|.||..|+. .....||-|+.++..
T Consensus 841 skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~~ 884 (933)
T KOG2114|consen 841 SKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELRG 884 (933)
T ss_pred eeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhhh
Confidence 589999888774 35667799999999998 455689999885543
No 92
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=91.56 E-value=0.11 Score=58.67 Aligned_cols=43 Identities=23% Similarity=0.619 Sum_probs=37.5
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
..|.||++.+.. .-.+.-|+|.||..|+..|+..+..||+|..
T Consensus 1154 ~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1154 FVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred cchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence 489999999983 2356679999999999999999999999975
No 93
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.79 E-value=0.14 Score=46.29 Aligned_cols=49 Identities=24% Similarity=0.713 Sum_probs=34.5
Q ss_pred ccccccccccccCC----cceeeccCceechhhHHHHhhc----CC-------CCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGN----EAREMPCKHIYHEDCILPWLKM----RN-------SCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~----~~~~lpC~H~FH~~CI~~WL~~----~~-------sCP~CR~~l~~ 245 (351)
..|.||+.---.|. ..--..|+.-||+-|+..||+. ++ .||.|-.+|..
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 35888876543333 2333459999999999999952 22 49999887754
No 94
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=90.69 E-value=0.086 Score=51.39 Aligned_cols=43 Identities=26% Similarity=0.784 Sum_probs=30.7
Q ss_pred cccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
.|--|---+.. .-+.+||+|+||.+|.+. ...+.||.|-.+|.
T Consensus 92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHHH
Confidence 46666554443 347889999999999764 34568999976654
No 95
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=90.32 E-value=0.24 Score=49.55 Aligned_cols=29 Identities=28% Similarity=0.912 Sum_probs=22.5
Q ss_pred cCceechhhHHHHhhcC-------------CCCCCCCCCCCc
Q 045745 217 CKHIYHEDCILPWLKMR-------------NSCPVCRQELPA 245 (351)
Q Consensus 217 C~H~FH~~CI~~WL~~~-------------~sCP~CR~~l~~ 245 (351)
|.=.+|.+|+-+|+..+ -.||+||+++.-
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 66778999999998532 259999998754
No 96
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=90.00 E-value=0.16 Score=50.10 Aligned_cols=51 Identities=22% Similarity=0.533 Sum_probs=37.2
Q ss_pred cccccccccccccCCc-ceeeccCceechhhHHHHhh-cCCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNE-AREMPCKHIYHEDCILPWLK-MRNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~-~~~lpC~H~FH~~CI~~WL~-~~~sCP~CR~~l~~~ 246 (351)
++-|+.|+|++...|. -.-.||+...|.-|....-+ .+..||.||+....+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de 66 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE 66 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence 3459999999987663 44566898888888655433 455899999976554
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=89.10 E-value=0.38 Score=40.43 Aligned_cols=34 Identities=26% Similarity=0.438 Sum_probs=27.6
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeecc
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIET 46 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~~ 46 (351)
...||..|...+.+.. ....||.|++..++-+..
T Consensus 69 ~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 69 VECECEDCSEEVSPEI---DLYRCPKCHGIMLQVRAG 102 (115)
T ss_pred cEEEcccCCCEEecCC---cCccCcCCcCCCcEEecC
Confidence 5799999999888865 368899999988776643
No 98
>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=88.57 E-value=0.27 Score=30.19 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=18.8
Q ss_pred cccCCceeecCcCCCCCccCCCCC
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCH 37 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~ 37 (351)
|..|.+.|..+.. ...+.||.|+
T Consensus 1 C~sC~~~i~~r~~-~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQ-AVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCccc-CceEeCCCCC
Confidence 7889998877653 5789999997
No 99
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.52 E-value=0.17 Score=55.44 Aligned_cols=37 Identities=22% Similarity=0.678 Sum_probs=30.0
Q ss_pred CCCcccccccccccccCCcceeeccCceechhhHHHHh
Q 045745 193 VSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWL 230 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL 230 (351)
++....|.+|...+-. ..-.+.||+|.||++||.+-.
T Consensus 814 ~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred ecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence 4566799999998765 345778999999999998764
No 100
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.94 E-value=0.49 Score=39.74 Aligned_cols=34 Identities=32% Similarity=0.883 Sum_probs=26.6
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeec
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~ 45 (351)
...||..|...+..... ....||.|++.-++-+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ--RVRRCPQCHGDMLRIVA 102 (114)
T ss_pred cEEEcccCCCeeecCCc--cCCcCcCcCCCCcEEcc
Confidence 57999999998877642 23679999998877664
No 101
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=87.87 E-value=0.33 Score=47.55 Aligned_cols=42 Identities=29% Similarity=0.699 Sum_probs=35.0
Q ss_pred ccccccccccccCCcceeecc--CceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGNEAREMPC--KHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC--~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
.+|+||.+.+.. -++.| +|+-|..|=. +.++.||.||.+|..
T Consensus 49 leCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 49 LDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN 92 (299)
T ss_pred ccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence 689999999985 45667 6999999965 467899999999974
No 102
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=87.51 E-value=0.26 Score=47.41 Aligned_cols=51 Identities=24% Similarity=0.561 Sum_probs=38.0
Q ss_pred cccccccccccccCCc-ceeeccC-----ceechhhHHHHhh--cCCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNE-AREMPCK-----HIYHEDCILPWLK--MRNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~-~~~lpC~-----H~FH~~CI~~WL~--~~~sCP~CR~~l~~~ 246 (351)
+..|-||.++...... ..+.||. +..|..|+..|+. ....|.+|.......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 4689999998765332 4667753 6789999999997 445799998865444
No 103
>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=87.19 E-value=0.51 Score=41.97 Aligned_cols=51 Identities=25% Similarity=0.593 Sum_probs=35.1
Q ss_pred cccccccccccccCCcceeec------------cCc-eechhhHHHHhhc------------------------------
Q 045745 196 ECHCAVCKEAFELGNEAREMP------------CKH-IYHEDCILPWLKM------------------------------ 232 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lp------------C~H-~FH~~CI~~WL~~------------------------------ 232 (351)
+..|+||||-=-. ++.|- |.. .=|..||++.-+.
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 5689999997443 44443 443 3478999987531
Q ss_pred -CCCCCCCCCCCCcchhh
Q 045745 233 -RNSCPVCRQELPAAAAA 249 (351)
Q Consensus 233 -~~sCP~CR~~l~~~~~~ 249 (351)
+-.||+||-+|..+...
T Consensus 79 ~~L~CPLCRG~V~GWtvv 96 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV 96 (162)
T ss_pred ccccCccccCceeceEEc
Confidence 12599999999888654
No 104
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.03 E-value=0.7 Score=32.29 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=27.2
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEee
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi 44 (351)
..|-|-.|...+..... ...+.||+|++-++-..
T Consensus 2 ~~y~C~~CG~~~~~~~~-~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDEY-GTGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECCC-CCceECCCCCCeEEEcc
Confidence 35999999999888754 33899999999888543
No 105
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=86.83 E-value=0.18 Score=54.51 Aligned_cols=48 Identities=21% Similarity=0.546 Sum_probs=39.0
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCC--CCCCCCCCCCcchh
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN--SCPVCRQELPAAAA 248 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~--sCP~CR~~l~~~~~ 248 (351)
..|.||++ -+.+...+|+|.||..|+..-+.... .||+||..+.....
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 68999999 24578889999999999999886433 59999998766543
No 106
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=86.44 E-value=0.32 Score=34.69 Aligned_cols=33 Identities=27% Similarity=0.742 Sum_probs=23.4
Q ss_pred eeccC-ceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 214 EMPCK-HIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 214 ~lpC~-H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
.+.|. |..|-.|+..-|.....||+|..+||..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 44575 9999999999999999999999998864
No 107
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=86.34 E-value=0.69 Score=38.78 Aligned_cols=33 Identities=33% Similarity=0.892 Sum_probs=26.4
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeec
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~ 45 (351)
..+||..|.....+.. ....||.|++.-++-+.
T Consensus 69 ~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ---HDAQCPHCHGERLRVDT 101 (113)
T ss_pred cEEEcccCCCEEecCC---cCccCcCCCCCCcEEcc
Confidence 5799999998887764 36779999998777654
No 108
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.03 E-value=0.66 Score=39.16 Aligned_cols=35 Identities=14% Similarity=0.338 Sum_probs=26.5
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeecc
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIET 46 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~~ 46 (351)
...||..|...+.+... ....||.|++..++-+..
T Consensus 70 ~~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 70 VELECKDCSHVFKPNAL--DYGVCEKCHSKNVIITQG 104 (117)
T ss_pred CEEEhhhCCCccccCCc--cCCcCcCCCCCceEEecC
Confidence 57999999987766542 244599999998886643
No 109
>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=85.85 E-value=0.55 Score=39.31 Aligned_cols=33 Identities=24% Similarity=0.422 Sum_probs=24.8
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceEeec
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~ 45 (351)
...||..|.....+... ...||.|++..++-+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEF---DFSCPRCGSPDVEIIS 101 (113)
T ss_dssp -EEEETTTS-EEECHHC---CHH-SSSSSS-EEEEE
T ss_pred CcEECCCCCCEEecCCC---CCCCcCCcCCCcEEcc
Confidence 57999999999998873 6899999999887664
No 110
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.36 E-value=0.41 Score=50.47 Aligned_cols=47 Identities=30% Similarity=0.788 Sum_probs=40.3
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcchh
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAAA 248 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~~ 248 (351)
....|.||++++ ..+..+|. |..|+.+|+..+..||+|+..+..++.
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~ 524 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDF 524 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhcccc
Confidence 346899999998 46888899 999999999999999999987766643
No 111
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.44 E-value=0.36 Score=46.06 Aligned_cols=51 Identities=29% Similarity=0.627 Sum_probs=35.8
Q ss_pred CCCcccccccccccccCCcc-eeecc-----CceechhhHHHHhhcC--------CCCCCCCCCC
Q 045745 193 VSSECHCAVCKEAFELGNEA-REMPC-----KHIYHEDCILPWLKMR--------NSCPVCRQEL 243 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~-~~lpC-----~H~FH~~CI~~WL~~~--------~sCP~CR~~l 243 (351)
.+.+..|-||...=++.-.. =+-|| .|-.|..||..|+..+ .+||.|+.+.
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 34567899999876643222 34465 3889999999999421 2599999864
No 112
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=84.41 E-value=0.45 Score=35.85 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=21.9
Q ss_pred ecccCCceeecCcCCCCCccCCCCCCC-ceEeecc
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCHGG-FIEQIET 46 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~~G-FvEEi~~ 46 (351)
=|+.|.+.+... .-+||.|++. |.||-..
T Consensus 6 AC~~Ck~l~~~d-----~e~CP~Cgs~~~te~W~G 35 (64)
T COG2093 6 ACKNCKRLTPED-----TEICPVCGSTDLTEEWFG 35 (64)
T ss_pred HHhhccccCCCC-----CccCCCCCCcccchhhcc
Confidence 399999876433 4689999996 8887654
No 113
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.01 E-value=0.97 Score=39.10 Aligned_cols=36 Identities=19% Similarity=0.285 Sum_probs=26.2
Q ss_pred CceecccCCceeecCc----------------CC--CCCccCCCCCCCceEeec
Q 045745 10 ESFWCYRCLRIVSSLS----------------QF--DGDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~----------------~~--~~~~~CP~C~~GFvEEi~ 45 (351)
..|||..|...+.... ++ .....||.|++.-++-+.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 6799999998887751 00 135779999998777553
No 114
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=83.67 E-value=0.55 Score=51.13 Aligned_cols=52 Identities=21% Similarity=0.662 Sum_probs=39.0
Q ss_pred CCcccccccccccccCCcceeeccC-----ceechhhHHHHhhcC--CCCCCCCCCCCcc
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCK-----HIYHEDCILPWLKMR--NSCPVCRQELPAA 246 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~-----H~FH~~CI~~WL~~~--~sCP~CR~~l~~~ 246 (351)
+++..|-||.-+=..++ +.-=||+ ...|.+|+..|+.-. ..|-+|+.++...
T Consensus 10 ~d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk 68 (1175)
T COG5183 10 EDKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFK 68 (1175)
T ss_pred ccchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeee
Confidence 34578999998866644 4566776 468999999999744 3699999977543
No 115
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.31 E-value=1.1 Score=45.03 Aligned_cols=47 Identities=28% Similarity=0.444 Sum_probs=40.8
Q ss_pred CCCcccccccccccccCCcceeeccCceechhhHHHHhhcCC---CCCCC
Q 045745 193 VSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN---SCPVC 239 (351)
Q Consensus 193 ~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~---sCP~C 239 (351)
..+-..|+|=++.-.+...+..|.|||+..++=|.+-.+... .||.|
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYC 380 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYC 380 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCC
Confidence 445678999999988888999999999999999999876544 69999
No 116
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=81.88 E-value=0.6 Score=47.61 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=31.0
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhhc
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM 232 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~ 232 (351)
+++..|+||...|++ +++|||+|..|..|...-|.+
T Consensus 2 eeelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFYRE---PIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhccC---ceEeecccHHHHHHHHhhccc
Confidence 456789999999986 899999999999999876643
No 117
>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=81.61 E-value=1.2 Score=29.73 Aligned_cols=29 Identities=31% Similarity=0.701 Sum_probs=22.8
Q ss_pred CceecccCCceeecCcCC--CCCccCCCCCC
Q 045745 10 ESFWCYRCLRIVSSLSQF--DGDTTCPHCHG 38 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~--~~~~~CP~C~~ 38 (351)
..|.|-.|...+.+.... ...+.||.|++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 579999999977665421 46789999998
No 118
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.21 E-value=0.82 Score=42.44 Aligned_cols=40 Identities=28% Similarity=0.690 Sum_probs=28.8
Q ss_pred ccccccccccCCcceeeccCce-echhhHHHHhhcCCCCCCCCCCCCc
Q 045745 199 CAVCKEAFELGNEAREMPCKHI-YHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~-FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
|-+|.+. +..|..+||.|. +|..|=.. -.+||+|+.....
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhhc
Confidence 7777665 345899999865 88999554 3459999886543
No 119
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.99 E-value=1.3 Score=44.87 Aligned_cols=38 Identities=18% Similarity=0.521 Sum_probs=28.0
Q ss_pred cccccccccc-cccCCcceeeccCceechhhHHHHhhcC
Q 045745 196 ECHCAVCKEA-FELGNEAREMPCKHIYHEDCILPWLKMR 233 (351)
Q Consensus 196 ~~~C~ICle~-~~~g~~~~~lpC~H~FH~~CI~~WL~~~ 233 (351)
..+|.||..+ ....+.....-|.|.||.+|+...++.+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~ 184 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK 184 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence 4689999944 4443444456699999999999988643
No 120
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.04 E-value=1.5 Score=37.43 Aligned_cols=36 Identities=14% Similarity=0.076 Sum_probs=25.0
Q ss_pred CceecccCCceeecCcCCC--C--CccCCCCCCCceEeecc
Q 045745 10 ESFWCYRCLRIVSSLSQFD--G--DTTCPHCHGGFIEQIET 46 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~--~--~~~CP~C~~GFvEEi~~ 46 (351)
...|| .|.....+...+. - ...||.|++.-++-+..
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 57999 9998866542100 0 25799999998886643
No 121
>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=78.80 E-value=1.1 Score=27.87 Aligned_cols=23 Identities=35% Similarity=0.691 Sum_probs=19.0
Q ss_pred cccCCceeecCcCCCCCccCCCCCCCce
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCHGGFI 41 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~~GFv 41 (351)
|-.|...|... ...||+|+=-|.
T Consensus 3 CP~C~~~V~~~-----~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPES-----AKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchhh-----cCcCCCCCCCCc
Confidence 78899998666 489999998774
No 122
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.62 E-value=1.2 Score=40.34 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=27.8
Q ss_pred CCCceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 8 TTESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 8 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
....|.|-.|.+.++...--+.++.||.|++-.+|
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 34689999999888765322578999999998777
No 123
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=78.48 E-value=1.1 Score=48.49 Aligned_cols=26 Identities=27% Similarity=0.835 Sum_probs=22.6
Q ss_pred eeeccCceechhhHHHHhhcCCCCCC
Q 045745 213 REMPCKHIYHEDCILPWLKMRNSCPV 238 (351)
Q Consensus 213 ~~lpC~H~FH~~CI~~WL~~~~sCP~ 238 (351)
.-..|+|+-|.+|...|+.....||.
T Consensus 1044 ~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1044 FCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred hhccccccccHHHHHHHHhcCCcCCC
Confidence 33459999999999999999999984
No 124
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=76.82 E-value=2.5 Score=29.64 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=26.1
Q ss_pred ceecccCCceeecCcCCCCCccCCCCCCCceEe
Q 045745 11 SFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 11 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
.|-|-.|...|.+.. .+.+.||+|+.-.|=.
T Consensus 2 ~Y~C~~Cg~~~~~~~--~~~irC~~CG~rIlyK 32 (44)
T smart00659 2 IYICGECGRENEIKS--KDVVRCRECGYRILYK 32 (44)
T ss_pred EEECCCCCCEeecCC--CCceECCCCCceEEEE
Confidence 499999999999885 4789999999876643
No 125
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=75.71 E-value=1.6 Score=39.90 Aligned_cols=26 Identities=23% Similarity=0.669 Sum_probs=20.1
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
.-|||-.|+-.+.. -.|+-|+++|-|
T Consensus 13 ~iyWCe~cNlPl~~-------~~c~~cg~~~~~ 38 (202)
T COG5270 13 PIYWCEKCNLPLLG-------RRCSVCGSKVEE 38 (202)
T ss_pred ceeehhhCCCcccc-------ccccccCCcceE
Confidence 46999999987643 469999976644
No 126
>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=75.64 E-value=1.9 Score=41.92 Aligned_cols=47 Identities=26% Similarity=0.523 Sum_probs=34.5
Q ss_pred cccccccccccCCccee--eccCceechhhHHHHhhcCC-CCCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEARE--MPCKHIYHEDCILPWLKMRN-SCPVCRQELP 244 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~--lpC~H~FH~~CI~~WL~~~~-sCP~CR~~l~ 244 (351)
.|++|+-.--....++. =+|+|..|..|++..+.... -||.|-..+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 59999876433332332 36999999999999986555 7999977653
No 127
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.95 E-value=1.5 Score=47.82 Aligned_cols=52 Identities=10% Similarity=0.181 Sum_probs=39.2
Q ss_pred ccccccccccccC-Ccceeec---cCceechhhHHHHhhc------CCCCCCCCCCCCcchh
Q 045745 197 CHCAVCKEAFELG-NEAREMP---CKHIYHEDCILPWLKM------RNSCPVCRQELPAAAA 248 (351)
Q Consensus 197 ~~C~ICle~~~~g-~~~~~lp---C~H~FH~~CI~~WL~~------~~sCP~CR~~l~~~~~ 248 (351)
..|.||.-++... |..-.+| |.|.||..||..|+.+ +-.|++|..-|..+..
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR 158 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR 158 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh
Confidence 5788888888762 2344556 9999999999999843 3468999887776653
No 128
>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=73.49 E-value=3.6 Score=26.90 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=21.5
Q ss_pred eecccCCceeecCcCCCCCccCCCCCCCce
Q 045745 12 FWCYRCLRIVSSLSQFDGDTTCPHCHGGFI 41 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~~~~~~CP~C~~GFv 41 (351)
|-|-.|...|.+... +.+.||+|+.-.|
T Consensus 1 Y~C~~Cg~~~~~~~~--~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKPG--DPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BSTS--STSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCCC--CcEECCcCCCeEE
Confidence 789999999997764 7899999986543
No 129
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.76 E-value=2.7 Score=30.29 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=25.4
Q ss_pred CCceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 9 TESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 9 ~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
+..|-|-.|.+.|.+. +....+.||+|++-.|=
T Consensus 4 ~~~Y~C~~Cg~~~~~~-~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 4 MMEYKCARCGREVELD-QETRGIRCPYCGSRILV 36 (49)
T ss_pred eEEEEhhhcCCeeehh-hccCceeCCCCCcEEEE
Confidence 4579999999999533 22579999999986543
No 130
>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=72.27 E-value=1.8 Score=38.40 Aligned_cols=38 Identities=16% Similarity=0.335 Sum_probs=27.6
Q ss_pred CCCceecccCCceeecCcCCCCCccCCCCCCCceEeecc
Q 045745 8 TTESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIET 46 (351)
Q Consensus 8 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~~ 46 (351)
...-|.|-.|...++...--+.++.||.|++- ++++++
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~-L~~~dn 143 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAMELNFTCPRCGAM-LDYLDN 143 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE-eeeccC
Confidence 35779999999887765322568999999987 444443
No 131
>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=72.11 E-value=4.4 Score=28.67 Aligned_cols=35 Identities=26% Similarity=0.549 Sum_probs=25.2
Q ss_pred CceecccCCceeecCcC--CCCCccCCCCCCCceEee
Q 045745 10 ESFWCYRCLRIVSSLSQ--FDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~--~~~~~~CP~C~~GFvEEi 44 (351)
..|.|-.|...+.++.. .+..+.||.|++.=++.+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 46999999996666532 135678999999655555
No 132
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=71.77 E-value=2.6 Score=45.78 Aligned_cols=39 Identities=21% Similarity=0.479 Sum_probs=30.3
Q ss_pred ccccccccccccCCcceeec--cCceechhhHHHHhhcCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMP--CKHIYHEDCILPWLKMRNSCPV 238 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lp--C~H~FH~~CI~~WL~~~~sCP~ 238 (351)
..|.||...+.. +..-+ |+|.-|.+|+.+|+..+.-||.
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 368888777653 22222 9999999999999999888876
No 133
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=71.73 E-value=2.6 Score=36.58 Aligned_cols=49 Identities=27% Similarity=0.621 Sum_probs=36.3
Q ss_pred cccccccccccccCCcceee-c---cCceechhhHHHHhh---cCCCCCCCCCCCCcch
Q 045745 196 ECHCAVCKEAFELGNEAREM-P---CKHIYHEDCILPWLK---MRNSCPVCRQELPAAA 247 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~l-p---C~H~FH~~CI~~WL~---~~~sCP~CR~~l~~~~ 247 (351)
-.+|-||.|...+. +.| | |+-..|..|-...++ .+..||+|+..+.+..
T Consensus 80 lYeCnIC~etS~ee---~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 80 LYECNICKETSAEE---RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred ceeccCcccccchh---hcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 36899999987653 233 3 898888888766554 5668999999886654
No 134
>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=69.40 E-value=3.8 Score=26.31 Aligned_cols=38 Identities=24% Similarity=0.586 Sum_probs=25.4
Q ss_pred cccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
.|..|.+.+..++.. ...=+..||..| ..|..|...|.
T Consensus 1 ~C~~C~~~i~~~~~~-~~~~~~~~H~~C--------f~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELV-LRALGKVWHPEC--------FKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEE-EEeCCccccccC--------CCCcccCCcCc
Confidence 378888888764222 222368899888 56888877663
No 135
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=68.80 E-value=2.3 Score=25.67 Aligned_cols=23 Identities=22% Similarity=0.693 Sum_probs=17.4
Q ss_pred ecccCCceeecCcCCCCCccCCCCCCCc
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~~GF 40 (351)
||..|-..|.. +...||.|+..|
T Consensus 1 ~Cp~CG~~~~~-----~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED-----DAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC-----cCcchhhhCCcC
Confidence 68889887754 368899998653
No 136
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.46 E-value=2.6 Score=42.71 Aligned_cols=43 Identities=28% Similarity=0.599 Sum_probs=33.4
Q ss_pred ccccccccccccCCcceee--ccCceechhhHHHHhhcCCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREM--PCKHIYHEDCILPWLKMRNSCPVC 239 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~l--pC~H~FH~~CI~~WL~~~~sCP~C 239 (351)
..|+.|.-.++...-...+ .|+|.|+..|...|......|..|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 5799999887765534333 489999999999998888877655
No 137
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.41 E-value=3.3 Score=36.07 Aligned_cols=36 Identities=28% Similarity=0.601 Sum_probs=26.6
Q ss_pred CCCceecccCCceeecCc-----CCCCCccCCCCCCCceEe
Q 045745 8 TTESFWCYRCLRIVSSLS-----QFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 8 ~~~~ywCh~C~r~V~~~~-----~~~~~~~CP~C~~GFvEE 43 (351)
....|.|-.|.+.+.... +.++.+.||.|++-.++.
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 346899999999887632 123449999999877663
No 138
>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=63.95 E-value=8.5 Score=26.39 Aligned_cols=35 Identities=20% Similarity=0.499 Sum_probs=24.3
Q ss_pred CceecccCCceeecCc--CCCCCccCCCCCCCceEee
Q 045745 10 ESFWCYRCLRIVSSLS--QFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~--~~~~~~~CP~C~~GFvEEi 44 (351)
..|-|-.|...+.+.. .++..+.||.|++.=++.+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGSTEVRRV 40 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEEe
Confidence 5699999995544432 2257899999999555443
No 139
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.93 E-value=5 Score=41.27 Aligned_cols=36 Identities=22% Similarity=0.627 Sum_probs=30.7
Q ss_pred CcccccccccccccCCcceeeccCceechhhHHHHhhc
Q 045745 195 SECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM 232 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~ 232 (351)
...+|-||.+.+.. ....+.|+|.|+..|+...|+.
T Consensus 69 ~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 69 GDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred ccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 44789999999875 5778889999999999999853
No 140
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=63.60 E-value=3.3 Score=38.58 Aligned_cols=43 Identities=33% Similarity=0.756 Sum_probs=35.0
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
..|.+|.+..-.| ++-=.|+-.||..|+...+.....||.|-.
T Consensus 182 k~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 182 KNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 5799999986643 233348999999999999999999999944
No 141
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.37 E-value=2.8 Score=40.89 Aligned_cols=30 Identities=20% Similarity=0.689 Sum_probs=23.1
Q ss_pred cCceechhhHHHHhhc-------------CCCCCCCCCCCCcc
Q 045745 217 CKHIYHEDCILPWLKM-------------RNSCPVCRQELPAA 246 (351)
Q Consensus 217 C~H~FH~~CI~~WL~~-------------~~sCP~CR~~l~~~ 246 (351)
|.-.+|.+|+.+|+.. +-+||+||+.+.-.
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~ 367 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR 367 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence 6677889999998732 34699999987654
No 142
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=62.68 E-value=4.5 Score=27.48 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=22.2
Q ss_pred cccCCceeecCcCCCCCccCCCCCCCceEeec
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~ 45 (351)
|+.|++.+.+.+ +.|.+|+.-|-.+--
T Consensus 1 C~~C~~~~~l~~-----f~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLTG-----FKCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCcccccC-----eECCccCCccccccC
Confidence 889999877763 899999999987653
No 143
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=62.63 E-value=2 Score=46.33 Aligned_cols=48 Identities=19% Similarity=0.630 Sum_probs=37.8
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcCC---CCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN---SCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~---sCP~CR~~l~~~ 246 (351)
..+|.||+..+.. ...+.|-|.|+..|+..-|...+ .||+|+..+...
T Consensus 21 ~lEc~ic~~~~~~---p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVKE---PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hccCCceeEEeec---cchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 3589999999886 36778999999999988775444 699999765443
No 144
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=61.00 E-value=2.4 Score=45.02 Aligned_cols=39 Identities=28% Similarity=0.860 Sum_probs=25.3
Q ss_pred ccccccccc-----cccCCcceee-ccCceechhhHHHHhhcCCCCCCC
Q 045745 197 CHCAVCKEA-----FELGNEAREM-PCKHIYHEDCILPWLKMRNSCPVC 239 (351)
Q Consensus 197 ~~C~ICle~-----~~~g~~~~~l-pC~H~FH~~CI~~WL~~~~sCP~C 239 (351)
..|-+|... |+. +.++.. -|+++||+.|+.. ...-||.|
T Consensus 512 fiCe~Cq~~~iiyPF~~-~~~~rC~~C~avfH~~C~~r---~s~~CPrC 556 (580)
T KOG1829|consen 512 FICELCQHNDIIYPFET-RNTRRCSTCLAVFHKKCLRR---KSPCCPRC 556 (580)
T ss_pred eeeeeccCCCccccccc-ccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence 567788432 332 334444 4999999999654 33449999
No 145
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.95 E-value=3.1 Score=44.54 Aligned_cols=42 Identities=24% Similarity=0.628 Sum_probs=32.3
Q ss_pred ccccccccccccCC-cceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 197 CHCAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 197 ~~C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
..|.||+..|.... .++.|-|+|..|..|+..- -+.+|| |++
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 57999999886543 5677779999999999874 456788 644
No 146
>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=60.58 E-value=2.7 Score=31.02 Aligned_cols=28 Identities=29% Similarity=0.780 Sum_probs=18.1
Q ss_pred ceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 11 SFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 11 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
+|-|--|..=+.... .-+||+|+|+||.
T Consensus 26 SfECTFC~~C~e~~l----~~~CPNCgGelv~ 53 (57)
T PF06906_consen 26 SFECTFCADCAETML----NGVCPNCGGELVR 53 (57)
T ss_pred eEeCcccHHHHHHHh----cCcCcCCCCcccc
Confidence 455555544443332 4689999999985
No 147
>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=57.31 E-value=2.7 Score=32.48 Aligned_cols=43 Identities=28% Similarity=0.526 Sum_probs=25.7
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
..|++|..+++... +|.++..|-.. ++....||-|..+|..-.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~Le~Lk 44 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPLEVLK 44 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-EEEE
T ss_pred CcCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHHHHHH
Confidence 57999999988532 67888888664 455668999998875543
No 148
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=56.93 E-value=4.9 Score=38.72 Aligned_cols=47 Identities=23% Similarity=0.604 Sum_probs=33.2
Q ss_pred ccccccccccc-cCCcceeec---cCceechhhHHHHhh-c--------CCCCCCCCCCC
Q 045745 197 CHCAVCKEAFE-LGNEAREMP---CKHIYHEDCILPWLK-M--------RNSCPVCRQEL 243 (351)
Q Consensus 197 ~~C~ICle~~~-~g~~~~~lp---C~H~FH~~CI~~WL~-~--------~~sCP~CR~~l 243 (351)
.+|-+|.+++. .+......+ |.-.+|..|+..-+. . ...||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 58999999994 433333332 889999999999442 1 33699998844
No 149
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.56 E-value=5.9 Score=38.53 Aligned_cols=37 Identities=22% Similarity=0.393 Sum_probs=29.3
Q ss_pred ccccccccccccCCcceeec--cCceechhhHHHHhhcCC
Q 045745 197 CHCAVCKEAFELGNEAREMP--CKHIYHEDCILPWLKMRN 234 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lp--C~H~FH~~CI~~WL~~~~ 234 (351)
..|.+|.|.+|+ .+-++.| =.|+||..|-+.-+|.+.
T Consensus 269 LcCTLC~ERLED-THFVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 269 LCCTLCHERLED-THFVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred eeehhhhhhhcc-CceeecCCCcccceecccCHHHHHhhc
Confidence 689999999997 3344555 369999999999998654
No 150
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=56.53 E-value=6.3 Score=36.29 Aligned_cols=39 Identities=31% Similarity=0.971 Sum_probs=28.0
Q ss_pred cccccccccc-----cccCCcceeec-cCceechhhHHHHhhcCCCCCCCC
Q 045745 196 ECHCAVCKEA-----FELGNEAREMP-CKHIYHEDCILPWLKMRNSCPVCR 240 (351)
Q Consensus 196 ~~~C~ICle~-----~~~g~~~~~lp-C~H~FH~~CI~~WL~~~~sCP~CR 240 (351)
...|-||.+. |.. +.+...+ |+-+||+.|..+ ..||-|-
T Consensus 152 GfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~~-----~~CpkC~ 196 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFRK-----KSCPKCA 196 (202)
T ss_pred CCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcCC-----CCCCCcH
Confidence 3578889753 333 2455566 999999999762 6799994
No 151
>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=56.44 E-value=5 Score=38.15 Aligned_cols=46 Identities=28% Similarity=0.658 Sum_probs=35.0
Q ss_pred cccccccccccccCCcceee--c-cCceechhhHHHHhhcCC-CCC--CCCC
Q 045745 196 ECHCAVCKEAFELGNEAREM--P-CKHIYHEDCILPWLKMRN-SCP--VCRQ 241 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~l--p-C~H~FH~~CI~~WL~~~~-sCP--~CR~ 241 (351)
+..|+||..+.-..-.++.| | |-|..|..|+++.+.... .|| -|-.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 45799999886554444444 5 999999999999997655 799 7744
No 152
>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=56.12 E-value=8.9 Score=29.85 Aligned_cols=33 Identities=18% Similarity=0.671 Sum_probs=16.5
Q ss_pred ceecccCCceeecCcCCCCCccCCCCCCCceEeeccC
Q 045745 11 SFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQIETE 47 (351)
Q Consensus 11 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi~~~ 47 (351)
-++||.|-...... .-..||.|+..=|..+.-.
T Consensus 9 vlrC~aCf~~t~~~----~k~FCp~CGn~TL~rvsvs 41 (73)
T PF08772_consen 9 VLRCHACFKITKDM----TKQFCPKCGNATLKRVSVS 41 (73)
T ss_dssp EEE-SSS--EES-S----S--S-SSS--S--EEEE-B
T ss_pred eEEccccccCcCCC----CceeCcccCCCcceEEEEE
Confidence 36899999887754 3699999999988888543
No 153
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.93 E-value=5.9 Score=24.35 Aligned_cols=23 Identities=22% Similarity=0.713 Sum_probs=16.9
Q ss_pred eecccCCceeecCcCCCCCccCCCCCCC
Q 045745 12 FWCYRCLRIVSSLSQFDGDTTCPHCHGG 39 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~~~~~~CP~C~~G 39 (351)
..|..|...|.. ++-.||+|+..
T Consensus 3 ~~Cp~Cg~~~~~-----~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-----DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-----ccccChhhCCC
Confidence 478999985422 47899999864
No 154
>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=52.81 E-value=9.9 Score=27.57 Aligned_cols=41 Identities=29% Similarity=0.673 Sum_probs=20.9
Q ss_pred ccccccccccCC------cceeec-cCceechhhHHHHhhcCCCCCCC
Q 045745 199 CAVCKEAFELGN------EAREMP-CKHIYHEDCILPWLKMRNSCPVC 239 (351)
Q Consensus 199 C~ICle~~~~g~------~~~~lp-C~H~FH~~CI~~WL~~~~sCP~C 239 (351)
|.-|+..|.... ....-| |++.|+.+|=.--=+.=..||-|
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC 49 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGC 49 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCC
Confidence 666777776542 234445 99999999943322333469988
No 155
>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=52.65 E-value=6.9 Score=25.87 Aligned_cols=30 Identities=17% Similarity=0.434 Sum_probs=22.2
Q ss_pred eecccCCceeecCcCC----CCCccCCCCCCCce
Q 045745 12 FWCYRCLRIVSSLSQF----DGDTTCPHCHGGFI 41 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~----~~~~~CP~C~~GFv 41 (351)
+-|-.|...+.+.... ...+.||.|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4588899988887521 23589999998774
No 156
>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=52.43 E-value=4 Score=29.20 Aligned_cols=42 Identities=24% Similarity=0.636 Sum_probs=21.8
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcC---C--CCCCCCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMR---N--SCPVCRQ 241 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~---~--sCP~CR~ 241 (351)
..|+|....++. .++...|.|.-+.+ +..||+.. . .||+|.+
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence 468888888774 46777799996543 55666432 2 5999975
No 157
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=52.11 E-value=5.6 Score=43.53 Aligned_cols=45 Identities=24% Similarity=0.543 Sum_probs=33.2
Q ss_pred cccccccccccc-cC---CcceeeccCceechhhHHHHhhcCCCCCCCCC
Q 045745 196 ECHCAVCKEAFE-LG---NEAREMPCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 196 ~~~C~ICle~~~-~g---~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
+..|.-|.+..- .+ +.++++-|+|.||+.|+.--..+++ |-.|-.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~ 832 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESG 832 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhc
Confidence 457999988654 23 4678889999999999988766555 666643
No 158
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=51.71 E-value=14 Score=26.15 Aligned_cols=39 Identities=21% Similarity=0.482 Sum_probs=28.1
Q ss_pred ccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 199 CAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 199 C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
|..|.+.+..++ .....-+..||..| .+|-.|...|...
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~H~~C--------f~C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFWHPEC--------FKCSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEEETTT--------SBETTTTCBTTTS
T ss_pred CCCCCCCccCcE-EEEEeCCcEEEccc--------cccCCCCCccCCC
Confidence 778888887533 22235778999988 5789998887654
No 159
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=51.66 E-value=13 Score=26.08 Aligned_cols=31 Identities=23% Similarity=0.567 Sum_probs=21.8
Q ss_pred ecccCCceeecCcCCC-CCccCCCCCCCceEeec
Q 045745 13 WCYRCLRIVSSLSQFD-GDTTCPHCHGGFIEQIE 45 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~-~~~~CP~C~~GFvEEi~ 45 (351)
||-.|...+....... ...+||.|+ |++.++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 7899988776664322 368999998 566554
No 160
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=51.15 E-value=14 Score=36.57 Aligned_cols=48 Identities=25% Similarity=0.435 Sum_probs=39.2
Q ss_pred CCCCcccccccccccccCCcceeeccCceechhhHHHHhhc---CCCCCCC
Q 045745 192 HVSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKM---RNSCPVC 239 (351)
Q Consensus 192 ~~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~---~~sCP~C 239 (351)
+..+-..|+|=.+.-.....+..|.|+|+.-+.-++..-+. ...||.|
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYC 382 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYC 382 (396)
T ss_pred cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCC
Confidence 44556789999999888888999999999999998886543 2369999
No 161
>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 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=50.04 E-value=9.6 Score=26.10 Aligned_cols=32 Identities=25% Similarity=0.546 Sum_probs=20.1
Q ss_pred eecccCCceeecCcCCCCCccCCCCCCCceEee
Q 045745 12 FWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEEi 44 (351)
|.|-.|.....+.....++++|+.| |--|||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~C-G~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNC-GLVLEEN 32 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT--BBEE-T
T ss_pred CCCcCCcCCceEEcCCCCeEECCCC-CCEeecc
Confidence 5688888765333333688999999 4444544
No 163
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=49.64 E-value=12 Score=37.06 Aligned_cols=49 Identities=22% Similarity=0.465 Sum_probs=35.9
Q ss_pred ccccccccccccCC-cceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..|+||.+.....+ ...-.||++.-|..|+..-...+.+||.||.....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYER 299 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcccc
Confidence 67999999874433 33334478887888888877888899999965443
No 164
>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=49.16 E-value=24 Score=26.12 Aligned_cols=47 Identities=26% Similarity=0.518 Sum_probs=34.6
Q ss_pred ccccccccccccCC-cceeeccCceechhhHHHHhhcCCCCCCCCCCCCc
Q 045745 197 CHCAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPA 245 (351)
Q Consensus 197 ~~C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~ 245 (351)
..|-.|-.++..+. ++.+..=...|+.+|...-| ++.||.|--+|..
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 35778888887755 45554434679999999866 7899999776643
No 165
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.06 E-value=8 Score=37.90 Aligned_cols=52 Identities=25% Similarity=0.528 Sum_probs=40.1
Q ss_pred CCCCCcccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 191 GHVSSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 191 ~~~~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
........|-||.-.+...+ +.-.|.|.|+..|...|....+-||.|+....
T Consensus 100 ~~~~~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~ 151 (324)
T KOG0824|consen 100 GFQQDHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKIS 151 (324)
T ss_pred cccCCccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCcC
Confidence 34445578999998877522 22239999999999999999999999987553
No 166
>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=47.65 E-value=11 Score=26.22 Aligned_cols=42 Identities=31% Similarity=0.711 Sum_probs=26.6
Q ss_pred cccccccccccCCcceeec-cCceechhhHHHHhhc------CCCCCCCC
Q 045745 198 HCAVCKEAFELGNEAREMP-CKHIYHEDCILPWLKM------RNSCPVCR 240 (351)
Q Consensus 198 ~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL~~------~~sCP~CR 240 (351)
.|.||...... +..+.-. |...||..|+..=+.. .-.||.|+
T Consensus 1 ~C~vC~~~~~~-~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDD-GDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTT-SSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCC-CCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 38899994333 2333333 9999999998765431 22577664
No 167
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=45.22 E-value=21 Score=35.38 Aligned_cols=51 Identities=29% Similarity=0.711 Sum_probs=35.7
Q ss_pred cccccccccccc-----cCCc-----------ceeeccCceechhhHHHHhhc---------CCCCCCCCCCCCcc
Q 045745 196 ECHCAVCKEAFE-----LGNE-----------AREMPCKHIYHEDCILPWLKM---------RNSCPVCRQELPAA 246 (351)
Q Consensus 196 ~~~C~ICle~~~-----~g~~-----------~~~lpC~H~FH~~CI~~WL~~---------~~sCP~CR~~l~~~ 246 (351)
+.+|++|+.+=. .|.+ -..-||+|+--.+-..-|-+. |..||.|-..|..+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 578999998621 1111 123479999999999999753 34699998777554
No 168
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=44.44 E-value=17 Score=26.07 Aligned_cols=35 Identities=23% Similarity=0.478 Sum_probs=26.2
Q ss_pred Cceecc--cCCceeecCc-CCCCCccCCCCCCCceEee
Q 045745 10 ESFWCY--RCLRIVSSLS-QFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 10 ~~ywCh--~C~r~V~~~~-~~~~~~~CP~C~~GFvEEi 44 (351)
..=||- .|...|.... .....+.||.|+--|--.-
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C 54 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRC 54 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCC
Confidence 345999 9999988862 2367899999998876443
No 169
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=44.32 E-value=5.9 Score=38.70 Aligned_cols=38 Identities=24% Similarity=0.569 Sum_probs=29.6
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhhcCC
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRN 234 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~ 234 (351)
.+|.+|+++|+.+.......|.-+||..|+..|+....
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTGA 252 (288)
T ss_pred eecHHHHHHHhcccccchhhcccccccccccccccccc
Confidence 48999999998766666666666999999999986554
No 170
>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=43.91 E-value=25 Score=23.47 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=25.9
Q ss_pred ceecccCCceeecCcC-CCCCccCCCCCCCceEe
Q 045745 11 SFWCYRCLRIVSSLSQ-FDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 11 ~ywCh~C~r~V~~~~~-~~~~~~CP~C~~GFvEE 43 (351)
+.-|-.|.+..++.-. +..+-+|..|++.+|+.
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 3568899999998643 36789999999987764
No 171
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.19 E-value=15 Score=27.64 Aligned_cols=20 Identities=25% Similarity=0.514 Sum_probs=14.3
Q ss_pred eecCcCCCCCccCCCCCCCc
Q 045745 21 VSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 21 V~~~~~~~~~~~CP~C~~GF 40 (351)
|.+.+..+++++||+|+--|
T Consensus 39 V~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 39 VFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred EEEEcCCCCcEecCccccEE
Confidence 34444447899999998655
No 172
>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=42.88 E-value=13 Score=26.62 Aligned_cols=11 Identities=55% Similarity=1.219 Sum_probs=6.6
Q ss_pred CccCCCCCCCc
Q 045745 30 DTTCPHCHGGF 40 (351)
Q Consensus 30 ~~~CP~C~~GF 40 (351)
.+.||+|+.+|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 45666666644
No 173
>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=42.19 E-value=24 Score=28.43 Aligned_cols=41 Identities=24% Similarity=0.587 Sum_probs=33.0
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHHhhcCCCCCCCCCCCCcchh
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAAA 248 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~~ 248 (351)
-..|.-|...+.--|.+= |..||..+..|..|+++|+..-.
T Consensus 33 rS~C~~C~~~L~~~~lIP------------i~S~l~lrGrCr~C~~~I~~~y~ 73 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP------------ILSYLLLRGRCRYCGAPIPPRYP 73 (92)
T ss_pred CCcCcCCCCcCcccccch------------HHHHHHhCCCCcccCCCCChHHH
Confidence 368999999988655332 78999999999999999987643
No 174
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=41.75 E-value=23 Score=26.53 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=21.6
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCC
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGG 39 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~G 39 (351)
..+.|-.|.+.|..... ...+.||+|+.-
T Consensus 6 ~~~~CtSCg~~i~~~~~-~~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGIEIAPREK-AVKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCCcccCCCc-cCEeeCCCCCCe
Confidence 34789999998876542 468999999763
No 175
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=40.83 E-value=16 Score=23.97 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=20.7
Q ss_pred eecccCCceeec-CcCCCCCccCCCCCCCc
Q 045745 12 FWCYRCLRIVSS-LSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 12 ywCh~C~r~V~~-~~~~~~~~~CP~C~~GF 40 (351)
+-|..|....-. .. ++..+|+.|+.-|
T Consensus 4 ~~C~~C~~~~i~~~~--~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKE--DDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEec--CCeEEcccCCcEe
Confidence 558889988766 33 5789999998754
No 176
>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=40.58 E-value=18 Score=30.27 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=22.9
Q ss_pred CceecccCCc-eeecCcCCCCCccCCCCCCCceEe
Q 045745 10 ESFWCYRCLR-IVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 10 ~~ywCh~C~r-~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
.-.-|..|-. |+-+.. .-++||+|+.-|--+
T Consensus 8 tKR~Cp~CG~kFYDLnk---~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK---DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCC---CCccCCCCCCccCcc
Confidence 3467999964 555555 468899999988776
No 177
>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=40.17 E-value=14 Score=28.21 Aligned_cols=12 Identities=17% Similarity=0.844 Sum_probs=8.7
Q ss_pred eechhhHHHHhh
Q 045745 220 IYHEDCILPWLK 231 (351)
Q Consensus 220 ~FH~~CI~~WL~ 231 (351)
-||..||.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999984
No 178
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.11 E-value=8.8 Score=29.92 Aligned_cols=29 Identities=24% Similarity=0.658 Sum_probs=18.6
Q ss_pred ceecccCCceeecCcCCCCCccCCCCCCCceEe
Q 045745 11 SFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 11 ~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
+|-|--|.--..... +-+||+|+|+||-.
T Consensus 26 tfEcTFCadCae~~l----~g~CPnCGGelv~R 54 (84)
T COG3813 26 TFECTFCADCAENRL----HGLCPNCGGELVAR 54 (84)
T ss_pred EEeeehhHhHHHHhh----cCcCCCCCchhhcC
Confidence 455555544444333 46899999999863
No 179
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.36 E-value=16 Score=29.86 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=28.6
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHh
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWL 230 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL 230 (351)
-.|.||-+.+..|+.-...+ +-..|.+|+..=.
T Consensus 7 wkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~ 39 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESK 39 (103)
T ss_pred eeEeeeCCEeeeccEEEEee-CCcchHHHHHHHH
Confidence 57999999999999877777 8899999998743
No 180
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.91 E-value=38 Score=28.55 Aligned_cols=44 Identities=23% Similarity=0.486 Sum_probs=32.1
Q ss_pred ccccccccccccCC----------cceeec-cCceechhhHHHHhhcCCCCCCCC
Q 045745 197 CHCAVCKEAFELGN----------EAREMP-CKHIYHEDCILPWLKMRNSCPVCR 240 (351)
Q Consensus 197 ~~C~ICle~~~~g~----------~~~~lp-C~H~FH~~CI~~WL~~~~sCP~CR 240 (351)
..|.-|+..|.... ..-.-+ |++.|+.+|=.-|-+.=..||-|-
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 35999998886421 112234 999999999888877767799995
No 181
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.47 E-value=13 Score=38.25 Aligned_cols=37 Identities=22% Similarity=0.454 Sum_probs=28.4
Q ss_pred ccccccccccccCC-----cceeeccCceechhhHHHHhhcC
Q 045745 197 CHCAVCKEAFELGN-----EAREMPCKHIYHEDCILPWLKMR 233 (351)
Q Consensus 197 ~~C~ICle~~~~g~-----~~~~lpC~H~FH~~CI~~WL~~~ 233 (351)
..|+.|+..++... .....+|+|.||..|+..|....
T Consensus 227 k~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 227 KECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred ccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 35999999988765 22333599999999999997654
No 182
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=38.10 E-value=18 Score=27.56 Aligned_cols=19 Identities=32% Similarity=0.849 Sum_probs=14.8
Q ss_pred cccCCceeecCcCCCCCccCCCCCCC
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCHGG 39 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~~G 39 (351)
|..|++-+ . +-+||.|++.
T Consensus 8 C~~C~~i~---~----~~~Cp~Cgs~ 26 (64)
T PRK06393 8 CKKCKRLT---P----EKTCPVHGDE 26 (64)
T ss_pred HhhCCccc---C----CCcCCCCCCC
Confidence 88898877 1 3499999983
No 183
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=37.21 E-value=29 Score=34.51 Aligned_cols=45 Identities=20% Similarity=0.513 Sum_probs=31.2
Q ss_pred cccccccccccccCCcceeec-cCceechhhHHHHhhcCCCCCCCCC
Q 045745 196 ECHCAVCKEAFELGNEAREMP-CKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
...|-.|.++..... ....+ |+|.||.+|=.---+.=..||-|-.
T Consensus 330 ~~~Cf~C~~~~~~~~-~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGELLSSG-RYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CcceeeeccccCCCC-cEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 345999977776543 33444 9999999995543344457999964
No 184
>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=36.82 E-value=18 Score=26.84 Aligned_cols=35 Identities=17% Similarity=0.503 Sum_probs=17.3
Q ss_pred cccccccccccccCCcceeec-cCceechhhHHHHh
Q 045745 196 ECHCAVCKEAFELGNEAREMP-CKHIYHEDCILPWL 230 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lp-C~H~FH~~CI~~WL 230 (351)
...|.+|...|..-..-..-. ||++|+.+|....+
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 358999999997532222222 99999999987654
No 185
>PRK10220 hypothetical protein; Provisional
Probab=36.40 E-value=28 Score=29.23 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=20.0
Q ss_pred cccCCceeecCcCCCCCccCCCCCCCceEe
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
|-+|+-...-... ..++||.|..-+-.+
T Consensus 6 CP~C~seytY~d~--~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYEDN--GMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEcCC--CeEECCcccCcCCcc
Confidence 7788877666653 678888888766544
No 186
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=35.76 E-value=17 Score=24.11 Aligned_cols=28 Identities=18% Similarity=0.339 Sum_probs=19.5
Q ss_pred ecccCCceeecCcC---C-CCCccCCCCCCCc
Q 045745 13 WCYRCLRIVSSLSQ---F-DGDTTCPHCHGGF 40 (351)
Q Consensus 13 wCh~C~r~V~~~~~---~-~~~~~CP~C~~GF 40 (351)
-|.+|+....+... + ...+.|+.|+--|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 47888888777642 1 4568898887654
No 187
>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=35.43 E-value=23 Score=36.14 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=22.5
Q ss_pred ecccCCceeecCcCC-CCCccCCCCCCCce
Q 045745 13 WCYRCLRIVSSLSQF-DGDTTCPHCHGGFI 41 (351)
Q Consensus 13 wCh~C~r~V~~~~~~-~~~~~CP~C~~GFv 41 (351)
=||.|+.-++....+ .+...||.|+.-..
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 499999988776432 46788999998764
No 188
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.98 E-value=8.4 Score=37.03 Aligned_cols=47 Identities=21% Similarity=0.480 Sum_probs=38.2
Q ss_pred cccccccccccccC---Ccceeec--------cCceechhhHHHHhhcCC-CCCCCCCC
Q 045745 196 ECHCAVCKEAFELG---NEAREMP--------CKHIYHEDCILPWLKMRN-SCPVCRQE 242 (351)
Q Consensus 196 ~~~C~ICle~~~~g---~~~~~lp--------C~H~FH~~CI~~WL~~~~-sCP~CR~~ 242 (351)
+..|.||...|... ...+++. |+|..+..|+..-+.... .||.|+..
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 35799999999842 2566777 999999999999987655 89999874
No 189
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=33.83 E-value=23 Score=26.63 Aligned_cols=19 Identities=32% Similarity=0.829 Sum_probs=14.3
Q ss_pred ecccCCceeecCcCCCCCccCCCCCC
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCHG 38 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~~ 38 (351)
=|-.|++-+ . +-+||.|++
T Consensus 5 AC~~C~~i~--~-----~~~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYIT--T-----EDRCPVCGS 23 (61)
T ss_pred hhhhCCccc--C-----CCcCCCCcC
Confidence 388898877 1 237999998
No 190
>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=33.27 E-value=9.9 Score=36.73 Aligned_cols=45 Identities=24% Similarity=0.418 Sum_probs=21.3
Q ss_pred cccccccccccccCCcceee---ccCceechhhHHHHhhcCCCCCCCCC
Q 045745 196 ECHCAVCKEAFELGNEAREM---PCKHIYHEDCILPWLKMRNSCPVCRQ 241 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~l---pC~H~FH~~CI~~WL~~~~sCP~CR~ 241 (351)
...|+||-..=..+. ++.- -=.|.+|.-|-..|-..+..||.|-.
T Consensus 172 ~g~CPvCGs~P~~s~-l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSV-LRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEE-EE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CCcCCCCCCcCceEE-EecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 368999977532210 0000 12588899999999888899999955
No 191
>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=32.12 E-value=13 Score=26.65 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=7.9
Q ss_pred CCCCCCCCCCcchh
Q 045745 235 SCPVCRQELPAAAA 248 (351)
Q Consensus 235 sCP~CR~~l~~~~~ 248 (351)
.||+|..+|..+..
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999877654
No 192
>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=31.94 E-value=28 Score=24.92 Aligned_cols=29 Identities=31% Similarity=0.737 Sum_probs=16.3
Q ss_pred eeccc--CCceeecCcCCCC-CccCCCCCCCc
Q 045745 12 FWCYR--CLRIVSSLSQFDG-DTTCPHCHGGF 40 (351)
Q Consensus 12 ywCh~--C~r~V~~~~~~~~-~~~CP~C~~GF 40 (351)
-||-. |...+........ .++|+.|+--|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 39988 9999988875322 28999998766
No 193
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.26 E-value=30 Score=28.85 Aligned_cols=19 Identities=37% Similarity=0.704 Sum_probs=14.2
Q ss_pred eeecCcCCCCCccCCCCCCCce
Q 045745 20 IVSSLSQFDGDTTCPHCHGGFI 41 (351)
Q Consensus 20 ~V~~~~~~~~~~~CP~C~~GFv 41 (351)
+|.+.. +...||.|+.+|=
T Consensus 42 yV~ie~---G~t~CP~Cg~~~e 60 (115)
T COG1885 42 YVEIEV---GSTSCPKCGEPFE 60 (115)
T ss_pred eEEEec---ccccCCCCCCccc
Confidence 455555 5889999998873
No 194
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=30.91 E-value=39 Score=34.16 Aligned_cols=30 Identities=27% Similarity=0.599 Sum_probs=22.2
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCce
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFI 41 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFv 41 (351)
--|+|+.|..+...... ..-.||+|++.++
T Consensus 243 ~~~~C~~c~~~~~~~~~--~~~~C~~c~~~~~ 272 (382)
T PRK04338 243 YVYYCPKCLYREEVEGL--PPEECPVCGGKFG 272 (382)
T ss_pred eEEECCCCCcEEEecCC--CCCCCCCCCCcce
Confidence 46899999998765432 3468999988655
No 195
>PRK12495 hypothetical protein; Provisional
Probab=30.79 E-value=28 Score=32.72 Aligned_cols=32 Identities=28% Similarity=0.553 Sum_probs=25.6
Q ss_pred CCCceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 8 TTESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 8 ~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
++..|+|-.|...|-.. .+.++||.|+.-+-+
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 45779999999998844 379999999965554
No 196
>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=30.60 E-value=39 Score=24.76 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=23.7
Q ss_pred eecccCCceeecCcCC-CCCccCCCCCCCce
Q 045745 12 FWCYRCLRIVSSLSQF-DGDTTCPHCHGGFI 41 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~-~~~~~CP~C~~GFv 41 (351)
+-|-.|...|.+.... ...+.||.|+--|-
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 5799999999886543 56789999987653
No 197
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=30.43 E-value=31 Score=24.45 Aligned_cols=35 Identities=20% Similarity=0.526 Sum_probs=24.1
Q ss_pred ccccccccccccCCcceee-ccCceechhhHHHHhh
Q 045745 197 CHCAVCKEAFELGNEAREM-PCKHIYHEDCILPWLK 231 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~l-pC~H~FH~~CI~~WL~ 231 (351)
..|.+|...|..-..-... .|+++|+..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 4799999888763322222 3899999999776543
No 198
>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=29.95 E-value=17 Score=29.41 Aligned_cols=24 Identities=29% Similarity=0.613 Sum_probs=14.3
Q ss_pred ecccCCceeecCcCC--------------CCCccCCCC
Q 045745 13 WCYRCLRIVSSLSQF--------------DGDTTCPHC 36 (351)
Q Consensus 13 wCh~C~r~V~~~~~~--------------~~~~~CP~C 36 (351)
.|+.|++.|++.... +=.++||.|
T Consensus 54 ~C~~C~~~lrl~V~as~~~Ir~lq~LLl~~L~lvCp~C 91 (92)
T PF00527_consen 54 CCGRCGKRLRLVVVASHEGIRTLQQLLLGDLSLVCPPC 91 (92)
T ss_dssp EBTTT--EEEEEEEC-HHHHHHHHHHHHCT-EE--CCC
T ss_pred ECCCCCCEEEEEEEeChhhHHHHHHHhhcCceEeCCCC
Confidence 599999999986532 337889888
No 199
>PHA02776 E7 protein; Provisional
Probab=29.84 E-value=25 Score=29.09 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=19.5
Q ss_pred ecccCCceeecCcCC--------------CCCccCCCCCC
Q 045745 13 WCYRCLRIVSSLSQF--------------DGDTTCPHCHG 38 (351)
Q Consensus 13 wCh~C~r~V~~~~~~--------------~~~~~CP~C~~ 38 (351)
-|+.|.+.|++.... +=.++||.|..
T Consensus 60 ~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~ 99 (101)
T PHA02776 60 CCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAP 99 (101)
T ss_pred ECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCC
Confidence 499999999886522 23789999964
No 200
>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=29.75 E-value=21 Score=24.08 Aligned_cols=12 Identities=17% Similarity=0.794 Sum_probs=5.5
Q ss_pred CceecccCCcee
Q 045745 10 ESFWCYRCLRIV 21 (351)
Q Consensus 10 ~~ywCh~C~r~V 21 (351)
++|||--|+..|
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 579999999988
No 201
>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=29.04 E-value=25 Score=23.54 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=8.9
Q ss_pred CCccCCCCCCC
Q 045745 29 GDTTCPHCHGG 39 (351)
Q Consensus 29 ~~~~CP~C~~G 39 (351)
-++.||+|++.
T Consensus 4 i~v~CP~C~s~ 14 (36)
T PF03811_consen 4 IDVHCPRCQST 14 (36)
T ss_pred EeeeCCCCCCC
Confidence 36899999974
No 202
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.71 E-value=26 Score=23.29 Aligned_cols=27 Identities=22% Similarity=0.498 Sum_probs=17.9
Q ss_pred cccCCceeecCcC----CCCCccCCCCCCCc
Q 045745 14 CYRCLRIVSSLSQ----FDGDTTCPHCHGGF 40 (351)
Q Consensus 14 Ch~C~r~V~~~~~----~~~~~~CP~C~~GF 40 (351)
|-.|.....+... ....+.||.|+--|
T Consensus 5 CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred CCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 6777777776542 14577888887655
No 203
>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=28.49 E-value=73 Score=23.56 Aligned_cols=32 Identities=16% Similarity=0.312 Sum_probs=20.0
Q ss_pred Cccccccccccccc--CCcceeec-cCceechhhH
Q 045745 195 SECHCAVCKEAFEL--GNEAREMP-CKHIYHEDCI 226 (351)
Q Consensus 195 ~~~~C~ICle~~~~--g~~~~~lp-C~H~FH~~CI 226 (351)
....|+.|-...+. .......| |++.+|.|-.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcHHH
Confidence 34579999988776 33344444 6666666543
No 204
>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=28.37 E-value=33 Score=25.32 Aligned_cols=15 Identities=47% Similarity=1.028 Sum_probs=12.2
Q ss_pred CCceecccCCceeec
Q 045745 9 TESFWCYRCLRIVSS 23 (351)
Q Consensus 9 ~~~ywCh~C~r~V~~ 23 (351)
+.+.|||.|+.+|..
T Consensus 47 ~~~i~C~~C~~~v~~ 61 (63)
T PF02148_consen 47 TGSIWCYACDDYVYD 61 (63)
T ss_dssp TTCEEETTTTEEEES
T ss_pred CCeEEEcCCCcEEeC
Confidence 356899999999864
No 205
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=28.24 E-value=38 Score=34.78 Aligned_cols=29 Identities=21% Similarity=0.502 Sum_probs=22.2
Q ss_pred eecccCCceeecCcCC-CCCccCCCCCCCc
Q 045745 12 FWCYRCLRIVSSLSQF-DGDTTCPHCHGGF 40 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~-~~~~~CP~C~~GF 40 (351)
-=||.|+.-++....+ .+...||.|+.-.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 3499999998876532 4567899999876
No 206
>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=27.96 E-value=41 Score=28.10 Aligned_cols=46 Identities=33% Similarity=0.606 Sum_probs=28.0
Q ss_pred CcccccccccccccCC-cceee-ccCceechhhHHHHhhcCC--CCCCCCC
Q 045745 195 SECHCAVCKEAFELGN-EAREM-PCKHIYHEDCILPWLKMRN--SCPVCRQ 241 (351)
Q Consensus 195 ~~~~C~ICle~~~~g~-~~~~l-pC~H~FH~~CI~~WL~~~~--sCP~CR~ 241 (351)
++..|.+|...|..-. ..... .|+|.+|..|-.. ..... .|-+|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 4568999999875432 22333 3999999999665 21122 4888854
No 207
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=27.17 E-value=33 Score=37.71 Aligned_cols=46 Identities=30% Similarity=0.637 Sum_probs=29.3
Q ss_pred Ccccccccccccc----cCCc-----ceeec-cCceechhhHHHHhhcCCCCCCCCCCCC
Q 045745 195 SECHCAVCKEAFE----LGNE-----AREMP-CKHIYHEDCILPWLKMRNSCPVCRQELP 244 (351)
Q Consensus 195 ~~~~C~ICle~~~----~g~~-----~~~lp-C~H~FH~~CI~~WL~~~~sCP~CR~~l~ 244 (351)
.+.+|+-|.-.|- .|.. .=..| |+|.-|..=|.+ ++.||+|...+.
T Consensus 1130 ~~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a~~~EIs~----y~~CPLCHs~~~ 1185 (1189)
T KOG2041|consen 1130 YDLQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRAHQHEISK----YNCCPLCHSMES 1185 (1189)
T ss_pred cCCCChhhcCcCceeeccCCccccceEEEccccccccccccccc----cccCccccChhh
Confidence 3456777766653 1211 11234 999999887765 689999977543
No 208
>PRK13794 hypothetical protein; Provisional
Probab=27.05 E-value=33 Score=35.81 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=20.9
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCC-ceEeec
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGG-FIEQIE 45 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~G-FvEEi~ 45 (351)
.-|||-.|+-+|-- -.|..|+.. |-=.|.
T Consensus 9 ~~~wc~~cn~p~~~-------~~c~~cg~~~~~~~~~ 38 (479)
T PRK13794 9 HLKWCDNCNVPVLG-------KKCAICGSETREVKVT 38 (479)
T ss_pred EEEEcCCCCCeecC-------CchhHhCCCeeEEecC
Confidence 36999999998743 359999985 433443
No 209
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.84 E-value=35 Score=21.56 Aligned_cols=22 Identities=32% Similarity=0.904 Sum_probs=13.7
Q ss_pred eecccCCceeecCcCCCCCccCCCCC
Q 045745 12 FWCYRCLRIVSSLSQFDGDTTCPHCH 37 (351)
Q Consensus 12 ywCh~C~r~V~~~~~~~~~~~CP~C~ 37 (351)
|||-.|.+.+...- -..|-.|.
T Consensus 1 ~~C~~C~~~~~~~~----~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY----FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE----eEEeCCCC
Confidence 67888877665541 25666665
No 210
>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=26.80 E-value=46 Score=28.70 Aligned_cols=31 Identities=10% Similarity=0.002 Sum_probs=23.0
Q ss_pred CceecccCCc-eeecCcCCCCCccCCCCCCCceEe
Q 045745 10 ESFWCYRCLR-IVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 10 ~~ywCh~C~r-~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
..+-|..|.. |+-+.. .-++||+|+.-|-.+
T Consensus 8 tKr~Cp~cg~kFYDLnk---~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNR---RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccccccCC---CCccCCCcCCccCcc
Confidence 4567999965 455554 579999999887655
No 211
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=25.90 E-value=34 Score=35.17 Aligned_cols=22 Identities=41% Similarity=0.711 Sum_probs=18.5
Q ss_pred ccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 15 YRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 15 h~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
|.|.|.|++. ..||.|+.-|--
T Consensus 286 HrC~RIV~vE------YrCPEC~KVFsC 307 (500)
T KOG3993|consen 286 HRCPRIVHVE------YRCPECDKVFSC 307 (500)
T ss_pred ccCCeeEEee------ecCCcccccccC
Confidence 8899988765 899999998854
No 212
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=25.90 E-value=31 Score=28.03 Aligned_cols=34 Identities=15% Similarity=0.393 Sum_probs=21.7
Q ss_pred cccccccccccccCCcceeeccCceechhhHHHH
Q 045745 196 ECHCAVCKEAFELGNEAREMPCKHIYHEDCILPW 229 (351)
Q Consensus 196 ~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~W 229 (351)
...|.||....-.--....-.|...||..|...+
T Consensus 55 ~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 55 KLKCSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 3589999998221001111228889999998764
No 213
>PRK03922 hypothetical protein; Provisional
Probab=25.33 E-value=45 Score=28.04 Aligned_cols=19 Identities=37% Similarity=0.644 Sum_probs=14.4
Q ss_pred ceeecCcCCCCCccCCCCCCCc
Q 045745 19 RIVSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 19 r~V~~~~~~~~~~~CP~C~~GF 40 (351)
.+|.+.. +...||.|+..|
T Consensus 41 ~yVeiev---G~~~cP~cge~~ 59 (113)
T PRK03922 41 DYVEVEV---GLTICPKCGEPF 59 (113)
T ss_pred CeEEEec---CcccCCCCCCcC
Confidence 3566665 589999999766
No 214
>PF14353 CpXC: CpXC protein
Probab=25.14 E-value=42 Score=28.15 Aligned_cols=18 Identities=39% Similarity=0.763 Sum_probs=15.5
Q ss_pred CccCCCCCCCceEeeccC
Q 045745 30 DTTCPHCHGGFIEQIETE 47 (351)
Q Consensus 30 ~~~CP~C~~GFvEEi~~~ 47 (351)
+++||+|+.-|--++...
T Consensus 1 ~itCP~C~~~~~~~v~~~ 18 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTS 18 (128)
T ss_pred CcCCCCCCCeeEEEEEeE
Confidence 479999999999998764
No 215
>PLN02189 cellulose synthase
Probab=24.84 E-value=56 Score=37.30 Aligned_cols=48 Identities=19% Similarity=0.438 Sum_probs=33.8
Q ss_pred cccccccccccc---CCcceeec-cCceechhhHHHHhh-cCCCCCCCCCCCC
Q 045745 197 CHCAVCKEAFEL---GNEAREMP-CKHIYHEDCILPWLK-MRNSCPVCRQELP 244 (351)
Q Consensus 197 ~~C~ICle~~~~---g~~~~~lp-C~H~FH~~CI~~WL~-~~~sCP~CR~~l~ 244 (351)
..|.||-|++.. |+.-+-.. |+--.|..|.+-=-+ .+++||.|+....
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 489999999763 23223333 778899999865443 4668999988654
No 216
>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=24.76 E-value=65 Score=20.85 Aligned_cols=24 Identities=17% Similarity=0.470 Sum_probs=18.6
Q ss_pred ecccCCceeecCcCCCCCccCCCCC
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCH 37 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~ 37 (351)
+|+.|+.....-.. ...+.|..|+
T Consensus 3 ~C~~C~t~L~yP~g-A~~vrCs~C~ 26 (31)
T TIGR01053 3 VCGGCRTLLMYPRG-ASSVRCALCQ 26 (31)
T ss_pred CcCCCCcEeecCCC-CCeEECCCCC
Confidence 69999988766543 5689999996
No 217
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=24.71 E-value=57 Score=35.36 Aligned_cols=50 Identities=30% Similarity=0.551 Sum_probs=29.2
Q ss_pred CCcccccccccccccCCcceeeccCceechhhHHHHhh-cC---C--CCCCCCCCCCcch
Q 045745 194 SSECHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLK-MR---N--SCPVCRQELPAAA 247 (351)
Q Consensus 194 ~~~~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~-~~---~--sCP~CR~~l~~~~ 247 (351)
.-...|+|++-.+.. .++-+.|+|+=|.+= .|+. .+ . .||+|-+....+.
T Consensus 304 ~vSL~CPl~~~Rm~~--P~r~~~CkHlQcFD~--~~~lq~n~~~pTW~CPVC~~~~~~e~ 359 (636)
T KOG2169|consen 304 RVSLNCPLSKMRMSL--PARGHTCKHLQCFDA--LSYLQMNEQKPTWRCPVCQKAAPFEG 359 (636)
T ss_pred eeEecCCcccceeec--CCcccccccceecch--hhhHHhccCCCeeeCccCCccccccc
Confidence 344679998877553 244555666544432 3432 21 1 4999988776654
No 218
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.63 E-value=31 Score=22.85 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=8.5
Q ss_pred ecccCCceeecCcCC---CCCccCCCCC
Q 045745 13 WCYRCLRIVSSLSQF---DGDTTCPHCH 37 (351)
Q Consensus 13 wCh~C~r~V~~~~~~---~~~~~CP~C~ 37 (351)
||-+|-..+.....+ -.-.+||.|+
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 455555554443321 2234555554
No 219
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.53 E-value=26 Score=21.34 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=10.3
Q ss_pred CccCCCCCCCceE
Q 045745 30 DTTCPHCHGGFIE 42 (351)
Q Consensus 30 ~~~CP~C~~GFvE 42 (351)
-+.||.|+--|.+
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 3679999998864
No 220
>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=24.31 E-value=41 Score=34.34 Aligned_cols=24 Identities=21% Similarity=0.663 Sum_probs=18.3
Q ss_pred ecccCCceeecCcCCCCCccCCCCCCCc
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~~GF 40 (351)
=||.|+..+.. .+...||.|+.-.
T Consensus 217 ~C~~Cd~~~~~----~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTILP----AQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCccCC----CCCcCCcCCCCcc
Confidence 49999996633 2468899999866
No 221
>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 KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=23.96 E-value=47 Score=32.92 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=20.6
Q ss_pred CCCCceecccCCceeecCcCCCCCccCCCCCCCce
Q 045745 7 TTTESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFI 41 (351)
Q Consensus 7 ~~~~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFv 41 (351)
++++.-+||.|...- ...+||.|+--..
T Consensus 3 pts~~~~C~ic~vq~-------~~YtCPRCn~~YC 30 (383)
T KOG4317|consen 3 PTSSFLACGICGVQK-------REYTCPRCNLLYC 30 (383)
T ss_pred CCCceeecccccccc-------ccccCCCCCccce
Confidence 455778999998633 2599999986553
No 223
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.94 E-value=53 Score=23.87 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=14.1
Q ss_pred ccCCCCCCCceEeeccCc
Q 045745 31 TTCPHCHGGFIEQIETEV 48 (351)
Q Consensus 31 ~~CP~C~~GFvEEi~~~~ 48 (351)
+.||+|+..|-=.|+...
T Consensus 1 i~CPyCge~~~~~iD~s~ 18 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSA 18 (52)
T ss_pred CCCCCCCCeeEEEEecCC
Confidence 579999998877776553
No 224
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.83 E-value=67 Score=25.12 Aligned_cols=47 Identities=26% Similarity=0.588 Sum_probs=31.6
Q ss_pred ccccccccccCC-cceeeccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 199 CAVCKEAFELGN-EAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 199 C~ICle~~~~g~-~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
|--|-.++-.+. .+++..=.|.||.+|... +.+..||.|--+|....
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~--~l~g~CPnCGGelv~RP 55 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAEN--RLHGLCPNCGGELVARP 55 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHH--hhcCcCCCCCchhhcCc
Confidence 555666665433 334433458999999886 35789999988776554
No 225
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=23.56 E-value=82 Score=24.93 Aligned_cols=49 Identities=20% Similarity=0.382 Sum_probs=20.5
Q ss_pred cccccccccccccCC--cce--eeccCceechhhHHHHhh-cCCCCCCCCCCCC
Q 045745 196 ECHCAVCKEAFELGN--EAR--EMPCKHIYHEDCILPWLK-MRNSCPVCRQELP 244 (351)
Q Consensus 196 ~~~C~ICle~~~~g~--~~~--~lpC~H~FH~~CI~~WL~-~~~sCP~CR~~l~ 244 (351)
...|-||-|++.... ++- -..|.--.|+.|..-=.+ .++.||.|+....
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 358999999875433 222 223888889999887665 5668999986543
No 226
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.55 E-value=63 Score=31.08 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=28.0
Q ss_pred ccccccccccccCCcceeeccCceechhhHHHHhh
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYHEDCILPWLK 231 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH~~CI~~WL~ 231 (351)
..|+.||.-+.. +++.|=+|+|+.+||...+.
T Consensus 44 dcCsLtLqPc~d---Pvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 44 DCCSLTLQPCRD---PVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ceeeeecccccC---CccCCCCeeeeHHHHHHHHH
Confidence 579999998875 78888999999999999863
No 227
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=22.40 E-value=54 Score=27.08 Aligned_cols=19 Identities=37% Similarity=0.709 Sum_probs=14.1
Q ss_pred ceeecCcCCCCCccCCCCCCCc
Q 045745 19 RIVSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 19 r~V~~~~~~~~~~~CP~C~~GF 40 (351)
.+|.+.. +...||.|+..|
T Consensus 39 ~~VeIev---G~~~cP~Cge~~ 57 (102)
T PF04475_consen 39 DYVEIEV---GDTICPKCGEEL 57 (102)
T ss_pred CeEEEec---CcccCCCCCCcc
Confidence 4566665 589999999654
No 228
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=22.22 E-value=58 Score=33.07 Aligned_cols=29 Identities=31% Similarity=0.665 Sum_probs=20.2
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCc
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGF 40 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GF 40 (351)
..|+|-.|. .+.... .+.+-.||+|++-|
T Consensus 239 ~~~~c~~cg-~~~~~~-~~~~~~c~~Cg~~~ 267 (380)
T COG1867 239 YIYHCSRCG-EIVGSF-REVDEKCPHCGGKV 267 (380)
T ss_pred cEEEccccc-ceeccc-ccccccCCcccccc
Confidence 469999998 332222 25789999999833
No 229
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=22.11 E-value=39 Score=33.13 Aligned_cols=32 Identities=28% Similarity=0.477 Sum_probs=21.0
Q ss_pred ecccCCceee--cCcCCCCCccCCCCCCCceEee
Q 045745 13 WCYRCLRIVS--SLSQFDGDTTCPHCHGGFIEQI 44 (351)
Q Consensus 13 wCh~C~r~V~--~~~~~~~~~~CP~C~~GFvEEi 44 (351)
||+.|.+.=. +.....++.+|+.|+--|=+.+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~ 35 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRI 35 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeecccc
Confidence 7888887533 2222378999999986544433
No 230
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.03 E-value=24 Score=32.08 Aligned_cols=33 Identities=24% Similarity=0.428 Sum_probs=25.0
Q ss_pred CceecccCCceeecCcCCCCCccCCCCCCCceE
Q 045745 10 ESFWCYRCLRIVSSLSQFDGDTTCPHCHGGFIE 42 (351)
Q Consensus 10 ~~ywCh~C~r~V~~~~~~~~~~~CP~C~~GFvE 42 (351)
.-|-|-.|.-.++.-..-...++||.|++-..|
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred CceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 458899998888776433567999999986443
No 231
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=21.97 E-value=92 Score=19.29 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=16.8
Q ss_pred cccCCceeecCcCCCCCccCCCCC
Q 045745 14 CYRCLRIVSSLSQFDGDTTCPHCH 37 (351)
Q Consensus 14 Ch~C~r~V~~~~~~~~~~~CP~C~ 37 (351)
|..|+..+.-... ...+.|..|+
T Consensus 1 C~~Cr~~L~yp~G-A~sVrCa~C~ 23 (25)
T PF06943_consen 1 CGGCRTLLMYPRG-APSVRCACCH 23 (25)
T ss_pred CCCCCceEEcCCC-CCCeECCccC
Confidence 7788887665432 5689999997
No 232
>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=21.94 E-value=74 Score=22.16 Aligned_cols=34 Identities=21% Similarity=0.363 Sum_probs=21.8
Q ss_pred Cccccccccccc--ccCCcceeeccCceechhhHHH
Q 045745 195 SECHCAVCKEAF--ELGNEAREMPCKHIYHEDCILP 228 (351)
Q Consensus 195 ~~~~C~ICle~~--~~g~~~~~lpC~H~FH~~CI~~ 228 (351)
....|.+|.+.+ ...+..+=.-|+-.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 446899999998 2222233334999999999765
No 233
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=21.29 E-value=54 Score=29.09 Aligned_cols=17 Identities=24% Similarity=0.544 Sum_probs=13.8
Q ss_pred ccCCCCCCCceEeeccC
Q 045745 31 TTCPHCHGGFIEQIETE 47 (351)
Q Consensus 31 ~~CP~C~~GFvEEi~~~ 47 (351)
+.||+|++.+.+-+++-
T Consensus 1 m~cp~c~~~~~~~~~s~ 17 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSR 17 (154)
T ss_pred CcCCCCCCCCCEeEecc
Confidence 47999999998877653
No 234
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.81 E-value=1.3e+02 Score=29.39 Aligned_cols=9 Identities=22% Similarity=0.829 Sum_probs=6.6
Q ss_pred CCCCCCCCC
Q 045745 234 NSCPVCRQE 242 (351)
Q Consensus 234 ~sCP~CR~~ 242 (351)
..||.|...
T Consensus 270 ~~C~~Cgt~ 278 (279)
T TIGR00627 270 PICKTCKTA 278 (279)
T ss_pred CCCCCCCCC
Confidence 478888764
No 235
>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=20.60 E-value=53 Score=22.74 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=9.2
Q ss_pred CCccCCCCCCC
Q 045745 29 GDTTCPHCHGG 39 (351)
Q Consensus 29 ~~~~CP~C~~G 39 (351)
+.++||+|++-
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 45899999986
No 236
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=20.51 E-value=53 Score=26.97 Aligned_cols=28 Identities=25% Similarity=0.653 Sum_probs=19.2
Q ss_pred ecccCCceeecCcCCCCCccCCCCCCCceEe
Q 045745 13 WCYRCLRIVSSLSQFDGDTTCPHCHGGFIEQ 43 (351)
Q Consensus 13 wCh~C~r~V~~~~~~~~~~~CP~C~~GFvEE 43 (351)
=|..|..-+.... -..-.||+|+ +|++-
T Consensus 5 AC~~C~~I~~~~q--f~~~gCpnC~-~~l~~ 32 (98)
T cd07973 5 ACLLCSLIKTEDQ--FERDGCPNCE-GYLDM 32 (98)
T ss_pred hhccCCccccccc--ccCCCCCCCc-chhcc
Confidence 3888988775432 1357899998 67653
No 237
>PLN02248 cellulose synthase-like protein
Probab=20.45 E-value=86 Score=36.14 Aligned_cols=37 Identities=19% Similarity=0.453 Sum_probs=29.1
Q ss_pred cceeeccCceechhhHHHHhhcCCCCCCCCCCCCcch
Q 045745 211 EAREMPCKHIYHEDCILPWLKMRNSCPVCRQELPAAA 247 (351)
Q Consensus 211 ~~~~lpC~H~FH~~CI~~WL~~~~sCP~CR~~l~~~~ 247 (351)
.+.-..|.+..|.+|..--++....||-|+.+....+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (1135)
T PLN02248 144 DLLPCECGFKICRDCYIDAVKSGGICPGCKEPYKVTD 180 (1135)
T ss_pred cCCcccccchhHHhHhhhhhhcCCCCCCCcccccccc
Confidence 3333448899999999999999889999998875443
No 238
>PRK05978 hypothetical protein; Provisional
Probab=20.36 E-value=55 Score=28.93 Aligned_cols=23 Identities=17% Similarity=0.654 Sum_probs=18.7
Q ss_pred ceechhhHHHHhhcCCCCCCCCCCCCcc
Q 045745 219 HIYHEDCILPWLKMRNSCPVCRQELPAA 246 (351)
Q Consensus 219 H~FH~~CI~~WL~~~~sCP~CR~~l~~~ 246 (351)
|.|+ .+|+.+..||+|-.++...
T Consensus 43 ~LF~-----g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 43 KLFR-----AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cccc-----cccccCCCccccCCccccC
Confidence 6665 7899999999998887654
No 239
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.20 E-value=28 Score=30.42 Aligned_cols=51 Identities=20% Similarity=0.509 Sum_probs=28.7
Q ss_pred CCCCcccccccccc-cccCCcceeeccCceechhhHHHHh-hcCC---CCCCCCCC
Q 045745 192 HVSSECHCAVCKEA-FELGNEAREMPCKHIYHEDCILPWL-KMRN---SCPVCRQE 242 (351)
Q Consensus 192 ~~~~~~~C~ICle~-~~~g~~~~~lpC~H~FH~~CI~~WL-~~~~---sCP~CR~~ 242 (351)
.+..+..|.||+.. |.+|---.-.-|.-.||..|--+-- +.+. .|-+|+..
T Consensus 61 Gv~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 61 GVGDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred ccCcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 34567899999984 5554211112255556666655542 2222 48888664
No 240
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.19 E-value=53 Score=31.08 Aligned_cols=26 Identities=19% Similarity=0.601 Sum_probs=19.9
Q ss_pred ccccccccccccCCcceeeccCceec
Q 045745 197 CHCAVCKEAFELGNEAREMPCKHIYH 222 (351)
Q Consensus 197 ~~C~ICle~~~~g~~~~~lpC~H~FH 222 (351)
..|+||...+...+.....+.+|.|-
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~fd 28 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQFD 28 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCCc
Confidence 47999999998766555666788883
No 241
>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=20.15 E-value=43 Score=23.01 Aligned_cols=12 Identities=25% Similarity=0.899 Sum_probs=9.9
Q ss_pred CccCCCCCCCce
Q 045745 30 DTTCPHCHGGFI 41 (351)
Q Consensus 30 ~~~CP~C~~GFv 41 (351)
.+.||+|+--|+
T Consensus 29 ~~~CpYCg~~yv 40 (40)
T PF10276_consen 29 PVVCPYCGTRYV 40 (40)
T ss_dssp EEEETTTTEEEE
T ss_pred eEECCCCCCEEC
Confidence 499999997765
No 242
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.10 E-value=48 Score=23.73 Aligned_cols=14 Identities=36% Similarity=1.039 Sum_probs=10.8
Q ss_pred ccCCCCCCCceEee
Q 045745 31 TTCPHCHGGFIEQI 44 (351)
Q Consensus 31 ~~CP~C~~GFvEEi 44 (351)
..||.|+++|+..-
T Consensus 21 ~fCP~Cg~~~m~~~ 34 (50)
T PRK00432 21 KFCPRCGSGFMAEH 34 (50)
T ss_pred CcCcCCCcchhecc
Confidence 48999998866544
No 243
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=20.02 E-value=72 Score=34.11 Aligned_cols=35 Identities=26% Similarity=0.687 Sum_probs=24.0
Q ss_pred Cccccccccccccc-----CC-----cceeeccCceechhhHHHH
Q 045745 195 SECHCAVCKEAFEL-----GN-----EAREMPCKHIYHEDCILPW 229 (351)
Q Consensus 195 ~~~~C~ICle~~~~-----g~-----~~~~lpC~H~FH~~CI~~W 229 (351)
....|+||.|.|+. .+ .++.+.=+-+||..|+..=
T Consensus 512 ~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~ 556 (579)
T KOG2071|consen 512 RQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEK 556 (579)
T ss_pred cccCCcccccccceeecchhhheeecceeeeccCceeeccccchH
Confidence 34679999999863 11 2334445889999998653
Done!