Query 028040
Match_columns 215
No_of_seqs 217 out of 697
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:19:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028040.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028040hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3970 Predicted E3 ubiquitin 100.0 3.7E-60 8.1E-65 415.3 7.0 156 1-165 1-159 (299)
2 PF13639 zf-RING_2: Ring finge 99.4 1.3E-13 2.8E-18 91.1 2.0 43 53-105 2-44 (44)
3 KOG4628 Predicted E3 ubiquitin 99.3 3.4E-12 7.4E-17 118.2 6.1 52 52-112 230-281 (348)
4 PF12678 zf-rbx1: RING-H2 zinc 99.0 5.3E-10 1.1E-14 82.0 4.4 56 39-105 10-73 (73)
5 COG5540 RING-finger-containing 99.0 2.7E-10 5.9E-15 104.5 3.4 51 52-111 324-374 (374)
6 COG5243 HRD1 HRD ubiquitin lig 98.9 1.9E-09 4.1E-14 101.3 6.8 51 52-110 288-347 (491)
7 cd00162 RING RING-finger (Real 98.8 4.3E-09 9.2E-14 66.4 4.1 45 53-108 1-45 (45)
8 PHA02929 N1R/p28-like protein; 98.8 4.8E-09 1E-13 93.0 4.5 50 52-109 175-227 (238)
9 PF12861 zf-Apc11: Anaphase-pr 98.7 1.7E-08 3.7E-13 77.3 4.3 52 52-108 22-81 (85)
10 KOG0802 E3 ubiquitin ligase [P 98.7 8E-09 1.7E-13 99.8 2.7 54 52-113 292-345 (543)
11 PLN03208 E3 ubiquitin-protein 98.6 4.1E-08 8.8E-13 85.0 4.8 55 52-111 19-81 (193)
12 smart00184 RING Ring finger. E 98.5 8.3E-08 1.8E-12 58.4 3.3 39 54-104 1-39 (39)
13 PF00097 zf-C3HC4: Zinc finger 98.5 5.4E-08 1.2E-12 62.7 2.5 41 54-104 1-41 (41)
14 PF13923 zf-C3HC4_2: Zinc fing 98.5 6.1E-08 1.3E-12 62.6 2.2 39 54-104 1-39 (39)
15 PF15227 zf-C3HC4_4: zinc fing 98.5 1.1E-07 2.3E-12 63.3 3.2 42 54-104 1-42 (42)
16 PF13920 zf-C3HC4_3: Zinc fing 98.4 2.4E-07 5.1E-12 62.7 3.1 45 52-109 3-48 (50)
17 KOG0317 Predicted E3 ubiquitin 98.4 1.4E-07 3.1E-12 85.7 2.4 48 52-112 240-287 (293)
18 COG5194 APC11 Component of SCF 98.4 3.3E-07 7.1E-12 70.0 3.3 48 52-109 32-81 (88)
19 smart00504 Ubox Modified RING 98.3 1.2E-06 2.7E-11 60.5 5.1 46 52-110 2-47 (63)
20 KOG0823 Predicted E3 ubiquitin 98.3 5.5E-07 1.2E-11 79.7 3.2 53 44-110 44-96 (230)
21 PF14634 zf-RING_5: zinc-RING 98.2 1.4E-06 3.1E-11 57.7 3.4 44 53-106 1-44 (44)
22 PF13445 zf-RING_UBOX: RING-ty 98.2 1E-06 2.3E-11 59.3 2.6 43 54-102 1-43 (43)
23 smart00744 RINGv The RING-vari 98.1 2E-06 4.3E-11 59.1 3.3 44 53-105 1-49 (49)
24 PHA02926 zinc finger-like prot 98.1 1.5E-06 3.2E-11 77.2 2.5 55 52-109 171-230 (242)
25 KOG1493 Anaphase-promoting com 98.0 1.1E-06 2.4E-11 66.7 0.3 50 52-107 21-79 (84)
26 PF11793 FANCL_C: FANCL C-term 98.0 6.7E-07 1.5E-11 65.4 -0.9 56 52-109 3-66 (70)
27 KOG0827 Predicted E3 ubiquitin 97.9 4.2E-06 9.2E-11 79.3 2.0 47 52-105 5-52 (465)
28 TIGR00599 rad18 DNA repair pro 97.9 2.3E-05 5.1E-10 74.2 6.0 49 50-111 25-73 (397)
29 KOG0828 Predicted E3 ubiquitin 97.8 6.7E-06 1.5E-10 79.9 1.6 52 51-110 571-635 (636)
30 KOG0804 Cytoplasmic Zn-finger 97.8 7.3E-06 1.6E-10 78.7 1.6 49 51-110 175-223 (493)
31 COG5574 PEX10 RING-finger-cont 97.8 1.3E-05 2.9E-10 72.4 2.4 49 52-112 216-265 (271)
32 KOG0320 Predicted E3 ubiquitin 97.8 1.5E-05 3.2E-10 68.8 2.4 47 52-109 132-178 (187)
33 KOG1734 Predicted RING-contain 97.7 7E-06 1.5E-10 74.9 -0.1 59 51-115 224-287 (328)
34 PF04564 U-box: U-box domain; 97.6 6.4E-05 1.4E-09 54.8 3.5 48 52-111 5-52 (73)
35 KOG1941 Acetylcholine receptor 97.6 3.3E-05 7E-10 73.7 2.5 47 52-105 366-412 (518)
36 KOG2164 Predicted E3 ubiquitin 97.5 7E-05 1.5E-09 72.8 2.9 53 51-111 186-238 (513)
37 KOG1940 Zn-finger protein [Gen 97.4 5.9E-05 1.3E-09 68.6 1.9 50 46-106 155-204 (276)
38 KOG1952 Transcription factor N 97.3 5.8E-05 1.3E-09 77.0 0.7 59 42-107 186-245 (950)
39 KOG0825 PHD Zn-finger protein 97.3 5.6E-05 1.2E-09 77.0 -0.4 75 52-136 124-199 (1134)
40 KOG4445 Uncharacterized conser 97.2 5E-05 1.1E-09 70.3 -0.9 68 40-110 105-187 (368)
41 KOG2177 Predicted E3 ubiquitin 97.2 0.00016 3.5E-09 59.1 1.6 43 51-106 13-55 (386)
42 COG5219 Uncharacterized conser 97.1 0.00015 3.2E-09 75.2 1.1 51 52-108 1470-1522(1525)
43 KOG2930 SCF ubiquitin ligase, 97.0 0.00049 1.1E-08 55.0 2.6 27 73-107 80-106 (114)
44 TIGR00570 cdk7 CDK-activating 96.8 0.0014 3E-08 60.7 4.1 51 52-111 4-56 (309)
45 PF10367 Vps39_2: Vacuolar sor 96.7 0.00059 1.3E-08 51.1 0.8 30 52-84 79-108 (109)
46 KOG1428 Inhibitor of type V ad 96.6 0.0014 3.1E-08 70.7 3.3 54 52-109 3487-3544(3738)
47 KOG1645 RING-finger-containing 96.6 0.0017 3.7E-08 62.2 3.5 50 52-108 5-55 (463)
48 KOG0287 Postreplication repair 96.2 0.0027 5.9E-08 60.0 2.5 87 52-162 24-110 (442)
49 PF14835 zf-RING_6: zf-RING of 96.1 0.0014 3E-08 48.2 0.0 46 52-112 8-54 (65)
50 PF11789 zf-Nse: Zinc-finger o 96.1 0.0039 8.4E-08 44.2 2.0 41 52-103 12-53 (57)
51 KOG0801 Predicted E3 ubiquitin 96.0 0.002 4.4E-08 55.5 0.5 64 15-80 134-204 (205)
52 KOG4265 Predicted E3 ubiquitin 96.0 0.0052 1.1E-07 57.7 3.2 48 51-111 290-338 (349)
53 KOG0978 E3 ubiquitin ligase in 95.9 0.0031 6.7E-08 63.8 1.2 49 51-111 643-691 (698)
54 COG5432 RAD18 RING-finger-cont 95.6 0.0078 1.7E-07 56.0 2.4 44 52-108 26-69 (391)
55 PF12906 RINGv: RING-variant d 95.3 0.0067 1.5E-07 41.2 0.7 42 54-104 1-47 (47)
56 PF05883 Baculo_RING: Baculovi 95.0 0.01 2.3E-07 49.1 1.3 34 52-87 27-66 (134)
57 KOG3268 Predicted E3 ubiquitin 94.9 0.014 3.1E-07 51.1 1.9 67 39-109 155-228 (234)
58 KOG1814 Predicted E3 ubiquitin 94.8 0.024 5.2E-07 54.5 3.2 72 53-136 186-257 (445)
59 KOG0311 Predicted E3 ubiquitin 94.5 0.011 2.3E-07 55.9 0.1 50 51-111 43-92 (381)
60 PHA02825 LAP/PHD finger-like p 94.4 0.046 1E-06 46.6 3.7 50 51-110 8-60 (162)
61 KOG4185 Predicted E3 ubiquitin 94.3 0.052 1.1E-06 48.2 4.1 50 52-108 4-54 (296)
62 KOG0824 Predicted E3 ubiquitin 94.3 0.021 4.6E-07 53.0 1.6 46 52-109 8-53 (324)
63 KOG1039 Predicted E3 ubiquitin 93.9 0.035 7.6E-07 52.1 2.3 56 51-108 161-220 (344)
64 PHA02862 5L protein; Provision 93.8 0.049 1.1E-06 46.0 2.7 47 52-110 3-54 (156)
65 KOG1002 Nucleotide excision re 93.7 0.038 8.2E-07 55.1 2.1 72 29-110 515-587 (791)
66 KOG1785 Tyrosine kinase negati 92.6 0.048 1E-06 52.8 1.0 48 53-111 371-418 (563)
67 KOG2114 Vacuolar assembly/sort 92.6 0.043 9.3E-07 56.8 0.7 40 52-106 841-880 (933)
68 KOG4172 Predicted E3 ubiquitin 92.5 0.038 8.3E-07 39.9 0.1 47 50-108 6-53 (62)
69 PF04641 Rtf2: Rtf2 RING-finge 92.1 0.28 6E-06 43.7 5.2 67 52-130 114-183 (260)
70 KOG2034 Vacuolar sorting prote 92.0 0.073 1.6E-06 55.3 1.5 36 52-90 818-853 (911)
71 KOG2660 Locus-specific chromos 91.9 0.043 9.3E-07 51.3 -0.3 48 52-111 16-63 (331)
72 KOG4159 Predicted E3 ubiquitin 91.5 0.11 2.5E-06 49.6 2.1 46 52-110 85-130 (398)
73 KOG2879 Predicted E3 ubiquitin 91.3 0.2 4.3E-06 46.2 3.3 50 51-110 239-288 (298)
74 PF14570 zf-RING_4: RING/Ubox 91.2 0.21 4.6E-06 34.7 2.7 45 54-108 1-47 (48)
75 KOG0297 TNF receptor-associate 90.5 0.21 4.5E-06 47.2 2.8 51 52-114 22-72 (391)
76 PF14447 Prok-RING_4: Prokaryo 89.8 0.15 3.2E-06 36.5 0.9 34 68-111 19-52 (55)
77 PF08746 zf-RING-like: RING-li 89.4 0.2 4.3E-06 33.5 1.3 43 54-104 1-43 (43)
78 smart00249 PHD PHD zinc finger 89.2 0.17 3.6E-06 31.8 0.8 46 53-104 1-47 (47)
79 KOG1571 Predicted E3 ubiquitin 89.0 0.19 4.1E-06 47.5 1.3 55 38-109 290-347 (355)
80 KOG3039 Uncharacterized conser 88.9 0.4 8.6E-06 44.0 3.2 49 52-110 222-271 (303)
81 PF07800 DUF1644: Protein of u 88.2 0.68 1.5E-05 39.6 4.0 54 52-110 3-92 (162)
82 KOG1813 Predicted E3 ubiquitin 88.1 0.29 6.4E-06 45.5 1.9 63 50-128 240-302 (313)
83 PF14446 Prok-RING_1: Prokaryo 87.9 0.61 1.3E-05 33.2 3.0 32 52-85 6-38 (54)
84 KOG0309 Conserved WD40 repeat- 87.7 0.36 7.7E-06 50.1 2.4 36 52-90 1029-1064(1081)
85 KOG2817 Predicted E3 ubiquitin 87.3 0.48 1E-05 45.4 2.9 51 51-108 334-384 (394)
86 KOG0827 Predicted E3 ubiquitin 85.0 0.08 1.7E-06 50.9 -3.5 49 52-109 197-245 (465)
87 KOG3800 Predicted E3 ubiquitin 83.4 1.1 2.3E-05 41.7 3.1 48 53-110 2-52 (300)
88 KOG3053 Uncharacterized conser 82.0 0.76 1.6E-05 42.3 1.5 60 51-113 20-89 (293)
89 COG5152 Uncharacterized conser 80.9 0.64 1.4E-05 41.5 0.7 47 51-110 196-242 (259)
90 KOG1609 Protein involved in mR 79.7 0.9 1.9E-05 39.8 1.2 53 52-111 79-136 (323)
91 COG5220 TFB3 Cdk activating ki 78.1 0.85 1.8E-05 41.8 0.6 47 51-106 10-61 (314)
92 PF05605 zf-Di19: Drought indu 77.9 1.8 4E-05 29.6 2.1 36 53-106 4-39 (54)
93 COG5236 Uncharacterized conser 77.3 2.1 4.6E-05 41.1 3.0 46 51-107 61-106 (493)
94 COG5222 Uncharacterized conser 77.3 1.4 3.1E-05 41.6 1.8 43 52-106 275-318 (427)
95 PF02891 zf-MIZ: MIZ/SP-RING z 76.0 3.4 7.3E-05 28.3 3.0 44 53-107 4-50 (50)
96 PF00628 PHD: PHD-finger; Int 74.0 0.12 2.6E-06 34.3 -4.5 47 54-105 2-49 (51)
97 PHA03096 p28-like protein; Pro 70.9 2.6 5.7E-05 38.7 1.9 39 52-90 179-220 (284)
98 TIGR00373 conserved hypothetic 69.9 3.9 8.4E-05 34.1 2.5 29 98-131 128-156 (158)
99 PRK06266 transcription initiat 68.7 5 0.00011 34.2 3.0 31 97-132 135-165 (178)
100 KOG2932 E3 ubiquitin ligase in 67.4 2.4 5.2E-05 40.1 0.9 69 52-136 91-165 (389)
101 PF06906 DUF1272: Protein of u 63.9 10 0.00023 27.4 3.4 48 52-112 6-55 (57)
102 KOG3002 Zn finger protein [Gen 62.6 6.7 0.00015 36.3 2.8 55 52-129 49-105 (299)
103 KOG3161 Predicted E3 ubiquitin 62.5 2.7 5.8E-05 43.2 0.2 46 52-109 12-57 (861)
104 PF13901 DUF4206: Domain of un 62.2 4.1 8.9E-05 35.1 1.3 38 52-105 153-196 (202)
105 KOG2066 Vacuolar assembly/sort 61.7 3 6.5E-05 43.4 0.4 38 52-89 785-824 (846)
106 PRK10144 formate-dependent nit 61.3 8.9 0.00019 31.5 3.0 29 98-131 40-68 (126)
107 KOG1701 Focal adhesion adaptor 60.5 4.7 0.0001 39.5 1.5 18 9-26 313-330 (468)
108 COG5175 MOT2 Transcriptional r 58.6 6.8 0.00015 37.7 2.1 55 51-114 14-68 (480)
109 TIGR03147 cyt_nit_nrfF cytochr 58.3 9.6 0.00021 31.3 2.7 29 98-131 40-68 (126)
110 COG5109 Uncharacterized conser 57.9 7.5 0.00016 37.0 2.3 46 52-104 337-382 (396)
111 KOG4362 Transcriptional regula 56.8 4.8 0.0001 41.3 0.9 51 51-111 21-71 (684)
112 KOG1829 Uncharacterized conser 56.0 2.9 6.3E-05 42.0 -0.8 26 68-104 530-556 (580)
113 KOG4739 Uncharacterized protei 53.4 5.5 0.00012 35.9 0.6 33 68-110 16-49 (233)
114 KOG1815 Predicted E3 ubiquitin 53.0 2.9 6.2E-05 40.0 -1.3 68 22-90 189-268 (444)
115 KOG1812 Predicted E3 ubiquitin 50.0 9.2 0.0002 36.3 1.6 56 51-109 146-203 (384)
116 KOG4275 Predicted E3 ubiquitin 48.6 3.3 7.2E-05 38.9 -1.6 41 52-109 301-342 (350)
117 PF00643 zf-B_box: B-box zinc 48.3 5.1 0.00011 25.5 -0.3 25 9-34 13-37 (42)
118 COG5183 SSM4 Protein involved 48.1 11 0.00025 39.8 2.0 48 52-108 13-65 (1175)
119 KOG2068 MOT2 transcription fac 47.9 16 0.00034 34.5 2.7 50 51-111 249-300 (327)
120 KOG0269 WD40 repeat-containing 46.6 19 0.00041 37.7 3.3 37 52-91 780-816 (839)
121 PF10272 Tmpp129: Putative tra 45.6 18 0.00039 34.4 2.8 35 74-108 311-350 (358)
122 PF03918 CcmH: Cytochrome C bi 44.8 22 0.00049 29.5 2.9 29 98-131 40-68 (148)
123 KOG1815 Predicted E3 ubiquitin 44.0 38 0.00082 32.5 4.7 88 52-147 71-161 (444)
124 KOG3005 GIY-YIG type nuclease 42.3 16 0.00034 33.8 1.7 53 52-107 183-241 (276)
125 smart00132 LIM Zinc-binding do 41.9 15 0.00032 21.9 1.1 37 53-108 1-37 (39)
126 KOG1701 Focal adhesion adaptor 41.6 17 0.00036 35.8 1.9 33 50-82 393-427 (468)
127 KOG1001 Helicase-like transcri 41.4 12 0.00026 38.2 1.0 47 52-110 455-501 (674)
128 PF04710 Pellino: Pellino; In 40.4 9.3 0.0002 37.1 0.0 50 52-106 278-336 (416)
129 PF15353 HECA: Headcase protei 40.2 21 0.00044 28.8 1.9 22 68-89 27-55 (107)
130 KOG2071 mRNA cleavage and poly 39.8 15 0.00033 37.0 1.4 38 52-89 514-559 (579)
131 PF00412 LIM: LIM domain; Int 39.4 8.4 0.00018 25.6 -0.3 40 54-112 1-40 (58)
132 smart00064 FYVE Protein presen 38.6 9.6 0.00021 26.6 -0.2 45 41-89 3-47 (68)
133 COG2888 Predicted Zn-ribbon RN 38.1 36 0.00079 24.9 2.7 46 51-105 9-57 (61)
134 KOG0826 Predicted E3 ubiquitin 37.5 30 0.00065 33.0 2.8 45 52-108 301-345 (357)
135 COG4847 Uncharacterized protei 37.3 32 0.00069 27.5 2.5 35 54-91 9-43 (103)
136 PF09943 DUF2175: Uncharacteri 37.2 26 0.00056 27.9 2.1 35 53-90 4-38 (101)
137 COG3088 CcmH Uncharacterized p 36.4 28 0.0006 29.7 2.2 27 98-129 44-70 (153)
138 smart00531 TFIIE Transcription 36.0 14 0.0003 30.2 0.4 17 97-113 122-138 (147)
139 PF04710 Pellino: Pellino; In 36.0 12 0.00026 36.3 0.0 75 36-110 312-402 (416)
140 PF13717 zinc_ribbon_4: zinc-r 35.5 22 0.00048 22.7 1.2 13 53-65 4-16 (36)
141 COG1675 TFA1 Transcription ini 34.8 35 0.00076 29.5 2.6 30 98-132 132-161 (176)
142 KOG4367 Predicted Zn-finger pr 34.7 26 0.00056 35.0 2.0 36 51-91 4-39 (699)
143 PF04423 Rad50_zn_hook: Rad50 32.2 13 0.00028 25.4 -0.3 26 100-130 22-47 (54)
144 PRK14890 putative Zn-ribbon RN 31.8 39 0.00084 24.6 2.1 46 51-105 7-55 (59)
145 cd00730 rubredoxin Rubredoxin; 31.8 29 0.00063 24.0 1.4 12 96-107 32-43 (50)
146 PF13240 zinc_ribbon_2: zinc-r 29.6 29 0.00063 20.3 0.9 8 101-108 16-23 (23)
147 PF00301 Rubredoxin: Rubredoxi 28.2 30 0.00064 23.7 0.9 12 96-107 32-43 (47)
148 KOG0825 PHD Zn-finger protein 27.9 30 0.00065 36.8 1.3 57 52-111 97-156 (1134)
149 cd04718 BAH_plant_2 BAH, or Br 27.1 25 0.00054 29.7 0.5 27 78-108 2-28 (148)
150 KOG0801 Predicted E3 ubiquitin 26.9 35 0.00076 29.9 1.3 16 97-112 137-152 (205)
151 PF13832 zf-HC5HC2H_2: PHD-zin 26.1 81 0.0018 23.8 3.1 30 52-86 56-88 (110)
152 PF13719 zinc_ribbon_5: zinc-r 25.3 35 0.00076 21.8 0.8 28 52-79 3-36 (37)
153 KOG1100 Predicted E3 ubiquitin 24.1 30 0.00064 30.3 0.4 41 52-109 159-200 (207)
154 PF13248 zf-ribbon_3: zinc-rib 24.1 51 0.0011 19.4 1.3 13 52-64 3-15 (26)
155 KOG3113 Uncharacterized conser 23.2 1.5E+02 0.0032 27.7 4.6 50 52-113 112-162 (293)
156 KOG0298 DEAD box-containing he 23.2 24 0.00052 38.9 -0.4 46 52-109 1154-1199(1394)
157 PF01927 Mut7-C: Mut7-C RNAse 22.9 57 0.0012 26.5 1.8 49 52-114 92-140 (147)
158 PF03854 zf-P11: P-11 zinc fin 22.8 28 0.0006 24.5 -0.0 28 73-108 17-45 (50)
159 KOG3842 Adaptor protein Pellin 22.6 1.1E+02 0.0023 29.6 3.7 74 36-111 325-416 (429)
160 PF01363 FYVE: FYVE zinc finge 22.4 21 0.00045 25.0 -0.8 40 41-87 2-44 (69)
161 PF05018 DUF667: Protein of un 22.4 60 0.0013 28.0 2.0 24 188-211 42-65 (190)
162 COG3813 Uncharacterized protei 22.3 98 0.0021 23.7 2.8 48 51-111 5-54 (84)
163 KOG4692 Predicted E3 ubiquitin 22.0 55 0.0012 31.9 1.8 46 51-109 422-467 (489)
164 PRK00420 hypothetical protein; 21.8 59 0.0013 26.2 1.7 13 51-63 23-35 (112)
No 1
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.7e-60 Score=415.25 Aligned_cols=156 Identities=37% Similarity=0.809 Sum_probs=144.3
Q ss_pred Cccccc--cccccceeeeeccCccCcccccCCCCceeeeecceeeccCCCCCCCccccccccccccccCCeeeecCCCcc
Q 028040 1 MVVCKC--RKATKLYCFVHKVPVCGECICFPEHQICVVRTYSEWVIDGEYDWPPKCCQCQAVLEEESGSETTRLGCLHVI 78 (215)
Q Consensus 1 MglCkC--rk~T~~fCf~Hrv~VC~~Ci~~~~H~~CvVqsYlqwL~Dsdyd~~~~C~ICle~L~~gD~~evvRL~C~HvF 78 (215)
|||||| |||||||||||||||||+|+| .||++||||||+|||+|+||+ ++|.+|...|+.|| ++||.|+|+|
T Consensus 1 MGLCKCPKRkVTNlFCfEHRVNVCEhClV-~nHpkCiVQSYLqWL~DsDY~--pNC~LC~t~La~gd---t~RLvCyhlf 74 (299)
T KOG3970|consen 1 MGLCKCPKRKVTNLFCFEHRVNVCEHCLV-ANHPKCIVQSYLQWLQDSDYN--PNCRLCNTPLASGD---TTRLVCYHLF 74 (299)
T ss_pred CCcccCchhhhhhhhhhhhhhhHHHHHHh-ccCchhhHHHHHHHHhhcCCC--CCCceeCCccccCc---ceeehhhhhH
Confidence 999999 889999999999999999997 999999999999999999999 99999999999986 9999999999
Q ss_pred CHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhhhhhhhhhcCCCCCCchh-cccCCCCCC
Q 028040 79 HTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIMLTGLEKNLFGNHPVSLAV-AESRGPPPA 157 (215)
Q Consensus 79 H~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q~~wAr~~lG~~l~~~~~-~~~~~~p~a 157 (215)
||+||++|..++|.||||+||+||.|..+|||+-|+ .|||+++|||+++|+||||++||++||+--. .+....||.
T Consensus 75 HW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nl---vsPva~aLre~L~qvNWaRagLGLpll~E~~sp~p~p~~p~ 151 (299)
T KOG3970|consen 75 HWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINL---VSPVAEALREQLKQVNWARAGLGLPLLPELNSPVPSPAPPQ 151 (299)
T ss_pred HHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccc---cchhHHHHHHHHHhhhHHhhccCCccchhhcCCCCCCCChh
Confidence 999999999999999999999999999999999886 5999999999999999999999999998221 222336777
Q ss_pred CCCCcccc
Q 028040 158 FASDPIVN 165 (215)
Q Consensus 158 f~~~~~~~ 165 (215)
-+|+|.++
T Consensus 152 ~~s~~~~~ 159 (299)
T KOG3970|consen 152 LKSAPVMH 159 (299)
T ss_pred hccchhhh
Confidence 88888877
No 2
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.39 E-value=1.3e-13 Score=91.07 Aligned_cols=43 Identities=33% Similarity=0.773 Sum_probs=37.6
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
+|+||+++|..++ .+++|+|+|+||.+||.+|+++. .+||+||
T Consensus 2 ~C~IC~~~~~~~~--~~~~l~C~H~fh~~Ci~~~~~~~--------~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGE--KVVKLPCGHVFHRSCIKEWLKRN--------NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTS--CEEEETTSEEEEHHHHHHHHHHS--------SB-TTTH
T ss_pred CCcCCChhhcCCC--eEEEccCCCeeCHHHHHHHHHhC--------CcCCccC
Confidence 6999999998865 89999999999999999999884 2699996
No 3
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.29 E-value=3.4e-12 Score=118.21 Aligned_cols=52 Identities=23% Similarity=0.550 Sum_probs=45.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
..|+||+|+|+.|| .++.|+|.|.||..|+|.||.... ..||+|++.|..+.
T Consensus 230 ~~CaIClEdY~~Gd--klRiLPC~H~FH~~CIDpWL~~~r-------~~CPvCK~di~~~~ 281 (348)
T KOG4628|consen 230 DTCAICLEDYEKGD--KLRILPCSHKFHVNCIDPWLTQTR-------TFCPVCKRDIRTDS 281 (348)
T ss_pred ceEEEeecccccCC--eeeEecCCCchhhccchhhHhhcC-------ccCCCCCCcCCCCC
Confidence 48999999999998 677799999999999999998752 24999999988764
No 4
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=98.98 E-value=5.3e-10 Score=82.04 Aligned_cols=56 Identities=27% Similarity=0.599 Sum_probs=38.2
Q ss_pred cceeeccCCCCCCCccccccccccc--------cccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 39 YSEWVIDGEYDWPPKCCQCQAVLEE--------ESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 39 YlqwL~Dsdyd~~~~C~ICle~L~~--------gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
...|-.|..- .+|+||+++|.+ ++.-.+....|+|.||..||.+||+... +||+||
T Consensus 10 v~~~~~~~~~---d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~--------~CP~CR 73 (73)
T PF12678_consen 10 VALWSWDIAD---DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN--------TCPLCR 73 (73)
T ss_dssp EEEEEESSCC---SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS--------B-TTSS
T ss_pred EEEEeecCcC---CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC--------cCCCCC
Confidence 3455545443 469999999943 1211233458999999999999998742 599997
No 5
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=2.7e-10 Score=104.53 Aligned_cols=51 Identities=27% Similarity=0.665 Sum_probs=44.9
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
-.|+||++.|-.+| ..+.|||.|.||..|+++|+..+. .+||+||++|-|+
T Consensus 324 veCaICms~fiK~d--~~~vlPC~H~FH~~Cv~kW~~~y~-------~~CPvCrt~iPPp 374 (374)
T COG5540 324 VECAICMSNFIKND--RLRVLPCDHRFHVGCVDKWLLGYS-------NKCPVCRTAIPPP 374 (374)
T ss_pred ceEEEEhhhhcccc--eEEEeccCceechhHHHHHHhhhc-------ccCCccCCCCCCC
Confidence 67999999999887 688899999999999999998653 3599999999764
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=1.9e-09 Score=101.33 Aligned_cols=51 Identities=25% Similarity=0.655 Sum_probs=42.0
Q ss_pred Cccccccccccccc--------cCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC-ccC
Q 028040 52 PKCCQCQAVLEEES--------GSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT-IWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD--------~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~-I~P 110 (215)
..|.||++++...+ ++...||+|||+||.+||..|++++. +||+||.| +|-
T Consensus 288 ~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ--------TCPICr~p~ifd 347 (491)
T COG5243 288 RTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ--------TCPICRRPVIFD 347 (491)
T ss_pred CeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc--------CCCcccCccccc
Confidence 78999999965433 14578999999999999999999863 49999999 543
No 7
>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=98.83 E-value=4.3e-09 Score=66.41 Aligned_cols=45 Identities=38% Similarity=0.722 Sum_probs=34.9
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
.|+||++.+.+ ....++|+|.||..|++.|++. ...+||.|++.+
T Consensus 1 ~C~iC~~~~~~----~~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFRE----PVVLLPCGHVFCRSCIDKWLKS-------GKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhC----ceEecCCCChhcHHHHHHHHHh-------CcCCCCCCCCcC
Confidence 49999999821 3444469999999999999986 234699999864
No 8
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.79 E-value=4.8e-09 Score=93.03 Aligned_cols=50 Identities=24% Similarity=0.467 Sum_probs=38.2
Q ss_pred Ccccccccccccccc--CCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESG--SETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~--~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|+||++++.+... .....| +|+|+||..||.+|++... +||+||+++.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~--------tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN--------TCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC--------CCCCCCCEee
Confidence 689999999875320 012344 7999999999999998642 4999999875
No 9
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.70 E-value=1.7e-08 Score=77.27 Aligned_cols=52 Identities=17% Similarity=0.468 Sum_probs=37.6
Q ss_pred Cccccccccccc--------cccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEE--------ESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~--------gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
..|.||...|+. ||+-.++.-.|+|.||..||.+||+.... .-+||+||++.
T Consensus 22 d~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPmCR~~w 81 (85)
T PF12861_consen 22 DVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPMCRQPW 81 (85)
T ss_pred CceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCCcCCee
Confidence 668888888762 44112333479999999999999997532 23799999864
No 10
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.68 E-value=8e-09 Score=99.76 Aligned_cols=54 Identities=30% Similarity=0.582 Sum_probs=46.4
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKN 113 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~ 113 (215)
..|.||+++|..++.....||+|+|+||..||.+|++++ + +||+||..+.....
T Consensus 292 ~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--q------tCP~CR~~~~~~~~ 345 (543)
T KOG0802|consen 292 ELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--Q------TCPTCRTVLYDYVL 345 (543)
T ss_pred CeeeeechhhccccccccceeecccchHHHHHHHHHHHh--C------cCCcchhhhhcccc
Confidence 789999999998874558899999999999999999985 3 49999997776543
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.61 E-value=4.1e-08 Score=84.96 Aligned_cols=55 Identities=15% Similarity=0.318 Sum_probs=41.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCC--------CCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPH--------TAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~n--------Tap~g~~CP~Cr~~I~P~ 111 (215)
..|+||++.+.+ .+.++|||+|+|.||.+|+...... ......+||+||++|...
T Consensus 19 ~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 19 FDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred cCCccCCCcCCC-----cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 679999998743 6668999999999999998643110 011346899999999753
No 12
>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=98.54 E-value=8.3e-08 Score=58.38 Aligned_cols=39 Identities=33% Similarity=0.763 Sum_probs=31.6
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|+||++.. ...+.++|+|+||..|++.|++. ...+||.|
T Consensus 1 C~iC~~~~-----~~~~~~~C~H~~c~~C~~~~~~~-------~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL-----KDPVVLPCGHTFCRSCIRKWLKS-------GNNTCPIC 39 (39)
T ss_pred CCcCccCC-----CCcEEecCCChHHHHHHHHHHHh-------CcCCCCCC
Confidence 78898882 25888999999999999999982 23469987
No 13
>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=98.53 E-value=5.4e-08 Score=62.73 Aligned_cols=41 Identities=29% Similarity=0.664 Sum_probs=34.2
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|+||++.+.+. ...++|+|.|+..||.+|++.. ..+.||+|
T Consensus 1 C~iC~~~~~~~----~~~~~C~H~fC~~C~~~~~~~~------~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP----VILLPCGHSFCRDCLRKWLENS------GSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE----EEETTTSEEEEHHHHHHHHHHT------SSSBTTTT
T ss_pred CCcCCccccCC----CEEecCCCcchHHHHHHHHHhc------CCccCCcC
Confidence 78999998652 4578999999999999999962 45779998
No 14
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.50 E-value=6.1e-08 Score=62.64 Aligned_cols=39 Identities=23% Similarity=0.572 Sum_probs=31.2
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|+||++.+.+ .++.++|||+|..+|+.+|++.. .+||+|
T Consensus 1 C~iC~~~~~~----~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD----PVVVTPCGHSFCKECIEKYLEKN--------PKCPVC 39 (39)
T ss_dssp ETTTTSB-SS----EEEECTTSEEEEHHHHHHHHHCT--------SB-TTT
T ss_pred CCCCCCcccC----cCEECCCCCchhHHHHHHHHHCc--------CCCcCC
Confidence 7899998865 25778999999999999999873 359998
No 15
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.49 E-value=1.1e-07 Score=63.31 Aligned_cols=42 Identities=31% Similarity=0.695 Sum_probs=31.4
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|+||++.|.+ .+.|.|||+|=.+||.+|.+.... .++.||.|
T Consensus 1 CpiC~~~~~~-----Pv~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD-----PVSLPCGHSFCRSCLERLWKEPSG----SGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS-----EEE-SSSSEEEHHHHHHHHCCSSS----ST---SSS
T ss_pred CCccchhhCC-----ccccCCcCHHHHHHHHHHHHccCC----cCCCCcCC
Confidence 8999999954 899999999999999999987532 34889998
No 16
>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=98.40 E-value=2.4e-07 Score=62.67 Aligned_cols=45 Identities=24% Similarity=0.502 Sum_probs=36.2
Q ss_pred CccccccccccccccCCeeeecCCCc-cCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHV-IHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~Hv-FH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|.||++... +++.++|+|+ |...|+.+|++.. .+||+||++|-
T Consensus 3 ~~C~iC~~~~~-----~~~~~pCgH~~~C~~C~~~~~~~~--------~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPR-----DVVLLPCGHLCFCEECAERLLKRK--------KKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBS-----SEEEETTCEEEEEHHHHHHHHHTT--------SBBTTTTBB-S
T ss_pred CCCccCCccCC-----ceEEeCCCChHHHHHHhHHhcccC--------CCCCcCChhhc
Confidence 57999999852 4888899999 9999999999843 35999999873
No 17
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.38 E-value=1.4e-07 Score=85.73 Aligned_cols=48 Identities=27% Similarity=0.603 Sum_probs=41.4
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
..|.+|++...+ ....+|||+|-|.||.+|...... ||+||...-|.+
T Consensus 240 ~kC~LCLe~~~~-----pSaTpCGHiFCWsCI~~w~~ek~e--------CPlCR~~~~psk 287 (293)
T KOG0317|consen 240 RKCSLCLENRSN-----PSATPCGHIFCWSCILEWCSEKAE--------CPLCREKFQPSK 287 (293)
T ss_pred CceEEEecCCCC-----CCcCcCcchHHHHHHHHHHccccC--------CCcccccCCCcc
Confidence 789999999644 678899999999999999987643 999999987754
No 18
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.35 E-value=3.3e-07 Score=70.03 Aligned_cols=48 Identities=27% Similarity=0.494 Sum_probs=38.5
Q ss_pred CccccccccccccccCCeee-e-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTR-L-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvR-L-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|+-|+.....+| +... - .|.|.||..||.+||..+. .||++++...
T Consensus 32 ~~C~eCq~~~~~~~--eC~v~wG~CnHaFH~HCI~rWL~Tk~--------~CPld~q~w~ 81 (88)
T COG5194 32 GTCPECQFGMTPGD--ECPVVWGVCNHAFHDHCIYRWLDTKG--------VCPLDRQTWV 81 (88)
T ss_pred CcCcccccCCCCCC--cceEEEEecchHHHHHHHHHHHhhCC--------CCCCCCceeE
Confidence 67888988887776 4443 3 7999999999999998753 4999998643
No 19
>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=98.31 E-value=1.2e-06 Score=60.46 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=38.5
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
-.|+||++.+.+ .+.++|||+|-++||.+|++.. .+||.|+.++-.
T Consensus 2 ~~Cpi~~~~~~~-----Pv~~~~G~v~~~~~i~~~~~~~--------~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-----PVILPSGQTYERRAIEKWLLSH--------GTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-----CEECCCCCEEeHHHHHHHHHHC--------CCCCCCcCCCCh
Confidence 359999999854 6778999999999999999862 259999998843
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=5.5e-07 Score=79.72 Aligned_cols=53 Identities=23% Similarity=0.524 Sum_probs=42.8
Q ss_pred ccCCCCCCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 44 IDGEYDWPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 44 ~Dsdyd~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
+++.|| |-|||+.- ++.|.-.|||+|-|-||-+||...+. ...||+|+..|--
T Consensus 44 ~~~~Fd----CNICLd~a-----kdPVvTlCGHLFCWpClyqWl~~~~~-----~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 44 DGGFFD----CNICLDLA-----KDPVVTLCGHLFCWPCLYQWLQTRPN-----SKECPVCKAEVSI 96 (230)
T ss_pred CCCcee----eeeecccc-----CCCEEeecccceehHHHHHHHhhcCC-----CeeCCcccccccc
Confidence 345566 99999874 35888899999999999999988653 4469999988754
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.20 E-value=1.4e-06 Score=57.75 Aligned_cols=44 Identities=25% Similarity=0.570 Sum_probs=34.5
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
.|.+|.+.+.+. .....|.|||+|..+||..+.. ....||+|++
T Consensus 1 ~C~~C~~~~~~~--~~~~l~~CgH~~C~~C~~~~~~--------~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEE--RRPRLTSCGHIFCEKCLKKLKG--------KSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCC--CCeEEcccCCHHHHHHHHhhcC--------CCCCCcCCCC
Confidence 489999999333 2455568999999999999991 2456999985
No 22
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.19 E-value=1e-06 Score=59.31 Aligned_cols=43 Identities=28% Similarity=0.566 Sum_probs=25.2
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCP 102 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP 102 (215)
|+||++ |.+.+ ...+.|+|||+|=++||++++++.. ...++||
T Consensus 1 CpIc~e-~~~~~-n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEE-NPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTS-S-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCC-CCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 75554 4678899999999999999998642 1467887
No 23
>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=98.15 E-value=2e-06 Score=59.07 Aligned_cols=44 Identities=23% Similarity=0.533 Sum_probs=33.7
Q ss_pred ccccccccccccccCCeeeecCC-----CccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCL-----HVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~-----HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
.|.||++..++ ++...+||. |.||..||.+|+...... +||+|+
T Consensus 1 ~CrIC~~~~~~---~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~------~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDE---GDPLVSPCRCKGSLKYVHQECLERWINESGNK------TCEICK 49 (49)
T ss_pred CccCCCCCCCC---CCeeEeccccCCchhHHHHHHHHHHHHHcCCC------cCCCCC
Confidence 48999983222 367788884 999999999999876433 599995
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.10 E-value=1.5e-06 Score=77.24 Aligned_cols=55 Identities=22% Similarity=0.451 Sum_probs=39.1
Q ss_pred Ccccccccccccc----ccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEE----SGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~g----D~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|+||++...+. + ..-..| +|+|+|...||..|.+....+ .....||+||..+.
T Consensus 171 ~eCgICmE~I~eK~~~~e-RrFGIL~~CnHsFCl~CIr~Wr~~r~~~--~~~rsCPiCR~~f~ 230 (242)
T PHA02926 171 KECGICYEVVYSKRLEND-RYFGLLDSCNHIFCITCINIWHRTRRET--GASDNCPICRTRFR 230 (242)
T ss_pred CCCccCcccccccccccc-ccccccCCCCchHHHHHHHHHHHhcccc--CcCCcCCCCcceee
Confidence 6799999987432 1 112334 799999999999999864321 13456999999764
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=1.1e-06 Score=66.66 Aligned_cols=50 Identities=22% Similarity=0.581 Sum_probs=37.6
Q ss_pred Cccccccccccc--------cccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEE--------ESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 52 ~~C~ICle~L~~--------gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
.+|.||..+|+. || +=...+ .|.|.||..||.+|+.... ++-.||+||+.
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgD-dCPLv~G~C~h~fh~hCI~~wl~~~t-----sq~~CPmcRq~ 79 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGD-DCPLVWGYCLHAFHAHCILKWLNTPT-----SQGQCPMCRQT 79 (84)
T ss_pred CccceEecccCCcCCCCcCCCC-CCccHHHHHHHHHHHHHHHHHhcCcc-----ccccCCcchhe
Confidence 478999888863 44 233444 5999999999999997643 34579999975
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.03 E-value=6.7e-07 Score=65.36 Aligned_cols=56 Identities=25% Similarity=0.460 Sum_probs=26.4
Q ss_pred CccccccccccccccCCeeee-----cCCCccCHHHHHHHHhcCCCCC---CCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRL-----GCLHVIHTSCLVSHIKSFPPHT---APAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-----~C~HvFH~~CLd~Wl~~~p~nT---ap~g~~CP~Cr~~I~ 109 (215)
..|.||.+.+.+++ ++.++ .|+..||..||.+||+..+... .|-.-+||.|+++|-
T Consensus 3 ~~C~IC~~~~~~~~--~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 3 LECGICYSYRLDDG--EIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -S-SSS--SS-TT-------B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCcCCcEecCCC--CcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 56999999876332 23232 5999999999999998754321 122235999999873
No 27
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=4.2e-06 Score=79.29 Aligned_cols=47 Identities=28% Similarity=0.668 Sum_probs=37.6
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
..|.|| .+|...+ .++... .|||+||..||.+|++.-|.| -.||+|+
T Consensus 5 A~C~Ic-~d~~p~~-~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpic~ 52 (465)
T KOG0827|consen 5 AECHIC-IDGRPND-HELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPICQ 52 (465)
T ss_pred ceeeEe-ccCCccc-cccccccchhhHHHHHHHHHHHccCCcc-----CCCCcee
Confidence 579999 7776655 455555 499999999999999987664 3599998
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.87 E-value=2.3e-05 Score=74.22 Aligned_cols=49 Identities=18% Similarity=0.465 Sum_probs=40.5
Q ss_pred CCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 50 WPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 50 ~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
....|+||++.|.+ .+.++|+|.|...||..|+... ..||+|+..+...
T Consensus 25 ~~l~C~IC~d~~~~-----PvitpCgH~FCs~CI~~~l~~~--------~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 25 TSLRCHICKDFFDV-----PVLTSCSHTFCSLCIRRCLSNQ--------PKCPLCRAEDQES 73 (397)
T ss_pred cccCCCcCchhhhC-----ccCCCCCCchhHHHHHHHHhCC--------CCCCCCCCccccc
Confidence 34789999999844 5668999999999999999763 2599999998753
No 29
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=6.7e-06 Score=79.94 Aligned_cols=52 Identities=27% Similarity=0.761 Sum_probs=38.0
Q ss_pred CCccccccccccc---cccCC------eee---e-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 51 PPKCCQCQAVLEE---ESGSE------TTR---L-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 51 ~~~C~ICle~L~~---gD~~e------vvR---L-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
...|+||+.+++- +. .. +.| + +|.|+||..||.+|++..+ ..||+||.++-|
T Consensus 571 t~dC~ICMt~I~l~~~~s-~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~yk-------l~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGS-DCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYK-------LICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccC-cchhhhhhhhccccccchHHHHHHHHHHHHHhhhc-------ccCCccCCCCCC
Confidence 3689999998862 11 01 111 2 8999999999999998543 359999998854
No 30
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.81 E-value=7.3e-06 Score=78.68 Aligned_cols=49 Identities=29% Similarity=0.649 Sum_probs=41.1
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
.|+|+|||+.|+.+. ..++...|.|.||-.||.+|-.. +||+||-..-|
T Consensus 175 LPTCpVCLERMD~s~-~gi~t~~c~Hsfh~~cl~~w~~~----------scpvcR~~q~p 223 (493)
T KOG0804|consen 175 LPTCPVCLERMDSST-TGILTILCNHSFHCSCLMKWWDS----------SCPVCRYCQSP 223 (493)
T ss_pred CCCcchhHhhcCccc-cceeeeecccccchHHHhhcccC----------cChhhhhhcCc
Confidence 489999999998764 34566689999999999999765 39999988774
No 31
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.3e-05 Score=72.39 Aligned_cols=49 Identities=33% Similarity=0.624 Sum_probs=40.7
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHH-HHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVS-HIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~-Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
-.|+||+++.. ...+.+|||+|-|.||.. |-.++.. -||+||+-..|..
T Consensus 216 ~kC~lC~e~~~-----~ps~t~CgHlFC~~Cl~~~~t~~k~~-------~CplCRak~~pk~ 265 (271)
T COG5574 216 YKCFLCLEEPE-----VPSCTPCGHLFCLSCLLISWTKKKYE-------FCPLCRAKVYPKK 265 (271)
T ss_pred cceeeeecccC-----CcccccccchhhHHHHHHHHHhhccc-------cCchhhhhccchh
Confidence 34999999864 488999999999999999 8776532 2999999998864
No 32
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.5e-05 Score=68.75 Aligned_cols=47 Identities=28% Similarity=0.562 Sum_probs=39.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
-.|+|||+.+.+. .++--.|||||-.+||..-++.. .+||+|++.|-
T Consensus 132 ~~CPiCl~~~sek---~~vsTkCGHvFC~~Cik~alk~~--------~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSVSEK---VPVSTKCGHVFCSQCIKDALKNT--------NKCPTCRKKIT 178 (187)
T ss_pred cCCCceecchhhc---cccccccchhHHHHHHHHHHHhC--------CCCCCcccccc
Confidence 4699999998773 46777999999999999999863 35999998664
No 33
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=7e-06 Score=74.90 Aligned_cols=59 Identities=22% Similarity=0.467 Sum_probs=44.5
Q ss_pred CCcccccccccccccc-----CCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCC
Q 028040 51 PPKCCQCQAVLEEESG-----SETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVK 115 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~-----~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~ 115 (215)
+..|+||.+.|..+.+ +.+-+|.|+|+||..||.-|---.+..| ||-|++.+.-.+.++
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqt------CPYCKekVdl~rmfs 287 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQT------CPYCKEKVDLKRMFS 287 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCC------CchHHHHhhHhhhcc
Confidence 4789999999975431 1356799999999999999955444444 999999887654443
No 34
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.60 E-value=6.4e-05 Score=54.80 Aligned_cols=48 Identities=13% Similarity=0.138 Sum_probs=36.1
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
-.|+|+.+-|. +.+++++||+|-+.+|.+||+.. +.+||.|+.++-..
T Consensus 5 f~CpIt~~lM~-----dPVi~~~G~tyer~~I~~~l~~~-------~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 5 FLCPITGELMR-----DPVILPSGHTYERSAIERWLEQN-------GGTDPFTRQPLSES 52 (73)
T ss_dssp GB-TTTSSB-S-----SEEEETTSEEEEHHHHHHHHCTT-------SSB-TTT-SB-SGG
T ss_pred cCCcCcCcHhh-----CceeCCcCCEEcHHHHHHHHHcC-------CCCCCCCCCcCCcc
Confidence 35999999984 48999999999999999999872 34699999988754
No 35
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.60 E-value=3.3e-05 Score=73.67 Aligned_cols=47 Identities=23% Similarity=0.542 Sum_probs=39.6
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
-.|..|.+.+-..+ +....|+|.|+||..|+..+|++... .+||.||
T Consensus 366 L~Cg~CGe~~Glk~-e~LqALpCsHIfH~rCl~e~L~~n~~------rsCP~Cr 412 (518)
T KOG1941|consen 366 LYCGLCGESIGLKN-ERLQALPCSHIFHLRCLQEILENNGT------RSCPNCR 412 (518)
T ss_pred hhhhhhhhhhcCCc-ccccccchhHHHHHHHHHHHHHhCCC------CCCccHH
Confidence 78999999987665 56777999999999999999987543 4599998
No 36
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=7e-05 Score=72.80 Aligned_cols=53 Identities=21% Similarity=0.422 Sum_probs=40.8
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
+..|+||+++... .++..|||+|-+.||-+++....-- ..-.||+|+..|.+.
T Consensus 186 ~~~CPICL~~~~~-----p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPiC~s~I~~k 238 (513)
T KOG2164|consen 186 DMQCPICLEPPSV-----PVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPICRSTITLK 238 (513)
T ss_pred CCcCCcccCCCCc-----ccccccCceeeHHHHHHHHhhhccc---CCccCCchhhhcccc
Confidence 3679999999633 6677799999999999998754111 234599999999883
No 37
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=97.44 E-value=5.9e-05 Score=68.60 Aligned_cols=50 Identities=30% Similarity=0.648 Sum_probs=42.8
Q ss_pred CCCCCCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 46 GEYDWPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 46 sdyd~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
...+ .+|+||.+.+..+. ..+..|+|+|..|..|+...... +|+||+|.+
T Consensus 155 ~~~~--~ncPic~e~l~~s~-~~~~~~~CgH~~h~~cf~e~~~~--------~y~CP~C~~ 204 (276)
T KOG1940|consen 155 RSSE--FNCPICKEYLFLSF-EDAGVLKCGHYMHSRCFEEMICE--------GYTCPICSK 204 (276)
T ss_pred hccc--CCCchhHHHhcccc-ccCCccCcccchHHHHHHHHhcc--------CCCCCcccc
Confidence 4444 77999999999886 56777999999999999999875 499999998
No 38
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=97.34 E-value=5.8e-05 Score=77.03 Aligned_cols=59 Identities=24% Similarity=0.646 Sum_probs=45.1
Q ss_pred eeccCCCCCCCccccccccccccccCCeee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q 028040 42 WVIDGEYDWPPKCCQCQAVLEEESGSETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 42 wL~Dsdyd~~~~C~ICle~L~~gD~~evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
-|....|+ |.||.+.+...+ .+-- -.||||||..||.+|.++ ...|.+++.+||.|...
T Consensus 186 ~l~~~~ye----CmIC~e~I~~t~--~~WSC~sCYhVFHl~CI~~WArs-~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 186 QLSNRKYE----CMICTERIKRTA--PVWSCKSCYHVFHLNCIKKWARS-SEKTGQDGWRCPACQSV 245 (950)
T ss_pred HHhcCceE----EEEeeeeccccC--CceecchhhhhhhHHHHHHHHHH-hhhccCccccCCcccch
Confidence 34445556 999999998764 2332 269999999999999988 45566789999999743
No 39
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.26 E-value=5.6e-05 Score=76.96 Aligned_cols=75 Identities=20% Similarity=0.253 Sum_probs=52.7
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcc-hHHHHHHHHhh
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGS-RLHSLLKEAIM 130 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S-~l~~~Lre~i~ 130 (215)
..|++|+..+.++. ...+-.|.|.||.+||+.|-+.- +| ||+||....--.-..-.++ ++...|..-..
T Consensus 124 ~~CP~Ci~s~~DqL--~~~~k~c~H~FC~~Ci~sWsR~a--qT------CPiDR~EF~~v~V~eS~~~~~~vR~lP~EEs 193 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQL--EESEKHTAHYFCEECVGSWSRCA--QT------CPVDRGEFGEVKVLESTGIEANVRCLPSEES 193 (1134)
T ss_pred hhhhHHHHHHHHHh--hccccccccccHHHHhhhhhhhc--cc------CchhhhhhheeeeeccccccceeEecchhhh
Confidence 67999999998875 67778999999999999998764 33 9999986543211111223 55555655555
Q ss_pred hhhhhh
Q 028040 131 LTGLEK 136 (215)
Q Consensus 131 q~~wAr 136 (215)
+.+.|+
T Consensus 194 ~~~~e~ 199 (1134)
T KOG0825|consen 194 ENILEK 199 (1134)
T ss_pred hhhhhh
Confidence 555544
No 40
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.25 E-value=5e-05 Score=70.29 Aligned_cols=68 Identities=24% Similarity=0.460 Sum_probs=50.2
Q ss_pred ceeeccCCCCCCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCC-----------C---C-CCCCCCCCCCC
Q 028040 40 SEWVIDGEYDWPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFP-----------P---H-TAPAGYVCPLC 104 (215)
Q Consensus 40 lqwL~Dsdyd~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p-----------~---n-Tap~g~~CP~C 104 (215)
.++|.++... -..|.|||--|.+++ +.++-.|.|.||..||.++|...- . | +.+-.-.||+|
T Consensus 105 ~e~LT~nn~p-~gqCvICLygfa~~~--~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVc 181 (368)
T KOG4445|consen 105 SEFLTENNHP-NGQCVICLYGFASSP--AFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVC 181 (368)
T ss_pred HHHcccCCCC-CCceEEEEEeecCCC--ceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHh
Confidence 3567776642 267999999999987 899999999999999998874320 0 1 12234469999
Q ss_pred CCCccC
Q 028040 105 STTIWP 110 (215)
Q Consensus 105 r~~I~P 110 (215)
|..|.-
T Consensus 182 re~i~~ 187 (368)
T KOG4445|consen 182 RERIKI 187 (368)
T ss_pred hhhccc
Confidence 998754
No 41
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00016 Score=59.08 Aligned_cols=43 Identities=26% Similarity=0.583 Sum_probs=36.6
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
.-.|+||++.|.. ...|+|+|.|=..||..++. ..+.||.||.
T Consensus 13 ~~~C~iC~~~~~~-----p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~cr~ 55 (386)
T KOG2177|consen 13 ELTCPICLEYFRE-----PVLLPCGHNFCRACLTRSWE--------GPLSCPVCRP 55 (386)
T ss_pred cccChhhHHHhhc-----CccccccchHhHHHHHHhcC--------CCcCCcccCC
Confidence 3679999999965 46788999999999999997 2367999994
No 42
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.14 E-value=0.00015 Score=75.25 Aligned_cols=51 Identities=33% Similarity=0.666 Sum_probs=38.4
Q ss_pred CccccccccccccccCCee-ee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEEESGSETT-RL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evv-RL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
..|+||-.-|..-|.+... |- .|.|-||.+||-+|+++...++ ||+||..|
T Consensus 1470 eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~------CPlCRsei 1522 (1525)
T COG5219 1470 EECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSN------CPLCRSEI 1522 (1525)
T ss_pred chhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCC------CCcccccc
Confidence 6899999998743311222 22 5999999999999999875554 99999766
No 43
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.00049 Score=55.04 Aligned_cols=27 Identities=33% Similarity=0.689 Sum_probs=23.6
Q ss_pred cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q 028040 73 GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 73 ~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
.|.|.||..||.+||+... +||+|.+.
T Consensus 80 ~CNHaFH~hCisrWlktr~--------vCPLdn~e 106 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRN--------VCPLDNKE 106 (114)
T ss_pred ecchHHHHHHHHHHHhhcC--------cCCCcCcc
Confidence 6999999999999999752 59999775
No 44
>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=96.78 E-value=0.0014 Score=60.67 Aligned_cols=51 Identities=20% Similarity=0.383 Sum_probs=36.2
Q ss_pred CccccccccccccccCCeeee--cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL--GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL--~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
..|++|+...--.. ...-| .|||.|-..|++..+... ...||.|+.++...
T Consensus 4 ~~CP~Ck~~~y~np--~~kl~i~~CGH~~C~sCv~~l~~~~-------~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 4 QGCPRCKTTKYRNP--SLKLMVNVCGHTLCESCVDLLFVRG-------SGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcCCCCCccCc--ccccccCCCCCcccHHHHHHHhcCC-------CCCCCCCCCccchh
Confidence 57999999532221 22222 699999999999987543 23699999988764
No 45
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.69 E-value=0.00059 Score=51.12 Aligned_cols=30 Identities=33% Similarity=0.654 Sum_probs=27.0
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLV 84 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd 84 (215)
..|++|...|.++ ..++.||+|+||..|++
T Consensus 79 ~~C~vC~k~l~~~---~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNS---VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCc---eEEEeCCCeEEeccccc
Confidence 7799999999875 58889999999999985
No 46
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.62 E-value=0.0014 Score=70.72 Aligned_cols=54 Identities=22% Similarity=0.479 Sum_probs=40.1
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCC----CCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAP----AGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap----~g~~CP~Cr~~I~ 109 (215)
..|.||..+--... -.++|.|+|+||..|...-|++.=. .| .-..||+|..+|-
T Consensus 3487 DmCmICFTE~L~AA--P~IqL~C~HiFHlqC~R~vLE~RW~--GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3487 DMCMICFTEALSAA--PAIQLDCSHIFHLQCCRRVLENRWL--GPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred ceEEEEehhhhCCC--cceecCCccchhHHHHHHHHHhccc--CCeeEEeeeecccccchhh
Confidence 77999987644332 6899999999999999888776411 11 2346999988874
No 47
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.61 E-value=0.0017 Score=62.21 Aligned_cols=50 Identities=22% Similarity=0.513 Sum_probs=39.5
Q ss_pred Cccccccccccc-cccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEE-ESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~-gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
.+|+||++.+.- || ..++.|.|+|.|-..|+.+||-+. .-.+||.|...-
T Consensus 5 ~tcpiclds~~~~g~-hr~vsl~cghlFgs~cie~wl~k~------~~~~cp~c~~ka 55 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGN-HRIVSLQCGHLFGSQCIEKWLGKK------TKMQCPLCSGKA 55 (463)
T ss_pred ccCceeeeeeeecCc-eEEeeecccccccHHHHHHHHhhh------hhhhCcccCChh
Confidence 689999999874 44 457778999999999999999532 234799997653
No 48
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.24 E-value=0.0027 Score=59.96 Aligned_cols=87 Identities=24% Similarity=0.504 Sum_probs=57.6
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhh
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIML 131 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q 131 (215)
-.|.||.+.|.. .+..+|+|.|-.-||..+|..+|. ||+|+.++-.+ .++ +.+ .|.|.+..
T Consensus 24 LRC~IC~eyf~i-----p~itpCsHtfCSlCIR~~L~~~p~--------CP~C~~~~~Es-~Lr--~n~---il~Eiv~S 84 (442)
T KOG0287|consen 24 LRCGICFEYFNI-----PMITPCSHTFCSLCIRKFLSYKPQ--------CPTCCVTVTES-DLR--NNR---ILDEIVKS 84 (442)
T ss_pred HHHhHHHHHhcC-----ceeccccchHHHHHHHHHhccCCC--------CCceecccchh-hhh--hhh---HHHHHHHH
Confidence 459999999954 566689999999999999998763 99997665432 221 112 25566666
Q ss_pred hhhhhhhcCCCCCCchhcccCCCCCCCCCCc
Q 028040 132 TGLEKNLFGNHPVSLAVAESRGPPPAFASDP 162 (215)
Q Consensus 132 ~~wAr~~lG~~l~~~~~~~~~~~p~af~~~~ 162 (215)
-+.+|+-|-.-|. ++..+-||-.+-|
T Consensus 85 ~~~~R~~Ll~fl~-----~~~~p~P~~~~~p 110 (442)
T KOG0287|consen 85 LNFARNHLLQFLL-----ESPAPSPASSSSP 110 (442)
T ss_pred HHHHHHHHHHHHh-----cCCCCCcccccCC
Confidence 7777755433222 2234556666666
No 49
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.14 E-value=0.0014 Score=48.22 Aligned_cols=46 Identities=35% Similarity=0.846 Sum_probs=24.0
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
-.|++|.+-|++ .+-| .|.|+|-+.|+..-+. ..||+|++|.|-.+
T Consensus 8 LrCs~C~~~l~~-----pv~l~~CeH~fCs~Ci~~~~~----------~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKE-----PVCLGGCEHIFCSSCIRDCIG----------SECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS------B---SSS--B-TTTGGGGTT----------TB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcC-----CceeccCccHHHHHHhHHhcC----------CCCCCcCChHHHHH
Confidence 469999999844 6666 7999999999977554 35999999999754
No 50
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.08 E-value=0.0039 Score=44.18 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=28.5
Q ss_pred CccccccccccccccCCeee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPL 103 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~ 103 (215)
..|+|.+.+|++ .++ ..|+|+|=++.|.+||++. ...+||+
T Consensus 12 ~~CPiT~~~~~~-----PV~s~~C~H~fek~aI~~~i~~~------~~~~CPv 53 (57)
T PF11789_consen 12 LKCPITLQPFED-----PVKSKKCGHTFEKEAILQYIQRN------GSKRCPV 53 (57)
T ss_dssp SB-TTTSSB-SS-----EEEESSS--EEEHHHHHHHCTTT------S-EE-SC
T ss_pred cCCCCcCChhhC-----CcCcCCCCCeecHHHHHHHHHhc------CCCCCCC
Confidence 789999999965 555 6999999999999999442 3567998
No 51
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.002 Score=55.50 Aligned_cols=64 Identities=23% Similarity=0.396 Sum_probs=41.2
Q ss_pred eeeccCccCccc--ccCCCC-----ceeeeecceeeccCCCCCCCccccccccccccccCCeeeecCCCccCH
Q 028040 15 FVHKVPVCGECI--CFPEHQ-----ICVVRTYSEWVIDGEYDWPPKCCQCQAVLEEESGSETTRLGCLHVIHT 80 (215)
Q Consensus 15 f~Hrv~VC~~Ci--~~~~H~-----~CvVqsYlqwL~Dsdyd~~~~C~ICle~L~~gD~~evvRL~C~HvFH~ 80 (215)
..|.-..|-.|- |.+|.- .|..+--+.|=+|-=-+..-.|.||||+|+.|| .|.||+|.-+||+
T Consensus 134 ~~~~g~KCPvC~K~V~sDd~e~HlvMCLtkPrlsYNdDVL~ddkGECvICLEdL~~Gd--tIARLPCLCIYHK 204 (205)
T KOG0801|consen 134 MDHSGMKCPVCHKVVPSDDAEIHLVMCLTKPRLSYNDDVLKDDKGECVICLEDLEAGD--TIARLPCLCIYHK 204 (205)
T ss_pred eccCCccCCccccccCCCcceEEEEEEecccccccccchhcccCCcEEEEhhhccCCC--ceeccceEEEeec
Confidence 345556677774 223321 455555555433311111256999999999998 8999999999996
No 52
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.0052 Score=57.70 Aligned_cols=48 Identities=25% Similarity=0.508 Sum_probs=37.4
Q ss_pred CCccccccccccccccCCeeeecCCCc-cCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHV-IHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~Hv-FH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
...|.||+.+- ++++.|||.|. +-..|.+..--+. | .||+||.+|-..
T Consensus 290 gkeCVIClse~-----rdt~vLPCRHLCLCs~Ca~~Lr~q~--n------~CPICRqpi~~l 338 (349)
T KOG4265|consen 290 GKECVICLSES-----RDTVVLPCRHLCLCSGCAKSLRYQT--N------NCPICRQPIEEL 338 (349)
T ss_pred CCeeEEEecCC-----cceEEecchhhehhHhHHHHHHHhh--c------CCCccccchHhh
Confidence 36899999986 35999999998 6788888775221 2 399999998754
No 53
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.89 E-value=0.0031 Score=63.75 Aligned_cols=49 Identities=20% Similarity=0.470 Sum_probs=40.7
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
--.|++|.... ++.+...|||+|-..|+...++.. .-+||.|.++.-|.
T Consensus 643 ~LkCs~Cn~R~-----Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 643 LLKCSVCNTRW-----KDAVITKCGHVFCEECVQTRYETR-------QRKCPKCNAAFGAN 691 (698)
T ss_pred ceeCCCccCch-----hhHHHHhcchHHHHHHHHHHHHHh-------cCCCCCCCCCCCcc
Confidence 36799999765 458889999999999999999874 33699999988764
No 54
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.58 E-value=0.0078 Score=56.01 Aligned_cols=44 Identities=23% Similarity=0.613 Sum_probs=36.5
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
..|-||.+.|.. .+.-+|||.|-.-||..+|..+|- ||+||.+.
T Consensus 26 lrC~IC~~~i~i-----p~~TtCgHtFCslCIR~hL~~qp~--------CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRISI-----PCETTCGHTFCSLCIRRHLGTQPF--------CPVCREDP 69 (391)
T ss_pred HHhhhhhheeec-----ceecccccchhHHHHHHHhcCCCC--------CccccccH
Confidence 579999999843 445589999999999999998763 99997653
No 55
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.25 E-value=0.0067 Score=41.22 Aligned_cols=42 Identities=31% Similarity=0.593 Sum_probs=27.1
Q ss_pred cccccccccccccCCeeeecCC-----CccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCL-----HVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~-----HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|-||++.-+++ +....+|. -..|.+||.+|+.... ..+|++|
T Consensus 1 CrIC~~~~~~~---~~li~pC~C~Gs~~~vH~~CL~~W~~~~~------~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED---EPLISPCRCKGSMKYVHRSCLERWIRESG------NRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS---S-EE-SSS-SSCCGSEECCHHHHHHHHHT-------SB-TTT
T ss_pred CeEeCCcCCCC---CceecccccCCCcchhHHHHHHHHHHhcC------CCcCCCC
Confidence 67898886554 34555653 3889999999998743 3459887
No 56
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=95.04 E-value=0.01 Score=49.07 Aligned_cols=34 Identities=9% Similarity=0.168 Sum_probs=30.0
Q ss_pred CccccccccccccccCCeeeecCC------CccCHHHHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCL------HVIHTSCLVSHI 87 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~------HvFH~~CLd~Wl 87 (215)
..|.||++.+.+++ .++.++|| |+||.+|+.+|-
T Consensus 27 ~EC~IC~~~I~~~~--GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 27 VECQICFDRIDNND--GVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred eeehhhhhhhhcCC--CEEEEecCCeehHHHHHHHHHHHHHH
Confidence 56999999998843 79999988 999999999993
No 57
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.94 E-value=0.014 Score=51.09 Aligned_cols=67 Identities=19% Similarity=0.406 Sum_probs=45.7
Q ss_pred cceeeccCCCCCCCcccccccccccccc--CCeeeecCCCccCHHHHHHHHhcCCCCCCCCCC-----CCCCCCCCcc
Q 028040 39 YSEWVIDGEYDWPPKCCQCQAVLEEESG--SETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGY-----VCPLCSTTIW 109 (215)
Q Consensus 39 YlqwL~Dsdyd~~~~C~ICle~L~~gD~--~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~-----~CP~Cr~~I~ 109 (215)
|.++|.-+|+- ..|.||...--+|.- ....-..|+--||.-||-.||+..- |....| .||.|.+||-
T Consensus 155 a~a~Lekdd~~--~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgil--TsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 155 AAAFLEKDDEL--GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGIL--TSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred HHHhcCcchhh--hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHh--hccceeeeeeccCCCCCCcce
Confidence 45666666666 678888766544421 1223357999999999999998763 222332 5999999885
No 58
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.80 E-value=0.024 Score=54.54 Aligned_cols=72 Identities=21% Similarity=0.264 Sum_probs=48.0
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhhh
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIMLT 132 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q~ 132 (215)
.|.||.++....+ ...-|+|+|||-+.|+..++...-.-.--...+||-+.-.=.-+.. .|+|.+...
T Consensus 186 ~C~ICf~e~~G~~--c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g----------~vKelvg~E 253 (445)
T KOG1814|consen 186 DCCICFEEQMGQH--CFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPG----------QVKELVGDE 253 (445)
T ss_pred cceeeehhhcCcc--eeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCch----------HHHHHHHHH
Confidence 4999999976544 6777899999999999999877643332345567766443222211 466666665
Q ss_pred hhhh
Q 028040 133 GLEK 136 (215)
Q Consensus 133 ~wAr 136 (215)
-.||
T Consensus 254 L~ar 257 (445)
T KOG1814|consen 254 LFAR 257 (445)
T ss_pred HHHH
Confidence 5555
No 59
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.49 E-value=0.011 Score=55.91 Aligned_cols=50 Identities=24% Similarity=0.519 Sum_probs=40.9
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
.-.|+|||+-|.. .....-|+|-|-.+||..=++.. +..||.||+.+.-.
T Consensus 43 ~v~c~icl~llk~----tmttkeClhrfc~~ci~~a~r~g-------n~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 43 QVICPICLSLLKK----TMTTKECLHRFCFDCIWKALRSG-------NNECPTCRKKLVSK 92 (381)
T ss_pred hhccHHHHHHHHh----hcccHHHHHHHHHHHHHHHHHhc-------CCCCchHHhhcccc
Confidence 3679999999966 35667899999999999999873 45699999987653
No 60
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.38 E-value=0.046 Score=46.56 Aligned_cols=50 Identities=20% Similarity=0.457 Sum_probs=34.3
Q ss_pred CCccccccccccccccCCeeeecCCC---ccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLH---VIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~H---vFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
+..|-||.++-. + +..-=.|.. ..|.+||.+|+..... -.|++|+++.--
T Consensus 8 ~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~------~~CeiC~~~Y~i 60 (162)
T PHA02825 8 DKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKN------KSCKICNGPYNI 60 (162)
T ss_pred CCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCC------CcccccCCeEEE
Confidence 488999987731 1 221113545 6799999999987533 359999988643
No 61
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.34 E-value=0.052 Score=48.22 Aligned_cols=50 Identities=30% Similarity=0.681 Sum_probs=40.8
Q ss_pred CccccccccccccccCCeee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEEESGSETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
+.|-||.++|..+|+..+-| |.|||.|=..|+.+.+... ...||.||.+.
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~-------~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNS-------RILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCc-------eeeccCCCCcc
Confidence 57999999999876434444 7899999999999998763 44689999986
No 62
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.31 E-value=0.021 Score=52.99 Aligned_cols=46 Identities=22% Similarity=0.410 Sum_probs=36.7
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|+||+..-. -.++|.|+|.|-..||.--..... ..|++||.+|.
T Consensus 8 ~eC~IC~nt~n-----~Pv~l~C~HkFCyiCiKGsy~ndk-------~~CavCR~pid 53 (324)
T KOG0824|consen 8 KECLICYNTGN-----CPVNLYCFHKFCYICIKGSYKNDK-------KTCAVCRFPID 53 (324)
T ss_pred CcceeeeccCC-----cCccccccchhhhhhhcchhhcCC-------CCCceecCCCC
Confidence 67999998753 369999999999999976554432 24999999985
No 63
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.95 E-value=0.035 Score=52.10 Aligned_cols=56 Identities=20% Similarity=0.514 Sum_probs=37.7
Q ss_pred CCccccccccccccccCCeee---e-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 51 PPKCCQCQAVLEEESGSETTR---L-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvR---L-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
+..|.||++...+-- ....| | +|.|.|-..|++.|-.....++ .-...||.||...
T Consensus 161 ~k~CGICme~i~ek~-~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~-~~sksCP~CRv~s 220 (344)
T KOG1039|consen 161 EKECGICMETINEKA-ASERRFGILPNCNHSFCLNCIRKWRQATQFES-KTSKSCPFCRVPS 220 (344)
T ss_pred cccceehhhhccccc-hhhhhcccCCCcchhhhhcHhHhhhhhhcccc-ccccCCCcccCcc
Confidence 478999999986532 11233 3 5999999999999974332111 1245699998764
No 64
>PHA02862 5L protein; Provisional
Probab=93.82 E-value=0.049 Score=46.02 Aligned_cols=47 Identities=26% Similarity=0.469 Sum_probs=34.0
Q ss_pred CccccccccccccccCCeeeecC-----CCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGC-----LHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C-----~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
+.|-||.++= ++ + + -+| .-..|.+||.+|+..... -.|++|+.+..-
T Consensus 3 diCWIC~~~~--~e--~-~-~PC~C~GS~K~VHq~CL~~WIn~S~k------~~CeLCkteY~I 54 (156)
T PHA02862 3 DICWICNDVC--DE--R-N-NFCGCNEEYKVVHIKCMQLWINYSKK------KECNLCKTKYNI 54 (156)
T ss_pred CEEEEecCcC--CC--C-c-ccccccCcchhHHHHHHHHHHhcCCC------cCccCCCCeEEE
Confidence 6799999872 22 2 2 344 578999999999965432 359999998754
No 65
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.68 E-value=0.038 Score=55.10 Aligned_cols=72 Identities=18% Similarity=0.389 Sum_probs=53.0
Q ss_pred CCCCceeeeecceee-ccCCCCCCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q 028040 29 PEHQICVVRTYSEWV-IDGEYDWPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 29 ~~H~~CvVqsYlqwL-~Dsdyd~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
.||+-=|+.|-..=| .++..+ ..|.+|.++-+ +.+.-.|+|+|-+.||.+++..+..+ ++.+||+|...
T Consensus 515 aDHP~LVl~S~~~n~~~enk~~--~~C~lc~d~ae-----d~i~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP~C~i~ 584 (791)
T KOG1002|consen 515 ADHPDLVLYSANANLPDENKGE--VECGLCHDPAE-----DYIESSCHHKFCRLCIKEYVESFMEN---NNVTCPVCHIG 584 (791)
T ss_pred ccCcceeeehhhcCCCccccCc--eeecccCChhh-----hhHhhhhhHHHHHHHHHHHHHhhhcc---cCCCCcccccc
Confidence 467777765433333 333344 78999998843 46777899999999999999987654 46899999877
Q ss_pred ccC
Q 028040 108 IWP 110 (215)
Q Consensus 108 I~P 110 (215)
+--
T Consensus 585 Lsi 587 (791)
T KOG1002|consen 585 LSI 587 (791)
T ss_pred ccc
Confidence 643
No 66
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.64 E-value=0.048 Score=52.77 Aligned_cols=48 Identities=29% Similarity=0.552 Sum_probs=38.0
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
.|-||-+. | +++..-+|||++-..||-.|-.+. .|..||-||..|--.
T Consensus 371 LCKICaen----d-KdvkIEPCGHLlCt~CLa~WQ~sd------~gq~CPFCRcEIKGt 418 (563)
T KOG1785|consen 371 LCKICAEN----D-KDVKIEPCGHLLCTSCLAAWQDSD------EGQTCPFCRCEIKGT 418 (563)
T ss_pred HHHHhhcc----C-CCcccccccchHHHHHHHhhcccC------CCCCCCceeeEeccc
Confidence 68888764 3 567778999999999999998764 255699999887543
No 67
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.62 E-value=0.043 Score=56.76 Aligned_cols=40 Identities=30% Similarity=0.673 Sum_probs=33.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
..|..|...|+- -.|...|+|.||..|+. ++ ...||.|+.
T Consensus 841 skCs~C~~~Ldl----P~VhF~CgHsyHqhC~e---~~--------~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDL----PFVHFLCGHSYHQHCLE---DK--------EDKCPKCLP 880 (933)
T ss_pred eeecccCCcccc----ceeeeecccHHHHHhhc---cC--------cccCCccch
Confidence 589999999966 47888999999999999 22 346999966
No 68
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.49 E-value=0.038 Score=39.95 Aligned_cols=47 Identities=23% Similarity=0.619 Sum_probs=32.2
Q ss_pred CCCccccccccccccccCCeeeecCCCc-cCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 50 WPPKCCQCQAVLEEESGSETTRLGCLHV-IHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 50 ~~~~C~ICle~L~~gD~~evvRL~C~Hv-FH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
|...|.||.+.-. +.+.-.|||. +-.+|-.+..+.. +-.||+||.+|
T Consensus 6 ~~dECTICye~pv-----dsVlYtCGHMCmCy~Cg~rl~~~~-------~g~CPiCRapi 53 (62)
T KOG4172|consen 6 WSDECTICYEHPV-----DSVLYTCGHMCMCYACGLRLKKAL-------HGCCPICRAPI 53 (62)
T ss_pred cccceeeeccCcc-----hHHHHHcchHHhHHHHHHHHHHcc-------CCcCcchhhHH
Confidence 4478999988632 2455589997 4567766655542 23699999887
No 69
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.14 E-value=0.28 Score=43.67 Aligned_cols=67 Identities=15% Similarity=0.188 Sum_probs=44.8
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCC--CCCCcchHHHHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKN--VKDSGSRLHSLLKEA 128 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~--i~d~~S~l~~~Lre~ 128 (215)
-.|+|...+|...- -.+.| +|||||=..+|.+-- .. -.||+|.++....+- +.+... -.+.|+++
T Consensus 114 ~~CPvt~~~~~~~~--~fv~l~~cG~V~s~~alke~k---~~------~~Cp~c~~~f~~~DiI~Lnp~~e-e~~~l~~~ 181 (260)
T PF04641_consen 114 FICPVTGKEFNGKH--KFVYLRPCGCVFSEKALKELK---KS------KKCPVCGKPFTEEDIIPLNPPEE-ELEKLRER 181 (260)
T ss_pred eECCCCCcccCCce--eEEEEcCCCCEeeHHHHHhhc---cc------ccccccCCccccCCEEEecCCcc-HHHHHHHH
Confidence 56999999995442 56666 899999999999983 11 139999999764331 222223 34556555
Q ss_pred hh
Q 028040 129 IM 130 (215)
Q Consensus 129 i~ 130 (215)
+.
T Consensus 182 ~~ 183 (260)
T PF04641_consen 182 ME 183 (260)
T ss_pred HH
Confidence 53
No 70
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.00 E-value=0.073 Score=55.26 Aligned_cols=36 Identities=28% Similarity=0.561 Sum_probs=30.8
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSF 90 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~ 90 (215)
..|.+|..+|... --...+|||.||+.||.+.....
T Consensus 818 d~C~~C~~~ll~~---pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 818 DSCDHCGRPLLIK---PFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred cchHHhcchhhcC---cceeeeccchHHHHHHHHHHHcc
Confidence 7899999999774 46667999999999999998765
No 71
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.90 E-value=0.043 Score=51.34 Aligned_cols=48 Identities=31% Similarity=0.630 Sum_probs=40.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
-.|.+|...|-+ .++.--|+|.|-+.||-++|+.. ++ ||.|...|--.
T Consensus 16 itC~LC~GYliD----ATTI~eCLHTFCkSCivk~l~~~--~~------CP~C~i~ih~t 63 (331)
T KOG2660|consen 16 ITCRLCGGYLID----ATTITECLHTFCKSCIVKYLEES--KY------CPTCDIVIHKT 63 (331)
T ss_pred eehhhccceeec----chhHHHHHHHHHHHHHHHHHHHh--cc------CCccceeccCc
Confidence 689999999976 36667899999999999999983 33 99999888653
No 72
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.45 E-value=0.11 Score=49.56 Aligned_cols=46 Identities=26% Similarity=0.586 Sum_probs=37.0
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
-.|.||..-|.. .+.++|||.|-..||++-+.+.. .||.||.++.-
T Consensus 85 f~c~vc~~~l~~-----pv~tpcghs~c~~Cl~r~ld~~~--------~cp~Cr~~l~e 130 (398)
T KOG4159|consen 85 FECCVCSRALYP-----PVVTPCGHSFCLECLDRSLDQET--------ECPLCRDELVE 130 (398)
T ss_pred hhhhhhHhhcCC-----CccccccccccHHHHHHHhccCC--------CCccccccccc
Confidence 459999888754 66669999999999999666432 49999999984
No 73
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.26 E-value=0.2 Score=46.23 Aligned_cols=50 Identities=22% Similarity=0.440 Sum_probs=38.9
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
..+|++|.+.=.. --+..+|+|+|---|+..-+.-. +.|+||.|..+.-|
T Consensus 239 ~~~C~~Cg~~Pti----P~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 239 DTECPVCGEPPTI----PHVIGKCGHIYCYYCIATSRLWD------ASFTCPLCGENVEP 288 (298)
T ss_pred CceeeccCCCCCC----Ceeeccccceeehhhhhhhhcch------hhcccCccCCCCcc
Confidence 3789999987432 24445799999999999887642 57889999998865
No 74
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=91.20 E-value=0.21 Score=34.69 Aligned_cols=45 Identities=24% Similarity=0.504 Sum_probs=20.5
Q ss_pred cccccccccccccCCeeee--cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 54 CCQCQAVLEEESGSETTRL--GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL--~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
|++|.++|+..| ...+ .|++-+-+.|...-++. .+-+||.||++.
T Consensus 1 cp~C~e~~d~~d---~~~~PC~Cgf~IC~~C~~~i~~~-------~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETD---KDFYPCECGFQICRFCYHDILEN-------EGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCC---TT--SSTTS----HHHHHHHTTS-------S-SB-TTT--B-
T ss_pred CCCcccccccCC---CccccCcCCCcHHHHHHHHHHhc-------cCCCCCCCCCCC
Confidence 789999996554 3444 58877777776666642 244799999863
No 75
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=90.50 E-value=0.21 Score=47.24 Aligned_cols=51 Identities=22% Similarity=0.572 Sum_probs=41.2
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNV 114 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i 114 (215)
-.|++|...+.+- +....|+|.|-..|+++|+..++ .||.|+..+.....+
T Consensus 22 l~C~~C~~vl~~p----~~~~~cgh~fC~~C~~~~~~~~~--------~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 22 LLCPICMSVLRDP----VQTTTCGHRFCAGCLLESLSNHQ--------KCPVCRQELTQAEEL 72 (391)
T ss_pred ccCccccccccCC----CCCCCCCCcccccccchhhccCc--------CCcccccccchhhcc
Confidence 5699999999663 33379999999999999998732 499999998875443
No 76
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.84 E-value=0.15 Score=36.52 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=26.7
Q ss_pred CeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 68 ETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 68 evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
.-+.|+|+|+.=..|.+-+=-+ -||.|.+++.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rYn----------gCPfC~~~~~~~ 52 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERYN----------GCPFCGTPFEFD 52 (55)
T ss_pred ccccccccceeeccccChhhcc----------CCCCCCCcccCC
Confidence 4566899999999998866433 299999999764
No 77
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=89.41 E-value=0.2 Score=33.55 Aligned_cols=43 Identities=19% Similarity=0.581 Sum_probs=21.7
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
|.+|.+-...|. .-....|.=.+|..|++.+++..... +||.|
T Consensus 1 C~~C~~iv~~G~--~C~~~~C~~r~H~~C~~~y~r~~~~~------~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQ--RCSNRDCNVRLHDDCFKKYFRHRSNP------KCPNC 43 (43)
T ss_dssp -TTT-SB-SSSE--E-SS--S--EE-HHHHHHHTTT-SS-------B-TTT
T ss_pred CcccchhHeeec--cCCCCccCchHHHHHHHHHHhcCCCC------CCcCC
Confidence 556666655442 22222477789999999999886432 59988
No 78
>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 KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.04 E-value=0.19 Score=47.54 Aligned_cols=55 Identities=25% Similarity=0.547 Sum_probs=36.0
Q ss_pred ecceeeccCCC---CCCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 38 TYSEWVIDGEY---DWPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 38 sYlqwL~Dsdy---d~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
+..|| +++-+ ..++.|.||+++.. +.+-++|||+-- |..-.. +.+ +||+||..|-
T Consensus 290 tr~~~-~~~~~~~~~~p~lcVVcl~e~~-----~~~fvpcGh~cc--ct~cs~-~l~--------~CPvCR~rI~ 347 (355)
T KOG1571|consen 290 TRIQN-ENGTFRELPQPDLCVVCLDEPK-----SAVFVPCGHVCC--CTLCSK-HLP--------QCPVCRQRIR 347 (355)
T ss_pred ccccc-ccCcccccCCCCceEEecCCcc-----ceeeecCCcEEE--chHHHh-hCC--------CCchhHHHHH
Confidence 33455 44433 34689999999864 478899999943 444332 211 3999998774
No 80
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.86 E-value=0.4 Score=43.98 Aligned_cols=49 Identities=18% Similarity=0.253 Sum_probs=41.0
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
-.|++|...|.+.. ....| +|||||-.+|..+.++.- -.||+|.+++--
T Consensus 222 yiCpvtrd~LtNt~--~ca~Lr~sg~Vv~~ecvEklir~D--------~v~pv~d~plkd 271 (303)
T KOG3039|consen 222 YICPVTRDTLTNTT--PCAVLRPSGHVVTKECVEKLIRKD--------MVDPVTDKPLKD 271 (303)
T ss_pred eecccchhhhcCcc--ceEEeccCCcEeeHHHHHHhcccc--------ccccCCCCcCcc
Confidence 45999999998864 56667 899999999999999863 469999988754
No 81
>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=88.22 E-value=0.68 Score=39.57 Aligned_cols=54 Identities=22% Similarity=0.447 Sum_probs=36.1
Q ss_pred CccccccccccccccCCeeeecC------------C-CccCHHHHHHHHhcCCCCC-----------------------C
Q 028040 52 PKCCQCQAVLEEESGSETTRLGC------------L-HVIHTSCLVSHIKSFPPHT-----------------------A 95 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C------------~-HvFH~~CLd~Wl~~~p~nT-----------------------a 95 (215)
..|+||++-=.+ .|-|.| . -.-|..|||++-+.....+ .
T Consensus 3 ~~CpICme~PHN-----AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 3 VTCPICMEHPHN-----AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred ccCceeccCCCc-----eEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 679999987543 444443 2 3459999999976653221 1
Q ss_pred CCCCCCCCCCCCccC
Q 028040 96 PAGYVCPLCSTTIWP 110 (215)
Q Consensus 96 p~g~~CP~Cr~~I~P 110 (215)
.....||+||..|.-
T Consensus 78 ~~~L~CPLCRG~V~G 92 (162)
T PF07800_consen 78 QPELACPLCRGEVKG 92 (162)
T ss_pred cccccCccccCceec
Confidence 126789999999874
No 82
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.10 E-value=0.29 Score=45.46 Aligned_cols=63 Identities=22% Similarity=0.329 Sum_probs=47.1
Q ss_pred CCCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcchHHHHHHHH
Q 028040 50 WPPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEA 128 (215)
Q Consensus 50 ~~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~ 128 (215)
.|..|-||.+.|.. .|+-.|+|.|-..|..+-++..+ .|.+|.+.+.-..+ .+.-|...|+..
T Consensus 240 ~Pf~c~icr~~f~~-----pVvt~c~h~fc~~ca~~~~qk~~--------~c~vC~~~t~g~~~---~akeL~~~L~~k 302 (313)
T KOG1813|consen 240 LPFKCFICRKYFYR-----PVVTKCGHYFCEVCALKPYQKGE--------KCYVCSQQTHGSFN---VAKELLVSLKLK 302 (313)
T ss_pred CCcccccccccccc-----chhhcCCceeehhhhccccccCC--------cceecccccccccc---hHHHHHHHHHhh
Confidence 35679999999954 78889999999999999887643 49999998875433 234455555443
No 83
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.89 E-value=0.61 Score=33.20 Aligned_cols=32 Identities=19% Similarity=0.396 Sum_probs=27.7
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVS 85 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~ 85 (215)
..|.+|.+.|.++| ++|+- .|+=.+|++|-+.
T Consensus 6 ~~C~~Cg~~~~~~d--DiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD--DIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCC--CEEECCCCCCcccHHHHhh
Confidence 78999999999776 78886 5999999999654
No 84
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=87.68 E-value=0.36 Score=50.06 Aligned_cols=36 Identities=25% Similarity=0.462 Sum_probs=28.8
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSF 90 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~ 90 (215)
..|++|--..... -.+-+.|+|+.|..|...|++..
T Consensus 1029 ~~C~~C~l~V~gs---s~~Cg~C~Hv~H~sc~~eWf~~g 1064 (1081)
T KOG0309|consen 1029 FQCAICHLAVRGS---SNFCGTCGHVGHTSCMMEWFRTG 1064 (1081)
T ss_pred eeeeeEeeEeecc---chhhccccccccHHHHHHHHhcC
Confidence 3488887766543 36667999999999999999975
No 85
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.28 E-value=0.48 Score=45.40 Aligned_cols=51 Identities=24% Similarity=0.340 Sum_probs=40.0
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
--.|+|=.+.=.+.. -..+|.||||.=++-|++..+... ..|+||-|-...
T Consensus 334 vF~CPVlKeqtsdeN--PPm~L~CGHVISkdAlnrLS~ng~-----~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 334 VFICPVLKEQTSDEN--PPMMLICGHVISKDALNRLSKNGS-----QSFKCPYCPVEQ 384 (394)
T ss_pred eeecccchhhccCCC--CCeeeeccceecHHHHHHHhhCCC-----eeeeCCCCCccc
Confidence 356888887765554 799999999999999999988643 258999994443
No 86
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.01 E-value=0.08 Score=50.92 Aligned_cols=49 Identities=16% Similarity=0.290 Sum_probs=41.0
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|+||.+.|...- +.+..+.|||++|..||.+||.... +||.|++.+-
T Consensus 197 ~sl~I~~~slK~~y-~k~~~~~~g~~~~~~kL~k~L~~~~--------kl~~~~rel~ 245 (465)
T KOG0827|consen 197 GSLSICFESLKQNY-DKISAIVCGHIYHHGKLSKWLATKR--------KLPSCRRELP 245 (465)
T ss_pred hhhHhhHHHHHHHH-HHHHHHhhcccchhhHHHHHHHHHH--------HhHHHHhhhh
Confidence 57999999998752 2577789999999999999998743 4999999874
No 87
>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=83.40 E-value=1.1 Score=41.71 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=35.1
Q ss_pred cccccccccc-ccccCCeeee--cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 53 KCCQCQAVLE-EESGSETTRL--GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 53 ~C~ICle~L~-~gD~~evvRL--~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
.|++|...-- +- ++..| +|+|..-.+|.|.-+... .+.||-|++.+--
T Consensus 2 ~Cp~CKt~~Y~np---~lk~~in~C~H~lCEsCvd~iF~~g-------~~~CpeC~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNP---DLKLMINECGHRLCESCVDRIFSLG-------PAQCPECMVILRK 52 (300)
T ss_pred CCcccccceecCc---cceeeeccccchHHHHHHHHHHhcC-------CCCCCcccchhhh
Confidence 4888876532 32 24333 799999999999999874 4579999887653
No 88
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.98 E-value=0.76 Score=42.27 Aligned_cols=60 Identities=25% Similarity=0.463 Sum_probs=41.8
Q ss_pred CCccccccccccccccCCee--eecCC-----CccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC---ccCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETT--RLGCL-----HVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT---IWPPKN 113 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evv--RL~C~-----HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~---I~P~~~ 113 (215)
+.-|=||...=++. ... .=||. |=.|.+||..|+..+..+.+-+.-.||.|++. ++|+-.
T Consensus 20 eR~CWiCF~TdeDn---~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~ 89 (293)
T KOG3053|consen 20 ERCCWICFATDEDN---RLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLG 89 (293)
T ss_pred ceeEEEEeccCccc---chhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccC
Confidence 47899998763221 111 12553 88999999999988766555577889999997 456543
No 89
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=80.93 E-value=0.64 Score=41.54 Aligned_cols=47 Identities=19% Similarity=0.448 Sum_probs=38.8
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
|-.|.||.++++. .+.-.|||.|-..|...-.+..+ .|-+|.+...-
T Consensus 196 PF~C~iCKkdy~s-----pvvt~CGH~FC~~Cai~~y~kg~--------~C~~Cgk~t~G 242 (259)
T COG5152 196 PFLCGICKKDYES-----PVVTECGHSFCSLCAIRKYQKGD--------ECGVCGKATYG 242 (259)
T ss_pred ceeehhchhhccc-----hhhhhcchhHHHHHHHHHhccCC--------cceecchhhcc
Confidence 4589999999854 77789999999999998887643 59999887664
No 90
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=79.68 E-value=0.9 Score=39.83 Aligned_cols=53 Identities=23% Similarity=0.402 Sum_probs=37.7
Q ss_pred CccccccccccccccCCeeeecCC-----CccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCL-----HVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~-----HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
..|.||..+..... .+....+|. +..|..|++.|+..+. ...|.+|.....+.
T Consensus 79 ~~cRIc~~~~~~~~-~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~------~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 79 PICRICHEEDEESN-GLLLISPCSCKGSLAYVHRSCLEKWFSIKG------NITCEICKSFFINV 136 (323)
T ss_pred CcEEEEeccccccc-ccccccCccccCcHHHHHHHHHHhhhcccc------Ceeeecccccceec
Confidence 56999999876543 123444553 7789999999998653 34599998866553
No 91
>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=78.08 E-value=0.85 Score=41.81 Aligned_cols=47 Identities=23% Similarity=0.501 Sum_probs=36.0
Q ss_pred CCccccccccccccccCCeeee--c-CCCccCHHHHHHHHhcCCCCCCCCCCCCC--CCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRL--G-CLHVIHTSCLVSHIKSFPPHTAPAGYVCP--LCST 106 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL--~-C~HvFH~~CLd~Wl~~~p~nTap~g~~CP--~Cr~ 106 (215)
+..|+||..+---.- ++..| | |+|-+-.+|.|+-|...|+ +|| -|.+
T Consensus 10 d~~CPvCksDrYLnP--dik~linPECyHrmCESCvdRIFs~GpA-------qCP~~gC~k 61 (314)
T COG5220 10 DRRCPVCKSDRYLNP--DIKILINPECYHRMCESCVDRIFSRGPA-------QCPYKGCGK 61 (314)
T ss_pred cccCCccccccccCC--CeEEEECHHHHHHHHHHHHHHHhcCCCC-------CCCCccHHH
Confidence 368999988754332 46666 4 9999999999999988765 599 7854
No 92
>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=77.94 E-value=1.8 Score=29.56 Aligned_cols=36 Identities=33% Similarity=0.645 Sum_probs=23.7
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
.|+.|.+.|.... |...+....... ...+.||+|.+
T Consensus 4 ~CP~C~~~~~~~~-----------------L~~H~~~~H~~~-~~~v~CPiC~~ 39 (54)
T PF05605_consen 4 TCPYCGKGFSESS-----------------LVEHCEDEHRSE-SKNVVCPICSS 39 (54)
T ss_pred CCCCCCCccCHHH-----------------HHHHHHhHCcCC-CCCccCCCchh
Confidence 4999999776544 555655443322 24689999975
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.33 E-value=2.1 Score=41.13 Aligned_cols=46 Identities=28% Similarity=0.531 Sum_probs=34.0
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
...|.||.+.+.- ..++||+|-.--.|-.+.-.-. ....||+||+.
T Consensus 61 n~~C~ICA~~~TY-----s~~~PC~H~~CH~Ca~RlRALY------~~K~C~~CrTE 106 (493)
T COG5236 61 NMNCQICAGSTTY-----SARYPCGHQICHACAVRLRALY------MQKGCPLCRTE 106 (493)
T ss_pred cceeEEecCCceE-----EEeccCCchHHHHHHHHHHHHH------hccCCCccccc
Confidence 4799999988744 6789999999888876652221 12249999986
No 94
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.31 E-value=1.4 Score=41.57 Aligned_cols=43 Identities=26% Similarity=0.675 Sum_probs=34.8
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
-.|++|..-|.+ .++- -|+|.|-.+||..-|.. ..|.||.|.+
T Consensus 275 LkCplc~~Llrn-----p~kT~cC~~~fc~eci~~al~d-------sDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRN-----PMKTPCCGHTFCDECIGTALLD-------SDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhC-----cccCccccchHHHHHHhhhhhh-------ccccCCCccc
Confidence 679999998866 3444 59999999999977654 3688999976
No 95
>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=76.03 E-value=3.4 Score=28.33 Aligned_cols=44 Identities=23% Similarity=0.561 Sum_probs=19.0
Q ss_pred ccccccccccccccCCeeee-cCCCccCHHHHH--HHHhcCCCCCCCCCCCCCCCCCC
Q 028040 53 KCCQCQAVLEEESGSETTRL-GCLHVIHTSCLV--SHIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd--~Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
.|+|-...+.. .+|- .|.|+ +|+| .||+....+ ..+.||+|+++
T Consensus 4 ~CPls~~~i~~-----P~Rg~~C~H~---~CFDl~~fl~~~~~~---~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIRI-----PVRGKNCKHL---QCFDLESFLESNQRT---PKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-SS-----EEEETT--SS-----EEHHHHHHHHHHS------B-TTT---
T ss_pred eCCCCCCEEEe-----CccCCcCccc---ceECHHHHHHHhhcc---CCeECcCCcCc
Confidence 57777777643 6664 79876 4643 455543322 34889999874
No 96
>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=74.00 E-value=0.12 Score=34.32 Aligned_cols=47 Identities=19% Similarity=0.444 Sum_probs=31.4
Q ss_pred cccccccccccccCCeee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 54 CCQCQAVLEEESGSETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 54 C~ICle~L~~gD~~evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
|.||.+...++ +.+. -.|.-.||..|+..-....... ...+.||.|+
T Consensus 2 C~vC~~~~~~~---~~i~C~~C~~~~H~~C~~~~~~~~~~~--~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQSDDDG---DMIQCDSCNRWYHQECVGPPEKAEEIP--SGDWYCPNCR 49 (51)
T ss_dssp BTTTTSSCTTS---SEEEBSTTSCEEETTTSTSSHSHHSHH--SSSBSSHHHH
T ss_pred CcCCCCcCCCC---CeEEcCCCChhhCcccCCCChhhccCC--CCcEECcCCc
Confidence 88998843332 3444 3799999999998776533211 1378899885
No 97
>PHA03096 p28-like protein; Provisional
Probab=70.92 E-value=2.6 Score=38.66 Aligned_cols=39 Identities=13% Similarity=0.141 Sum_probs=28.1
Q ss_pred Ccccccccccccccc--CCeeee-cCCCccCHHHHHHHHhcC
Q 028040 52 PKCCQCQAVLEEESG--SETTRL-GCLHVIHTSCLVSHIKSF 90 (215)
Q Consensus 52 ~~C~ICle~L~~gD~--~evvRL-~C~HvFH~~CLd~Wl~~~ 90 (215)
-.|.||++...+... ..-..| .|.|.|-..|+..|....
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~ 220 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTES 220 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhh
Confidence 469999998765310 112225 599999999999998764
No 98
>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=69.92 E-value=3.9 Score=34.08 Aligned_cols=29 Identities=24% Similarity=0.437 Sum_probs=23.9
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIML 131 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q 131 (215)
+|.||.|...+..-+ +|.+.++|+++|.+
T Consensus 128 ~F~Cp~Cg~~L~~~d-----n~~~i~~l~~~i~~ 156 (158)
T TIGR00373 128 NFTCPRCGAMLDYLD-----NSEAIEKLEEQIKF 156 (158)
T ss_pred CCcCCCCCCEeeecc-----CHHHHHHHHHHHHh
Confidence 789999999987654 47888999988864
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.75 E-value=5 Score=34.20 Aligned_cols=31 Identities=32% Similarity=0.461 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhhh
Q 028040 97 AGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIMLT 132 (215)
Q Consensus 97 ~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q~ 132 (215)
.+|.||.|...+..-. ++.+.+.|+++|.+-
T Consensus 135 ~~F~Cp~Cg~~L~~~d-----n~~~~~~l~~~I~~l 165 (178)
T PRK06266 135 YGFRCPQCGEMLEEYD-----NSELIKELKEQIKEL 165 (178)
T ss_pred cCCcCCCCCCCCeecc-----cHHHHHHHHHHHHHH
Confidence 3789999999998754 477889999888864
No 100
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=67.42 E-value=2.4 Score=40.15 Aligned_cols=69 Identities=23% Similarity=0.462 Sum_probs=41.8
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcc-----hHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGS-----RLHSLL 125 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S-----~l~~~L 125 (215)
--|--|-.++.. --|| +|.|||-.+|...--. ..||.|...|.-=+.+ ..++ .+.--+
T Consensus 91 HfCd~Cd~PI~I-----YGRmIPCkHvFCl~CAr~~~d----------K~Cp~C~d~VqrIeq~-~~g~iFmC~~~~GC~ 154 (389)
T KOG2932|consen 91 HFCDRCDFPIAI-----YGRMIPCKHVFCLECARSDSD----------KICPLCDDRVQRIEQI-MMGGIFMCAAPHGCL 154 (389)
T ss_pred EeecccCCccee-----eecccccchhhhhhhhhcCcc----------ccCcCcccHHHHHHHh-cccceEEeecchhHH
Confidence 357777777643 4566 8999999999754432 2499998877542221 1122 222246
Q ss_pred HHHhhhhhhhh
Q 028040 126 KEAIMLTGLEK 136 (215)
Q Consensus 126 re~i~q~~wAr 136 (215)
|.-|+|..+..
T Consensus 155 RTyLsqrDlqA 165 (389)
T KOG2932|consen 155 RTYLSQRDLQA 165 (389)
T ss_pred HHHhhHHHHHH
Confidence 66666666544
No 101
>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=63.92 E-value=10 Score=27.35 Aligned_cols=48 Identities=23% Similarity=0.528 Sum_probs=37.8
Q ss_pred CccccccccccccccCCeeeecCC--CccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCL--HVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~--HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
++|-.|..+|..+. .....|. -.|-.+|.+..|.. .||.|...+.+.+
T Consensus 6 pnCE~C~~dLp~~s---~~A~ICSfECTFC~~C~e~~l~~----------~CPNCgGelv~RP 55 (57)
T PF06906_consen 6 PNCECCDKDLPPDS---PEAYICSFECTFCADCAETMLNG----------VCPNCGGELVRRP 55 (57)
T ss_pred CCccccCCCCCCCC---CcceEEeEeCcccHHHHHHHhcC----------cCcCCCCccccCC
Confidence 88999999998753 4455554 47999999999965 4999999888753
No 102
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=62.56 E-value=6.7 Score=36.28 Aligned_cols=55 Identities=27% Similarity=0.487 Sum_probs=35.2
Q ss_pred CccccccccccccccCCeeeecC--CCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCCCCCcchHHHHHHHHh
Q 028040 52 PKCCQCQAVLEEESGSETTRLGC--LHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAI 129 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C--~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i 129 (215)
..|+||.+.|.. -.+.| ||+.-..|-.+-.. +||.||.+|- ++ .++..+++-|.+
T Consensus 49 leCPvC~~~l~~------Pi~QC~nGHlaCssC~~~~~~-----------~CP~Cr~~~g---~~---R~~amEkV~e~~ 105 (299)
T KOG3002|consen 49 LDCPVCFNPLSP------PIFQCDNGHLACSSCRTKVSN-----------KCPTCRLPIG---NI---RCRAMEKVAEAV 105 (299)
T ss_pred ccCchhhccCcc------cceecCCCcEehhhhhhhhcc-----------cCCccccccc---cH---HHHHHHHHHHhc
Confidence 579999999844 34566 45555555442222 4999999886 33 466677765543
No 103
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.54 E-value=2.7 Score=43.20 Aligned_cols=46 Identities=22% Similarity=0.368 Sum_probs=36.7
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|.||+..|.... -+.+-|.|||+.-..|+..-..+ +|| |+..=+
T Consensus 12 l~c~ic~n~f~~~~-~~Pvsl~cghtic~~c~~~lyn~----------scp-~~~De~ 57 (861)
T KOG3161|consen 12 LLCDICLNLFVVQR-LEPVSLQCGHTICGHCVQLLYNA----------SCP-TKRDED 57 (861)
T ss_pred hhchHHHHHHHHHh-cCcccccccchHHHHHHHhHhhc----------cCC-CCcccc
Confidence 57999999998765 57788999999999999887765 399 655433
No 104
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=62.16 E-value=4.1 Score=35.13 Aligned_cols=38 Identities=32% Similarity=0.718 Sum_probs=25.5
Q ss_pred Cccccccc-----cccccccCCeee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQA-----VLEEESGSETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 52 ~~C~ICle-----~L~~gD~~evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
..|.+|.. +|+.+ .+++ -.|+-+||.+|..+ . .||-|.
T Consensus 153 fiCe~C~~~~~IfPF~~~---~~~~C~~C~~v~H~~C~~~---~----------~CpkC~ 196 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQID---TTVRCPKCKSVFHKSCFRK---K----------SCPKCA 196 (202)
T ss_pred CCCccCCCCCCCCCCCCC---CeeeCCcCccccchhhcCC---C----------CCCCcH
Confidence 34777764 22221 4666 47999999999983 1 299994
No 105
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.67 E-value=3 Score=43.40 Aligned_cols=38 Identities=18% Similarity=0.418 Sum_probs=28.2
Q ss_pred Ccccccccccccccc--CCeeeecCCCccCHHHHHHHHhc
Q 028040 52 PKCCQCQAVLEEESG--SETTRLGCLHVIHTSCLVSHIKS 89 (215)
Q Consensus 52 ~~C~ICle~L~~gD~--~evvRL~C~HvFH~~CLd~Wl~~ 89 (215)
..|..|.++...... ..++++-|+|+||++|+-.-..+
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~ 824 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLR 824 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHh
Confidence 578888777652210 25889999999999999877655
No 106
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=61.31 E-value=8.9 Score=31.52 Aligned_cols=29 Identities=17% Similarity=0.479 Sum_probs=22.2
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIML 131 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q 131 (215)
..+||+|.. .++.|++++++..||+.+.+
T Consensus 40 ~LRC~vCqn-----qsiadSna~iA~dmR~~Vr~ 68 (126)
T PRK10144 40 QLRCPQCQN-----QNLLESNAPVAVSMRHQVYS 68 (126)
T ss_pred cCCCCCCCC-----CChhhcCCHHHHHHHHHHHH
Confidence 467999954 45777788999998877663
No 107
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=60.49 E-value=4.7 Score=39.45 Aligned_cols=18 Identities=28% Similarity=0.573 Sum_probs=14.8
Q ss_pred cccceeeeeccCccCccc
Q 028040 9 ATKLYCFVHKVPVCGECI 26 (215)
Q Consensus 9 ~T~~fCf~Hrv~VC~~Ci 26 (215)
+-..|=++-.+.-||.|+
T Consensus 313 ~Gq~FY~v~~k~~CE~cy 330 (468)
T KOG1701|consen 313 AGQSFYQVDGKPYCEGCY 330 (468)
T ss_pred ccccccccCCcccchHHH
Confidence 667777888888899987
No 108
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=58.63 E-value=6.8 Score=37.73 Aligned_cols=55 Identities=18% Similarity=0.301 Sum_probs=36.3
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNV 114 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i 114 (215)
+.-|++|.++++-.| +.----+||--.-.-|.+.--+.+ |. +||.||+-.. .+|+
T Consensus 14 ed~cplcie~mditd-knf~pc~cgy~ic~fc~~~irq~l--ng-----rcpacrr~y~-denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITD-KNFFPCPCGYQICQFCYNNIRQNL--NG-----RCPACRRKYD-DENV 68 (480)
T ss_pred cccCccccccccccc-CCcccCCcccHHHHHHHHHHHhhc--cC-----CChHhhhhcc-ccce
Confidence 367999999998876 444445788666566655444432 33 6999998654 3443
No 109
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=58.26 E-value=9.6 Score=31.32 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=21.8
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIML 131 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q 131 (215)
..+||.|.. .++.|++++++..||+.+.+
T Consensus 40 ~LRC~vCqn-----qsiadS~a~iA~dmR~~Vr~ 68 (126)
T TIGR03147 40 SLRCPQCQN-----QNLVESNSPIAYDLRHEVYS 68 (126)
T ss_pred hCCCCCCCC-----CChhhcCCHHHHHHHHHHHH
Confidence 467999954 45677788999888877663
No 110
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.87 E-value=7.5 Score=37.02 Aligned_cols=46 Identities=24% Similarity=0.418 Sum_probs=36.0
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
-.|++=.+.-.+.. -.+-|.||||.-.+-|+..-+... -.|+||-|
T Consensus 337 FiCPVlKe~~t~EN--pP~ml~CgHVIskeal~~LS~nG~-----~~FKCPYC 382 (396)
T COG5109 337 FICPVLKELCTDEN--PPVMLECGHVISKEALSVLSQNGV-----LSFKCPYC 382 (396)
T ss_pred eeccccHhhhcccC--CCeeeeccceeeHHHHHHHhhcCc-----EEeeCCCC
Confidence 57888777655543 678889999999999998776532 37999999
No 111
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=56.76 E-value=4.8 Score=41.26 Aligned_cols=51 Identities=25% Similarity=0.439 Sum_probs=41.5
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
...|+||.+...+ .+.+.|.|.|=..|+..-|...+ +...||+|+..+--.
T Consensus 21 ~lEc~ic~~~~~~-----p~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVKE-----PSLLKCDHIFLKFCLNKLFESKK-----GPKQCALCKSDIEKR 71 (684)
T ss_pred hccCCceeEEeec-----cchhhhhHHHHhhhhhceeeccC-----ccccchhhhhhhhhh
Confidence 3679999999855 57889999999999999988754 256799999877543
No 112
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=55.96 E-value=2.9 Score=42.03 Aligned_cols=26 Identities=42% Similarity=0.896 Sum_probs=19.6
Q ss_pred Ceee-ecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCC
Q 028040 68 ETTR-LGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLC 104 (215)
Q Consensus 68 evvR-L~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~C 104 (215)
.+.| ..|+++||..|+..--. .||.|
T Consensus 530 ~~~rC~~C~avfH~~C~~r~s~-----------~CPrC 556 (580)
T KOG1829|consen 530 NTRRCSTCLAVFHKKCLRRKSP-----------CCPRC 556 (580)
T ss_pred cceeHHHHHHHHHHHHHhccCC-----------CCCch
Confidence 4555 68999999999875332 29999
No 113
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=53.40 E-value=5.5 Score=35.86 Aligned_cols=33 Identities=36% Similarity=0.703 Sum_probs=23.9
Q ss_pred Ceeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 68 ETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 68 evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
+.-.| .|+|||-..|...=.. -.||+|+++|--
T Consensus 16 ~~f~LTaC~HvfC~~C~k~~~~----------~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 16 DPFFLTACRHVFCEPCLKASSP----------DVCPLCKKSIRI 49 (233)
T ss_pred CceeeeechhhhhhhhcccCCc----------cccccccceeee
Confidence 35666 6999999999753322 169999998643
No 114
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.03 E-value=2.9 Score=39.99 Aligned_cols=68 Identities=24% Similarity=0.465 Sum_probs=47.4
Q ss_pred cCcccccCCCCceeeeecceeeccCCCC-----C----CCccccccccccccccCC-eee--ecCCCccCHHHHHHHHhc
Q 028040 22 CGECICFPEHQICVVRTYSEWVIDGEYD-----W----PPKCCQCQAVLEEESGSE-TTR--LGCLHVIHTSCLVSHIKS 89 (215)
Q Consensus 22 C~~Ci~~~~H~~CvVqsYlqwL~Dsdyd-----~----~~~C~ICle~L~~gD~~e-vvR--L~C~HvFH~~CLd~Wl~~ 89 (215)
|..|. .+.|.-+..+....|++....+ | ...|+.|..+.+...+-. ... ..|.|.|+|-|+..|-.+
T Consensus 189 C~~C~-~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 189 CFACG-EESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred Hhhcc-ccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 66676 4788888888888888753321 1 244999999997653111 122 249999999999999876
Q ss_pred C
Q 028040 90 F 90 (215)
Q Consensus 90 ~ 90 (215)
.
T Consensus 268 ~ 268 (444)
T KOG1815|consen 268 G 268 (444)
T ss_pred c
Confidence 4
No 115
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.01 E-value=9.2 Score=36.30 Aligned_cols=56 Identities=21% Similarity=0.361 Sum_probs=36.5
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCC--CCCCCcc
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCP--LCSTTIW 109 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP--~Cr~~I~ 109 (215)
..+|.||..+....+ +.-..+.|+|-|-.+|+.++++.+- ..-...+|| .|...+-
T Consensus 146 ~~~C~iC~~e~~~~~-~~f~~~~C~H~fC~~C~k~~iev~~--~~~~~~~C~~~~C~~~l~ 203 (384)
T KOG1812|consen 146 KEECGICFVEDPEAE-DMFSVLKCGHRFCKDCVKQHIEVKL--LSGTVIRCPHDGCESRLT 203 (384)
T ss_pred cccCccCccccccHh-hhHHHhcccchhhhHHhHHHhhhhh--ccCCCccCCCCCCCccCC
Confidence 368999996655543 1233568999999999999998662 222344564 3544443
No 116
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.62 E-value=3.3 Score=38.90 Aligned_cols=41 Identities=27% Similarity=0.554 Sum_probs=28.6
Q ss_pred CccccccccccccccCCeeeecCCCcc-CHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVI-HTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvF-H~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|.||.+-- .+.+-|.|||.. -.+|=...- .||+||+-|.
T Consensus 301 ~LC~ICmDaP-----~DCvfLeCGHmVtCt~CGkrm~------------eCPICRqyi~ 342 (350)
T KOG4275|consen 301 RLCAICMDAP-----RDCVFLECGHMVTCTKCGKRMN------------ECPICRQYIV 342 (350)
T ss_pred HHHHHHhcCC-----cceEEeecCcEEeehhhccccc------------cCchHHHHHH
Confidence 6799998763 358999999975 344433222 3999998765
No 117
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=48.35 E-value=5.1 Score=25.52 Aligned_cols=25 Identities=28% Similarity=0.635 Sum_probs=20.7
Q ss_pred cccceeeeeccCccCcccccCCCCce
Q 028040 9 ATKLYCFVHKVPVCGECICFPEHQIC 34 (215)
Q Consensus 9 ~T~~fCf~Hrv~VC~~Ci~~~~H~~C 34 (215)
..++||...++.+|..|+. ..|..-
T Consensus 13 ~~~~~C~~C~~~~C~~C~~-~~H~~H 37 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCSECTV-SGHKGH 37 (42)
T ss_dssp BEEEEETTTTEEEEHHHHH-TSTTTS
T ss_pred ceEEEecCCCCccCccCCC-CCCCCC
Confidence 3899999999999999996 447653
No 118
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=48.15 E-value=11 Score=39.84 Aligned_cols=48 Identities=19% Similarity=0.414 Sum_probs=34.9
Q ss_pred CccccccccccccccCCeeeecCC-----CccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCL-----HVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~-----HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
..|.||..+=..+| ..-=||. -..|.+||-+|+.... ...|-+|..++
T Consensus 13 ~~CRICr~e~~~d~---pLfhPCKC~GSIkYiH~eCL~eW~~~s~------~~kCdiChy~~ 65 (1175)
T COG5183 13 RSCRICRTEDIRDD---PLFHPCKCSGSIKYIHRECLMEWMECSG------TKKCDICHYEY 65 (1175)
T ss_pred hhceeecCCCCCCC---cCcccccccchhHHHHHHHHHHHHhcCC------Ccceeeeccee
Confidence 78999998855543 3333554 4689999999998542 34699999765
No 119
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=47.95 E-value=16 Score=34.54 Aligned_cols=50 Identities=22% Similarity=0.347 Sum_probs=37.4
Q ss_pred CCccccccccccccccCCeeee--cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRL--GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL--~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
++.|++|-+++...| -..| +|++..++.|+..-.... .+||.||++.+-.
T Consensus 249 ~~s~p~~~~~~~~~d---~~~lP~~~~~~~~l~~~~t~~~~~--------~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTD---SNFLPCPCGFRLCLFCHKTISDGD--------GRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCCcccccc---cccccccccccchhhhhhcccccC--------CCCCccCCccccC
Confidence 488999999997665 4444 688888888877766543 3699999887753
No 120
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=46.59 E-value=19 Score=37.65 Aligned_cols=37 Identities=27% Similarity=0.290 Sum_probs=27.0
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFP 91 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p 91 (215)
..|.+|.-.+..- .+---.|+|.-|.+||.+|+....
T Consensus 780 ~~CtVC~~vi~G~---~~~c~~C~H~gH~sh~~sw~~~~s 816 (839)
T KOG0269|consen 780 AKCTVCDLVIRGV---DVWCQVCGHGGHDSHLKSWFFKAS 816 (839)
T ss_pred cCceeecceeeee---EeecccccccccHHHHHHHHhcCC
Confidence 4688887776442 122236999999999999998753
No 121
>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=45.60 E-value=18 Score=34.42 Aligned_cols=35 Identities=20% Similarity=0.482 Sum_probs=25.5
Q ss_pred CCCccCHHHHHHHHhcCCCCCCC-----CCCCCCCCCCCc
Q 028040 74 CLHVIHTSCLVSHIKSFPPHTAP-----AGYVCPLCSTTI 108 (215)
Q Consensus 74 C~HvFH~~CLd~Wl~~~p~nTap-----~g~~CP~Cr~~I 108 (215)
|.-..-.+|+-+|+.+...+..| +.-.||+||+..
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 55667789999999776544443 345699999875
No 122
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=44.80 E-value=22 Score=29.53 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=18.8
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIML 131 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q 131 (215)
..+||.|.. .++.|++++++..||+.|.+
T Consensus 40 ~LrCp~Cq~-----qsi~~s~a~~A~dmR~~I~~ 68 (148)
T PF03918_consen 40 ELRCPVCQN-----QSIADSNAPIARDMRREIRE 68 (148)
T ss_dssp CCE-TTTTS------CTTT--SHHHHHHHHHHHH
T ss_pred cccCCCCCC-----CchhhcCcHHHHHHHHHHHH
Confidence 467999954 35666778999998877763
No 123
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.96 E-value=38 Score=32.47 Aligned_cols=88 Identities=20% Similarity=0.275 Sum_probs=56.7
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCC-CCCCC--CCCCccCCCCCCCCcchHHHHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAG-YVCPL--CSTTIWPPKNVKDSGSRLHSLLKEA 128 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g-~~CP~--Cr~~I~P~~~i~d~~S~l~~~Lre~ 128 (215)
..|.||.+.+.. +++++.|+|.|=..|...++..+-... +.. .+||. |...+-+. .+....++. ..+++
T Consensus 71 ~~c~ic~~~~~~----~~~~~~c~H~~c~~cw~~yl~~kI~~~-~~~~i~cp~~~C~a~v~~~-~i~~~~s~~--~~~~k 142 (444)
T KOG1815|consen 71 VQCGICVESYDG----EIIGLGCGHPFCPPCWTGYLGTKIHEG-EEAKIKCPAHGCPALVGED-TVEKLVSDK--EDKEK 142 (444)
T ss_pred ccCCcccCCCcc----hhhhcCCCcHHHHHHHHHHhhheeecc-ccccccCCCCCccccCCCc-eeeeecCCH--HHHHH
Confidence 679999999855 489999999999999999998763322 121 45654 54444332 233233332 35666
Q ss_pred hhhhhhhhhhcCCCCCCch
Q 028040 129 IMLTGLEKNLFGNHPVSLA 147 (215)
Q Consensus 129 i~q~~wAr~~lG~~l~~~~ 147 (215)
+...-+..++=++..++.-
T Consensus 143 y~~~i~~syve~~~~lkwC 161 (444)
T KOG1815|consen 143 YQRYILRSYVEDNVPLKWC 161 (444)
T ss_pred HHHHHHHHHHhcCCccccC
Confidence 6666666777777765533
No 124
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=42.34 E-value=16 Score=33.85 Aligned_cols=53 Identities=25% Similarity=0.516 Sum_probs=39.6
Q ss_pred CccccccccccccccCCeeeec-----CCCccCHHHHHH-HHhcCCCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLG-----CLHVIHTSCLVS-HIKSFPPHTAPAGYVCPLCSTT 107 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~-----C~HvFH~~CLd~-Wl~~~p~nTap~g~~CP~Cr~~ 107 (215)
..|-+|.+++.+.| -.|+. |.=++|..||-. -+...+.|--|-+-.||.|++-
T Consensus 183 ~~celc~~ei~e~~---~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~ 241 (276)
T KOG3005|consen 183 VECELCEKEILETD---WSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKF 241 (276)
T ss_pred hhhHHHHHHhcccc---ceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhce
Confidence 58999999996543 44443 788999999999 4555555555667789999884
No 125
>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=41.87 E-value=15 Score=21.95 Aligned_cols=37 Identities=24% Similarity=0.582 Sum_probs=23.5
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
.|..|.+.+..++ ..+. .=+..||.+|+ +|..|+.+|
T Consensus 1 ~C~~C~~~i~~~~--~~~~-~~~~~~H~~Cf----------------~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGE--LVLR-ALGKVWHPECF----------------KCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCc--EEEE-eCCccccccCC----------------CCcccCCcC
Confidence 3788888886652 2222 23667887764 477787765
No 126
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=41.59 E-value=17 Score=35.80 Aligned_cols=33 Identities=27% Similarity=0.706 Sum_probs=24.9
Q ss_pred CCCcccccccccccccc-CCeeeecCC-CccCHHH
Q 028040 50 WPPKCCQCQAVLEEESG-SETTRLGCL-HVIHTSC 82 (215)
Q Consensus 50 ~~~~C~ICle~L~~gD~-~evvRL~C~-HvFH~~C 82 (215)
..+.|++|-+++--.|+ +|++|..+. --||.+|
T Consensus 393 fAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~C 427 (468)
T KOG1701|consen 393 FAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNC 427 (468)
T ss_pred cCcchhhccCCccCCCCCcceEEEEEccccccccc
Confidence 34999999999975554 458998775 4677777
No 127
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=41.35 E-value=12 Score=38.24 Aligned_cols=47 Identities=26% Similarity=0.449 Sum_probs=36.4
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWP 110 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P 110 (215)
..|.+|++ + + ..+.-.|+|.|-.+|+..-++.... ..||.||..+--
T Consensus 455 ~~c~ic~~-~---~--~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD-L---D--SFFITRCGHDFCVECLKKSIQQSEN------APCPLCRNVLKE 501 (674)
T ss_pred cccccccc-c---c--cceeecccchHHHHHHHhccccccC------CCCcHHHHHHHH
Confidence 46999999 2 1 4777899999999999999876422 169999987654
No 128
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=40.44 E-value=9.3 Score=37.08 Aligned_cols=50 Identities=26% Similarity=0.346 Sum_probs=0.0
Q ss_pred Cccccccccccccc---------cCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 028040 52 PKCCQCQAVLEEES---------GSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCST 106 (215)
Q Consensus 52 ~~C~ICle~L~~gD---------~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~ 106 (215)
+.|+|=+..|.-.. .+--+-|.||||+-+ ..|-..... .+...+||+|++
T Consensus 278 pQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~--~~~~r~CPlCr~ 336 (416)
T PF04710_consen 278 PQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDR--DPRSRTCPLCRQ 336 (416)
T ss_dssp ----------------------------------------------------------------
T ss_pred CCCCcCCCccccccccccccccccCceeeccccceeee---ccccccccc--ccccccCCCccc
Confidence 67777777664110 011344789999865 467654321 123677999975
No 129
>PF15353 HECA: Headcase protein family homologue
Probab=40.16 E-value=21 Score=28.82 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=17.4
Q ss_pred CeeeecC-------CCccCHHHHHHHHhc
Q 028040 68 ETTRLGC-------LHVIHTSCLVSHIKS 89 (215)
Q Consensus 68 evvRL~C-------~HvFH~~CLd~Wl~~ 89 (215)
+.+++.| ++.+|.+|+++|=.+
T Consensus 27 d~vkv~Cnne~Cp~~~~MH~~CF~~wE~~ 55 (107)
T PF15353_consen 27 DGVKVICNNESCPFGQYMHRECFEKWEDS 55 (107)
T ss_pred ccEEEEeCCCCCCCCCchHHHHHHHHHHH
Confidence 5777644 689999999999554
No 130
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=39.80 E-value=15 Score=37.05 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=28.8
Q ss_pred Cccccccccccc----ccc----CCeeeecCCCccCHHHHHHHHhc
Q 028040 52 PKCCQCQAVLEE----ESG----SETTRLGCLHVIHTSCLVSHIKS 89 (215)
Q Consensus 52 ~~C~ICle~L~~----gD~----~evvRL~C~HvFH~~CLd~Wl~~ 89 (215)
..|+||.+.|++ .++ ++.|+|.=|-+||..|+..-..+
T Consensus 514 ~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~~~ 559 (579)
T KOG2071|consen 514 ASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKRAQ 559 (579)
T ss_pred cCCcccccccceeecchhhheeecceeeeccCceeeccccchHHHh
Confidence 789999999973 110 44777778899999999876533
No 131
>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=39.45 E-value=8.4 Score=25.57 Aligned_cols=40 Identities=18% Similarity=0.426 Sum_probs=29.5
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPK 112 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~ 112 (215)
|..|.+.+..+ +.+...-+..||.+|+ +|=.|+++|.+..
T Consensus 1 C~~C~~~I~~~---~~~~~~~~~~~H~~Cf----------------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT---EIVIKAMGKFWHPECF----------------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS---SEEEEETTEEEETTTS----------------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc---EEEEEeCCcEEEcccc----------------ccCCCCCccCCCe
Confidence 77899998764 3554466778997764 5999999887643
No 132
>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 COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=38.14 E-value=36 Score=24.90 Aligned_cols=46 Identities=24% Similarity=0.596 Sum_probs=33.9
Q ss_pred CCccccccccccccccCCeeee---cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRL---GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL---~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
++.|.-|...|..++ .-+.. +||-+.=+.|..---.. +-|+||.|.
T Consensus 9 ~~~CtSCg~~i~p~e--~~v~F~CPnCGe~~I~Rc~~CRk~g-------~~Y~Cp~CG 57 (61)
T COG2888 9 PPVCTSCGREIAPGE--TAVKFPCPNCGEVEIYRCAKCRKLG-------NPYRCPKCG 57 (61)
T ss_pred CceeccCCCEeccCC--ceeEeeCCCCCceeeehhhhHHHcC-------CceECCCcC
Confidence 578999999997764 44444 58988888887654433 469999995
No 134
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=37.49 E-value=30 Score=33.02 Aligned_cols=45 Identities=18% Similarity=0.284 Sum_probs=34.8
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
..|+||+..-.+ .++--.-|=||-+.|+.+++..+. .||+=..|+
T Consensus 301 ~~CpvClk~r~N----ptvl~vSGyVfCY~Ci~~Yv~~~~--------~CPVT~~p~ 345 (357)
T KOG0826|consen 301 EVCPVCLKKRQN----PTVLEVSGYVFCYPCIFSYVVNYG--------HCPVTGYPA 345 (357)
T ss_pred ccChhHHhccCC----CceEEecceEEeHHHHHHHHHhcC--------CCCccCCcc
Confidence 689999999766 255556788999999999998653 399865443
No 135
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.29 E-value=32 Score=27.48 Aligned_cols=35 Identities=20% Similarity=0.410 Sum_probs=27.1
Q ss_pred cccccccccccccCCeeeecCCCccCHHHHHHHHhcCC
Q 028040 54 CCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFP 91 (215)
Q Consensus 54 C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p 91 (215)
|.||.++..+|. .-...=.--.|++|+.+-.++++
T Consensus 9 C~VCg~~iieGq---kFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 9 CYVCGGTIIEGQ---KFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred EeeeCCEeeecc---EEEEeeCCcchHHHHHHHHhcCc
Confidence 999999999984 33332266789999999988764
No 136
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=37.22 E-value=26 Score=27.92 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=26.1
Q ss_pred ccccccccccccccCCeeeecCCCccCHHHHHHHHhcC
Q 028040 53 KCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSF 90 (215)
Q Consensus 53 ~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~ 90 (215)
.|.||.+++..|. .-...=.=..||+|+..-+...
T Consensus 4 kC~iCg~~I~~gq---lFTF~~kG~VH~~C~~~~~~~k 38 (101)
T PF09943_consen 4 KCYICGKPIYEGQ---LFTFTKKGPVHYECFREKASKK 38 (101)
T ss_pred EEEecCCeeeecc---eEEEecCCcEeHHHHHHHHhhh
Confidence 4999999998874 3333333588999999988754
No 137
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=36.37 E-value=28 Score=29.70 Aligned_cols=27 Identities=22% Similarity=0.562 Sum_probs=20.7
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAI 129 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i 129 (215)
..+||.| ...+|.|++.+++--||..+
T Consensus 44 ~LRCp~C-----QNqsIadSnA~IA~DlR~~V 70 (153)
T COG3088 44 ELRCPQC-----QNQSIADSNAPIARDLRHQV 70 (153)
T ss_pred hcCCCcC-----CCCChhhhccHHHHHHHHHH
Confidence 5679999 44568888899988887544
No 138
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=36.03 E-value=14 Score=30.18 Aligned_cols=17 Identities=24% Similarity=0.681 Sum_probs=14.0
Q ss_pred CCCCCCCCCCCccCCCC
Q 028040 97 AGYVCPLCSTTIWPPKN 113 (215)
Q Consensus 97 ~g~~CP~Cr~~I~P~~~ 113 (215)
..|.||.|...|....|
T Consensus 122 ~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 122 GTFTCPRCGEELEEDDN 138 (147)
T ss_pred CcEECCCCCCEEEEcCc
Confidence 44999999999987654
No 139
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=36.01 E-value=12 Score=36.33 Aligned_cols=75 Identities=24% Similarity=0.336 Sum_probs=0.0
Q ss_pred eeecceeeccCCCC-CCCccccccccc-----ccc-------ccCC-eee-ecCCCccCHHHHHHHHhcC-CCCCCCCCC
Q 028040 36 VRTYSEWVIDGEYD-WPPKCCQCQAVL-----EEE-------SGSE-TTR-LGCLHVIHTSCLVSHIKSF-PPHTAPAGY 99 (215)
Q Consensus 36 VqsYlqwL~Dsdyd-~~~~C~ICle~L-----~~g-------D~~e-vvR-L~C~HvFH~~CLd~Wl~~~-p~nTap~g~ 99 (215)
|+-|-.|-.+.+-+ ...+|++|+..= .-| |.+. +-. -||||+--.+...-|-+-- |..|.--.-
T Consensus 312 VhG~h~Wg~~~~~~~~~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a 391 (416)
T PF04710_consen 312 VHGYHNWGQDSDRDPRSRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHA 391 (416)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred eeeecccccccccccccccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccc
Confidence 78888998766631 237899998641 111 1011 222 2799999999999996543 333322234
Q ss_pred CCCCCCCCccC
Q 028040 100 VCPLCSTTIWP 110 (215)
Q Consensus 100 ~CP~Cr~~I~P 110 (215)
.||-|..+|-.
T Consensus 392 ~CPFCa~~L~g 402 (416)
T PF04710_consen 392 ACPFCATPLDG 402 (416)
T ss_dssp -----------
T ss_pred cCCcccCcccC
Confidence 69999888864
No 140
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=35.54 E-value=22 Score=22.75 Aligned_cols=13 Identities=38% Similarity=0.723 Sum_probs=9.7
Q ss_pred ccccccccccccc
Q 028040 53 KCCQCQAVLEEES 65 (215)
Q Consensus 53 ~C~ICle~L~~gD 65 (215)
.|+-|...|+-.|
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 5888888887654
No 141
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.77 E-value=35 Score=29.49 Aligned_cols=30 Identities=20% Similarity=0.361 Sum_probs=22.6
Q ss_pred CCCCCCCCCCccCCCCCCCCcchHHHHHHHHhhhh
Q 028040 98 GYVCPLCSTTIWPPKNVKDSGSRLHSLLKEAIMLT 132 (215)
Q Consensus 98 g~~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~q~ 132 (215)
+|+||.|...+---. +|+..+.|++++.+.
T Consensus 132 ~F~Cp~Cg~~L~~~d-----~s~~i~~l~~~i~~l 161 (176)
T COG1675 132 GFTCPKCGEDLEEYD-----SSEEIEELESELDEL 161 (176)
T ss_pred CCCCCCCCchhhhcc-----chHHHHHHHHHHHHH
Confidence 578999999886433 477888888777653
No 142
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=34.69 E-value=26 Score=35.00 Aligned_cols=36 Identities=25% Similarity=0.482 Sum_probs=29.6
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFP 91 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p 91 (215)
+-.|+||..-|+ +.+.|+|+|-+-..|...-+-+-|
T Consensus 4 elkc~vc~~f~~-----epiil~c~h~lc~~ca~~~~~~tp 39 (699)
T KOG4367|consen 4 ELKCPVCGSFYR-----EPIILPCSHNLCQACARNILVQTP 39 (699)
T ss_pred cccCceehhhcc-----CceEeecccHHHHHHHHhhcccCC
Confidence 367999998874 489999999999999987776544
No 143
>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=32.25 E-value=13 Score=25.36 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=13.5
Q ss_pred CCCCCCCCccCCCCCCCCcchHHHHHHHHhh
Q 028040 100 VCPLCSTTIWPPKNVKDSGSRLHSLLKEAIM 130 (215)
Q Consensus 100 ~CP~Cr~~I~P~~~i~d~~S~l~~~Lre~i~ 130 (215)
.||+|.+++-+.. ...|...+++.+.
T Consensus 22 ~CPlC~r~l~~e~-----~~~li~~~~~~i~ 47 (54)
T PF04423_consen 22 CCPLCGRPLDEEH-----RQELIKKYKSEIE 47 (54)
T ss_dssp E-TTT--EE-HHH-----HHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHH-----HHHHHHHHHHHHH
Confidence 7999999997643 2455555555443
No 144
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=31.80 E-value=39 Score=24.56 Aligned_cols=46 Identities=30% Similarity=0.738 Sum_probs=28.9
Q ss_pred CCccccccccccccccCCeeee---cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRL---GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCS 105 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL---~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr 105 (215)
+..|..|...|...+ .-++. .||.+.=+.|-.=--+. +.|+||.|.
T Consensus 7 ~~~CtSCg~~i~~~~--~~~~F~CPnCG~~~I~RC~~CRk~~-------~~Y~CP~CG 55 (59)
T PRK14890 7 PPKCTSCGIEIAPRE--KAVKFLCPNCGEVIIYRCEKCRKQS-------NPYTCPKCG 55 (59)
T ss_pred CccccCCCCcccCCC--ccCEeeCCCCCCeeEeechhHHhcC-------CceECCCCC
Confidence 367888888887653 24554 47777555554432222 468999985
No 145
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=31.76 E-value=29 Score=24.04 Aligned_cols=12 Identities=42% Similarity=1.309 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCC
Q 028040 96 PAGYVCPLCSTT 107 (215)
Q Consensus 96 p~g~~CP~Cr~~ 107 (215)
|..++||+|+.+
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 467899999753
No 146
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.62 E-value=29 Score=20.28 Aligned_cols=8 Identities=50% Similarity=1.389 Sum_probs=5.2
Q ss_pred CCCCCCCc
Q 028040 101 CPLCSTTI 108 (215)
Q Consensus 101 CP~Cr~~I 108 (215)
||.|.++|
T Consensus 16 C~~CG~~l 23 (23)
T PF13240_consen 16 CPNCGTPL 23 (23)
T ss_pred hhhhCCcC
Confidence 77776654
No 147
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.21 E-value=30 Score=23.73 Aligned_cols=12 Identities=42% Similarity=1.342 Sum_probs=7.1
Q ss_pred CCCCCCCCCCCC
Q 028040 96 PAGYVCPLCSTT 107 (215)
Q Consensus 96 p~g~~CP~Cr~~ 107 (215)
|..++||+|..+
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 467899999764
No 148
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=27.94 E-value=30 Score=36.78 Aligned_cols=57 Identities=9% Similarity=0.080 Sum_probs=40.3
Q ss_pred CccccccccccccccCCeeee---cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL---GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL---~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
..|.+|..+|.+.+ +..-.+ .|+|-|-..||..|+.++-. ++..-.|+.|...|.-=
T Consensus 97 ~Ss~~C~~E~S~~~-ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~--~~k~c~H~FC~~Ci~sW 156 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDV-DSSNICPVQTHVENQCPNCLKSCNDQLEE--SEKHTAHYFCEECVGSW 156 (1134)
T ss_pred cccchhheecCCcc-cccCcCchhhhhhhhhhHHHHHHHHHhhc--cccccccccHHHHhhhh
Confidence 57889988887743 233334 49999999999999887632 33444588887777643
No 149
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=27.06 E-value=25 Score=29.70 Aligned_cols=27 Identities=30% Similarity=0.869 Sum_probs=21.0
Q ss_pred cCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 78 IHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 78 FH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
||..||+.=|..-|. ....||.|...-
T Consensus 2 ~H~~CL~Ppl~~~P~----g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPPLKEVPE----GDWICPFCEVEK 28 (148)
T ss_pred cccccCCCCCCCCCC----CCcCCCCCcCCC
Confidence 899999998876654 357899998543
No 150
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.91 E-value=35 Score=29.86 Aligned_cols=16 Identities=25% Similarity=0.758 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCccCCC
Q 028040 97 AGYVCPLCSTTIWPPK 112 (215)
Q Consensus 97 ~g~~CP~Cr~~I~P~~ 112 (215)
+|++||+|.+.+.+.+
T Consensus 137 ~g~KCPvC~K~V~sDd 152 (205)
T KOG0801|consen 137 SGMKCPVCHKVVPSDD 152 (205)
T ss_pred CCccCCccccccCCCc
Confidence 6899999999887754
No 151
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=26.13 E-value=81 Score=23.84 Aligned_cols=30 Identities=23% Similarity=0.550 Sum_probs=22.9
Q ss_pred CccccccccccccccCCeee---ecCCCccCHHHHHHH
Q 028040 52 PKCCQCQAVLEEESGSETTR---LGCLHVIHTSCLVSH 86 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvR---L~C~HvFH~~CLd~W 86 (215)
..|.||... .| ..++ -.|...||..|....
T Consensus 56 ~~C~iC~~~--~G---~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 56 LKCSICGKS--GG---ACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CcCcCCCCC--Cc---eeEEcCCCCCCcCCCHHHHHHC
Confidence 889999998 33 3444 249999999998654
No 152
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.33 E-value=35 Score=21.81 Aligned_cols=28 Identities=25% Similarity=0.490 Sum_probs=16.7
Q ss_pred Ccccccccccccccc-----CCeeee-cCCCccC
Q 028040 52 PKCCQCQAVLEEESG-----SETTRL-GCLHVIH 79 (215)
Q Consensus 52 ~~C~ICle~L~~gD~-----~evvRL-~C~HvFH 79 (215)
-.|+-|...|.-.|. +..+|= .|+|+|+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 358889888876541 112232 4777775
No 153
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.15 E-value=30 Score=30.33 Aligned_cols=41 Identities=27% Similarity=0.641 Sum_probs=26.2
Q ss_pred CccccccccccccccCCeeeecCCCccC-HHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIH-TSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH-~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|-.|.+. + ..++-|||.|+-| ..|-.. +. .||+|+.+..
T Consensus 159 ~~Cr~C~~~--~---~~VlllPCrHl~lC~~C~~~-~~-----------~CPiC~~~~~ 200 (207)
T KOG1100|consen 159 RSCRKCGER--E---ATVLLLPCRHLCLCGICDES-LR-----------ICPICRSPKT 200 (207)
T ss_pred ccceecCcC--C---ceEEeecccceEeccccccc-Cc-----------cCCCCcChhh
Confidence 337777765 2 1366679998754 455544 32 3999988664
No 154
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.13 E-value=51 Score=19.45 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=7.0
Q ss_pred Ccccccccccccc
Q 028040 52 PKCCQCQAVLEEE 64 (215)
Q Consensus 52 ~~C~ICle~L~~g 64 (215)
..|+-|...+..+
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 3466666655443
No 155
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.17 E-value=1.5e+02 Score=27.68 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=34.5
Q ss_pred CccccccccccccccCCeeee-cCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRL-GCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKN 113 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~ 113 (215)
-.|+|=.-+|... ..-..| .|||||-..-|.+.=.+ .|++|....--.+.
T Consensus 112 fiCPvtgleMng~--~~F~~l~~CGcV~SerAlKeikas----------~C~~C~a~y~~~dv 162 (293)
T KOG3113|consen 112 FICPVTGLEMNGK--YRFCALRCCGCVFSERALKEIKAS----------VCHVCGAAYQEDDV 162 (293)
T ss_pred eecccccceecce--EEEEEEeccceeccHHHHHHhhhc----------cccccCCcccccCe
Confidence 4588877776432 133334 79999999998876543 49999998765443
No 156
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=23.17 E-value=24 Score=38.94 Aligned_cols=46 Identities=22% Similarity=0.411 Sum_probs=37.5
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
..|.+|++.+.+ .-.+-.|+|-+--.|+..|+.++. .||+|+....
T Consensus 1154 ~~c~ic~dil~~----~~~I~~cgh~~c~~c~~~~l~~~s--------~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1154 FVCEICLDILRN----QGGIAGCGHEPCCRCDELWLYASS--------RCPICKSIKG 1199 (1394)
T ss_pred cchHHHHHHHHh----cCCeeeechhHhhhHHHHHHHHhc--------cCcchhhhhh
Confidence 689999999975 245668999999999999999753 5999985443
No 157
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=22.85 E-value=57 Score=26.51 Aligned_cols=49 Identities=20% Similarity=0.414 Sum_probs=28.9
Q ss_pred CccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCCCCC
Q 028040 52 PKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPPKNV 114 (215)
Q Consensus 52 ~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~~~i 114 (215)
..|+.|...|..-+.+++... +-.... ++...-+.||.|++-.|+-+..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~----------vp~~v~----~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDR----------VPPYVY----ETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CccCCCCcEeeechhhccccc----------cCcccc----ccCCeEEECCCCCCEecccccH
Confidence 689999999976541222222 001111 1112356799999999987654
No 158
>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=22.76 E-value=28 Score=24.55 Aligned_cols=28 Identities=25% Similarity=0.719 Sum_probs=19.6
Q ss_pred cCC-CccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCc
Q 028040 73 GCL-HVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTI 108 (215)
Q Consensus 73 ~C~-HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I 108 (215)
.|. |..-..||...|.... .||+|..++
T Consensus 17 ~C~dHYLCl~CLt~ml~~s~--------~C~iC~~~L 45 (50)
T PF03854_consen 17 KCSDHYLCLNCLTLMLSRSD--------RCPICGKPL 45 (50)
T ss_dssp E-SS-EEEHHHHHHT-SSSS--------EETTTTEE-
T ss_pred eecchhHHHHHHHHHhcccc--------CCCcccCcC
Confidence 454 8899999999997643 599998876
No 159
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=22.59 E-value=1.1e+02 Score=29.56 Aligned_cols=74 Identities=22% Similarity=0.381 Sum_probs=48.7
Q ss_pred eeecceeeccCC-CCCCCccccccccc---------------cccccCCeeee-cCCCccCHHHHHHHHhcC-CCCCCCC
Q 028040 36 VRTYSEWVIDGE-YDWPPKCCQCQAVL---------------EEESGSETTRL-GCLHVIHTSCLVSHIKSF-PPHTAPA 97 (215)
Q Consensus 36 VqsYlqwL~Dsd-yd~~~~C~ICle~L---------------~~gD~~evvRL-~C~HvFH~~CLd~Wl~~~-p~nTap~ 97 (215)
|+-|-+|=.+.+ ...+..|++|+..= +.|- ..-.. +|||+--..=..-|-+-- |.-|.-.
T Consensus 325 V~G~H~WG~~e~~g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~--pthaF~PCGHv~sekt~~YWs~iplPhGT~~f 402 (429)
T KOG3842|consen 325 VHGYHNWGVRENTGQRERECPMCRVVGPYVPLWLGCEAGFYVDAGP--PTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAF 402 (429)
T ss_pred cccccccccccccCcccCcCCeeeeecceeeeeccccceeEecCCC--cccccCCcccccchhhhhHhhcCcCCCccccc
Confidence 778888976655 33357899998641 1121 12223 799999999999997643 3334334
Q ss_pred CCCCCCCCCCccCC
Q 028040 98 GYVCPLCSTTIWPP 111 (215)
Q Consensus 98 g~~CP~Cr~~I~P~ 111 (215)
+-.||-|.+.+.-.
T Consensus 403 ~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 403 HAACPFCATQLAGE 416 (429)
T ss_pred cccCcchhhhhccC
Confidence 55799998887654
No 160
>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=22.45 E-value=21 Score=24.98 Aligned_cols=40 Identities=30% Similarity=0.570 Sum_probs=19.9
Q ss_pred eeeccCCCCCCCccccccccccccccCCeeee---cCCCccCHHHHHHHH
Q 028040 41 EWVIDGEYDWPPKCCQCQAVLEEESGSETTRL---GCLHVIHTSCLVSHI 87 (215)
Q Consensus 41 qwL~Dsdyd~~~~C~ICle~L~~gD~~evvRL---~C~HvFH~~CLd~Wl 87 (215)
+|+.|.+- ..|.+|...|.- ...|- .||++|=..|....+
T Consensus 2 ~W~~d~~~---~~C~~C~~~F~~----~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 2 HWVPDSEA---SNCMICGKKFSL----FRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp -SSSGGG----SB-TTT--B-BS----SS-EEE-TTT--EEECCCS-EEE
T ss_pred CcCCCCCC---CcCcCcCCcCCC----ceeeEccCCCCCEECCchhCCEE
Confidence 58877654 489999999933 22332 688888777776554
No 161
>PF05018 DUF667: Protein of unknown function (DUF667); InterPro: IPR007714 This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature.
Probab=22.44 E-value=60 Score=27.96 Aligned_cols=24 Identities=25% Similarity=0.404 Sum_probs=19.7
Q ss_pred cccceeeecCCCCcccccccCCCC
Q 028040 188 TVSEIMEIDGPSPAGNFIKSSSPV 211 (215)
Q Consensus 188 ~~~~~~~~~~~~~~~~~~~~~~~~ 211 (215)
.-+-+.||+|+.+++|||+-|...
T Consensus 42 iks~V~ei~G~~~~~t~I~~P~~~ 65 (190)
T PF05018_consen 42 IKSYVLEIQGSNSATTYITCPKDP 65 (190)
T ss_pred cceEEEEEeccccccCeEECCCCc
Confidence 445689999999999999988543
No 162
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.35 E-value=98 Score=23.73 Aligned_cols=48 Identities=23% Similarity=0.528 Sum_probs=37.5
Q ss_pred CCccccccccccccccCCeeeecC--CCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCccCC
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGC--LHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIWPP 111 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C--~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~P~ 111 (215)
-++|--|-.+|-.+. ...+.| -|.|-..|...-|... ||.|...+.-.
T Consensus 5 RPnCECCDrDLpp~s---~dA~ICtfEcTFCadCae~~l~g~----------CPnCGGelv~R 54 (84)
T COG3813 5 RPNCECCDRDLPPDS---TDARICTFECTFCADCAENRLHGL----------CPNCGGELVAR 54 (84)
T ss_pred cCCCcccCCCCCCCC---CceeEEEEeeehhHhHHHHhhcCc----------CCCCCchhhcC
Confidence 378999999997653 445555 4899999999988763 99999887754
No 163
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.98 E-value=55 Score=31.87 Aligned_cols=46 Identities=24% Similarity=0.421 Sum_probs=34.7
Q ss_pred CCccccccccccccccCCeeeecCCCccCHHHHHHHHhcCCCCCCCCCCCCCCCCCCcc
Q 028040 51 PPKCCQCQAVLEEESGSETTRLGCLHVIHTSCLVSHIKSFPPHTAPAGYVCPLCSTTIW 109 (215)
Q Consensus 51 ~~~C~ICle~L~~gD~~evvRL~C~HvFH~~CLd~Wl~~~p~nTap~g~~CP~Cr~~I~ 109 (215)
+..|+||-.-=. ..+--+|+|-=-..||.+++.+.+ .|=-|++.+.
T Consensus 422 d~lCpICyA~pi-----~Avf~PC~H~SC~~CI~qHlmN~k--------~CFfCktTv~ 467 (489)
T KOG4692|consen 422 DNLCPICYAGPI-----NAVFAPCSHRSCYGCITQHLMNCK--------RCFFCKTTVI 467 (489)
T ss_pred cccCcceecccc-----hhhccCCCCchHHHHHHHHHhcCC--------eeeEecceee
Confidence 378999965411 234459999999999999998643 5999988776
No 164
>PRK00420 hypothetical protein; Validated
Probab=21.84 E-value=59 Score=26.20 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=10.7
Q ss_pred CCccccccccccc
Q 028040 51 PPKCCQCQAVLEE 63 (215)
Q Consensus 51 ~~~C~ICle~L~~ 63 (215)
...|++|..+|..
T Consensus 23 ~~~CP~Cg~pLf~ 35 (112)
T PRK00420 23 SKHCPVCGLPLFE 35 (112)
T ss_pred cCCCCCCCCccee
Confidence 3689999999875
Done!