Query 033301
Match_columns 122
No_of_seqs 125 out of 1081
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 12:14:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033301hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814 Predicted E3 ubiquitin 99.8 1.5E-21 3.3E-26 148.5 3.3 115 6-121 164-279 (445)
2 KOG1812 Predicted E3 ubiquitin 99.6 2.8E-16 6.1E-21 121.4 5.6 96 24-122 144-240 (384)
3 KOG1815 Predicted E3 ubiquitin 99.5 6.7E-15 1.5E-19 115.7 6.0 96 24-122 68-165 (444)
4 PF15227 zf-C3HC4_4: zinc fing 99.0 8.6E-11 1.9E-15 63.8 0.4 40 29-76 1-40 (42)
5 PF13639 zf-RING_2: Ring finge 98.9 2.2E-10 4.7E-15 62.7 0.5 35 28-63 2-36 (44)
6 PF00097 zf-C3HC4: Zinc finger 98.9 1.2E-09 2.6E-14 58.7 2.7 39 29-76 1-39 (41)
7 PF13445 zf-RING_UBOX: RING-ty 98.9 1.6E-09 3.5E-14 59.0 2.5 43 29-76 1-43 (43)
8 PLN03208 E3 ubiquitin-protein 98.9 1.8E-09 3.8E-14 76.1 3.3 67 23-95 15-89 (193)
9 KOG0320 Predicted E3 ubiquitin 98.8 2.1E-09 4.5E-14 74.5 2.9 59 21-91 126-184 (187)
10 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.7E-09 3.6E-14 57.7 1.1 32 29-63 1-32 (39)
11 PHA02926 zinc finger-like prot 98.7 1.4E-08 3.1E-13 72.8 4.6 62 20-85 164-230 (242)
12 PF14634 zf-RING_5: zinc-RING 98.7 1.7E-08 3.8E-13 55.1 2.5 43 28-81 1-43 (44)
13 cd00162 RING RING-finger (Real 98.6 3.5E-08 7.6E-13 52.9 3.2 44 28-83 1-44 (45)
14 PF13920 zf-C3HC4_3: Zinc fing 98.5 5.7E-08 1.2E-12 54.4 2.4 46 26-85 2-48 (50)
15 KOG2164 Predicted E3 ubiquitin 98.5 9.2E-08 2E-12 75.5 3.7 64 25-97 185-248 (513)
16 smart00504 Ubox Modified RING 98.4 2.8E-07 6E-12 53.6 3.9 51 27-91 2-52 (63)
17 PHA02929 N1R/p28-like protein; 98.4 3.2E-07 7E-12 67.0 4.2 52 24-85 172-227 (238)
18 KOG0317 Predicted E3 ubiquitin 98.4 1.3E-07 2.9E-12 70.0 2.0 53 24-90 237-289 (293)
19 smart00184 RING Ring finger. E 98.4 3E-07 6.5E-12 47.6 2.7 30 29-62 1-30 (39)
20 TIGR00599 rad18 DNA repair pro 98.4 3.7E-07 8.1E-12 71.0 4.1 66 24-103 24-90 (397)
21 KOG0823 Predicted E3 ubiquitin 98.2 7.6E-07 1.7E-11 64.1 2.8 60 23-93 44-103 (230)
22 KOG0006 E3 ubiquitin-protein l 98.2 2.4E-06 5.3E-11 64.4 4.7 96 22-122 217-322 (446)
23 TIGR00570 cdk7 CDK-activating 98.1 6.1E-06 1.3E-10 62.2 5.4 53 27-89 4-58 (309)
24 KOG1039 Predicted E3 ubiquitin 98.1 6.2E-06 1.3E-10 63.2 4.9 96 23-121 158-265 (344)
25 KOG0978 E3 ubiquitin ligase in 98.0 2.3E-06 5.1E-11 70.3 2.0 56 24-92 641-696 (698)
26 KOG1002 Nucleotide excision re 98.0 4.1E-06 8.8E-11 66.9 2.9 81 21-110 531-611 (791)
27 KOG2177 Predicted E3 ubiquitin 98.0 2.5E-06 5.3E-11 62.1 1.6 46 23-82 10-55 (386)
28 KOG0287 Postreplication repair 97.9 5.5E-06 1.2E-10 62.9 1.2 65 24-102 21-86 (442)
29 PF11789 zf-Nse: Zinc-finger o 97.8 1.7E-05 3.6E-10 45.7 2.3 50 23-81 8-57 (57)
30 KOG4628 Predicted E3 ubiquitin 97.8 1.1E-05 2.3E-10 61.8 1.9 49 27-85 230-278 (348)
31 COG5540 RING-finger-containing 97.7 3.4E-05 7.4E-10 57.9 3.2 54 23-86 320-373 (374)
32 COG5574 PEX10 RING-finger-cont 97.6 4.2E-05 9E-10 56.3 2.5 52 26-89 215-266 (271)
33 PF12678 zf-rbx1: RING-H2 zinc 97.5 3.6E-05 7.8E-10 46.4 1.3 39 25-63 18-65 (73)
34 PF04564 U-box: U-box domain; 97.5 8.4E-05 1.8E-09 44.7 2.4 53 24-89 2-54 (73)
35 COG5432 RAD18 RING-finger-cont 97.4 0.00012 2.6E-09 54.8 2.5 66 24-103 23-89 (391)
36 PF11793 FANCL_C: FANCL C-term 97.3 0.0001 2.2E-09 44.1 1.4 59 26-86 2-67 (70)
37 KOG2660 Locus-specific chromos 97.0 0.00045 9.7E-09 52.3 2.5 52 23-87 12-63 (331)
38 PF14835 zf-RING_6: zf-RING of 97.0 5.4E-05 1.2E-09 44.4 -2.0 50 26-90 7-56 (65)
39 KOG0824 Predicted E3 ubiquitin 96.9 0.00055 1.2E-08 51.4 1.7 53 24-89 5-57 (324)
40 COG5152 Uncharacterized conser 96.8 0.00048 1E-08 49.0 0.8 32 24-59 194-225 (259)
41 COG5243 HRD1 HRD ubiquitin lig 96.8 0.0016 3.5E-08 50.4 3.7 52 23-84 284-344 (491)
42 KOG0802 E3 ubiquitin ligase [P 96.8 0.00099 2.2E-08 54.1 2.6 50 22-82 287-338 (543)
43 PHA03096 p28-like protein; Pro 96.7 0.00032 6.9E-09 52.6 -0.4 54 27-84 179-236 (284)
44 smart00647 IBR In Between Ring 96.5 0.0018 4E-08 37.2 1.7 24 99-122 1-25 (64)
45 KOG4159 Predicted E3 ubiquitin 96.4 0.0036 7.8E-08 49.1 3.7 49 24-86 82-130 (398)
46 KOG2879 Predicted E3 ubiquitin 96.4 0.0028 6.1E-08 47.1 2.9 52 24-86 237-288 (298)
47 PF14570 zf-RING_4: RING/Ubox 96.3 0.0038 8.1E-08 34.6 2.4 45 29-83 1-46 (48)
48 KOG0311 Predicted E3 ubiquitin 96.2 0.0005 1.1E-08 52.6 -1.9 49 24-84 41-89 (381)
49 KOG1428 Inhibitor of type V ad 96.2 0.0044 9.6E-08 55.3 3.3 75 24-101 3484-3562(3738)
50 KOG4739 Uncharacterized protei 96.1 0.0018 3.8E-08 47.2 0.4 57 27-97 4-60 (233)
51 PF05883 Baculo_RING: Baculovi 95.8 0.0037 8.1E-08 41.8 1.0 39 22-61 22-66 (134)
52 PF12861 zf-Apc11: Anaphase-pr 95.7 0.0094 2E-07 36.9 2.3 54 25-85 20-82 (85)
53 PF01485 IBR: IBR domain; Int 95.6 0.0021 4.6E-08 36.9 -0.8 24 99-122 1-25 (64)
54 PF04641 Rtf2: Rtf2 RING-finge 95.4 0.032 7E-07 41.3 4.7 73 22-105 109-182 (260)
55 KOG4265 Predicted E3 ubiquitin 95.3 0.013 2.7E-07 45.1 2.4 50 23-86 287-337 (349)
56 smart00744 RINGv The RING-vari 95.3 0.019 4E-07 31.9 2.4 36 28-65 1-41 (49)
57 KOG1645 RING-finger-containing 95.3 0.0097 2.1E-07 46.6 1.6 53 26-87 4-58 (463)
58 KOG4172 Predicted E3 ubiquitin 95.2 0.0048 1E-07 35.0 -0.2 46 27-85 8-54 (62)
59 KOG1952 Transcription factor N 95.1 0.03 6.5E-07 47.5 4.0 59 21-82 186-244 (950)
60 KOG1734 Predicted RING-contain 94.9 0.0048 1E-07 45.9 -1.0 56 24-89 222-285 (328)
61 KOG4445 Uncharacterized conser 94.8 0.019 4.1E-07 43.4 1.9 62 22-86 111-187 (368)
62 KOG3002 Zn finger protein [Gen 94.7 0.033 7.1E-07 42.2 3.0 59 21-86 43-122 (299)
63 KOG4185 Predicted E3 ubiquitin 94.5 0.083 1.8E-06 39.5 4.8 59 25-92 2-64 (296)
64 KOG0828 Predicted E3 ubiquitin 94.4 0.025 5.4E-07 45.4 1.9 54 23-86 568-635 (636)
65 KOG0297 TNF receptor-associate 94.1 0.039 8.5E-07 43.3 2.5 38 23-63 18-55 (391)
66 COG5175 MOT2 Transcriptional r 93.9 0.11 2.4E-06 40.0 4.5 58 24-91 12-70 (480)
67 KOG1813 Predicted E3 ubiquitin 93.6 0.022 4.7E-07 42.9 0.2 47 24-84 239-285 (313)
68 KOG1001 Helicase-like transcri 93.4 0.016 3.6E-07 48.3 -0.8 50 27-89 455-504 (674)
69 KOG4692 Predicted E3 ubiquitin 93.3 0.069 1.5E-06 41.4 2.4 37 24-64 420-456 (489)
70 COG5220 TFB3 Cdk activating ki 93.2 0.018 4E-07 42.3 -0.7 53 25-84 9-63 (314)
71 COG5219 Uncharacterized conser 92.6 0.054 1.2E-06 46.8 1.1 54 25-86 1468-1524(1525)
72 KOG3039 Uncharacterized conser 92.0 0.12 2.6E-06 38.2 2.3 60 22-91 217-276 (303)
73 KOG0827 Predicted E3 ubiquitin 91.9 0.12 2.7E-06 40.4 2.3 53 26-85 4-56 (465)
74 KOG0826 Predicted E3 ubiquitin 91.1 0.13 2.8E-06 39.4 1.6 52 22-84 296-347 (357)
75 KOG1941 Acetylcholine receptor 90.5 0.074 1.6E-06 41.7 -0.1 51 24-83 363-414 (518)
76 KOG2817 Predicted E3 ubiquitin 90.3 0.29 6.3E-06 38.3 2.9 63 22-92 330-392 (394)
77 KOG0825 PHD Zn-finger protein 90.2 0.099 2.1E-06 44.3 0.3 21 45-65 118-138 (1134)
78 PF05290 Baculo_IE-1: Baculovi 90.1 0.43 9.4E-06 32.0 3.3 57 23-86 77-133 (140)
79 PF10571 UPF0547: Uncharacteri 89.3 0.26 5.5E-06 23.7 1.3 23 28-52 2-24 (26)
80 KOG0804 Cytoplasmic Zn-finger 89.1 0.18 3.9E-06 40.1 1.0 39 24-62 173-211 (493)
81 KOG1785 Tyrosine kinase negati 88.3 0.22 4.8E-06 39.3 1.0 36 24-63 367-402 (563)
82 PF06844 DUF1244: Protein of u 88.1 0.52 1.1E-05 27.7 2.3 16 52-67 12-27 (68)
83 PF10367 Vps39_2: Vacuolar sor 88.1 0.14 2.9E-06 32.2 -0.2 33 24-58 76-108 (109)
84 KOG1493 Anaphase-promoting com 88.0 0.098 2.1E-06 31.8 -0.8 54 25-85 19-81 (84)
85 KOG2034 Vacuolar sorting prote 87.2 0.33 7.3E-06 41.5 1.5 40 24-65 815-854 (911)
86 PF08746 zf-RING-like: RING-li 87.0 0.35 7.5E-06 26.0 1.0 41 29-76 1-41 (43)
87 KOG1940 Zn-finger protein [Gen 86.9 0.35 7.5E-06 36.3 1.3 51 22-82 154-204 (276)
88 PF14446 Prok-RING_1: Prokaryo 86.8 0.73 1.6E-05 26.1 2.3 36 24-59 3-38 (54)
89 KOG4367 Predicted Zn-finger pr 86.6 0.27 5.8E-06 39.3 0.6 33 26-62 4-36 (699)
90 KOG3053 Uncharacterized conser 85.3 1.3 2.7E-05 33.1 3.5 56 23-82 17-79 (293)
91 PF14447 Prok-RING_4: Prokaryo 85.3 0.31 6.8E-06 27.7 0.3 46 27-88 8-53 (55)
92 KOG3161 Predicted E3 ubiquitin 83.5 0.37 8E-06 40.2 0.1 37 26-62 11-47 (861)
93 KOG4275 Predicted E3 ubiquitin 82.0 0.41 8.9E-06 36.3 -0.1 28 26-57 300-328 (350)
94 COG5194 APC11 Component of SCF 81.8 1.1 2.3E-05 27.5 1.7 19 46-64 52-70 (88)
95 KOG0801 Predicted E3 ubiquitin 81.6 0.5 1.1E-05 32.8 0.2 31 22-53 173-203 (205)
96 COG5236 Uncharacterized conser 80.8 2 4.4E-05 33.5 3.2 54 24-89 59-112 (493)
97 COG3492 Uncharacterized protei 80.0 1.7 3.6E-05 27.3 2.1 17 51-67 42-58 (104)
98 COG5222 Uncharacterized conser 79.9 3.4 7.3E-05 31.6 4.1 44 27-82 275-318 (427)
99 KOG2932 E3 ubiquitin ligase in 78.2 1.1 2.3E-05 34.4 1.0 31 26-59 90-120 (389)
100 KOG4362 Transcriptional regula 76.9 1.1 2.3E-05 37.7 0.7 68 13-91 8-75 (684)
101 KOG3970 Predicted E3 ubiquitin 75.0 4.6 0.0001 29.7 3.5 62 24-89 48-110 (299)
102 KOG3268 Predicted E3 ubiquitin 74.1 5.7 0.00012 28.2 3.7 59 24-85 163-228 (234)
103 KOG2930 SCF ubiquitin ligase, 73.9 1.9 4E-05 27.8 1.1 39 26-64 46-97 (114)
104 KOG3800 Predicted E3 ubiquitin 72.5 8 0.00017 29.3 4.3 51 28-87 2-53 (300)
105 KOG3039 Uncharacterized conser 70.8 4.6 0.0001 30.1 2.7 38 25-66 42-79 (303)
106 KOG3579 Predicted E3 ubiquitin 69.8 2.7 5.9E-05 31.9 1.4 52 24-82 266-322 (352)
107 cd00065 FYVE FYVE domain; Zinc 68.4 4.5 9.8E-05 22.3 1.9 38 27-64 3-40 (57)
108 PHA02825 LAP/PHD finger-like p 67.4 5.2 0.00011 27.7 2.3 51 23-86 5-60 (162)
109 PF07975 C1_4: TFIIH C1-like d 66.7 3.4 7.4E-05 23.1 1.1 16 41-57 21-36 (51)
110 KOG2114 Vacuolar assembly/sort 66.6 3.1 6.8E-05 35.8 1.3 40 27-82 841-880 (933)
111 PF14445 Prok-RING_2: Prokaryo 65.0 1.4 3.1E-05 24.6 -0.7 36 24-60 5-40 (57)
112 PF10426 zf-RAG1: Recombinatio 64.3 2 4.2E-05 21.3 -0.2 17 72-88 2-18 (30)
113 KOG1571 Predicted E3 ubiquitin 61.9 4.4 9.6E-05 31.5 1.2 47 23-86 302-348 (355)
114 smart00064 FYVE Protein presen 60.7 8.9 0.00019 22.0 2.2 39 26-64 10-48 (68)
115 KOG2979 Protein involved in DN 58.5 40 0.00087 25.2 5.6 75 24-110 174-250 (262)
116 KOG0825 PHD Zn-finger protein 57.9 8.5 0.00018 33.3 2.3 49 28-87 125-173 (1134)
117 KOG0309 Conserved WD40 repeat- 57.7 10 0.00022 32.7 2.7 40 23-64 1025-1064(1081)
118 KOG2807 RNA polymerase II tran 57.5 4.5 9.7E-05 31.3 0.6 36 27-64 331-366 (378)
119 PF01363 FYVE: FYVE zinc finge 55.7 2.2 4.8E-05 24.7 -1.0 36 24-60 7-43 (69)
120 PF05605 zf-Di19: Drought indu 54.9 4.9 0.00011 22.3 0.3 40 26-84 2-41 (54)
121 PF07503 zf-HYPF: HypF finger; 54.2 5.4 0.00012 20.4 0.4 32 52-85 1-32 (35)
122 PF14471 DUF4428: Domain of un 54.0 13 0.00029 20.5 2.0 30 28-60 1-30 (51)
123 KOG3113 Uncharacterized conser 51.8 21 0.00045 26.8 3.3 76 23-110 108-184 (293)
124 KOG0298 DEAD box-containing he 51.3 10 0.00022 34.4 1.8 40 23-65 1150-1189(1394)
125 PF13240 zinc_ribbon_2: zinc-r 49.7 10 0.00022 17.4 1.0 21 29-51 2-22 (23)
126 PLN02638 cellulose synthase A 49.7 15 0.00033 32.7 2.7 51 23-82 14-67 (1079)
127 PF12906 RINGv: RING-variant d 48.6 12 0.00026 20.2 1.3 34 29-64 1-39 (47)
128 PF09889 DUF2116: Uncharacteri 47.4 23 0.0005 20.3 2.4 30 27-66 4-34 (59)
129 PF14353 CpXC: CpXC protein 46.5 18 0.0004 23.5 2.1 23 61-85 27-49 (128)
130 PF10497 zf-4CXXC_R1: Zinc-fin 46.3 43 0.00094 21.3 3.8 35 46-82 31-69 (105)
131 PF14569 zf-UDP: Zinc-binding 45.8 39 0.00084 20.6 3.2 51 23-82 6-59 (80)
132 PF01194 RNA_pol_N: RNA polyme 45.8 30 0.00064 20.0 2.6 15 70-86 2-16 (60)
133 PF10272 Tmpp129: Putative tra 45.5 15 0.00032 28.7 1.8 40 48-87 311-353 (358)
134 PF10764 Gin: Inhibitor of sig 45.2 7.4 0.00016 21.2 0.1 35 28-67 1-35 (46)
135 PHA02862 5L protein; Provision 44.8 29 0.00063 23.8 2.9 45 27-84 3-52 (156)
136 PF06906 DUF1272: Protein of u 44.6 22 0.00047 20.3 1.9 46 27-86 6-53 (57)
137 PLN02436 cellulose synthase A 44.5 20 0.00043 32.0 2.5 51 23-82 33-86 (1094)
138 PLN02189 cellulose synthase 44.4 20 0.00043 31.9 2.5 51 23-82 31-84 (1040)
139 PF09538 FYDLN_acid: Protein o 43.9 7 0.00015 25.2 -0.2 17 69-87 23-39 (108)
140 PF02891 zf-MIZ: MIZ/SP-RING z 43.8 20 0.00044 19.6 1.7 47 27-82 3-49 (50)
141 PF02148 zf-UBP: Zn-finger in 41.9 18 0.00038 20.6 1.3 33 29-64 1-37 (63)
142 PF15616 TerY-C: TerY-C metal 41.5 16 0.00034 24.5 1.2 43 27-89 78-120 (131)
143 PF06467 zf-FCS: MYM-type Zinc 41.1 23 0.00049 18.2 1.6 36 24-60 4-43 (43)
144 COG5112 UFD2 U1-like Zn-finger 40.6 17 0.00038 23.5 1.3 22 45-66 50-71 (126)
145 PLN02195 cellulose synthase A 40.5 28 0.0006 30.8 2.8 54 23-85 3-59 (977)
146 KOG4577 Transcription factor L 39.0 9.4 0.0002 29.1 -0.2 45 10-55 104-148 (383)
147 KOG0006 E3 ubiquitin-protein l 37.7 15 0.00033 28.4 0.8 19 45-63 339-357 (446)
148 PLN02915 cellulose synthase A 36.6 31 0.00067 30.8 2.5 52 23-83 12-66 (1044)
149 COG1996 RPC10 DNA-directed RNA 36.1 7.7 0.00017 21.5 -0.8 28 52-85 8-35 (49)
150 COG5109 Uncharacterized conser 35.9 38 0.00083 26.3 2.7 56 24-87 334-389 (396)
151 PF00412 LIM: LIM domain; Int 35.0 20 0.00043 19.5 0.8 37 21-60 21-57 (58)
152 PLN02400 cellulose synthase 34.7 23 0.0005 31.7 1.5 52 23-83 33-87 (1085)
153 KOG1100 Predicted E3 ubiquitin 34.2 23 0.0005 25.5 1.2 25 29-57 161-186 (207)
154 PF13248 zf-ribbon_3: zinc-rib 34.1 27 0.00058 16.3 1.1 22 27-50 3-24 (26)
155 PTZ00218 40S ribosomal protein 33.5 48 0.001 18.7 2.2 36 22-63 12-47 (54)
156 PF02318 FYVE_2: FYVE-type zin 33.2 28 0.00061 22.5 1.4 33 25-58 53-87 (118)
157 KOG2169 Zn-finger transcriptio 32.6 42 0.00092 28.2 2.7 42 45-89 317-360 (636)
158 PF13719 zinc_ribbon_5: zinc-r 32.0 43 0.00093 17.0 1.7 14 69-84 22-35 (37)
159 PF01530 zf-C2HC: Zinc finger, 31.8 25 0.00054 17.5 0.8 11 73-83 2-12 (31)
160 PRK14892 putative transcriptio 31.3 77 0.0017 20.1 3.1 40 69-111 39-79 (99)
161 PF13834 DUF4193: Domain of un 31.1 17 0.00038 23.1 0.2 33 22-56 66-98 (99)
162 KOG2789 Putative Zn-finger pro 29.3 20 0.00043 28.6 0.2 34 25-60 73-106 (482)
163 PF07649 C1_3: C1-like domain; 28.1 38 0.00082 16.2 1.1 29 27-56 1-29 (30)
164 KOG2066 Vacuolar assembly/sort 27.3 18 0.00039 31.2 -0.4 40 24-64 782-825 (846)
165 smart00249 PHD PHD zinc finger 26.7 39 0.00085 16.9 1.1 32 28-60 1-32 (47)
166 cd02335 ZZ_ADA2 Zinc finger, Z 26.6 63 0.0014 17.4 1.9 32 28-60 2-34 (49)
167 KOG0269 WD40 repeat-containing 25.9 56 0.0012 28.3 2.2 60 22-86 775-834 (839)
168 PF11781 RRN7: RNA polymerase 25.4 25 0.00053 18.0 0.1 13 24-36 6-18 (36)
169 PF00569 ZZ: Zinc finger, ZZ t 24.9 75 0.0016 16.8 2.0 34 25-59 3-37 (46)
170 PF04710 Pellino: Pellino; In 24.6 25 0.00054 28.0 0.0 59 25-86 327-402 (416)
171 PF07191 zinc-ribbons_6: zinc- 24.3 17 0.00038 21.6 -0.7 40 27-85 2-41 (70)
172 cd02249 ZZ Zinc finger, ZZ typ 24.3 61 0.0013 17.1 1.5 32 27-60 1-33 (46)
173 PF13465 zf-H2C2_2: Zinc-finge 23.7 71 0.0015 14.6 1.5 20 17-36 5-24 (26)
174 PF07800 DUF1644: Protein of u 23.2 2.3E+02 0.0051 19.7 4.5 72 20-110 74-157 (162)
175 TIGR02098 MJ0042_CXXC MJ0042 f 22.6 74 0.0016 15.8 1.6 12 71-84 24-35 (38)
176 KOG3408 U1-like Zn-finger-cont 22.5 42 0.00091 22.3 0.8 21 45-65 52-72 (129)
177 PF03107 C1_2: C1 domain; Int 22.4 43 0.00092 16.1 0.6 25 27-52 1-25 (30)
178 PF01258 zf-dskA_traR: Prokary 22.3 45 0.00098 16.7 0.7 31 27-60 4-34 (36)
179 KOG3362 Predicted BBOX Zn-fing 22.0 31 0.00067 23.6 0.1 37 22-63 114-151 (156)
180 PF09943 DUF2175: Uncharacteri 21.8 73 0.0016 20.4 1.7 39 26-66 2-40 (101)
181 KOG2594 Uncharacterized conser 21.5 67 0.0014 25.4 1.8 19 49-67 31-49 (396)
182 PF13453 zf-TFIIB: Transcripti 21.0 1E+02 0.0022 15.8 2.0 9 93-101 30-38 (41)
183 PF00643 zf-B_box: B-box zinc 20.7 73 0.0016 16.1 1.4 31 25-59 2-32 (42)
184 PF00628 PHD: PHD-finger; Int 20.6 28 0.00061 18.5 -0.3 35 28-63 1-35 (51)
185 PRK13130 H/ACA RNA-protein com 20.5 1.4E+02 0.003 16.9 2.5 36 72-109 17-52 (56)
186 TIGR02300 FYDLN_acid conserved 20.4 26 0.00056 23.4 -0.5 18 69-88 23-40 (129)
187 COG2260 Predicted Zn-ribbon RN 20.2 1.7E+02 0.0038 16.8 2.9 35 74-110 19-53 (59)
188 TIGR00622 ssl1 transcription f 20.1 66 0.0014 21.0 1.3 31 27-58 56-97 (112)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.83 E-value=1.5e-21 Score=148.46 Aligned_cols=115 Identities=23% Similarity=0.496 Sum_probs=105.7
Q ss_pred CCCCCCcchHHHHHHhhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 6 QTPKENLAKEEEEEEESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
++++..+..++++.+.+..+.+.|.||+++..+...| ..++|+|+||+.|++.|+...|++|....++||+.+|+...+
T Consensus 164 l~~~Il~~deea~~~~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~ 242 (445)
T KOG1814|consen 164 LKKEILQFDEEATLEKFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAP 242 (445)
T ss_pred HHHHHHhhhHHHHHHHHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCC
Confidence 3455566788888899999999999999999887777 499999999999999999999999999999999999999999
Q ss_pred hhhcccCCCHHHHHHHHHHHHhhhh-cCCCceecCCC
Q 033301 86 PFSCEPIVPASLFSKWCDVLCEDYV-LGFERSYCPNT 121 (122)
Q Consensus 86 ~~~i~~~l~~~~~~ky~~~~~~~~i-~~~~~~~CP~~ 121 (122)
+..++.+|+.++++||++++++..+ .+++.+|||++
T Consensus 243 ~g~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr~ 279 (445)
T KOG1814|consen 243 PGQVKELVGDELFARYEKLMLQKTLELMSDVVYCPRA 279 (445)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCChh
Confidence 9999999999999999999999999 57788999985
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.63 E-value=2.8e-16 Score=121.37 Aligned_cols=96 Identities=28% Similarity=0.565 Sum_probs=84.5
Q ss_pred CCcccccccccccccc-ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAAS-KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPASLFSKWC 102 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~ky~ 102 (122)
....+|.||+.+.+.. ++|. ...|+|.||.+||+.||+.+. +....|+||+.+|...++.+....+|++++.+.|+
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~iev~~--~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e 220 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIEVKL--LSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWE 220 (384)
T ss_pred cccccCccCccccccHhhhHH-HhcccchhhhHHhHHHhhhhh--ccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHH
Confidence 3567999999555444 6674 899999999999999999993 36789999999999999999999999999999999
Q ss_pred HHHHhhhhcCCCceecCCCC
Q 033301 103 DVLCEDYVLGFERSYCPNTN 122 (122)
Q Consensus 103 ~~~~~~~i~~~~~~~CP~~~ 122 (122)
+++.+.++...++.|||+|+
T Consensus 221 ~~~~e~~i~~~~~~ycp~~~ 240 (384)
T KOG1812|consen 221 QRLKEEVIPSLDRVYCPYPR 240 (384)
T ss_pred HHHHHHhhhhhhcccCCCCC
Confidence 99999999877777999985
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.55 E-value=6.7e-15 Score=115.71 Aligned_cols=96 Identities=25% Similarity=0.518 Sum_probs=84.9
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCH-HHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPA-SLFSKWC 102 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~ky~ 102 (122)
.....|+||++..+. .+ +.+.|+|.||..||..|+..+|.++....|+||..+|.+.+..++|..++++ ++.++|.
T Consensus 68 ~~~~~c~ic~~~~~~--~~-~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EI-IGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CccccCCcccCCCcc--hh-hhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 556899999999975 23 4899999999999999999999886555599999999999999999999988 5999999
Q ss_pred HHHHhhhhcCCC-ceecCCCC
Q 033301 103 DVLCEDYVLGFE-RSYCPNTN 122 (122)
Q Consensus 103 ~~~~~~~i~~~~-~~~CP~~~ 122 (122)
+++.++||..+. .+|||+|+
T Consensus 145 ~~i~~syve~~~~lkwCP~~~ 165 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPG 165 (444)
T ss_pred HHHHHHHHhcCCccccCCCCC
Confidence 999999997765 49999975
No 4
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.99 E-value=8.6e-11 Score=63.84 Aligned_cols=40 Identities=23% Similarity=0.683 Sum_probs=28.3
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCC
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECP 76 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP 76 (122)
|+||++.+..+ +.++|||.||..|+..++...- ...+.||
T Consensus 1 CpiC~~~~~~P----v~l~CGH~FC~~Cl~~~~~~~~----~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFKDP----VSLPCGHSFCRSCLERLWKEPS----GSGFSCP 40 (42)
T ss_dssp ETTTTSB-SSE----EE-SSSSEEEHHHHHHHHCCSS----SST---S
T ss_pred CCccchhhCCc----cccCCcCHHHHHHHHHHHHccC----CcCCCCc
Confidence 89999999766 5899999999999999986542 2227888
No 5
>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=98.93 E-value=2.2e-10 Score=62.68 Aligned_cols=35 Identities=31% Similarity=0.765 Sum_probs=30.5
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
+|+||++++...+.+ +.++|+|.||.+||..|+..
T Consensus 2 ~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEKV-VKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSCE-EEETTSEEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCeE-EEccCCCeeCHHHHHHHHHh
Confidence 699999999766566 47889999999999999976
No 6
>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=98.90 E-value=1.2e-09 Score=58.69 Aligned_cols=39 Identities=33% Similarity=0.933 Sum_probs=32.4
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCC
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECP 76 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP 76 (122)
|+||++.+.... .+++|||.||.+||..|+.. ...++||
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~~~------~~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWLEN------SGSVKCP 39 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHHHHHH------TSSSBTT
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHHHHHh------cCCccCC
Confidence 899999987653 27999999999999999998 2355688
No 7
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.86 E-value=1.6e-09 Score=59.03 Aligned_cols=43 Identities=28% Similarity=0.650 Sum_probs=23.3
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCC
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECP 76 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP 76 (122)
|+||.+ +...+.....|+|||.||++|+.+.+.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 655333324788999999999999998542 4577887
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.86 E-value=1.8e-09 Score=76.13 Aligned_cols=67 Identities=30% Similarity=0.663 Sum_probs=49.9
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhh--------cCCCceecCCCCCCCCCCChhhcccCCC
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQ--------DDNTAKIECPGLECRHDLDPFSCEPIVP 94 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~--------~~~~~~i~CP~~~C~~~i~~~~i~~~l~ 94 (122)
....+.|+||++.+..+ +...|||.||..|+..|+...-. .......+|| .|+..|+...+..+..
T Consensus 15 ~~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiyg 88 (193)
T PLN03208 15 SGGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYG 88 (193)
T ss_pred CCCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeec
Confidence 45678999999988544 36789999999999999865311 0123467999 6999999887776654
Q ss_pred H
Q 033301 95 A 95 (122)
Q Consensus 95 ~ 95 (122)
.
T Consensus 89 r 89 (193)
T PLN03208 89 R 89 (193)
T ss_pred c
Confidence 3
No 9
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=2.1e-09 Score=74.50 Aligned_cols=59 Identities=20% Similarity=0.595 Sum_probs=45.3
Q ss_pred hhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc
Q 033301 21 ESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP 91 (122)
Q Consensus 21 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 91 (122)
..+...+.|+||++.+.....+ ...|||.||..|++..+... .+|| .|+..|+..++..
T Consensus 126 ~~~~~~~~CPiCl~~~sek~~v--sTkCGHvFC~~Cik~alk~~--------~~CP--~C~kkIt~k~~~r 184 (187)
T KOG0320|consen 126 LRKEGTYKCPICLDSVSEKVPV--STKCGHVFCSQCIKDALKNT--------NKCP--TCRKKITHKQFHR 184 (187)
T ss_pred cccccccCCCceecchhhcccc--ccccchhHHHHHHHHHHHhC--------CCCC--Ccccccchhhhee
Confidence 3456668999999999654333 79999999999999877653 3899 5887887766544
No 10
>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=98.80 E-value=1.7e-09 Score=57.70 Aligned_cols=32 Identities=31% Similarity=0.881 Sum_probs=26.2
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
|+||++.+.. .+ +.++|||.||.+||..|++.
T Consensus 1 C~iC~~~~~~--~~-~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD--PV-VVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS--EE-EECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC--cC-EECCCCCchhHHHHHHHHHC
Confidence 8999999864 32 37999999999999999875
No 11
>PHA02926 zinc finger-like protein; Provisional
Probab=98.74 E-value=1.4e-08 Score=72.79 Aligned_cols=62 Identities=24% Similarity=0.496 Sum_probs=46.3
Q ss_pred HhhCCCcccccccccccc-----ccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 20 EESSGSSFTCEICIEPMA-----ASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 20 ~~~~~~~~~C~IC~~~~~-----~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
....+...+|+||++.+. ....|.++.+|+|.||..|++.|...+-. ....-.|| .|+..+.
T Consensus 164 ~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--~~~~rsCP--iCR~~f~ 230 (242)
T PHA02926 164 VYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE--TGASDNCP--ICRTRFR 230 (242)
T ss_pred HHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc--cCcCCcCC--CCcceee
Confidence 344567799999999863 22345568899999999999999997532 34556899 6997654
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.66 E-value=1.7e-08 Score=55.14 Aligned_cols=43 Identities=30% Similarity=0.796 Sum_probs=34.4
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCC
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECR 81 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~ 81 (122)
.|+||++.+.....+ .++.|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~-~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRP-RLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCe-EEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 499999999544455 499999999999999887 35678984 75
No 13
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.63 E-value=3.5e-08 Score=52.94 Aligned_cols=44 Identities=34% Similarity=0.804 Sum_probs=33.3
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD 83 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~ 83 (122)
.|+||++.+. +.+ ...+|+|.||..|+..|+.. ...+|| .|+..
T Consensus 1 ~C~iC~~~~~--~~~-~~~~C~H~~c~~C~~~~~~~-------~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPV-VLLPCGHVFCRSCIDKWLKS-------GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhhh--Cce-EecCCCChhcHHHHHHHHHh-------CcCCCC--CCCCc
Confidence 5899999983 233 25669999999999999875 345798 57754
No 14
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.54 E-value=5.7e-08 Score=54.40 Aligned_cols=46 Identities=28% Similarity=0.694 Sum_probs=35.6
Q ss_pred ccccccccccccccccccccCCcCCc-chHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHP-FSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
...|.||++.... . ++++|||. ||.+|+..++. ...+|| -|+..|.
T Consensus 2 ~~~C~iC~~~~~~--~--~~~pCgH~~~C~~C~~~~~~--------~~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD--V--VLLPCGHLCFCEECAERLLK--------RKKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS--E--EEETTCEEEEEHHHHHHHHH--------TTSBBT--TTTBB-S
T ss_pred cCCCccCCccCCc--e--EEeCCCChHHHHHHhHHhcc--------cCCCCC--cCChhhc
Confidence 3689999998643 2 47899999 99999999998 345899 5998765
No 15
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=9.2e-08 Score=75.47 Aligned_cols=64 Identities=25% Similarity=0.568 Sum_probs=51.3
Q ss_pred CccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCHHH
Q 033301 25 SSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPASL 97 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~ 97 (122)
....||||+++.+.+ ....|||.||-.||..||.... .....+|| -|...|...+++-+.-.++
T Consensus 185 t~~~CPICL~~~~~p----~~t~CGHiFC~~CiLqy~~~s~---~~~~~~CP--iC~s~I~~kdl~pv~~e~~ 248 (513)
T KOG2164|consen 185 TDMQCPICLEPPSVP----VRTNCGHIFCGPCILQYWNYSA---IKGPCSCP--ICRSTITLKDLLPVFIEDD 248 (513)
T ss_pred cCCcCCcccCCCCcc----cccccCceeeHHHHHHHHhhhc---ccCCccCC--chhhhccccceeeeeeccc
Confidence 378999999998665 3566999999999999999983 34578999 6999999987766554433
No 16
>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=98.45 E-value=2.8e-07 Score=53.60 Aligned_cols=51 Identities=20% Similarity=0.256 Sum_probs=40.7
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP 91 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 91 (122)
+.|+||.+.+..+ +.++|||.||+.|+..|+.. ..+|| -|+..++..++..
T Consensus 2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~--------~~~cP--~~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLS--------HGTDP--VTGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHH--------CCCCC--CCcCCCChhhcee
Confidence 5799999998765 36899999999999999975 23799 4888887666544
No 17
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.41 E-value=3.2e-07 Score=66.96 Aligned_cols=52 Identities=29% Similarity=0.622 Sum_probs=38.7
Q ss_pred CCccccccccccccccc----cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 24 GSSFTCEICIEPMAASK----KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
....+|+||++.+.... .+.++.+|+|.||.+|+..|+.. ...|| -|+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCC--CCCCEee
Confidence 45689999999875432 12246789999999999998753 23899 5997665
No 18
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.40 E-value=1.3e-07 Score=69.97 Aligned_cols=53 Identities=26% Similarity=0.676 Sum_probs=44.5
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcc
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCE 90 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 90 (122)
.....|.+|++....+ +..+|||.||-.|+..|...+-+ || -|+..+.+..+.
T Consensus 237 ~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~e--------CP--lCR~~~~pskvi 289 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKAE--------CP--LCREKFQPSKVI 289 (293)
T ss_pred CCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHccccC--------CC--cccccCCCccee
Confidence 4457899999999655 47999999999999999987642 99 699999988764
No 19
>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=98.39 E-value=3e-07 Score=47.56 Aligned_cols=30 Identities=33% Similarity=0.826 Sum_probs=24.8
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHH
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQ 62 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~ 62 (122)
|+||++... .. ..++|+|.||..|+..|+.
T Consensus 1 C~iC~~~~~---~~-~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEELK---DP-VVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCCC---Cc-EEecCCChHHHHHHHHHHH
Confidence 789999842 22 3789999999999999987
No 20
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.38 E-value=3.7e-07 Score=70.99 Aligned_cols=66 Identities=20% Similarity=0.495 Sum_probs=49.3
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcc-cCCCHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCE-PIVPASLFSKWC 102 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~-~~l~~~~~~ky~ 102 (122)
...+.|+||.+.+..+ +.++|||.||..|+..|+.. ...|| .|+..+....+. ..+-.++++.|.
T Consensus 24 e~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~--------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 24 DTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSN--------QPKCP--LCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred ccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhC--------CCCCC--CCCCccccccCccchHHHHHHHHHH
Confidence 3567999999988544 37899999999999998853 12799 699888765443 344567777775
Q ss_pred H
Q 033301 103 D 103 (122)
Q Consensus 103 ~ 103 (122)
.
T Consensus 90 ~ 90 (397)
T TIGR00599 90 N 90 (397)
T ss_pred H
Confidence 4
No 21
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.23 E-value=7.6e-07 Score=64.14 Aligned_cols=60 Identities=27% Similarity=0.689 Sum_probs=48.7
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCC
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIV 93 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l 93 (122)
....++|-||+|...++ ++..|||.||=-||..|+..+.+ .-.|| -|+..++.+.+.-|.
T Consensus 44 ~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~-----~~~cP--VCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPN-----SKECP--VCKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCC-----CeeCC--ccccccccceEEeee
Confidence 57789999999998665 58899999999999999998743 33678 599988887765543
No 22
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=2.4e-06 Score=64.40 Aligned_cols=96 Identities=19% Similarity=0.408 Sum_probs=74.4
Q ss_pred hCCCccccccccccccccccccccCCcC--CcchHHHHHHHHHHHhhcCC-------CceecCCCCCCCCCCC-hhhccc
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCT--HPFSQDCIAKYIQVKVQDDN-------TAKIECPGLECRHDLD-PFSCEP 91 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~C~~~~i~~~i~~~~-------~~~i~CP~~~C~~~i~-~~~i~~ 91 (122)
.+.....|..|-+.-+. + ..++|+ |..|.+|++.|..+++++.+ ...+.||. +|...+- .-.-.+
T Consensus 217 ~N~~ni~C~~Ctdv~~~---v-lvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ 291 (446)
T KOG0006|consen 217 TNSRNITCITCTDVRSP---V-LVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR 291 (446)
T ss_pred cccccceeEEecCCccc---e-EEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence 45778899999887642 2 268899 99999999999999996522 23567774 7875433 323356
Q ss_pred CCCHHHHHHHHHHHHhhhhcCCCceecCCCC
Q 033301 92 IVPASLFSKWCDVLCEDYVLGFERSYCPNTN 122 (122)
Q Consensus 92 ~l~~~~~~ky~~~~~~~~i~~~~~~~CP~~~ 122 (122)
+|..+.|.+|+++..|.+|......-||+|.
T Consensus 292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pg 322 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPG 322 (446)
T ss_pred ecchhHHHHHHHhhhhhheeecCCEecCCCC
Confidence 8999999999999999999877789999974
No 23
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.10 E-value=6.1e-06 Score=62.20 Aligned_cols=53 Identities=19% Similarity=0.460 Sum_probs=37.8
Q ss_pred ccccccccccccccc--ccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 27 FTCEICIEPMAASKK--FKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~--~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
..||+|..+...... +.+. .|||.||..|+...+. . .+..|| .|+..+....+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~----~---~~~~CP--~C~~~lrk~~f 58 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV----R---GSGSCP--ECDTPLRKNNF 58 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhc----C---CCCCCC--CCCCccchhhc
Confidence 579999997433322 2223 7999999999999873 1 234899 79987776654
No 24
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=6.2e-06 Score=63.17 Aligned_cols=96 Identities=21% Similarity=0.382 Sum_probs=60.5
Q ss_pred CCCccccccccccccccc----cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC----CChhhc--ccC
Q 033301 23 SGSSFTCEICIEPMAASK----KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD----LDPFSC--EPI 92 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~----i~~~~i--~~~ 92 (122)
+.+...|+||++.+...- .|.++++|.|.||..|++.|-...-. +....-.|| .|+.. ++...+ ..-
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP--~CRv~s~~v~pS~~Wv~t~~ 234 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCP--FCRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCC--cccCccccccccceeeeecc
Confidence 467889999999986431 15567899999999999999866554 356677899 59853 222222 112
Q ss_pred CCHHHHHHHHHHHHhhhh--cCCCceecCCC
Q 033301 93 VPASLFSKWCDVLCEDYV--LGFERSYCPNT 121 (122)
Q Consensus 93 l~~~~~~ky~~~~~~~~i--~~~~~~~CP~~ 121 (122)
-...+.+.|++.+....- -......||..
T Consensus 235 ~k~~li~e~~~~~s~~~c~yf~~~~g~cPf~ 265 (344)
T KOG1039|consen 235 EKQKLIEEYEAEMSAKDCKYFSQGLGSCPFG 265 (344)
T ss_pred cccccHHHHHHHhhccchhhhcCCCCCCCCC
Confidence 233455666655433221 13344667764
No 25
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=2.3e-06 Score=70.29 Aligned_cols=56 Identities=18% Similarity=0.544 Sum_probs=45.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccC
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPI 92 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 92 (122)
.....|++|.... -+. +...|+|.||.+|+...+..+- . +|| +|+..|++.+|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~--vI~kC~H~FC~~Cvq~r~etRq----R---KCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDA--VITKCGHVFCEECVQTRYETRQ----R---KCP--KCNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhH--HHHhcchHHHHHHHHHHHHHhc----C---CCC--CCCCCCCccccccc
Confidence 5567899999444 334 3799999999999999999873 2 899 79999999998764
No 26
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=98.00 E-value=4.1e-06 Score=66.91 Aligned_cols=81 Identities=19% Similarity=0.506 Sum_probs=56.1
Q ss_pred hhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCHHHHHH
Q 033301 21 ESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPASLFSK 100 (122)
Q Consensus 21 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~k 100 (122)
.++.....|.+|-++.. .+ +...|.|.||+-|++.|+....+. ..++|| .|...|+.+.-..-+..-..+.
T Consensus 531 ~enk~~~~C~lc~d~ae---d~-i~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP--~C~i~LsiDlse~alek~~l~~ 601 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAE---DY-IESSCHHKFCRLCIKEYVESFMEN---NNVTCP--VCHIGLSIDLSEPALEKTDLKG 601 (791)
T ss_pred ccccCceeecccCChhh---hh-HhhhhhHHHHHHHHHHHHHhhhcc---cCCCCc--cccccccccccchhhhhcchhh
Confidence 34566789999988863 23 488999999999999999998764 348999 6998777654444444444444
Q ss_pred HHHHHHhhhh
Q 033301 101 WCDVLCEDYV 110 (122)
Q Consensus 101 y~~~~~~~~i 110 (122)
|.....-..|
T Consensus 602 Fk~sSIlnRi 611 (791)
T KOG1002|consen 602 FKASSILNRI 611 (791)
T ss_pred hhhHHHhhhc
Confidence 5444433333
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.00 E-value=2.5e-06 Score=62.12 Aligned_cols=46 Identities=28% Similarity=0.710 Sum_probs=39.2
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
......|+||++.+..+ ..++|+|.||+.|+...+. ..+.|| .|+.
T Consensus 10 ~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp--~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCP--VCRP 55 (386)
T ss_pred ccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCc--ccCC
Confidence 35678999999999766 2799999999999999998 458999 6984
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.85 E-value=5.5e-06 Score=62.93 Aligned_cols=65 Identities=22% Similarity=0.487 Sum_probs=50.5
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc-CCCHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP-IVPASLFSKWC 102 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~~~ky~ 102 (122)
.....|.||++-+..+ ...+|+|.||.=||+.|+..+ ..|| .|...+....++. .+-.++++.|.
T Consensus 21 D~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~~~--------p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLSYK--------PQCP--TCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhccC--------CCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence 3456899999999766 357799999999999999864 3688 6998888887765 34556666663
No 29
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.79 E-value=1.7e-05 Score=45.72 Aligned_cols=50 Identities=26% Similarity=0.670 Sum_probs=33.1
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECR 81 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~ 81 (122)
....+.|||-...+..+ + ....|+|.|-++.+..|| ++...++||..+|.
T Consensus 8 ~~~~~~CPiT~~~~~~P--V-~s~~C~H~fek~aI~~~i------~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDP--V-KSKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE--E-EESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC--c-CcCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 34568999999998644 4 367999999999999999 24678899999995
No 30
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=1.1e-05 Score=61.80 Aligned_cols=49 Identities=31% Similarity=0.781 Sum_probs=41.0
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
..|.||+|++..++..+ .|+|+|.|...|+-.|+... .-.|| -|+..+.
T Consensus 230 ~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-------r~~CP--vCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-------RTFCP--VCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-------CccCC--CCCCcCC
Confidence 69999999999988886 79999999999999999875 22599 4776443
No 31
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.69 E-value=3.4e-05 Score=57.89 Aligned_cols=54 Identities=24% Similarity=0.698 Sum_probs=44.3
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
.....+|.||++++-..+.+. .++|.|.|.+.|+..|+.. ..-+|| -|+..|++
T Consensus 320 a~~GveCaICms~fiK~d~~~-vlPC~H~FH~~Cv~kW~~~-------y~~~CP--vCrt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLR-VLPCDHRFHVGCVDKWLLG-------YSNKCP--VCRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEE-EeccCceechhHHHHHHhh-------hcccCC--ccCCCCCC
Confidence 345589999999998777774 9999999999999999873 234899 59988875
No 32
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=4.2e-05 Score=56.27 Aligned_cols=52 Identities=25% Similarity=0.526 Sum_probs=40.6
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
.+.|.||++....+ +..+|||.||-.|+...+..+- .-.|| -|++...+..+
T Consensus 215 d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~k------~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKKK------YEFCP--LCRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCc----ccccccchhhHHHHHHHHHhhc------cccCc--hhhhhccchhh
Confidence 56799999998544 4799999999999998655432 33699 69988877766
No 33
>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=97.54 E-value=3.6e-05 Score=46.42 Aligned_cols=39 Identities=26% Similarity=0.553 Sum_probs=28.1
Q ss_pred Ccccccccccccccc---------ccccccCCcCCcchHHHHHHHHHH
Q 033301 25 SSFTCEICIEPMAAS---------KKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~---------~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
....|.||++++... +.......|||.|...||..|+..
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc
Confidence 345699999999321 121135679999999999999954
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=97.49 E-value=8.4e-05 Score=44.72 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=38.3
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
...+.|+|+.+-+..+ +.+++||.|++.+|..|+.. ....|| .++..++..++
T Consensus 2 P~~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~-------~~~~~P--~t~~~l~~~~l 54 (73)
T PF04564_consen 2 PDEFLCPITGELMRDP----VILPSGHTYERSAIERWLEQ-------NGGTDP--FTRQPLSESDL 54 (73)
T ss_dssp SGGGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCT-------TSSB-T--TT-SB-SGGGS
T ss_pred CcccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHc-------CCCCCC--CCCCcCCcccc
Confidence 3568999999999766 47899999999999999986 345788 47777887655
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.38 E-value=0.00012 Score=54.79 Aligned_cols=66 Identities=21% Similarity=0.392 Sum_probs=47.1
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc-CCCHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP-IVPASLFSKWC 102 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~~~ky~ 102 (122)
.....|.||-+-+..+ ....|||.||.=||+.|+.++ ..|| -|+...-...++. .+..++.+.|.
T Consensus 23 Ds~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~~q--------p~CP--~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 23 DSMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLGTQ--------PFCP--VCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hhHHHhhhhhheeecc----eecccccchhHHHHHHHhcCC--------CCCc--cccccHHhhhcccchhHHHHHHhhh
Confidence 3456799999998765 478999999999999998754 3688 5876555444433 44556666664
Q ss_pred H
Q 033301 103 D 103 (122)
Q Consensus 103 ~ 103 (122)
.
T Consensus 89 ~ 89 (391)
T COG5432 89 R 89 (391)
T ss_pred h
Confidence 4
No 36
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.33 E-value=0.0001 Score=44.09 Aligned_cols=59 Identities=17% Similarity=0.355 Sum_probs=28.3
Q ss_pred ccccccccccccccc----cccccCCcCCcchHHHHHHHHHHHhhcCCCc---eecCCCCCCCCCCCh
Q 033301 26 SFTCEICIEPMAASK----KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTA---KIECPGLECRHDLDP 86 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~---~i~CP~~~C~~~i~~ 86 (122)
...|+||+......+ .+-....|++.|...||..|+...-.....+ .-+|| .|...|..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 468999999865221 1112347899999999999998776542222 33699 69987754
No 37
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.03 E-value=0.00045 Score=52.34 Aligned_cols=52 Identities=25% Similarity=0.602 Sum_probs=41.5
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~ 87 (122)
-..-.+|.+|-.-+-+..+ ...|-|.||+.||..|++. ...|| .|...|...
T Consensus 12 ~n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~--------~~~CP--~C~i~ih~t 63 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEE--------SKYCP--TCDIVIHKT 63 (331)
T ss_pred cccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHH--------hccCC--ccceeccCc
Confidence 3566899999998866643 5899999999999999997 23799 688776654
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.01 E-value=5.4e-05 Score=44.36 Aligned_cols=50 Identities=26% Similarity=0.555 Sum_probs=22.5
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcc
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCE 90 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 90 (122)
...|++|.+.+..+ + .+..|.|.||..|+...+. -.|| -|.......+++
T Consensus 7 lLrCs~C~~~l~~p--v-~l~~CeH~fCs~Ci~~~~~----------~~CP--vC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEP--V-CLGGCEHIFCSSCIRDCIG----------SECP--VCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS---B----SSS--B-TTTGGGGTT----------TB-S--SS--B-S-SS--
T ss_pred hcCCcHHHHHhcCC--c-eeccCccHHHHHHhHHhcC----------CCCC--CcCChHHHHHHH
Confidence 46799999998655 3 2689999999999966222 2499 588766655554
No 39
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.86 E-value=0.00055 Score=51.38 Aligned_cols=53 Identities=25% Similarity=0.425 Sum_probs=40.9
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
....+|.||+.+..-+ +.+.|+|.||.-|+++-+... ...|+ -|+..|+.+.+
T Consensus 5 ~~~~eC~IC~nt~n~P----v~l~C~HkFCyiCiKGsy~nd-------k~~Ca--vCR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP----VNLYCFHKFCYICIKGSYKND-------KKTCA--VCRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCcC----ccccccchhhhhhhcchhhcC-------CCCCc--eecCCCCcchh
Confidence 3457899999998655 589999999999998866543 22588 59988877644
No 40
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.78 E-value=0.00048 Score=49.05 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=26.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAK 59 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~ 59 (122)
.-.|.|.||-.++..+ +...|||.||..|...
T Consensus 194 ~IPF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~ 225 (259)
T COG5152 194 KIPFLCGICKKDYESP----VVTECGHSFCSLCAIR 225 (259)
T ss_pred CCceeehhchhhccch----hhhhcchhHHHHHHHH
Confidence 4457999999999766 5789999999999654
No 41
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.0016 Score=50.37 Aligned_cols=52 Identities=25% Similarity=0.651 Sum_probs=38.8
Q ss_pred CCCccccccccccccccc---------cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAASK---------KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
.++...|.||+|++-.++ +-.-.++|||.+..+|++.|.+.+- +|| -|+..+
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ--------TCP--ICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ--------TCP--ICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc--------CCC--cccCcc
Confidence 577789999999953221 1113789999999999999998651 788 588653
No 42
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.75 E-value=0.00099 Score=54.09 Aligned_cols=50 Identities=26% Similarity=0.663 Sum_probs=39.2
Q ss_pred hCCCcccccccccccccccc--ccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 22 SSGSSFTCEICIEPMAASKK--FKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~--~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
.......|.||.|++..... - ..++|+|.|+..|++.|++.+ + .|| -|+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~-~rL~C~Hifh~~CL~~W~er~--q------tCP--~CR~ 338 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITP-KRLPCGHIFHDSCLRSWFERQ--Q------TCP--TCRT 338 (543)
T ss_pred hhhcCCeeeeechhhcccccccc-ceeecccchHHHHHHHHHHHh--C------cCC--cchh
Confidence 44667899999999865311 2 489999999999999999983 2 788 5776
No 43
>PHA03096 p28-like protein; Provisional
Probab=96.73 E-value=0.00032 Score=52.63 Aligned_cols=54 Identities=20% Similarity=0.336 Sum_probs=39.7
Q ss_pred cccccccccccc----cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 27 FTCEICIEPMAA----SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 27 ~~C~IC~~~~~~----~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
..|+||++.+.. ...|.++..|.|.||..|++.|...+.. ....-.|| .|...+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~--~e~~~~c~--~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY--KETEPENR--RLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh--cccCcccc--chhhHH
Confidence 789999999753 3356578899999999999999998763 34344455 355444
No 44
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=96.46 E-value=0.0018 Score=37.20 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=19.9
Q ss_pred HHHHHHHHhhhhcC-CCceecCCCC
Q 033301 99 SKWCDVLCEDYVLG-FERSYCPNTN 122 (122)
Q Consensus 99 ~ky~~~~~~~~i~~-~~~~~CP~~~ 122 (122)
+||++++.+.+|.. ++.+|||+|+
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~ 25 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPD 25 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCC
Confidence 48999999999965 4569999875
No 45
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.0036 Score=49.07 Aligned_cols=49 Identities=29% Similarity=0.752 Sum_probs=37.5
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
.+.+.|-||+..+..+ +..+|||.||..|+.+ .++ -...|| .|+..+..
T Consensus 82 ~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r----~ld----~~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP----VVTPCGHSFCLECLDR----SLD----QETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCCC----ccccccccccHHHHHH----Hhc----cCCCCc--cccccccc
Confidence 7889999999888655 4679999999999666 332 344788 59877663
No 46
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.42 E-value=0.0028 Score=47.09 Aligned_cols=52 Identities=29% Similarity=0.595 Sum_probs=40.1
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
....+|++|.+.-..+ + +...|+|.||--|+..-.... ..++|| .|++...+
T Consensus 237 t~~~~C~~Cg~~PtiP--~-~~~~C~HiyCY~Ci~ts~~~~------asf~Cp--~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP--H-VIGKCGHIYCYYCIATSRLWD------ASFTCP--LCGENVEP 288 (298)
T ss_pred cCCceeeccCCCCCCC--e-eeccccceeehhhhhhhhcch------hhcccC--ccCCCCcc
Confidence 5567899999987655 3 367799999999998766643 467999 79987663
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.35 E-value=0.0038 Score=34.60 Aligned_cols=45 Identities=22% Similarity=0.615 Sum_probs=21.6
Q ss_pred cccccccccccc-cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC
Q 033301 29 CEICIEPMAASK-KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD 83 (122)
Q Consensus 29 C~IC~~~~~~~~-~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~ 83 (122)
|++|.++++..+ .|. --.|++..|+.||..-.+ + ..-+|| +|+..
T Consensus 1 cp~C~e~~d~~d~~~~-PC~Cgf~IC~~C~~~i~~----~---~~g~CP--gCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFY-PCECGFQICRFCYHDILE----N---EGGRCP--GCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT---SSTTS----HHHHHHHTT----S---S-SB-T--TT--B
T ss_pred CCCcccccccCCCccc-cCcCCCcHHHHHHHHHHh----c---cCCCCC--CCCCC
Confidence 789999985443 342 567999999999987655 1 233899 68753
No 48
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.24 E-value=0.0005 Score=52.60 Aligned_cols=49 Identities=35% Similarity=0.802 Sum_probs=36.2
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
...+.|+||++-+... + +...|.|+||.+||-.-+.. |+. .|| .|+..+
T Consensus 41 ~~~v~c~icl~llk~t--m-ttkeClhrfc~~ci~~a~r~----gn~---ecp--tcRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLKKT--M-TTKECLHRFCFDCIWKALRS----GNN---ECP--TCRKKL 89 (381)
T ss_pred hhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHHh----cCC---CCc--hHHhhc
Confidence 4567899999998644 3 37899999999998765543 233 688 688644
No 49
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.20 E-value=0.0044 Score=55.30 Aligned_cols=75 Identities=16% Similarity=0.406 Sum_probs=58.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCC--CceecCCCCCCCCCCChhhcccCCCH--HHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDN--TAKIECPGLECRHDLDPFSCEPIVPA--SLFS 99 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~--~~~i~CP~~~C~~~i~~~~i~~~l~~--~~~~ 99 (122)
.....|-||+-+......- +.++|+|.|...|.+.-++.+-.... ..-|.|| -|+..|....++.+|++ ++++
T Consensus 3484 D~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldPiKel~e 3560 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDPIKELYE 3560 (3738)
T ss_pred ccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHHHHHHHH
Confidence 4456899999997665444 58999999999999999998876432 3478899 69999999988888875 4554
Q ss_pred HH
Q 033301 100 KW 101 (122)
Q Consensus 100 ky 101 (122)
..
T Consensus 3561 dV 3562 (3738)
T KOG1428|consen 3561 DV 3562 (3738)
T ss_pred HH
Confidence 44
No 50
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.09 E-value=0.0018 Score=47.21 Aligned_cols=57 Identities=19% Similarity=0.536 Sum_probs=39.1
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPASL 97 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~ 97 (122)
..|..|+---+ .+.|+ +..|+|+||..|...- .+-.|| .|+..|....+..-|+..+
T Consensus 4 VhCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~----------~~~~C~--lCkk~ir~i~l~~slp~~i 60 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFF-LTACRHVFCEPCLKAS----------SPDVCP--LCKKSIRIIQLNRSLPTDI 60 (233)
T ss_pred EEeccccccCC-CCcee-eeechhhhhhhhcccC----------Cccccc--cccceeeeeecccccchhH
Confidence 46888888776 55665 9999999999997531 122899 6998766555544444433
No 51
>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=95.82 E-value=0.0037 Score=41.84 Aligned_cols=39 Identities=15% Similarity=0.351 Sum_probs=30.8
Q ss_pred hCCCccccccccccccccccccccCCcC------CcchHHHHHHHH
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCT------HPFSQDCIAKYI 61 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~------H~fC~~C~~~~i 61 (122)
......+|.||++.+...+.+ +.+.|+ |+||.+|+++|-
T Consensus 22 w~~~~~EC~IC~~~I~~~~Gv-V~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 22 WPRCTVECQICFDRIDNNDGV-VYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred ccccCeeehhhhhhhhcCCCE-EEEecCCeehHHHHHHHHHHHHHH
Confidence 456688999999999873444 366776 789999999994
No 52
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.71 E-value=0.0094 Score=36.92 Aligned_cols=54 Identities=28% Similarity=0.600 Sum_probs=37.2
Q ss_pred Ccccccccccccccc---------ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 25 SSFTCEICIEPMAAS---------KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~---------~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
+...|+||...+... +.-.+.-.|+|.|...||..++.++- ..-.|| .|++...
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~-----~~~~CP--mCR~~w~ 82 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS-----SKGQCP--MCRQPWK 82 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc-----CCCCCC--CcCCeee
Confidence 356788888777521 11113457999999999999999852 233899 6987654
No 53
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=95.60 E-value=0.0021 Score=36.90 Aligned_cols=24 Identities=25% Similarity=0.548 Sum_probs=14.2
Q ss_pred HHHHHHHHhhhhcCC-CceecCCCC
Q 033301 99 SKWCDVLCEDYVLGF-ERSYCPNTN 122 (122)
Q Consensus 99 ~ky~~~~~~~~i~~~-~~~~CP~~~ 122 (122)
+||++++++.+|..+ +.+|||+||
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~ 25 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPD 25 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSS
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCC
Confidence 589999999999544 448999986
No 54
>PF04641 Rtf2: Rtf2 RING-finger
Probab=95.38 E-value=0.032 Score=41.29 Aligned_cols=73 Identities=19% Similarity=0.398 Sum_probs=52.3
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCCCH-HHHHH
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIVPA-SLFSK 100 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~k 100 (122)
.....+.|||...++.....|..+-+|||+|+..++...= . .-.|| .|...+...+|..|-+. +.++.
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~-----~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~ 177 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K-----SKKCP--VCGKPFTEEDIIPLNPPEEELEK 177 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c-----ccccc--ccCCccccCCEEEecCCccHHHH
Confidence 3567789999999997655554477999999999988771 1 12499 69999998888776653 34444
Q ss_pred HHHHH
Q 033301 101 WCDVL 105 (122)
Q Consensus 101 y~~~~ 105 (122)
....+
T Consensus 178 l~~~~ 182 (260)
T PF04641_consen 178 LRERM 182 (260)
T ss_pred HHHHH
Confidence 44443
No 55
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.34 E-value=0.013 Score=45.06 Aligned_cols=50 Identities=24% Similarity=0.503 Sum_probs=37.7
Q ss_pred CCCccccccccccccccccccccCCcCCc-chHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHP-FSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
..+..+|.||+.+..+ . +.|+|.|. .|.+|.+..-.+. =+|| -|++.|..
T Consensus 287 ~~~gkeCVIClse~rd--t--~vLPCRHLCLCs~Ca~~Lr~q~--------n~CP--ICRqpi~~ 337 (349)
T KOG4265|consen 287 SESGKECVICLSESRD--T--VVLPCRHLCLCSGCAKSLRYQT--------NNCP--ICRQPIEE 337 (349)
T ss_pred ccCCCeeEEEecCCcc--e--EEecchhhehhHhHHHHHHHhh--------cCCC--ccccchHh
Confidence 3557899999999743 3 48999999 9999988766221 1699 59987654
No 56
>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=95.27 E-value=0.019 Score=31.88 Aligned_cols=36 Identities=19% Similarity=0.528 Sum_probs=27.4
Q ss_pred ccccccccccccccccccCCcC-----CcchHHHHHHHHHHHh
Q 033301 28 TCEICIEPMAASKKFKNKNLCT-----HPFSQDCIAKYIQVKV 65 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~C~~~~i~~~i 65 (122)
.|-||++...+.+.+ ..+|. |.+..+|+..|+..+-
T Consensus 1 ~CrIC~~~~~~~~~l--~~PC~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPL--VSPCRCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCee--EeccccCCchhHHHHHHHHHHHHHcC
Confidence 488999844444444 57885 8899999999999763
No 57
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.26 E-value=0.0097 Score=46.57 Aligned_cols=53 Identities=26% Similarity=0.694 Sum_probs=40.0
Q ss_pred ccccccccccccc--cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChh
Q 033301 26 SFTCEICIEPMAA--SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 26 ~~~C~IC~~~~~~--~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~ 87 (122)
..+|+||++.+.- +..+ +.+.|||-|=.+|+++|+- +.....|| .|...-...
T Consensus 4 g~tcpiclds~~~~g~hr~-vsl~cghlFgs~cie~wl~------k~~~~~cp--~c~~katkr 58 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRI-VSLQCGHLFGSQCIEKWLG------KKTKMQCP--LCSGKATKR 58 (463)
T ss_pred cccCceeeeeeeecCceEE-eeecccccccHHHHHHHHh------hhhhhhCc--ccCChhHHH
Confidence 4689999999753 2334 6899999999999999993 34667899 587544433
No 58
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.20 E-value=0.0048 Score=35.04 Aligned_cols=46 Identities=26% Similarity=0.470 Sum_probs=33.9
Q ss_pred cccccccccccccccccccCCcCCc-chHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHP-FSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
.+|.||++.-.+. ++-.|||+ +|.+|-.+.+.. ..-.|| -|+..|.
T Consensus 8 dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~-------~~g~CP--iCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKA-------LHGCCP--ICRAPIK 54 (62)
T ss_pred cceeeeccCcchH----HHHHcchHHhHHHHHHHHHHc-------cCCcCc--chhhHHH
Confidence 6899999986544 37789999 899998776654 233688 5886553
No 59
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.07 E-value=0.03 Score=47.46 Aligned_cols=59 Identities=24% Similarity=0.577 Sum_probs=46.0
Q ss_pred hhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 21 ESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 21 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
.-.....+|.||++.+.....+.+--.|-|+|-..||+.|..+.-.+ +...-+|| .|..
T Consensus 186 ~l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~-~~~~WrCP--~Cqs 244 (950)
T KOG1952|consen 186 QLSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKT-GQDGWRCP--ACQS 244 (950)
T ss_pred HHhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhc-cCccccCC--cccc
Confidence 34577889999999997654332567799999999999999994444 45677999 6874
No 60
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.87 E-value=0.0048 Score=45.88 Aligned_cols=56 Identities=29% Similarity=0.576 Sum_probs=42.8
Q ss_pred CCcccccccccccccc--------ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 24 GSSFTCEICIEPMAAS--------KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~--------~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
.+...|.||...+... +.+ .+.|+|.|...|+++|...- ..-.|| =|++.++...+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty--~LsCnHvFHEfCIrGWcivG------KkqtCP--YCKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTY--KLSCNHVFHEFCIRGWCIVG------KKQTCP--YCKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhhe--eeecccchHHHhhhhheeec------CCCCCc--hHHHHhhHhhh
Confidence 5567899998877543 245 79999999999999998753 234899 59988876544
No 61
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.75 E-value=0.019 Score=43.43 Aligned_cols=62 Identities=24% Similarity=0.569 Sum_probs=46.8
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhc---------------CCCceecCCCCCCCCCCCh
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQD---------------DNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~---------------~~~~~i~CP~~~C~~~i~~ 86 (122)
.+.+.+.|.||+.-+.+.+.| +...|.|+|...|+.+|+.....+ ...+...|| -|+..|..
T Consensus 111 nn~p~gqCvICLygfa~~~~f-t~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp--Vcre~i~~ 187 (368)
T KOG4445|consen 111 NNHPNGQCVICLYGFASSPAF-TVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP--VCRERIKI 187 (368)
T ss_pred CCCCCCceEEEEEeecCCCce-eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh--Hhhhhccc
Confidence 356778999999999888778 599999999999999999854421 123445599 48876543
No 62
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=94.67 E-value=0.033 Score=42.21 Aligned_cols=59 Identities=19% Similarity=0.412 Sum_probs=39.8
Q ss_pred hhCCCccccccccccccccccccccCCc--CCcchHHHH-----------------HHHHHHHhhcCCCceecCCC--CC
Q 033301 21 ESSGSSFTCEICIEPMAASKKFKNKNLC--THPFSQDCI-----------------AKYIQVKVQDDNTAKIECPG--LE 79 (122)
Q Consensus 21 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C--~H~fC~~C~-----------------~~~i~~~i~~~~~~~i~CP~--~~ 79 (122)
....+..+||||++.+..+ ...| ||..|.+|- +.++..++-+ ...+.||. .+
T Consensus 43 ~~~~~lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV~e--~~~vpC~~~~~G 115 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSPP-----IFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKVAE--AVLVPCKNAKLG 115 (299)
T ss_pred ccchhhccCchhhccCccc-----ceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHHHH--hceecccccccC
Confidence 3356778999999999876 4566 799999996 4455555543 34556663 46
Q ss_pred CCCCCCh
Q 033301 80 CRHDLDP 86 (122)
Q Consensus 80 C~~~i~~ 86 (122)
|...++.
T Consensus 116 C~~~~~Y 122 (299)
T KOG3002|consen 116 CTKSFPY 122 (299)
T ss_pred Cceeecc
Confidence 6655544
No 63
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.48 E-value=0.083 Score=39.52 Aligned_cols=59 Identities=27% Similarity=0.557 Sum_probs=41.8
Q ss_pred Ccccccccccccccc--ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC--CChhhcccC
Q 033301 25 SSFTCEICIEPMAAS--KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD--LDPFSCEPI 92 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~--i~~~~i~~~ 92 (122)
+...|.||-++++.. +...-.+.|||.+|..|+...+.. ..|.|| -|+.. ++...++.+
T Consensus 2 ~~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cp--fcR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 2 SFPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCP--FCRETTEIPDGDVKSL 64 (296)
T ss_pred CCCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeecc--CCCCcccCCchhHhhh
Confidence 356899999999765 222236789999999999877653 456676 68876 555555443
No 64
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.40 E-value=0.025 Score=45.43 Aligned_cols=54 Identities=28% Similarity=0.752 Sum_probs=40.4
Q ss_pred CCCcccccccccccccc----c----------cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAAS----K----------KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~----~----------~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
......|.||+.+++.- + .| .+.+|.|.|.+.|+..|.... .+-|| .|+..|++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nY-m~tPC~HifH~~CL~~WMd~y-------kl~CP--vCR~pLPp 635 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNY-MLTPCHHIFHRQCLLQWMDTY-------KLICP--VCRCPLPP 635 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccc-cccchHHHHHHHHHHHHHhhh-------cccCC--ccCCCCCC
Confidence 57778999999988521 1 12 256999999999999998742 36799 58887764
No 65
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=94.13 E-value=0.039 Score=43.26 Aligned_cols=38 Identities=18% Similarity=0.573 Sum_probs=30.2
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
......|++|...+.++ + ....|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~~p--~-~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDP--V-QTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccccCC--C-CCCCCCCcccccccchhhcc
Confidence 34568899999998655 3 13599999999999988876
No 66
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.89 E-value=0.11 Score=40.04 Aligned_cols=58 Identities=28% Similarity=0.553 Sum_probs=41.3
Q ss_pred CCccccccccccccccc-cccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc
Q 033301 24 GSSFTCEICIEPMAASK-KFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP 91 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~-~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 91 (122)
.....|++|+++++..+ .|+ --+||-..|+=||.. |.+.+ +-+|| .|+...+.+-++.
T Consensus 12 deed~cplcie~mditdknf~-pc~cgy~ic~fc~~~-irq~l------ngrcp--acrr~y~denv~~ 70 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFF-PCPCGYQICQFCYNN-IRQNL------NGRCP--ACRRKYDDENVRY 70 (480)
T ss_pred cccccCcccccccccccCCcc-cCCcccHHHHHHHHH-HHhhc------cCCCh--HhhhhccccceeE
Confidence 33445999999998654 453 788999999999964 33333 44899 6998777766544
No 67
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.58 E-value=0.022 Score=42.87 Aligned_cols=47 Identities=26% Similarity=0.417 Sum_probs=34.0
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
.-.+.|.||...+..+ +...|+|.||..|....+.. .-+|+ .|.+.+
T Consensus 239 ~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk--------~~~c~--vC~~~t 285 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQK--------GEKCY--VCSQQT 285 (313)
T ss_pred cCCccccccccccccc----hhhcCCceeehhhhcccccc--------CCcce--eccccc
Confidence 3456799999999765 57999999999997655442 23566 477543
No 68
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.36 E-value=0.016 Score=48.30 Aligned_cols=50 Identities=32% Similarity=0.675 Sum_probs=37.6
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
..|.||.+ . ...+ ...|+|.||.+||..+|...-.. .|| .|+..+....+
T Consensus 455 ~~c~ic~~-~--~~~~--it~c~h~~c~~c~~~~i~~~~~~------~~~--~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD-L--DSFF--ITRCGHDFCVECLKKSIQQSENA------PCP--LCRNVLKEKKL 504 (674)
T ss_pred cccccccc-c--ccce--eecccchHHHHHHHhccccccCC------CCc--HHHHHHHHHHH
Confidence 99999999 2 2233 78999999999999999865321 777 68876665544
No 69
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.25 E-value=0.069 Score=41.37 Aligned_cols=37 Identities=19% Similarity=0.336 Sum_probs=28.7
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
+..-.|+||+..--. .+ ..+|+|.-|..||..|+.+.
T Consensus 420 sEd~lCpICyA~pi~--Av--f~PC~H~SC~~CI~qHlmN~ 456 (489)
T KOG4692|consen 420 SEDNLCPICYAGPIN--AV--FAPCSHRSCYGCITQHLMNC 456 (489)
T ss_pred cccccCcceecccch--hh--ccCCCCchHHHHHHHHHhcC
Confidence 344579999987532 33 68999999999999998753
No 70
>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=93.22 E-value=0.018 Score=42.25 Aligned_cols=53 Identities=17% Similarity=0.428 Sum_probs=38.0
Q ss_pred Ccccccccccccccc-cc-ccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 25 SSFTCEICIEPMAAS-KK-FKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~-~~-~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
....||||-.+.-.+ +. +.+...|-|..|.+|+-+-+. ..+..||..+|..+|
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHHH
Confidence 345799999886432 22 224556999999999876554 457899999998544
No 71
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.58 E-value=0.054 Score=46.80 Aligned_cols=54 Identities=20% Similarity=0.570 Sum_probs=38.5
Q ss_pred Cccccccccccccccc-ccc--ccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 25 SSFTCEICIEPMAASK-KFK--NKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~-~~~--~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
.-.+|.|||.-..--+ .+. .-..|.|.|...|+.+|+.+..+ -+|| -|+..|+.
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~------s~CP--lCRseitf 1524 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSAR------SNCP--LCRSEITF 1524 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCC------CCCC--cccccccc
Confidence 3458999998764111 110 14679999999999999998643 3899 69987763
No 72
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.05 E-value=0.12 Score=38.16 Aligned_cols=60 Identities=12% Similarity=0.261 Sum_probs=44.0
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP 91 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 91 (122)
.....+.|+||.+.+.......++-+|||+||.+|...+|..- +.|| -|...+...+|..
T Consensus 217 a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D--------~v~p--v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 217 AASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD--------MVDP--VTDKPLKDRDIIG 276 (303)
T ss_pred hhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc--------cccc--CCCCcCcccceEe
Confidence 3457889999999997654433588999999999999887643 3456 3666666666543
No 73
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.93 E-value=0.12 Score=40.40 Aligned_cols=53 Identities=23% Similarity=0.604 Sum_probs=36.2
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
.-.|.||-+-.+........-.|||.|...|+..|++..-. .=.|| .|+..++
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps-----~R~cp--ic~ik~~ 56 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS-----NRGCP--ICQIKLQ 56 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCc-----cCCCC--ceeeccc
Confidence 35799996666555455434459999999999999986532 23688 4664333
No 74
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=91.05 E-value=0.13 Score=39.37 Aligned_cols=52 Identities=15% Similarity=0.340 Sum_probs=38.9
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
-......|+||......+ .+ +.-=|=+||-.|+-.|+.+ .| +||..+|...+
T Consensus 296 l~~~~~~CpvClk~r~Np-tv--l~vSGyVfCY~Ci~~Yv~~---~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 296 LPPDREVCPVCLKKRQNP-TV--LEVSGYVFCYPCIFSYVVN---YG-----HCPVTGYPASV 347 (357)
T ss_pred CCCccccChhHHhccCCC-ce--EEecceEEeHHHHHHHHHh---cC-----CCCccCCcchH
Confidence 346677899999998655 22 4445899999999999983 22 79988887544
No 75
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=90.55 E-value=0.074 Score=41.70 Aligned_cols=51 Identities=22% Similarity=0.642 Sum_probs=38.5
Q ss_pred CCcccccccccccccc-ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC
Q 033301 24 GSSFTCEICIEPMAAS-KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD 83 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~ 83 (122)
.....|..|.+.+... +.. ..++|.|.|...|+..|++. ..+=.|| .|+..
T Consensus 363 e~~L~Cg~CGe~~Glk~e~L-qALpCsHIfH~rCl~e~L~~------n~~rsCP--~Crkl 414 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERL-QALPCSHIFHLRCLQEILEN------NGTRSCP--NCRKL 414 (518)
T ss_pred HHhhhhhhhhhhhcCCcccc-cccchhHHHHHHHHHHHHHh------CCCCCCc--cHHHH
Confidence 4557899999987543 344 48999999999999999943 2355899 68843
No 76
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.25 E-value=0.29 Score=38.29 Aligned_cols=63 Identities=17% Similarity=0.367 Sum_probs=45.0
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccC
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPI 92 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 92 (122)
.-.+.|.|||=.+.-+.++.- ..+.|||+.+++=+.+... |+....+|| =|......++.+++
T Consensus 330 ~fHSvF~CPVlKeqtsdeNPP-m~L~CGHVISkdAlnrLS~-----ng~~sfKCP--YCP~e~~~~~~kql 392 (394)
T KOG2817|consen 330 HFHSVFICPVLKEQTSDENPP-MMLICGHVISKDALNRLSK-----NGSQSFKCP--YCPVEQLASDTKQL 392 (394)
T ss_pred cccceeecccchhhccCCCCC-eeeeccceecHHHHHHHhh-----CCCeeeeCC--CCCcccCHHhcccc
Confidence 346789999988877655433 3899999999976554433 345589999 49977776665543
No 77
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.17 E-value=0.099 Score=44.34 Aligned_cols=21 Identities=5% Similarity=0.026 Sum_probs=13.4
Q ss_pred cCCcCCcchHHHHHHHHHHHh
Q 033301 45 KNLCTHPFSQDCIAKYIQVKV 65 (122)
Q Consensus 45 ~~~C~H~fC~~C~~~~i~~~i 65 (122)
+..|+|.||-.||..+....+
T Consensus 118 ~~~~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 118 VQTHVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhhhhHHHHHHHHHhh
Confidence 334777777777776666554
No 78
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=90.10 E-value=0.43 Score=32.00 Aligned_cols=57 Identities=21% Similarity=0.497 Sum_probs=45.1
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
+....+|.||-|...+....+...-||=..|.-|....|... .....|| -|+..+-.
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~-----~~ypvCP--vCkTSFKs 133 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFC-----NLYPVCP--VCKTSFKS 133 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHc-----ccCCCCC--cccccccc
Confidence 347789999999987665544556699999999999999986 3788999 59876643
No 79
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=89.34 E-value=0.26 Score=23.68 Aligned_cols=23 Identities=35% Similarity=0.582 Sum_probs=17.4
Q ss_pred ccccccccccccccccccCCcCCcc
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPF 52 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~f 52 (122)
.||-|...++....+ -..|||.|
T Consensus 2 ~CP~C~~~V~~~~~~--Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKF--CPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCc--CCCCCCCC
Confidence 689999998766444 56789887
No 80
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=89.10 E-value=0.18 Score=40.13 Aligned_cols=39 Identities=31% Similarity=0.587 Sum_probs=29.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQ 62 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~ 62 (122)
....+|+||++-++..-.......|.|.|--.|+..|..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~ 211 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD 211 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhccc
Confidence 455789999999976533224788999999999876643
No 81
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=88.31 E-value=0.22 Score=39.29 Aligned_cols=36 Identities=25% Similarity=0.512 Sum_probs=27.8
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
+.-..|.||-+...+ ++ ..+|||..|..|+..|-..
T Consensus 367 sTFeLCKICaendKd---vk-IEPCGHLlCt~CLa~WQ~s 402 (563)
T KOG1785|consen 367 STFELCKICAENDKD---VK-IEPCGHLLCTSCLAAWQDS 402 (563)
T ss_pred chHHHHHHhhccCCC---cc-cccccchHHHHHHHhhccc
Confidence 344579999988643 32 7899999999999988543
No 82
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=88.12 E-value=0.52 Score=27.74 Aligned_cols=16 Identities=19% Similarity=0.760 Sum_probs=12.8
Q ss_pred chHHHHHHHHHHHhhc
Q 033301 52 FSQDCIAKYIQVKVQD 67 (122)
Q Consensus 52 fC~~C~~~~i~~~i~~ 67 (122)
||++|+..|......+
T Consensus 12 FCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 12 FCRNCLSKWYREAAEE 27 (68)
T ss_dssp --HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999998876
No 83
>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=88.11 E-value=0.14 Score=32.24 Aligned_cols=33 Identities=30% Similarity=0.600 Sum_probs=26.7
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIA 58 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~ 58 (122)
.....|++|...+... .| ...+|||.|...|+.
T Consensus 76 ~~~~~C~vC~k~l~~~-~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNS-VF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCc-eE-EEeCCCeEEeccccc
Confidence 4456799999999654 55 589999999999975
No 84
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=88.00 E-value=0.098 Score=31.75 Aligned_cols=54 Identities=28% Similarity=0.607 Sum_probs=36.4
Q ss_pred Ccccccccccccccc---------ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 25 SSFTCEICIEPMAAS---------KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~---------~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
+..+|+||...++.. +.-.+.--|.|.|-..|+..++...-++ -.|| .|++...
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CP--mcRq~~~ 81 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCP--MCRQTWQ 81 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCC--cchheeE
Confidence 334899998887532 1110233589999999999999876543 4688 6887543
No 85
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.21 E-value=0.33 Score=41.54 Aligned_cols=40 Identities=23% Similarity=0.521 Sum_probs=32.5
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHh
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKV 65 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i 65 (122)
-+...|.+|.-.+... .|. ..+|||.|..+|+..++..-.
T Consensus 815 ep~d~C~~C~~~ll~~-pF~-vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIK-PFY-VFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred cCccchHHhcchhhcC-cce-eeeccchHHHHHHHHHHHccc
Confidence 4567899999998655 453 899999999999998887554
No 86
>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=87.01 E-value=0.35 Score=25.99 Aligned_cols=41 Identities=27% Similarity=0.729 Sum_probs=21.4
Q ss_pred cccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCC
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECP 76 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP 76 (122)
|.+|.+-+..+..- ...+|+=.+...|+..|+..+- .+ +||
T Consensus 1 C~~C~~iv~~G~~C-~~~~C~~r~H~~C~~~y~r~~~-----~~-~CP 41 (43)
T PF08746_consen 1 CEACKEIVTQGQRC-SNRDCNVRLHDDCFKKYFRHRS-----NP-KCP 41 (43)
T ss_dssp -TTT-SB-SSSEE--SS--S--EE-HHHHHHHTTT-S-----S--B-T
T ss_pred CcccchhHeeeccC-CCCccCchHHHHHHHHHHhcCC-----CC-CCc
Confidence 66787777655444 2457888999999999998652 22 788
No 87
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=86.86 E-value=0.35 Score=36.30 Aligned_cols=51 Identities=27% Similarity=0.517 Sum_probs=38.2
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
+......||||.+.+.........+.|||..-..|+..++.. + .+|| .|..
T Consensus 154 e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-----~---y~CP--~C~~ 204 (276)
T KOG1940|consen 154 ERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-----G---YTCP--ICSK 204 (276)
T ss_pred hhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-----C---CCCC--cccc
Confidence 445666799999998655433358999999999888877653 2 6899 5887
No 88
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.80 E-value=0.73 Score=26.09 Aligned_cols=36 Identities=19% Similarity=0.480 Sum_probs=27.8
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAK 59 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~ 59 (122)
.....|++|-+.+.+.+..-+-..|+-.+.++||..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 345689999999974443325889999999999964
No 89
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=86.59 E-value=0.27 Score=39.29 Aligned_cols=33 Identities=18% Similarity=0.438 Sum_probs=26.5
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHH
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQ 62 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~ 62 (122)
...|+||..-+..+ +.++|+|..|+.|.+.-+.
T Consensus 4 elkc~vc~~f~~ep----iil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGSFYREP----IILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehhhccCc----eEeecccHHHHHHHHhhcc
Confidence 46799999888554 5899999999999875443
No 90
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.31 E-value=1.3 Score=33.07 Aligned_cols=56 Identities=20% Similarity=0.557 Sum_probs=41.8
Q ss_pred CCCccccccccccccccc--cccccCCcC-----CcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAASK--KFKNKNLCT-----HPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~--~~~~~~~C~-----H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
......|-||+....++. .+ .-+|. |.....|+..||..+-.......+.|| +|..
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~W--V~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~--QCqT 79 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAW--VHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCP--QCQT 79 (293)
T ss_pred cccceeEEEEeccCcccchhhh--cccccccCccHHHHHHHHHHHHhHHhcCCCCceeech--hhcc
Confidence 345578999999876542 23 45664 668999999999988764357799999 5984
No 91
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=85.31 E-value=0.31 Score=27.66 Aligned_cols=46 Identities=17% Similarity=0.329 Sum_probs=29.6
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhh
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFS 88 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~ 88 (122)
..|-.|....... +.++|+|..|..||-. ...-.|| -|...|...+
T Consensus 8 ~~~~~~~~~~~~~----~~~pCgH~I~~~~f~~----------~rYngCP--fC~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFVGTKG----TVLPCGHLICDNCFPG----------ERYNGCP--FCGTPFEFDD 53 (55)
T ss_pred eeEEEcccccccc----ccccccceeeccccCh----------hhccCCC--CCCCcccCCC
Confidence 3455555443222 4899999999999842 2233688 5887776654
No 92
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.53 E-value=0.37 Score=40.17 Aligned_cols=37 Identities=16% Similarity=0.455 Sum_probs=28.3
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHH
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQ 62 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~ 62 (122)
...|+||+..+.......+++.|||..|..|+.....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 3579999888765544446899999999999875443
No 93
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.95 E-value=0.41 Score=36.27 Aligned_cols=28 Identities=21% Similarity=0.397 Sum_probs=22.1
Q ss_pred ccccccccccccccccccccCCcCCc-chHHHH
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHP-FSQDCI 57 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~ 57 (122)
...|.|||+-. -+.| +|.|||. -|..|=
T Consensus 300 ~~LC~ICmDaP--~DCv--fLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCV--FLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcCC--cceE--EeecCcEEeehhhc
Confidence 56799999975 4566 7999998 688773
No 94
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=81.82 E-value=1.1 Score=27.53 Aligned_cols=19 Identities=32% Similarity=0.975 Sum_probs=16.9
Q ss_pred CCcCCcchHHHHHHHHHHH
Q 033301 46 NLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 46 ~~C~H~fC~~C~~~~i~~~ 64 (122)
--|+|.|-..|+.+|+.++
T Consensus 52 G~CnHaFH~HCI~rWL~Tk 70 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDTK 70 (88)
T ss_pred EecchHHHHHHHHHHHhhC
Confidence 3499999999999999983
No 95
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.56 E-value=0.5 Score=32.84 Aligned_cols=31 Identities=19% Similarity=0.428 Sum_probs=24.2
Q ss_pred hCCCccccccccccccccccccccCCcCCcch
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFS 53 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC 53 (122)
-+....+|.||+|++...+.+ ..|+|-..|-
T Consensus 173 L~ddkGECvICLEdL~~GdtI-ARLPCLCIYH 203 (205)
T KOG0801|consen 173 LKDDKGECVICLEDLEAGDTI-ARLPCLCIYH 203 (205)
T ss_pred hcccCCcEEEEhhhccCCCce-eccceEEEee
Confidence 346778999999999888887 4888876553
No 96
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.79 E-value=2 Score=33.48 Aligned_cols=54 Identities=20% Similarity=0.557 Sum_probs=36.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
-....|.||-+.+.-. ..++|+|..|--|-.+.-..- ..-.|| -|+..-....+
T Consensus 59 Een~~C~ICA~~~TYs----~~~PC~H~~CH~Ca~RlRALY------~~K~C~--~CrTE~e~V~f 112 (493)
T COG5236 59 EENMNCQICAGSTTYS----ARYPCGHQICHACAVRLRALY------MQKGCP--LCRTETEAVVF 112 (493)
T ss_pred cccceeEEecCCceEE----EeccCCchHHHHHHHHHHHHH------hccCCC--ccccccceEEE
Confidence 4557899999887433 589999999999976654432 233688 58764443333
No 97
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.99 E-value=1.7 Score=27.32 Aligned_cols=17 Identities=12% Similarity=0.579 Sum_probs=15.0
Q ss_pred cchHHHHHHHHHHHhhc
Q 033301 51 PFSQDCIAKYIQVKVQD 67 (122)
Q Consensus 51 ~fC~~C~~~~i~~~i~~ 67 (122)
-||++|+..|.....+.
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 39999999999988865
No 98
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.87 E-value=3.4 Score=31.65 Aligned_cols=44 Identities=25% Similarity=0.748 Sum_probs=32.0
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
..|+.|-.-.-. .++ ...|+|.||.+|+..-+.. ...+|| .|..
T Consensus 275 LkCplc~~Llrn--p~k-T~cC~~~fc~eci~~al~d-------sDf~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLLRN--PMK-TPCCGHTFCDECIGTALLD-------SDFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhhhC--ccc-CccccchHHHHHHhhhhhh-------ccccCC--Cccc
Confidence 789999887643 343 5789999999998765432 356899 5864
No 99
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=78.22 E-value=1.1 Score=34.41 Aligned_cols=31 Identities=26% Similarity=0.527 Sum_probs=23.1
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHH
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAK 59 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~ 59 (122)
...|.-|--.+..-. -+++|.|+||.+|.+.
T Consensus 90 VHfCd~Cd~PI~IYG---RmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYG---RMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcceeee---cccccchhhhhhhhhc
Confidence 457888877665332 3789999999999764
No 100
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=76.85 E-value=1.1 Score=37.72 Aligned_cols=68 Identities=22% Similarity=0.468 Sum_probs=49.2
Q ss_pred chHHHHHHhhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc
Q 033301 13 AKEEEEEEESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP 91 (122)
Q Consensus 13 ~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 91 (122)
+.+.++-...-....+|+||+..+..+ +++.|.|.||.-||-.-+...- ....|| -|+..++-..++.
T Consensus 8 ~~~~~~vi~~~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~--lc~~~~eK~s~~E 75 (684)
T KOG4362|consen 8 VREVAQVINAMQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKK-----GPKQCA--LCKSDIEKRSLRE 75 (684)
T ss_pred HHHHHhHHHHHhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccC-----ccccch--hhhhhhhhhhccc
Confidence 334444455566778999999999766 5899999999999988877652 266787 5776666555444
No 101
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.00 E-value=4.6 Score=29.68 Aligned_cols=62 Identities=21% Similarity=0.515 Sum_probs=44.0
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC-CCChhhc
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH-DLDPFSC 89 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~-~i~~~~i 89 (122)
.=...|..|.-.+...++. .+.|-|.|.-+|+..+..+--..-.-.-..|| .|.. ++++.-+
T Consensus 48 DY~pNC~LC~t~La~gdt~--RLvCyhlfHW~ClneraA~lPanTAPaGyqCP--~Cs~eiFPp~Nl 110 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTT--RLVCYHLFHWKCLNERAANLPANTAPAGYQCP--CCSQEIFPPINL 110 (299)
T ss_pred CCCCCCceeCCccccCcce--eehhhhhHHHHHhhHHHhhCCCcCCCCcccCC--CCCCccCCCccc
Confidence 4456899999998877775 79999999999999887654433223455788 5775 4444433
No 102
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.12 E-value=5.7 Score=28.18 Aligned_cols=59 Identities=22% Similarity=0.542 Sum_probs=39.6
Q ss_pred CCcccccccccccccc----ccccccCCcCCcchHHHHHHHHHHHhhcCCCcee---cCCCCCCCCCCC
Q 033301 24 GSSFTCEICIEPMAAS----KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKI---ECPGLECRHDLD 85 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i---~CP~~~C~~~i~ 85 (122)
...+.|+|||.--.++ +.. -...||..|..-|+..|+..-+...+.+.| .|| -|...|.
T Consensus 163 d~~~~cgicyayqldGTipDqtC-dN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pia 228 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTC-DNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIA 228 (234)
T ss_pred hhhhcccceeeeecCCccccccc-cccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCcce
Confidence 4557899998754322 122 367899999999999999877755444444 577 4665544
No 103
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=73.94 E-value=1.9 Score=27.77 Aligned_cols=39 Identities=21% Similarity=0.576 Sum_probs=26.6
Q ss_pred ccccccccccccc-------------cccccccCCcCCcchHHHHHHHHHHH
Q 033301 26 SFTCEICIEPMAA-------------SKKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 26 ~~~C~IC~~~~~~-------------~~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
.-+|.||...+.+ .+....=-.|+|.|..-|+..|+.++
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr 97 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTR 97 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhc
Confidence 3468888776531 11111234599999999999999986
No 104
>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=72.47 E-value=8 Score=29.33 Aligned_cols=51 Identities=22% Similarity=0.436 Sum_probs=33.5
Q ss_pred ccccccccccc-cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChh
Q 033301 28 TCEICIEPMAA-SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 28 ~C~IC~~~~~~-~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~ 87 (122)
.|++|--+.-. ++.+.-.-.|+|..|.+|+-..+. ..+-.|| +|..++--.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cp--eC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCP--ECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCC--cccchhhhc
Confidence 48888777532 222211338999999999876554 3455799 898765543
No 105
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.82 E-value=4.6 Score=30.07 Aligned_cols=38 Identities=16% Similarity=0.266 Sum_probs=29.4
Q ss_pred CccccccccccccccccccccCCcCCcchHHHHHHHHHHHhh
Q 033301 25 SSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQ 66 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~ 66 (122)
+-.-|+.|+.+.-.+ +..+=||.||++||..||..+-+
T Consensus 42 ~FdcCsLtLqPc~dP----vit~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDP----VITPDGYLFDREAILEYILAQKK 79 (303)
T ss_pred CcceeeeecccccCC----ccCCCCeeeeHHHHHHHHHHHHH
Confidence 334689999888555 24666999999999999987754
No 106
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.82 E-value=2.7 Score=31.86 Aligned_cols=52 Identities=21% Similarity=0.555 Sum_probs=39.5
Q ss_pred CCccccccccccccccccccccCCc----CCcchHHHHHHHHHHHhhcCCCceecCCC-CCCCC
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLC----THPFSQDCIAKYIQVKVQDDNTAKIECPG-LECRH 82 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C----~H~fC~~C~~~~i~~~i~~~~~~~i~CP~-~~C~~ 82 (122)
....-|.+|-|.+.+ +. ...| .|.||.-|-+..|..+- ....+-||. .+|.-
T Consensus 266 ~apLcCTLC~ERLED--TH--FVQCPSVp~HKFCFPCSResIK~Qg---~sgevYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLED--TH--FVQCPSVPSHKFCFPCSRESIKQQG---ASGEVYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhcc--Cc--eeecCCCcccceecccCHHHHHhhc---CCCceeCCCCCcCcc
Confidence 444789999999843 33 3566 69999999999999874 455899995 47873
No 107
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=68.37 E-value=4.5 Score=22.29 Aligned_cols=38 Identities=18% Similarity=0.453 Sum_probs=25.8
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
..|.+|-..+.....-..--.||+.||.+|........
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~ 40 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLP 40 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeecC
Confidence 46888877765432111356899999999998776543
No 108
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=67.35 E-value=5.2 Score=27.69 Aligned_cols=51 Identities=20% Similarity=0.472 Sum_probs=35.4
Q ss_pred CCCccccccccccccccccccccCCcCC-----cchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTH-----PFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
......|-||.++... . .-+|.. ...++|+..|+..+ ...+|+ .|+.....
T Consensus 5 s~~~~~CRIC~~~~~~---~--~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Ce--iC~~~Y~i 60 (162)
T PHA02825 5 SLMDKCCWICKDEYDV---V--TNYCNCKNENKIVHKECLEEWINTS------KNKSCK--ICNGPYNI 60 (162)
T ss_pred CCCCCeeEecCCCCCC---c--cCCcccCCCchHHHHHHHHHHHhcC------CCCccc--ccCCeEEE
Confidence 4556799999999642 2 235543 45999999999953 466898 59875443
No 109
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=66.71 E-value=3.4 Score=23.08 Aligned_cols=16 Identities=25% Similarity=0.659 Sum_probs=8.6
Q ss_pred cccccCCcCCcchHHHH
Q 033301 41 KFKNKNLCTHPFSQDCI 57 (122)
Q Consensus 41 ~~~~~~~C~H~fC~~C~ 57 (122)
.| .-..|++.||.+|=
T Consensus 21 ~y-~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RY-RCPKCKNHFCIDCD 36 (51)
T ss_dssp EE---TTTT--B-HHHH
T ss_pred eE-ECCCCCCccccCcC
Confidence 34 37789999999993
No 110
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.57 E-value=3.1 Score=35.83 Aligned_cols=40 Identities=28% Similarity=0.704 Sum_probs=31.7
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
-.|..|--+...+- +-..|||.|.+.|+. + ..-+|| .|..
T Consensus 841 skCs~C~~~LdlP~---VhF~CgHsyHqhC~e--------~---~~~~CP--~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLPF---VHFLCGHSYHQHCLE--------D---KEDKCP--KCLP 880 (933)
T ss_pred eeecccCCccccce---eeeecccHHHHHhhc--------c---CcccCC--ccch
Confidence 48999999987763 357999999999998 2 244898 6885
No 111
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=65.01 E-value=1.4 Score=24.59 Aligned_cols=36 Identities=19% Similarity=0.353 Sum_probs=28.3
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~ 60 (122)
-+.+.|..|-+..+..+.- .-.-||..-|..||+.-
T Consensus 5 Fsry~CDLCn~~~p~~~LR-QCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 5 FSRYSCDLCNSSHPISELR-QCVLCGRWACNSCWQDE 40 (57)
T ss_pred HhhHhHHhhcccCcHHHHH-HHhhhchhhhhhhhhhh
Confidence 3567899999998766443 46779999999999853
No 112
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=64.31 E-value=2 Score=21.34 Aligned_cols=17 Identities=18% Similarity=0.538 Sum_probs=8.8
Q ss_pred eecCCCCCCCCCCChhh
Q 033301 72 KIECPGLECRHDLDPFS 88 (122)
Q Consensus 72 ~i~CP~~~C~~~i~~~~ 88 (122)
.++||..+|.+.+....
T Consensus 2 ~vrCPvkdC~EEv~lgK 18 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGK 18 (30)
T ss_dssp EEE--STT---EEEHHH
T ss_pred ccccccccCcchhhhhh
Confidence 57999999998776543
No 113
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.90 E-value=4.4 Score=31.49 Aligned_cols=47 Identities=19% Similarity=0.407 Sum_probs=31.6
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
.+....|.||.++..+. ..++|||.-| |...+- -.+.|| -|++.|..
T Consensus 302 ~~~p~lcVVcl~e~~~~----~fvpcGh~cc--ct~cs~---------~l~~CP--vCR~rI~~ 348 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSA----VFVPCGHVCC--CTLCSK---------HLPQCP--VCRQRIRL 348 (355)
T ss_pred cCCCCceEEecCCccce----eeecCCcEEE--chHHHh---------hCCCCc--hhHHHHHH
Confidence 45567899999997543 4799999977 543321 123499 58876654
No 114
>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 KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=58.49 E-value=40 Score=25.21 Aligned_cols=75 Identities=19% Similarity=0.262 Sum_probs=46.6
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC--CCChhhcccCCCHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH--DLDPFSCEPIVPASLFSKW 101 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~--~i~~~~i~~~l~~~~~~ky 101 (122)
.-...|||=+.++..+ + ++-.|||.|=++=+..++.. ...++||..+|.. .+.... ++....++++
T Consensus 174 ~fs~rdPis~~~I~nP--v-iSkkC~HvydrDsI~~~l~~------~~~i~CPv~gC~~~~~~~~~~---l~~d~el~~k 241 (262)
T KOG2979|consen 174 VFSNRDPISKKPIVNP--V-ISKKCGHVYDRDSIMQILCD------EITIRCPVLGCENPYYIQPGH---LDEDKELQQK 241 (262)
T ss_pred hhcccCchhhhhhhch--h-hhcCcCcchhhhhHHHHhcc------CceeecccccCCccccccccc---cCchHHHHHH
Confidence 3345677777776444 2 48899999988777666543 5688999999992 222221 2233356666
Q ss_pred HHHHHhhhh
Q 033301 102 CDVLCEDYV 110 (122)
Q Consensus 102 ~~~~~~~~i 110 (122)
.+...+..+
T Consensus 242 Ir~~qe~~~ 250 (262)
T KOG2979|consen 242 IRQSQEPAI 250 (262)
T ss_pred HHHhccccc
Confidence 555555444
No 116
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=57.91 E-value=8.5 Score=33.30 Aligned_cols=49 Identities=16% Similarity=0.508 Sum_probs=33.8
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChh
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~ 87 (122)
.|++|+........- .-..|+|.||..|+..|-... + +|| .|+..+...
T Consensus 125 ~CP~Ci~s~~DqL~~-~~k~c~H~FC~~Ci~sWsR~a--q------TCP--iDR~EF~~v 173 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEE-SEKHTAHYFCEECVGSWSRCA--Q------TCP--VDRGEFGEV 173 (1134)
T ss_pred hhhHHHHHHHHHhhc-cccccccccHHHHhhhhhhhc--c------cCc--hhhhhhhee
Confidence 467777666544222 467899999999999986543 2 788 587665543
No 117
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=57.71 E-value=10 Score=32.74 Aligned_cols=40 Identities=25% Similarity=0.603 Sum_probs=32.6
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHH
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
....+.|.||--.+.....| -..|+|....+|.+.|+...
T Consensus 1025 ~~~~~~C~~C~l~V~gss~~--Cg~C~Hv~H~sc~~eWf~~g 1064 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSNF--CGTCGHVGHTSCMMEWFRTG 1064 (1081)
T ss_pred ccceeeeeeEeeEeeccchh--hccccccccHHHHHHHHhcC
Confidence 45667799998887666454 79999999999999999863
No 118
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=57.48 E-value=4.5 Score=31.26 Aligned_cols=36 Identities=22% Similarity=0.511 Sum_probs=27.5
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
..|-.|.++..+...| .-..|.|.||.+|=. +|...
T Consensus 331 ~~Cf~C~~~~~~~~~y-~C~~Ck~~FCldCDv-~iHes 366 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRY-RCESCKNVFCLDCDV-FIHES 366 (378)
T ss_pred cceeeeccccCCCCcE-EchhccceeeccchH-HHHhh
Confidence 3499998888777777 489999999999953 34433
No 119
>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=55.71 E-value=2.2 Score=24.69 Aligned_cols=36 Identities=14% Similarity=0.379 Sum_probs=17.7
Q ss_pred CCccccccccccccccc-cccccCCcCCcchHHHHHHH
Q 033301 24 GSSFTCEICIEPMAASK-KFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~-~~~~~~~C~H~fC~~C~~~~ 60 (122)
.....|.+|...+.... .. .--.||+.||.+|....
T Consensus 7 ~~~~~C~~C~~~F~~~~rrh-hCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRH-HCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EE-E-TTT--EEECCCS-EE
T ss_pred CCCCcCcCcCCcCCCceeeE-ccCCCCCEECCchhCCE
Confidence 34568999999985431 12 35679999999887543
No 120
>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=54.93 E-value=4.9 Score=22.26 Aligned_cols=40 Identities=23% Similarity=0.562 Sum_probs=22.8
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
.+.||.|.+.++.. =+..++...=.. ....+.|| .|...+
T Consensus 2 ~f~CP~C~~~~~~~----------------~L~~H~~~~H~~-~~~~v~CP--iC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSES----------------SLVEHCEDEHRS-ESKNVVCP--ICSSRV 41 (54)
T ss_pred CcCCCCCCCccCHH----------------HHHHHHHhHCcC-CCCCccCC--Cchhhh
Confidence 57899998854322 123344443222 34478999 588643
No 121
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=54.19 E-value=5.4 Score=20.43 Aligned_cols=32 Identities=19% Similarity=0.495 Sum_probs=15.8
Q ss_pred chHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 52 FSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 52 fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
+|.+|++.|..-.-..-....|.|+ .|+-.++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~--~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCT--NCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BT--TCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCC--CCCCCEE
Confidence 4788888876543222235678888 5875543
No 122
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=54.03 E-value=13 Score=20.54 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=21.3
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHH
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~ 60 (122)
.|.||..++..-..+ .+.=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~--k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF--KIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce--eccCc-cchHHHHHHh
Confidence 489999998644333 34455 7999999776
No 123
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.81 E-value=21 Score=26.76 Aligned_cols=76 Identities=13% Similarity=0.166 Sum_probs=51.9
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhcccCC-CHHHHHHH
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEPIV-PASLFSKW 101 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l-~~~~~~ky 101 (122)
....|.|+|=.-++++...|..+-.|||+|=-. ++++ +-.-.|+ .|.+....+++.-|- +++.++-|
T Consensus 108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~Ser--------AlKe--ikas~C~--~C~a~y~~~dvIvlNg~~E~~dll 175 (293)
T KOG3113|consen 108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSER--------ALKE--IKASVCH--VCGAAYQEDDVIVLNGTEEDVDLL 175 (293)
T ss_pred ccceeecccccceecceEEEEEEeccceeccHH--------HHHH--hhhcccc--ccCCcccccCeEeeCCCHHHHHHH
Confidence 356789999999998776666688999998652 2222 3345798 599998887765443 45666666
Q ss_pred HHHHHhhhh
Q 033301 102 CDVLCEDYV 110 (122)
Q Consensus 102 ~~~~~~~~i 110 (122)
..++.+...
T Consensus 176 k~rme~~ka 184 (293)
T KOG3113|consen 176 KTRMEERKA 184 (293)
T ss_pred HHHHHHHHH
Confidence 655555443
No 124
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=51.28 E-value=10 Score=34.41 Aligned_cols=40 Identities=20% Similarity=0.397 Sum_probs=32.2
Q ss_pred CCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHh
Q 033301 23 SGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKV 65 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i 65 (122)
....+.|+||.+.+-.. .+ ...|||.+|-.|...+...+.
T Consensus 1150 ~~~~~~c~ic~dil~~~-~~--I~~cgh~~c~~c~~~~l~~~s 1189 (1394)
T KOG0298|consen 1150 LSGHFVCEICLDILRNQ-GG--IAGCGHEPCCRCDELWLYASS 1189 (1394)
T ss_pred hhcccchHHHHHHHHhc-CC--eeeechhHhhhHHHHHHHHhc
Confidence 35566999999998533 33 589999999999999988764
No 125
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.69 E-value=10 Score=17.36 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=12.3
Q ss_pred cccccccccccccccccCCcCCc
Q 033301 29 CEICIEPMAASKKFKNKNLCTHP 51 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~ 51 (122)
|+-|-.++.....| -..||+.
T Consensus 2 Cp~CG~~~~~~~~f--C~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAKF--CPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCcc--hhhhCCc
Confidence 77777777655444 4455543
No 126
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=49.69 E-value=15 Score=32.67 Aligned_cols=51 Identities=25% Similarity=0.756 Sum_probs=34.6
Q ss_pred CCCccccccccccccc---cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAA---SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
..+...|.||.|++.. ++.|-.--.|+-..|+.|. +...++|+. .|| .|+.
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY----EYEr~eG~q---~CP--qCkt 67 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY----EYERKDGNQ---SCP--QCKT 67 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCCCccccchh----hhhhhcCCc---cCC--ccCC
Confidence 3455699999999753 2334234457778999998 445556555 799 4875
No 127
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=48.56 E-value=12 Score=20.22 Aligned_cols=34 Identities=21% Similarity=0.622 Sum_probs=22.7
Q ss_pred cccccccccccccccccCCcCC-----cchHHHHHHHHHHH
Q 033301 29 CEICIEPMAASKKFKNKNLCTH-----PFSQDCIAKYIQVK 64 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H-----~fC~~C~~~~i~~~ 64 (122)
|-||+++......+ ..+|+- ....+|+..|+..+
T Consensus 1 CrIC~~~~~~~~~l--i~pC~C~Gs~~~vH~~CL~~W~~~~ 39 (47)
T PF12906_consen 1 CRICLEGEEEDEPL--ISPCRCKGSMKYVHRSCLERWIRES 39 (47)
T ss_dssp ETTTTEE-SSSS-E--E-SSS-SSCCGSEECCHHHHHHHHH
T ss_pred CeEeCCcCCCCCce--ecccccCCCcchhHHHHHHHHHHhc
Confidence 67999987655433 466653 46889999999984
No 128
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=47.37 E-value=23 Score=20.34 Aligned_cols=30 Identities=20% Similarity=0.607 Sum_probs=21.5
Q ss_pred cccccccccccccccccccCCcCCcch-HHHHHHHHHHHhh
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFS-QDCIAKYIQVKVQ 66 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC-~~C~~~~i~~~i~ 66 (122)
..|++|...++.+ -.|| .+|=..|...+-+
T Consensus 4 kHC~~CG~~Ip~~----------~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 4 KHCPVCGKPIPPD----------ESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CcCCcCCCcCCcc----------hhhhCHHHHHHHHHHHHH
Confidence 5799998888654 3478 4888888776543
No 129
>PF14353 CpXC: CpXC protein
Probab=46.48 E-value=18 Score=23.49 Aligned_cols=23 Identities=26% Similarity=0.699 Sum_probs=17.8
Q ss_pred HHHHhhcCCCceecCCCCCCCCCCC
Q 033301 61 IQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 61 i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
+..+|.+|..+.++|| .|+..+.
T Consensus 27 l~e~il~g~l~~~~CP--~Cg~~~~ 49 (128)
T PF14353_consen 27 LKEKILDGSLFSFTCP--SCGHKFR 49 (128)
T ss_pred HHHHHHcCCcCEEECC--CCCCcee
Confidence 4566778899999999 6987544
No 130
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=46.26 E-value=43 Score=21.35 Aligned_cols=35 Identities=23% Similarity=0.625 Sum_probs=24.2
Q ss_pred CCc---CCcchHHHHHHHHHHHhhcC-CCceecCCCCCCCC
Q 033301 46 NLC---THPFSQDCIAKYIQVKVQDD-NTAKIECPGLECRH 82 (122)
Q Consensus 46 ~~C---~H~fC~~C~~~~i~~~i~~~-~~~~i~CP~~~C~~ 82 (122)
..| .-.||..||.......+.+- ....-.|| .|+.
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crg 69 (105)
T PF10497_consen 31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRG 69 (105)
T ss_pred CCCccCcceehHhHHHHHHhhhHHHHhcCCceECC--CCCC
Confidence 455 77799999998877766431 23456888 4664
No 131
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=45.82 E-value=39 Score=20.62 Aligned_cols=51 Identities=22% Similarity=0.606 Sum_probs=20.9
Q ss_pred CCCccccccccccccc---cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAA---SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
..+...|.||-+++-. .+.|..-..|+-..|+.|+. ...++|+. .|| .|+.
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE----YErkeg~q---~Cp--qCkt 59 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE----YERKEGNQ---VCP--QCKT 59 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH----HHHHTS-S---B-T--TT--
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHH----HHhhcCcc---ccc--ccCC
Confidence 4566789999999853 23453456788889999974 45556544 788 4774
No 132
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=45.81 E-value=30 Score=19.99 Aligned_cols=15 Identities=13% Similarity=0.430 Sum_probs=10.0
Q ss_pred CceecCCCCCCCCCCCh
Q 033301 70 TAKIECPGLECRHDLDP 86 (122)
Q Consensus 70 ~~~i~CP~~~C~~~i~~ 86 (122)
..||+|. .|+.+|..
T Consensus 2 iiPVRCF--TCGkvi~~ 16 (60)
T PF01194_consen 2 IIPVRCF--TCGKVIGN 16 (60)
T ss_dssp --SSS-S--TTTSBTCG
T ss_pred CCceecC--CCCCChhH
Confidence 3689999 69988873
No 133
>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=45.51 E-value=15 Score=28.74 Aligned_cols=40 Identities=18% Similarity=0.497 Sum_probs=26.3
Q ss_pred cCCcchHHHHHHHHHHHhhcC---CCceecCCCCCCCCCCChh
Q 033301 48 CTHPFSQDCIAKYIQVKVQDD---NTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 48 C~H~fC~~C~~~~i~~~i~~~---~~~~i~CP~~~C~~~i~~~ 87 (122)
|.-+.|.+|+.+|+.++-++. .+..=+||-+.|++.+=..
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil 353 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL 353 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence 445579999999999887531 3444444444799865433
No 134
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=45.15 E-value=7.4 Score=21.16 Aligned_cols=35 Identities=17% Similarity=0.403 Sum_probs=26.2
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHHHhhc
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQD 67 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~ 67 (122)
.|.||-.....+ ..--|+..|.+|-+..+....++
T Consensus 1 ~CiiC~~~~~~G-----I~I~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEEG-----IHIYGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCCC-----EEEECeEehHHHHHHhccCCCCC
Confidence 488898887543 23348999999999988877654
No 135
>PHA02862 5L protein; Provisional
Probab=44.85 E-value=29 Score=23.77 Aligned_cols=45 Identities=24% Similarity=0.564 Sum_probs=31.9
Q ss_pred cccccccccccccccccccCCcC-----CcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCT-----HPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDL 84 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i 84 (122)
..|-||.++.... .-+|. ....++|+..|+.. ..+..|+ .|+...
T Consensus 3 diCWIC~~~~~e~-----~~PC~C~GS~K~VHq~CL~~WIn~------S~k~~Ce--LCkteY 52 (156)
T PHA02862 3 DICWICNDVCDER-----NNFCGCNEEYKVVHIKCMQLWINY------SKKKECN--LCKTKY 52 (156)
T ss_pred CEEEEecCcCCCC-----cccccccCcchhHHHHHHHHHHhc------CCCcCcc--CCCCeE
Confidence 5799999996432 23554 45889999999943 3567999 588644
No 136
>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=44.61 E-value=22 Score=20.30 Aligned_cols=46 Identities=24% Similarity=0.598 Sum_probs=28.9
Q ss_pred cccccccccccccccccccCCcC--CcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 27 FTCEICIEPMAASKKFKNKNLCT--HPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
..|..|-.+++....- ..-|. ..||.+|....+. =.|| .|+..|..
T Consensus 6 pnCE~C~~dLp~~s~~--A~ICSfECTFC~~C~e~~l~----------~~CP--NCgGelv~ 53 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPE--AYICSFECTFCADCAETMLN----------GVCP--NCGGELVR 53 (57)
T ss_pred CCccccCCCCCCCCCc--ceEEeEeCcccHHHHHHHhc----------CcCc--CCCCcccc
Confidence 4688898888765311 23344 3499999866542 2688 68765543
No 137
>PLN02436 cellulose synthase A
Probab=44.50 E-value=20 Score=32.05 Aligned_cols=51 Identities=29% Similarity=0.742 Sum_probs=33.2
Q ss_pred CCCcccccccccccc---ccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMA---ASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
......|.||.|++. .++.|..--.|+-..|+.|+ .| ..++|+. .|| .|+.
T Consensus 33 ~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-ey---er~eg~~---~Cp--qckt 86 (1094)
T PLN02436 33 ELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EY---ERREGNQ---ACP--QCKT 86 (1094)
T ss_pred ccCCccccccccccCcCCCCCEEEeeccCCCccccchh-hh---hhhcCCc---cCc--ccCC
Confidence 345569999999973 23344223348888999998 33 3444444 788 4875
No 138
>PLN02189 cellulose synthase
Probab=44.38 E-value=20 Score=31.89 Aligned_cols=51 Identities=25% Similarity=0.688 Sum_probs=33.5
Q ss_pred CCCccccccccccccc---cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAA---SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
......|.||.+++.. ++.|..--.|+-..|+.|+ .| ..++|+. .|| .|+.
T Consensus 31 ~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-ey---er~eg~q---~Cp--qCkt 84 (1040)
T PLN02189 31 NLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EY---ERREGTQ---NCP--QCKT 84 (1040)
T ss_pred cccCccccccccccCcCCCCCEEEeeccCCCccccchh-hh---hhhcCCc---cCc--ccCC
Confidence 3455689999999752 2344233448888999998 33 4445444 799 4875
No 139
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=43.86 E-value=7 Score=25.23 Aligned_cols=17 Identities=35% Similarity=0.849 Sum_probs=14.2
Q ss_pred CCceecCCCCCCCCCCChh
Q 033301 69 NTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 69 ~~~~i~CP~~~C~~~i~~~ 87 (122)
+..||.|| .|+..++..
T Consensus 23 nk~PivCP--~CG~~~~~~ 39 (108)
T PF09538_consen 23 NKDPIVCP--KCGTEFPPE 39 (108)
T ss_pred CCCCccCC--CCCCccCcc
Confidence 45899999 799888877
No 140
>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=43.84 E-value=20 Score=19.59 Aligned_cols=47 Identities=17% Similarity=0.530 Sum_probs=23.6
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRH 82 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~ 82 (122)
..|+|-+..+..+-. ...|.|.-|.| +..|+....+.+ .-+|| -|.+
T Consensus 3 L~CPls~~~i~~P~R---g~~C~H~~CFD-l~~fl~~~~~~~---~W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVR---GKNCKHLQCFD-LESFLESNQRTP---KWKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-SSEEE---ETT--SS--EE-HHHHHHHHHHS------B-T--TT--
T ss_pred eeCCCCCCEEEeCcc---CCcCcccceEC-HHHHHHHhhccC---CeECc--CCcC
Confidence 468888877755422 57899998765 567777766543 37898 4764
No 141
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=41.90 E-value=18 Score=20.64 Aligned_cols=33 Identities=15% Similarity=0.132 Sum_probs=21.5
Q ss_pred cccccccccccccccccCCcCCcchHH----HHHHHHHHH
Q 033301 29 CEICIEPMAASKKFKNKNLCTHPFSQD----CIAKYIQVK 64 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~fC~~----C~~~~i~~~ 64 (122)
|..|... ..+.+ +-|.|++.+|.+ ....|....
T Consensus 1 C~~C~~~--~~~lw-~CL~Cg~~~C~~~~~~Ha~~H~~~~ 37 (63)
T PF02148_consen 1 CSVCGST--NSNLW-LCLTCGYVGCGRYSNGHALKHYKET 37 (63)
T ss_dssp -SSSHTC--SSSEE-EETTTS-EEETTTSTSHHHHHHHHH
T ss_pred CCCCCCc--CCceE-EeCCCCcccccCCcCcHHHHhhccc
Confidence 5566644 23355 489999999996 788887743
No 142
>PF15616 TerY-C: TerY-C metal binding domain
Probab=41.54 E-value=16 Score=24.51 Aligned_cols=43 Identities=21% Similarity=0.380 Sum_probs=32.0
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
.-||-|-... .| +.-.||+.||. + +...+.|| .|.........
T Consensus 78 PgCP~CGn~~----~f-a~C~CGkl~Ci------------~-g~~~~~CP--wCg~~g~~~~~ 120 (131)
T PF15616_consen 78 PGCPHCGNQY----AF-AVCGCGKLFCI------------D-GEGEVTCP--WCGNEGSFGAG 120 (131)
T ss_pred CCCCCCcChh----cE-EEecCCCEEEe------------C-CCCCEECC--CCCCeeeeccc
Confidence 6799998876 33 36799999997 2 35588999 89987665443
No 143
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=41.06 E-value=23 Score=18.22 Aligned_cols=36 Identities=17% Similarity=0.360 Sum_probs=20.5
Q ss_pred CCcccccccccccccccc---ccccCCcCCcchH-HHHHHH
Q 033301 24 GSSFTCEICIEPMAASKK---FKNKNLCTHPFSQ-DCIAKY 60 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~---~~~~~~C~H~fC~-~C~~~~ 60 (122)
.....|..|...+..... + ..-+-.|.||. .|+..|
T Consensus 4 ~~~~~C~~C~~~~~~~~~~~~~-~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPNKPTMIEV-QYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp -SCEE-TTT--EEECCC----E-E-TTTTSCCSSHHHHHHH
T ss_pred CcCCcCcccCCcccCCCccccc-cccCcccChhCHHHHhhC
Confidence 455689999988865542 3 24567788886 677654
No 144
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=40.62 E-value=17 Score=23.51 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=18.1
Q ss_pred cCCcCCcchHHHHHHHHHHHhh
Q 033301 45 KNLCTHPFSQDCIAKYIQVKVQ 66 (122)
Q Consensus 45 ~~~C~H~fC~~C~~~~i~~~i~ 66 (122)
+.+=||.||.+|-+.++..+.-
T Consensus 50 lPGlGqhYCieCaryf~t~~aL 71 (126)
T COG5112 50 LPGLGQHYCIECARYFITEKAL 71 (126)
T ss_pred CCCCceeeeehhHHHHHHHHHH
Confidence 5666999999999988887763
No 145
>PLN02195 cellulose synthase A
Probab=40.47 E-value=28 Score=30.83 Aligned_cols=54 Identities=19% Similarity=0.551 Sum_probs=37.0
Q ss_pred CCCcccccccccccccc---ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAAS---KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
++....|.||.+++... +.|..--.|+-..|+.|. +...++|+. .|| .|+..-.
T Consensus 3 ~~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy----eyer~eg~q---~Cp--qCkt~Yk 59 (977)
T PLN02195 3 ESGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACL----EYEIKEGRK---VCL--RCGGPYD 59 (977)
T ss_pred cCCCccceecccccCcCCCCCeEEEeccCCCccccchh----hhhhhcCCc---cCC--ccCCccc
Confidence 34566899999987532 334345568888999998 445555555 899 5987655
No 146
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=38.97 E-value=9.4 Score=29.11 Aligned_cols=45 Identities=16% Similarity=0.202 Sum_probs=36.7
Q ss_pred CCcchHHHHHHhhCCCccccccccccccccccccccCCcCCcchHH
Q 033301 10 ENLAKEEEEEEESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQD 55 (122)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~ 55 (122)
-|+|.+++|.......-|.|.||--.+...+.|+ ++.=+...|++
T Consensus 104 PtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFY-LmeD~rLvCK~ 148 (383)
T KOG4577|consen 104 PTQVVRKAQDFVYHLHCFACFICKRQLATGDEFY-LMEDARLVCKD 148 (383)
T ss_pred hHHHHHHhhcceeehhhhhhHhhhcccccCCeeE-Eeccceeehhh
Confidence 4678999998888999999999999988777776 55557777774
No 147
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=37.67 E-value=15 Score=28.43 Aligned_cols=19 Identities=21% Similarity=0.564 Sum_probs=15.2
Q ss_pred cCCcCCcchHHHHHHHHHH
Q 033301 45 KNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 45 ~~~C~H~fC~~C~~~~i~~ 63 (122)
--+||-.||++|+.+|-+.
T Consensus 339 ~~gCgf~FCR~C~e~yh~g 357 (446)
T KOG0006|consen 339 EGGCGFAFCRECKEAYHEG 357 (446)
T ss_pred CCCchhHhHHHHHhhhccc
Confidence 3459999999999988653
No 148
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=36.61 E-value=31 Score=30.77 Aligned_cols=52 Identities=23% Similarity=0.650 Sum_probs=34.6
Q ss_pred CCCcccccccccccccc---ccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAAS---KKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD 83 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~ 83 (122)
..+...|.||.|++... +.|..--.|+-..|+.|+ +...++|+. .|| .|+..
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy----eye~~~g~~---~cp--~c~t~ 66 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY----EYERSEGNQ---CCP--QCNTR 66 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchh----hhhhhcCCc---cCC--ccCCc
Confidence 44667899999997532 334234457777999998 444555544 788 48753
No 149
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=36.11 E-value=7.7 Score=21.48 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=17.0
Q ss_pred chHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 52 FSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 52 fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
-|..|++.+ ..+. ....|+|| .|+..|-
T Consensus 8 ~C~~Cg~~~--~~~~--~~~~irCp--~Cg~rIl 35 (49)
T COG1996 8 KCARCGREV--ELDQ--ETRGIRCP--YCGSRIL 35 (49)
T ss_pred EhhhcCCee--ehhh--ccCceeCC--CCCcEEE
Confidence 356666655 1121 46789999 5887553
No 150
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=35.94 E-value=38 Score=26.25 Aligned_cols=56 Identities=18% Similarity=0.303 Sum_probs=36.3
Q ss_pred CCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChh
Q 033301 24 GSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPF 87 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~ 87 (122)
.+.|.||+=-+.......- .++.|||..=.+=+. ++...+....+|| -|...-..+
T Consensus 334 Hs~FiCPVlKe~~t~ENpP-~ml~CgHVIskeal~-----~LS~nG~~~FKCP--YCP~~~~~~ 389 (396)
T COG5109 334 HSLFICPVLKELCTDENPP-VMLECGHVISKEALS-----VLSQNGVLSFKCP--YCPEMSKYE 389 (396)
T ss_pred cceeeccccHhhhcccCCC-eeeeccceeeHHHHH-----HHhhcCcEEeeCC--CCCcchhhh
Confidence 5778999977666544332 389999998765443 2222256699999 487544333
No 151
>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=35.01 E-value=20 Score=19.46 Aligned_cols=37 Identities=22% Similarity=0.494 Sum_probs=26.5
Q ss_pred hhCCCccccccccccccccccccccCCcCCcchHHHHHHH
Q 033301 21 ESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 21 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~ 60 (122)
.+-..=+.|..|...+.....+ ..=+..||.+|..+.
T Consensus 21 ~~H~~Cf~C~~C~~~l~~~~~~---~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 21 FWHPECFKCSKCGKPLNDGDFY---EKDGKPYCKDCYQKR 57 (58)
T ss_dssp EEETTTSBETTTTCBTTTSSEE---EETTEEEEHHHHHHH
T ss_pred EEEccccccCCCCCccCCCeeE---eECCEEECHHHHhhh
Confidence 3446678999999998766532 233589999998753
No 152
>PLN02400 cellulose synthase
Probab=34.74 E-value=23 Score=31.68 Aligned_cols=52 Identities=23% Similarity=0.608 Sum_probs=34.9
Q ss_pred CCCccccccccccccc---cccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCC
Q 033301 23 SGSSFTCEICIEPMAA---SKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHD 83 (122)
Q Consensus 23 ~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~ 83 (122)
......|.||-|++.. .+.|..--.|+-..|+.|. +...++|+. .|| .|+..
T Consensus 33 ~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY----EYERkeGnq---~CP--QCkTr 87 (1085)
T PLN02400 33 NLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY----EYERKDGTQ---CCP--QCKTR 87 (1085)
T ss_pred ccCCceeeecccccCcCCCCCEEEEEccCCCccccchh----heecccCCc---cCc--ccCCc
Confidence 3455689999999743 2344344567788999998 445555554 799 48753
No 153
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.17 E-value=23 Score=25.48 Aligned_cols=25 Identities=28% Similarity=0.397 Sum_probs=19.5
Q ss_pred cccccccccccccccccCCcCCc-chHHHH
Q 033301 29 CEICIEPMAASKKFKNKNLCTHP-FSQDCI 57 (122)
Q Consensus 29 C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~ 57 (122)
|-.|.+.-. .+ .+++|.|. +|..|=
T Consensus 161 Cr~C~~~~~---~V-lllPCrHl~lC~~C~ 186 (207)
T KOG1100|consen 161 CRKCGEREA---TV-LLLPCRHLCLCGICD 186 (207)
T ss_pred ceecCcCCc---eE-EeecccceEeccccc
Confidence 999988753 33 48999997 898874
No 154
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=34.11 E-value=27 Score=16.27 Aligned_cols=22 Identities=23% Similarity=0.452 Sum_probs=12.2
Q ss_pred cccccccccccccccccccCCcCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTH 50 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H 50 (122)
..|+-|-..+.....| -..||+
T Consensus 3 ~~Cp~Cg~~~~~~~~f--C~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKF--CPNCGA 24 (26)
T ss_pred CCCcccCCcCCccccc--ChhhCC
Confidence 4677777765544333 344444
No 155
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=33.53 E-value=48 Score=18.71 Aligned_cols=36 Identities=11% Similarity=0.263 Sum_probs=25.8
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
+......|.+|-..... .-.-+-..|+.|++.+...
T Consensus 12 yGkGsr~C~vCg~~~gl------iRkygL~~CRqCFRe~A~~ 47 (54)
T PTZ00218 12 YGKGSRQCRVCSNRHGL------IRKYGLNVCRQCFRENAEL 47 (54)
T ss_pred CCCCCCeeecCCCcchh------hhhcCcchhhHHHHHhhHh
Confidence 34455789999886532 3445778999999988764
No 156
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=33.22 E-value=28 Score=22.47 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=20.9
Q ss_pred Ccccccccccccccc--ccccccCCcCCcchHHHHH
Q 033301 25 SSFTCEICIEPMAAS--KKFKNKNLCTHPFSQDCIA 58 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~C~~ 58 (122)
+...|.+|...+... ... .-..|.|.+|..|-.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~-~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGR-VCVDCKHRVCKKCGV 87 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCE-EETTTTEEEETTSEE
T ss_pred CCcchhhhCCcccccCCCCC-cCCcCCccccCccCC
Confidence 567899998875321 112 357899999998843
No 157
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=32.56 E-value=42 Score=28.23 Aligned_cols=42 Identities=10% Similarity=0.233 Sum_probs=31.7
Q ss_pred cCCcCCcchH--HHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhc
Q 033301 45 KNLCTHPFSQ--DCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSC 89 (122)
Q Consensus 45 ~~~C~H~fC~--~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i 89 (122)
.++|.+..|. .|+-.-+..++++ ..-.-.|| .|...+..+.+
T Consensus 317 ~~P~r~~~CkHlQcFD~~~~lq~n~-~~pTW~CP--VC~~~~~~e~l 360 (636)
T KOG2169|consen 317 SLPARGHTCKHLQCFDALSYLQMNE-QKPTWRCP--VCQKAAPFEGL 360 (636)
T ss_pred ecCCcccccccceecchhhhHHhcc-CCCeeeCc--cCCccccccch
Confidence 6777888887 8888777777766 56677999 59887776654
No 158
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.01 E-value=43 Score=16.99 Aligned_cols=14 Identities=36% Similarity=0.982 Sum_probs=9.2
Q ss_pred CCceecCCCCCCCCCC
Q 033301 69 NTAKIECPGLECRHDL 84 (122)
Q Consensus 69 ~~~~i~CP~~~C~~~i 84 (122)
+...++|| .|+..+
T Consensus 22 ~~~~vrC~--~C~~~f 35 (37)
T PF13719_consen 22 GGRKVRCP--KCGHVF 35 (37)
T ss_pred CCcEEECC--CCCcEe
Confidence 34577887 577654
No 159
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=31.78 E-value=25 Score=17.52 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=7.1
Q ss_pred ecCCCCCCCCC
Q 033301 73 IECPGLECRHD 83 (122)
Q Consensus 73 i~CP~~~C~~~ 83 (122)
.+||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 58999999854
No 160
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=31.31 E-value=77 Score=20.11 Aligned_cols=40 Identities=20% Similarity=0.367 Sum_probs=30.6
Q ss_pred CCceecCCCCCCCCCCChhhcccCCCH-HHHHHHHHHHHhhhhc
Q 033301 69 NTAKIECPGLECRHDLDPFSCEPIVPA-SLFSKWCDVLCEDYVL 111 (122)
Q Consensus 69 ~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~ky~~~~~~~~i~ 111 (122)
+...+.|| .|..-... .|..|..+ ++|.+|.+...+..|.
T Consensus 39 ~~~h~~C~--~CG~y~~~-~V~~l~epIDVY~~wiD~~~eg~i~ 79 (99)
T PRK14892 39 NIAIITCG--NCGLYTEF-EVPSVYDEVDVYNKFIDLYLEGKIE 79 (99)
T ss_pred CcceEECC--CCCCccCE-ECCccccchhhHHHHHHHHHhcCCC
Confidence 47899999 69976655 36555544 9999999999888773
No 161
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=31.07 E-value=17 Score=23.09 Aligned_cols=33 Identities=24% Similarity=0.508 Sum_probs=21.2
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHH
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDC 56 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C 56 (122)
.....|+|.-||=-..-...- ...=|+.+|++|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa--~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLA--REKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhc--cccCCCEecccc
Confidence 356778999998766443222 233377888887
No 162
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=29.34 E-value=20 Score=28.60 Aligned_cols=34 Identities=21% Similarity=0.592 Sum_probs=27.2
Q ss_pred CccccccccccccccccccccCCcCCcchHHHHHHH
Q 033301 25 SSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~ 60 (122)
...+|+||+--++....+ .--|.-..|.+|+..+
T Consensus 73 r~~ecpicflyyps~~n~--~rcC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNL--VRCCSETICGECFAPF 106 (482)
T ss_pred ccccCceeeeecccccch--hhhhccchhhhheecc
Confidence 346899999999875554 6789999999998754
No 163
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=28.12 E-value=38 Score=16.16 Aligned_cols=29 Identities=21% Similarity=0.706 Sum_probs=8.6
Q ss_pred cccccccccccccccccccCCcCCcchHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDC 56 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C 56 (122)
+.|.+|.........| .-..|.-.+..+|
T Consensus 1 ~~C~~C~~~~~~~~~Y-~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFY-RCSECDFDLHEEC 29 (30)
T ss_dssp ---TTTS----S--EE-E-TTT-----HHH
T ss_pred CcCCcCCCcCCCCceE-ECccCCCccChhc
Confidence 3577887777652233 3566666666555
No 164
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.28 E-value=18 Score=31.21 Aligned_cols=40 Identities=20% Similarity=0.401 Sum_probs=30.1
Q ss_pred CCcccccccccccccc----ccccccCCcCCcchHHHHHHHHHHH
Q 033301 24 GSSFTCEICIEPMAAS----KKFKNKNLCTHPFSQDCIAKYIQVK 64 (122)
Q Consensus 24 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fC~~C~~~~i~~~ 64 (122)
.-...|..|++..... +.+ ..+.|||.|...|+..+....
T Consensus 782 ~~e~rc~~c~~~~l~~~~~~~~~-~v~~c~h~yhk~c~~~~~~~~ 825 (846)
T KOG2066|consen 782 SVEERCSSCFEPNLPSGAAFDSV-VVFHCGHMYHKECLMMESLRN 825 (846)
T ss_pred eehhhhhhhcccccccCccccee-eEEEccchhhhcccccHHHhc
Confidence 3344799999997633 234 478999999999999877654
No 165
>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 cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.64 E-value=63 Score=17.39 Aligned_cols=32 Identities=16% Similarity=0.501 Sum_probs=20.8
Q ss_pred ccccccccccccccccccCCcCCc-chHHHHHHH
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHP-FSQDCIAKY 60 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~~ 60 (122)
.|..|..+....-.+. -+.|... .|.+|+..-
T Consensus 2 ~Cd~C~~~~~~g~r~~-C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIK-CAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEE-CCCCCCcchhHHhhhCc
Confidence 5788887775544453 6677443 888887743
No 167
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=25.92 E-value=56 Score=28.26 Aligned_cols=60 Identities=18% Similarity=0.258 Sum_probs=41.5
Q ss_pred hCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCCh
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDP 86 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~ 86 (122)
+......|.+|-..+.+-..+ -..|||--..+|++.|+.-.-.. ...-||...|...+.+
T Consensus 775 ~s~a~~~CtVC~~vi~G~~~~--c~~C~H~gH~sh~~sw~~~~s~c---a~~~C~~~c~~~~~~D 834 (839)
T KOG0269|consen 775 ESRASAKCTVCDLVIRGVDVW--CQVCGHGGHDSHLKSWFFKASPC---AKSICPHLCHYSSFID 834 (839)
T ss_pred HHHhhcCceeecceeeeeEee--cccccccccHHHHHHHHhcCCCC---ccccCCccccccccch
Confidence 345556799998887655444 78999999999999999865322 2222887666655544
No 168
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=25.44 E-value=25 Score=17.99 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=9.3
Q ss_pred CCccccccccccc
Q 033301 24 GSSFTCEICIEPM 36 (122)
Q Consensus 24 ~~~~~C~IC~~~~ 36 (122)
...+.|++|-...
T Consensus 6 ~~~~~C~~C~~~~ 18 (36)
T PF11781_consen 6 GPNEPCPVCGSRW 18 (36)
T ss_pred cCCCcCCCCCCeE
Confidence 4456699998774
No 169
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=24.91 E-value=75 Score=16.84 Aligned_cols=34 Identities=21% Similarity=0.559 Sum_probs=21.2
Q ss_pred CccccccccccccccccccccCCcCCc-chHHHHHH
Q 033301 25 SSFTCEICIEPMAASKKFKNKNLCTHP-FSQDCIAK 59 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~ 59 (122)
....|..|..+......|. -+.|... +|.+|+..
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~-C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYH-CLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SSCE-SSS-SSSEESSEEE-ESSSSS-EEEHHHHHH
T ss_pred CCeECcCCCCCcCcCCeEE-CCCCCCCchhhHHHhC
Confidence 3567889987433344563 7778765 99999876
No 170
>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=24.59 E-value=25 Score=27.96 Aligned_cols=59 Identities=24% Similarity=0.422 Sum_probs=0.0
Q ss_pred Ccccccccccccc----------------ccccccccCCcCCcchHHHHHHHHHHHhhcC-CCceecCCCCCCCCCCCh
Q 033301 25 SSFTCEICIEPMA----------------ASKKFKNKNLCTHPFSQDCIAKYIQVKVQDD-NTAKIECPGLECRHDLDP 86 (122)
Q Consensus 25 ~~~~C~IC~~~~~----------------~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~-~~~~i~CP~~~C~~~i~~ 86 (122)
...+|++|...-+ ..-.+ ..-+|||+-=....+-|-...|=.| ..+...|| =|...|.-
T Consensus 327 ~~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pth-aF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CP--FCa~~L~g 402 (416)
T PF04710_consen 327 RSRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTH-AFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACP--FCATPLDG 402 (416)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred ccccCCCccccCCceeEeeccccceeecCCCCce-eecccccccchhhhhhhhcCCCCCCcccccccCC--cccCcccC
Confidence 4789999986532 11123 3678999988888888877777665 46788999 48877763
No 171
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=24.34 E-value=17 Score=21.62 Aligned_cols=40 Identities=25% Similarity=0.615 Sum_probs=21.3
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCC
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLD 85 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~ 85 (122)
..||.|-.++... . +|.+|..|-..| .....|| +|.+.|.
T Consensus 2 ~~CP~C~~~L~~~-----~---~~~~C~~C~~~~---------~~~a~CP--dC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQ-----G---GHYHCEACQKDY---------KKEAFCP--DCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEE-----T---TEEEETTT--EE---------EEEEE-T--TT-SB-E
T ss_pred CcCCCCCCccEEe-----C---CEEECccccccc---------eecccCC--CcccHHH
Confidence 4799998887433 1 778888776632 3456788 6887664
No 172
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=24.28 E-value=61 Score=17.11 Aligned_cols=32 Identities=22% Similarity=0.719 Sum_probs=21.8
Q ss_pred cccccccccccccccccccCCcCCc-chHHHHHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHP-FSQDCIAKY 60 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~C~~~~ 60 (122)
+.|.+|..++.+ ..| .-+.|... +|.+|+..-
T Consensus 1 ~~C~~C~~~i~g-~r~-~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 1 YSCDGCLKPIVG-VRY-HCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCCcCCCCCCcC-CEE-ECCCCCCCcCHHHHHCcC
Confidence 358888887654 355 36777743 899988743
No 173
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.73 E-value=71 Score=14.63 Aligned_cols=20 Identities=10% Similarity=0.441 Sum_probs=14.1
Q ss_pred HHHHhhCCCccccccccccc
Q 033301 17 EEEEESSGSSFTCEICIEPM 36 (122)
Q Consensus 17 ~~~~~~~~~~~~C~IC~~~~ 36 (122)
..+.+.....+.|++|-..+
T Consensus 5 H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEE
T ss_pred HhhhcCCCCCCCCCCCcCee
Confidence 34456677789999996554
No 174
>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=23.17 E-value=2.3e+02 Score=19.66 Aligned_cols=72 Identities=13% Similarity=0.219 Sum_probs=47.2
Q ss_pred HhhCCCccccccccccccccccccccCCcCCcchHHHHHHHHHHHhhcCCCceecCCCCCCCCCCChhhccc--------
Q 033301 20 EESSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQDDNTAKIECPGLECRHDLDPFSCEP-------- 91 (122)
Q Consensus 20 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-------- 91 (122)
.........||+|..++.+= .+ . +-.+.|+. ...=.|+..+|...-++.++++
T Consensus 74 ~~~~~~~L~CPLCRG~V~GW-tv--v---------e~AR~~LN-------~K~RsC~~e~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 74 ESQEQPELACPLCRGEVKGW-TV--V---------EPARRFLN-------AKKRSCSQESCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred cccccccccCccccCceece-EE--c---------hHHHHHhc-------cCCccCcccccccccCHHHHHHHHHhhCCC
Confidence 34456678999999998533 22 1 11223332 2344799999998877776644
Q ss_pred ----CCCHHHHHHHHHHHHhhhh
Q 033301 92 ----IVPASLFSKWCDVLCEDYV 110 (122)
Q Consensus 92 ----~l~~~~~~ky~~~~~~~~i 110 (122)
-+|+....+|+++..+.-+
T Consensus 135 ~rP~~vDP~rq~~W~~le~~re~ 157 (162)
T PF07800_consen 135 ARPSEVDPQRQRDWERLEREREY 157 (162)
T ss_pred CCCccCCHHHHHHHHHHHHhhhh
Confidence 3678888889888766543
No 175
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=22.56 E-value=74 Score=15.81 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=8.5
Q ss_pred ceecCCCCCCCCCC
Q 033301 71 AKIECPGLECRHDL 84 (122)
Q Consensus 71 ~~i~CP~~~C~~~i 84 (122)
..++|| .|+..|
T Consensus 24 ~~v~C~--~C~~~~ 35 (38)
T TIGR02098 24 GKVRCG--KCGHVW 35 (38)
T ss_pred CEEECC--CCCCEE
Confidence 478888 587655
No 176
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=22.52 E-value=42 Score=22.27 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=17.2
Q ss_pred cCCcCCcchHHHHHHHHHHHh
Q 033301 45 KNLCTHPFSQDCIAKYIQVKV 65 (122)
Q Consensus 45 ~~~C~H~fC~~C~~~~i~~~i 65 (122)
+.+=|+.||..|-+.++....
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~ 72 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKA 72 (129)
T ss_pred CCCCceeehhhhhhhhcchHH
Confidence 556699999999988887665
No 177
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.44 E-value=43 Score=16.09 Aligned_cols=25 Identities=16% Similarity=0.518 Sum_probs=13.7
Q ss_pred cccccccccccccccccccCCcCCcc
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPF 52 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~f 52 (122)
+.|.||...+.....| .-..|+-.+
T Consensus 1 ~~C~~C~~~~~~~~~Y-~C~~c~f~l 25 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFY-HCSECCFTL 25 (30)
T ss_pred CCCCCCCCCcCCCEeE-EeCCCCCeE
Confidence 3688897777544323 234444333
No 178
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=22.26 E-value=45 Score=16.65 Aligned_cols=31 Identities=19% Similarity=0.372 Sum_probs=18.6
Q ss_pred cccccccccccccccccccCCcCCcchHHHHHHH
Q 033301 27 FTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKY 60 (122)
Q Consensus 27 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~ 60 (122)
..|..|-+.++..... ..+ +-.+|.+|-..+
T Consensus 4 g~C~~CGe~I~~~Rl~--~~p-~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLV--AVP-GATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHH--HCT-TECS-HHHHHHH
T ss_pred CCccccCChHHHHHHH--hCC-CcEECHHHhCcc
Confidence 4599999999765332 222 556888886543
No 179
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=21.97 E-value=31 Score=23.57 Aligned_cols=37 Identities=14% Similarity=0.283 Sum_probs=25.3
Q ss_pred hCCCccccccccccccccccccccCCcCCcchH-HHHHHHHHH
Q 033301 22 SSGSSFTCEICIEPMAASKKFKNKNLCTHPFSQ-DCIAKYIQV 63 (122)
Q Consensus 22 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~-~C~~~~i~~ 63 (122)
++.....|.||...- .+ +-..||-.||. .|+..|-++
T Consensus 114 ~KP~r~fCaVCG~~S----~y-sC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 114 FKPLRKFCAVCGYDS----KY-SCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred CCCcchhhhhcCCCc----hh-HHHhcCCceeechhhhhcccc
Confidence 445667899998332 23 36899999986 777665443
No 180
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=21.75 E-value=73 Score=20.37 Aligned_cols=39 Identities=21% Similarity=0.456 Sum_probs=28.8
Q ss_pred ccccccccccccccccccccCCcCCcchHHHHHHHHHHHhh
Q 033301 26 SFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQVKVQ 66 (122)
Q Consensus 26 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~~i~ 66 (122)
.+.|.||.+++-.++.|. .. =+-...-+||..-+...+.
T Consensus 2 kWkC~iCg~~I~~gqlFT-F~-~kG~VH~~C~~~~~~~k~~ 40 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFT-FT-KKGPVHYECFREKASKKLY 40 (101)
T ss_pred ceEEEecCCeeeecceEE-Ee-cCCcEeHHHHHHHHhhhcc
Confidence 468999999998887773 22 2367788888887776654
No 181
>KOG2594 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.49 E-value=67 Score=25.37 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=16.5
Q ss_pred CCcchHHHHHHHHHHHhhc
Q 033301 49 THPFSQDCIAKYIQVKVQD 67 (122)
Q Consensus 49 ~H~fC~~C~~~~i~~~i~~ 67 (122)
.-.||.+|+..++..++..
T Consensus 31 k~~~C~eCFv~~v~~KfR~ 49 (396)
T KOG2594|consen 31 KDAFCDECFVNNVRNKFRL 49 (396)
T ss_pred chhHHHHHHHHHHHHHHHH
Confidence 4589999999999998864
No 182
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.00 E-value=1e+02 Score=15.78 Aligned_cols=9 Identities=22% Similarity=0.154 Sum_probs=3.6
Q ss_pred CCHHHHHHH
Q 033301 93 VPASLFSKW 101 (122)
Q Consensus 93 l~~~~~~ky 101 (122)
|+...++++
T Consensus 30 ~d~~el~~~ 38 (41)
T PF13453_consen 30 FDAGELEKL 38 (41)
T ss_pred ccHHHHHHH
Confidence 334444433
No 183
>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=20.69 E-value=73 Score=16.08 Aligned_cols=31 Identities=19% Similarity=0.376 Sum_probs=20.6
Q ss_pred CccccccccccccccccccccCCcCCcchHHHHHH
Q 033301 25 SSFTCEICIEPMAASKKFKNKNLCTHPFSQDCIAK 59 (122)
Q Consensus 25 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~ 59 (122)
+...|..+-+.. ...| -..|+-.+|..|+..
T Consensus 2 ~~~~C~~H~~~~--~~~~--C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 2 QEPKCPEHPEEP--LSLF--CEDCNEPLCSECTVS 32 (42)
T ss_dssp SSSB-SSTTTSB--EEEE--ETTTTEEEEHHHHHT
T ss_pred cCccCccCCccc--eEEE--ecCCCCccCccCCCC
Confidence 345677776653 2233 688999999999864
No 184
>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=20.58 E-value=28 Score=18.48 Aligned_cols=35 Identities=14% Similarity=0.424 Sum_probs=20.5
Q ss_pred ccccccccccccccccccCCcCCcchHHHHHHHHHH
Q 033301 28 TCEICIEPMAASKKFKNKNLCTHPFSQDCIAKYIQV 63 (122)
Q Consensus 28 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~C~~~~i~~ 63 (122)
.|.||.......+++ .=..|+..|...|+.-....
T Consensus 1 ~C~vC~~~~~~~~~i-~C~~C~~~~H~~C~~~~~~~ 35 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMI-QCDSCNRWYHQECVGPPEKA 35 (51)
T ss_dssp EBTTTTSSCTTSSEE-EBSTTSCEEETTTSTSSHSH
T ss_pred eCcCCCCcCCCCCeE-EcCCCChhhCcccCCCChhh
Confidence 377887754444444 25567766766666555443
No 185
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=20.51 E-value=1.4e+02 Score=16.92 Aligned_cols=36 Identities=19% Similarity=0.289 Sum_probs=25.2
Q ss_pred eecCCCCCCCCCCChhhcccCCCHHHHHHHHHHHHhhh
Q 033301 72 KIECPGLECRHDLDPFSCEPIVPASLFSKWCDVLCEDY 109 (122)
Q Consensus 72 ~i~CP~~~C~~~i~~~~i~~~l~~~~~~ky~~~~~~~~ 109 (122)
...|| .|+.......=..+-+.+-+.+|...+....
T Consensus 17 k~~CP--~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 17 KEICP--VCGGKTKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred cccCc--CCCCCCCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 45688 5887666555556677788899987776554
No 186
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.44 E-value=26 Score=23.38 Aligned_cols=18 Identities=17% Similarity=0.182 Sum_probs=13.8
Q ss_pred CCceecCCCCCCCCCCChhh
Q 033301 69 NTAKIECPGLECRHDLDPFS 88 (122)
Q Consensus 69 ~~~~i~CP~~~C~~~i~~~~ 88 (122)
+..+|.|| .|+..++...
T Consensus 23 nk~p~vcP--~cg~~~~~~~ 40 (129)
T TIGR02300 23 NRRPAVSP--YTGEQFPPEE 40 (129)
T ss_pred CCCCccCC--CcCCccCcch
Confidence 46899999 7998776663
No 187
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.22 E-value=1.7e+02 Score=16.76 Aligned_cols=35 Identities=20% Similarity=0.328 Sum_probs=22.3
Q ss_pred cCCCCCCCCCCChhhcccCCCHHHHHHHHHHHHhhhh
Q 033301 74 ECPGLECRHDLDPFSCEPIVPASLFSKWCDVLCEDYV 110 (122)
Q Consensus 74 ~CP~~~C~~~i~~~~i~~~l~~~~~~ky~~~~~~~~i 110 (122)
+|| .|+...-...=..+-+.+-+.+|...+.+...
T Consensus 19 ~Cp--~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~ 53 (59)
T COG2260 19 KCP--VCGGDTKVPHPPRFSPEDKYGKYRRELKKRLG 53 (59)
T ss_pred cCC--CCCCccccCCCCCCCccchHHHHHHHHHHHhc
Confidence 688 57754433333445667888999887766553
No 188
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.08 E-value=66 Score=20.95 Aligned_cols=31 Identities=23% Similarity=0.538 Sum_probs=22.1
Q ss_pred ccccccccccccc-----------ccccccCCcCCcchHHHHH
Q 033301 27 FTCEICIEPMAAS-----------KKFKNKNLCTHPFSQDCIA 58 (122)
Q Consensus 27 ~~C~IC~~~~~~~-----------~~~~~~~~C~H~fC~~C~~ 58 (122)
..|--|...++.. ..| .-..|.+.||.+|=.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y-~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRY-VCAVCKNVFCVDCDV 97 (112)
T ss_pred CcccCcCCCCCCcccccccccccccce-eCCCCCCccccccch
Confidence 4699998876532 234 367899999999943
Done!