Query 020290
Match_columns 328
No_of_seqs 333 out of 1581
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 08:33:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3002 Zn finger protein [Gen 100.0 1.7E-41 3.8E-46 318.0 10.4 227 87-313 41-279 (299)
2 PF03145 Sina: Seven in absent 100.0 8.5E-30 1.8E-34 228.0 5.6 184 139-322 1-198 (198)
3 cd03829 Sina Seven in absentia 99.4 9.7E-14 2.1E-18 112.4 3.8 97 228-325 22-127 (127)
4 KOG0297 TNF receptor-associate 99.3 1.6E-12 3.5E-17 127.6 5.3 116 93-213 20-144 (391)
5 PF15227 zf-C3HC4_4: zinc fing 98.5 2E-08 4.4E-13 67.5 0.8 34 97-132 1-42 (42)
6 PLN03208 E3 ubiquitin-protein 98.5 4.9E-08 1.1E-12 86.2 1.9 46 91-138 15-80 (193)
7 PF14835 zf-RING_6: zf-RING of 98.5 7.3E-08 1.6E-12 69.9 2.1 52 94-147 7-64 (65)
8 smart00504 Ubox Modified RING 98.4 1E-07 2.3E-12 69.1 2.3 54 95-150 2-62 (63)
9 KOG0823 Predicted E3 ubiquitin 98.4 2.5E-07 5.4E-12 83.3 3.7 45 91-137 44-95 (230)
10 KOG0320 Predicted E3 ubiquitin 98.3 2.5E-07 5.5E-12 80.0 2.1 42 94-137 131-178 (187)
11 PF13923 zf-C3HC4_2: Zinc fing 98.3 2.5E-07 5.4E-12 61.0 0.7 34 97-132 1-39 (39)
12 TIGR00599 rad18 DNA repair pro 98.3 3.3E-07 7.1E-12 89.7 1.8 57 93-151 25-88 (397)
13 PF13920 zf-C3HC4_3: Zinc fing 98.2 4.4E-07 9.4E-12 63.2 0.5 42 94-137 2-48 (50)
14 KOG0287 Postreplication repair 98.1 1.8E-07 3.8E-12 88.1 -2.8 58 92-151 21-85 (442)
15 PF04564 U-box: U-box domain; 98.0 1.4E-06 3E-11 65.6 0.9 58 92-151 2-67 (73)
16 PF02176 zf-TRAF: TRAF-type zi 98.0 2.1E-06 4.6E-11 61.8 0.5 52 149-202 6-60 (60)
17 PF00097 zf-C3HC4: Zinc finger 97.9 3.3E-06 7.2E-11 56.0 1.0 34 97-132 1-41 (41)
18 PF14634 zf-RING_5: zinc-RING 97.9 2.6E-06 5.6E-11 57.7 0.1 37 96-134 1-44 (44)
19 PHA02929 N1R/p28-like protein; 97.8 5.3E-06 1.1E-10 76.1 1.0 44 93-138 173-228 (238)
20 PF13639 zf-RING_2: Ring finge 97.8 5E-06 1.1E-10 56.1 0.2 36 96-133 2-44 (44)
21 KOG0317 Predicted E3 ubiquitin 97.6 1.5E-05 3.2E-10 74.0 0.9 44 93-138 238-285 (293)
22 cd00162 RING RING-finger (Real 97.6 1.6E-05 3.4E-10 52.6 0.5 38 96-135 1-44 (45)
23 PF13445 zf-RING_UBOX: RING-ty 97.6 1.7E-05 3.8E-10 53.5 0.0 26 97-125 1-31 (43)
24 COG5432 RAD18 RING-finger-cont 97.5 1.8E-05 3.8E-10 73.4 -0.8 108 94-207 25-183 (391)
25 PHA02926 zinc finger-like prot 97.4 2.5E-05 5.5E-10 70.1 -0.4 43 94-138 170-231 (242)
26 TIGR00570 cdk7 CDK-activating 97.3 9.8E-05 2.1E-09 69.9 2.1 43 93-137 2-54 (309)
27 KOG2164 Predicted E3 ubiquitin 97.3 5.7E-05 1.2E-09 75.1 0.4 43 94-138 186-237 (513)
28 smart00184 RING Ring finger. E 97.3 6.3E-05 1.4E-09 47.9 0.0 34 97-132 1-39 (39)
29 KOG0311 Predicted E3 ubiquitin 97.3 1.9E-05 4E-10 75.1 -3.6 44 94-139 43-92 (381)
30 KOG2177 Predicted E3 ubiquitin 97.2 6.1E-05 1.3E-09 69.3 -0.6 62 92-155 11-77 (386)
31 KOG0978 E3 ubiquitin ligase in 97.1 0.00011 2.3E-09 76.3 -0.2 44 93-138 642-690 (698)
32 PF02176 zf-TRAF: TRAF-type zi 97.0 0.00024 5.2E-09 50.9 0.9 43 174-216 1-43 (60)
33 COG5574 PEX10 RING-finger-cont 97.0 0.00016 3.5E-09 66.5 -0.2 44 92-137 213-262 (271)
34 PLN03086 PRLI-interacting fact 96.7 0.0012 2.5E-08 67.7 3.2 106 91-206 404-537 (567)
35 PLN03086 PRLI-interacting fact 96.5 0.0063 1.4E-07 62.4 7.0 37 170-208 529-565 (567)
36 PF07800 DUF1644: Protein of u 96.4 0.0019 4E-08 55.3 2.1 28 182-209 107-134 (162)
37 PF12678 zf-rbx1: RING-H2 zinc 96.2 0.0024 5.2E-08 48.0 1.8 36 96-133 21-73 (73)
38 COG5152 Uncharacterized conser 96.1 0.0013 2.8E-08 58.2 -0.2 54 95-150 197-256 (259)
39 KOG1813 Predicted E3 ubiquitin 96.0 0.0041 8.8E-08 58.2 2.4 43 95-139 242-288 (313)
40 KOG2879 Predicted E3 ubiquitin 95.8 0.0049 1.1E-07 57.1 2.0 42 94-137 239-287 (298)
41 PF11789 zf-Nse: Zinc-finger o 95.5 0.0032 7E-08 45.1 -0.2 30 94-125 11-42 (57)
42 PF14570 zf-RING_4: RING/Ubox 95.2 0.0061 1.3E-07 42.0 0.3 40 97-136 1-47 (48)
43 KOG4172 Predicted E3 ubiquitin 95.1 0.0022 4.7E-08 45.1 -2.0 41 95-137 8-54 (62)
44 KOG4159 Predicted E3 ubiquitin 95.1 0.005 1.1E-07 60.7 -0.5 44 92-137 82-129 (398)
45 KOG2660 Locus-specific chromos 95.1 0.0049 1.1E-07 58.5 -0.5 43 93-137 14-61 (331)
46 PF05290 Baculo_IE-1: Baculovi 94.8 0.0097 2.1E-07 49.5 0.5 51 84-137 71-132 (140)
47 COG5175 MOT2 Transcriptional r 94.6 0.0076 1.6E-07 57.4 -0.6 46 91-137 12-64 (480)
48 KOG0824 Predicted E3 ubiquitin 94.6 0.014 2.9E-07 54.9 1.0 41 95-137 8-53 (324)
49 KOG0802 E3 ubiquitin ligase [P 94.0 0.014 2.9E-07 60.2 -0.5 41 94-136 291-340 (543)
50 COG5222 Uncharacterized conser 93.8 0.016 3.6E-07 54.3 -0.1 38 95-134 275-318 (427)
51 PF12861 zf-Apc11: Anaphase-pr 93.8 0.018 3.9E-07 44.5 0.1 40 96-137 34-82 (85)
52 KOG4739 Uncharacterized protei 93.6 0.035 7.6E-07 50.7 1.6 43 93-137 2-48 (233)
53 KOG4275 Predicted E3 ubiquitin 93.5 0.017 3.8E-07 54.0 -0.5 40 94-136 300-341 (350)
54 PF14447 Prok-RING_4: Prokaryo 93.4 0.071 1.5E-06 37.7 2.5 41 95-137 8-50 (55)
55 KOG1002 Nucleotide excision re 93.0 0.025 5.3E-07 56.9 -0.5 46 90-137 532-586 (791)
56 KOG4265 Predicted E3 ubiquitin 92.3 0.041 8.8E-07 53.0 0.1 42 94-137 290-336 (349)
57 KOG4692 Predicted E3 ubiquitin 91.8 0.025 5.4E-07 54.3 -1.9 48 88-137 416-467 (489)
58 KOG3161 Predicted E3 ubiquitin 91.4 0.029 6.4E-07 57.5 -2.0 36 93-130 10-51 (861)
59 KOG1785 Tyrosine kinase negati 91.2 0.042 9.2E-07 53.5 -1.1 40 96-137 371-416 (563)
60 COG5540 RING-finger-containing 89.4 0.15 3.3E-06 48.2 0.9 41 95-137 324-372 (374)
61 KOG4367 Predicted Zn-finger pr 89.3 0.081 1.8E-06 52.1 -0.9 30 93-124 3-33 (699)
62 PF05605 zf-Di19: Drought indu 89.2 0.23 4.9E-06 34.8 1.6 49 153-208 3-54 (54)
63 PF04641 Rtf2: Rtf2 RING-finge 88.7 0.24 5.2E-06 46.3 1.8 44 92-137 111-161 (260)
64 KOG1039 Predicted E3 ubiquitin 88.2 0.19 4.1E-06 48.8 0.8 44 93-138 160-222 (344)
65 KOG3039 Uncharacterized conser 87.9 0.21 4.6E-06 45.8 0.8 43 94-138 221-271 (303)
66 COG5236 Uncharacterized conser 87.1 0.11 2.4E-06 49.8 -1.5 44 91-136 58-107 (493)
67 KOG1571 Predicted E3 ubiquitin 85.8 0.26 5.7E-06 47.6 0.3 44 91-137 302-347 (355)
68 KOG0825 PHD Zn-finger protein 85.4 0.14 3E-06 53.9 -1.9 41 95-137 124-171 (1134)
69 PF07191 zinc-ribbons_6: zinc- 85.1 0.42 9E-06 35.6 1.0 38 95-137 2-41 (70)
70 KOG4185 Predicted E3 ubiquitin 84.6 0.58 1.3E-05 44.2 2.1 41 94-136 3-54 (296)
71 KOG1812 Predicted E3 ubiquitin 83.4 0.35 7.6E-06 47.8 -0.1 30 94-125 146-180 (384)
72 COG5243 HRD1 HRD ubiquitin lig 83.3 0.51 1.1E-05 45.9 1.0 42 93-136 286-344 (491)
73 KOG2817 Predicted E3 ubiquitin 83.1 0.44 9.6E-06 46.6 0.5 41 93-135 333-383 (394)
74 KOG4628 Predicted E3 ubiquitin 82.9 0.88 1.9E-05 44.2 2.5 41 95-137 230-278 (348)
75 KOG3800 Predicted E3 ubiquitin 82.4 0.4 8.6E-06 45.1 -0.1 39 96-136 2-50 (300)
76 PF11793 FANCL_C: FANCL C-term 82.3 0.32 6.9E-06 36.2 -0.6 43 95-137 3-66 (70)
77 PF10083 DUF2321: Uncharacteri 81.8 0.37 7.9E-06 41.3 -0.5 28 110-137 9-50 (158)
78 PF02891 zf-MIZ: MIZ/SP-RING z 81.6 0.44 9.5E-06 33.1 -0.1 39 95-135 3-50 (50)
79 COG5219 Uncharacterized conser 79.7 0.4 8.6E-06 51.6 -1.2 44 94-137 1469-1523(1525)
80 KOG0804 Cytoplasmic Zn-finger 79.4 0.59 1.3E-05 46.4 -0.1 41 93-135 174-220 (493)
81 PF12660 zf-TFIIIC: Putative z 78.0 0.92 2E-05 36.1 0.7 40 96-136 16-65 (99)
82 KOG3039 Uncharacterized conser 77.8 0.93 2E-05 41.8 0.7 29 95-124 44-72 (303)
83 KOG2231 Predicted E3 ubiquitin 77.3 1.1 2.4E-05 47.0 1.2 40 96-137 2-52 (669)
84 COG4306 Uncharacterized protei 76.2 0.96 2.1E-05 37.4 0.3 28 110-137 9-50 (160)
85 KOG3579 Predicted E3 ubiquitin 75.9 1.2 2.5E-05 41.9 0.9 31 94-124 268-301 (352)
86 KOG2932 E3 ubiquitin ligase in 75.0 1.9 4.1E-05 41.0 2.0 75 94-176 90-168 (389)
87 KOG1645 RING-finger-containing 74.1 0.98 2.1E-05 44.4 -0.1 39 95-135 5-54 (463)
88 PRK11088 rrmA 23S rRNA methylt 73.7 1.3 2.9E-05 41.2 0.7 23 95-117 3-27 (272)
89 KOG1001 Helicase-like transcri 73.1 0.88 1.9E-05 48.2 -0.8 39 95-136 455-499 (674)
90 KOG1814 Predicted E3 ubiquitin 72.4 1.5 3.3E-05 43.2 0.7 84 94-182 184-303 (445)
91 COG5194 APC11 Component of SCF 72.1 1 2.2E-05 34.4 -0.5 44 95-138 21-82 (88)
92 PF13909 zf-H2C2_5: C2H2-type 72.0 1.1 2.5E-05 25.6 -0.1 23 184-208 2-24 (24)
93 PF07975 C1_4: TFIIH C1-like d 71.8 2.1 4.5E-05 29.9 1.1 37 97-133 2-50 (51)
94 PF13913 zf-C2HC_2: zinc-finge 70.2 1.8 3.8E-05 25.5 0.4 22 153-178 3-24 (25)
95 PF10367 Vps39_2: Vacuolar sor 68.7 2.9 6.3E-05 32.8 1.5 29 96-124 80-109 (109)
96 KOG1734 Predicted RING-contain 65.4 1.2 2.7E-05 41.5 -1.4 41 95-137 225-281 (328)
97 KOG2114 Vacuolar assembly/sort 64.9 2.5 5.4E-05 45.2 0.5 38 95-134 841-880 (933)
98 PF05605 zf-Di19: Drought indu 64.6 3.7 8E-05 28.6 1.2 28 183-212 3-30 (54)
99 PF13834 DUF4193: Domain of un 64.2 14 0.00031 29.4 4.5 38 84-121 58-98 (99)
100 KOG3002 Zn finger protein [Gen 64.2 3.9 8.3E-05 39.1 1.6 53 150-206 78-132 (299)
101 COG2888 Predicted Zn-ribbon RN 62.7 5.5 0.00012 28.7 1.8 34 151-195 26-61 (61)
102 PHA00616 hypothetical protein 60.9 7.4 0.00016 26.3 2.1 33 182-216 1-34 (44)
103 COG3813 Uncharacterized protei 60.7 4.5 9.8E-05 30.2 1.1 29 110-138 24-53 (84)
104 PF10571 UPF0547: Uncharacteri 60.5 4.1 8.9E-05 24.3 0.7 9 97-105 3-11 (26)
105 PRK04023 DNA polymerase II lar 60.2 10 0.00022 41.7 4.1 43 93-137 625-674 (1121)
106 PF10235 Cript: Microtubule-as 60.1 4.7 0.0001 31.6 1.1 36 96-138 46-81 (90)
107 KOG1493 Anaphase-promoting com 59.8 1.5 3.2E-05 33.2 -1.6 26 110-137 50-81 (84)
108 PF01363 FYVE: FYVE zinc finge 59.2 5.1 0.00011 29.1 1.2 33 92-124 7-42 (69)
109 KOG3608 Zn finger proteins [Ge 58.7 3.7 7.9E-05 39.9 0.4 112 93-208 206-346 (467)
110 PF04606 Ogr_Delta: Ogr/Delta- 58.3 4.3 9.3E-05 27.6 0.6 39 128-168 1-39 (47)
111 PF05253 zf-U11-48K: U11-48K-l 56.8 4.6 0.0001 24.2 0.5 24 153-179 3-26 (27)
112 smart00734 ZnF_Rad18 Rad18-lik 53.3 8 0.00017 23.0 1.1 21 183-205 2-22 (26)
113 KOG2462 C2H2-type Zn-finger pr 53.1 13 0.00028 34.9 3.0 15 92-106 128-142 (279)
114 PF04216 FdhE: Protein involve 52.2 7.4 0.00016 36.8 1.3 41 95-135 173-220 (290)
115 COG5109 Uncharacterized conser 51.8 7.5 0.00016 37.2 1.3 40 93-134 335-384 (396)
116 KOG4362 Transcriptional regula 51.2 3.7 8E-05 43.2 -1.0 41 94-136 21-68 (684)
117 PF08209 Sgf11: Sgf11 (transcr 49.7 7.6 0.00016 24.6 0.7 24 152-179 4-27 (33)
118 PRK14559 putative protein seri 49.7 11 0.00024 39.8 2.3 10 96-105 3-12 (645)
119 KOG1100 Predicted E3 ubiquitin 47.5 13 0.00027 33.7 2.0 38 97-137 161-200 (207)
120 PF06906 DUF1272: Protein of u 47.1 12 0.00025 26.7 1.3 42 96-137 7-52 (57)
121 PF12773 DZR: Double zinc ribb 46.8 13 0.00029 25.1 1.6 9 97-105 15-23 (50)
122 PRK14890 putative Zn-ribbon RN 46.4 15 0.00033 26.4 1.9 35 151-195 24-59 (59)
123 KOG0827 Predicted E3 ubiquitin 45.6 5.6 0.00012 39.1 -0.6 37 95-133 5-52 (465)
124 TIGR01562 FdhE formate dehydro 44.8 16 0.00035 35.0 2.4 41 95-135 185-233 (305)
125 smart00301 DM Doublesex DNA-bi 44.6 13 0.00027 26.3 1.2 39 162-202 8-46 (54)
126 KOG0828 Predicted E3 ubiquitin 43.8 5.3 0.00012 40.4 -1.1 26 110-137 605-634 (636)
127 PRK14892 putative transcriptio 42.5 27 0.0006 27.8 3.0 38 85-123 12-50 (99)
128 PRK09678 DNA-binding transcrip 42.4 14 0.00029 27.8 1.1 46 128-175 3-48 (72)
129 KOG0826 Predicted E3 ubiquitin 41.4 11 0.00024 36.2 0.7 46 91-136 297-345 (357)
130 smart00064 FYVE Protein presen 41.2 15 0.00032 26.5 1.2 32 93-124 9-43 (68)
131 PF13240 zinc_ribbon_2: zinc-r 40.5 13 0.00028 21.4 0.6 7 128-134 15-21 (23)
132 smart00647 IBR In Between Ring 39.3 23 0.00049 24.8 1.9 33 93-125 17-58 (64)
133 PF05502 Dynactin_p62: Dynacti 39.3 20 0.00043 36.6 2.2 34 128-165 54-95 (483)
134 KOG0298 DEAD box-containing he 38.8 5 0.00011 45.0 -2.3 43 93-137 1152-1199(1394)
135 PF14446 Prok-RING_1: Prokaryo 38.6 14 0.00031 26.1 0.7 37 94-131 5-44 (54)
136 PF01485 IBR: IBR domain; Int 38.3 25 0.00054 24.5 2.0 35 91-125 15-58 (64)
137 COG5220 TFB3 Cdk activating ki 37.7 5.1 0.00011 36.9 -2.1 40 94-135 10-62 (314)
138 PF05883 Baculo_RING: Baculovi 37.2 5.7 0.00012 33.4 -1.7 32 94-125 26-65 (134)
139 KOG2462 C2H2-type Zn-finger pr 37.1 15 0.00032 34.6 0.7 103 92-209 159-269 (279)
140 PF13894 zf-C2H2_4: C2H2-type 36.7 12 0.00027 20.3 0.1 22 184-207 2-24 (24)
141 PF14445 Prok-RING_2: Prokaryo 36.5 3 6.5E-05 29.0 -2.9 43 94-136 7-51 (57)
142 PF00412 LIM: LIM domain; Int 35.5 14 0.0003 25.5 0.2 32 93-124 25-56 (58)
143 PF00751 DM: DM DNA binding do 35.0 4 8.8E-05 28.0 -2.4 31 165-197 11-41 (47)
144 KOG2068 MOT2 transcription fac 35.0 25 0.00054 33.9 2.0 43 95-137 250-298 (327)
145 PRK00420 hypothetical protein; 34.0 24 0.00051 28.8 1.4 25 95-123 24-48 (112)
146 COG1645 Uncharacterized Zn-fin 33.7 22 0.00047 29.8 1.2 24 95-123 29-52 (131)
147 PF03145 Sina: Seven in absent 33.2 18 0.00038 32.1 0.6 47 132-178 24-70 (198)
148 PRK03564 formate dehydrogenase 32.8 34 0.00073 32.9 2.5 41 94-134 187-234 (309)
149 PF10426 zf-RAG1: Recombinatio 32.3 16 0.00035 22.6 0.2 22 183-204 3-24 (30)
150 PRK14714 DNA polymerase II lar 31.3 44 0.00096 37.9 3.3 42 94-137 667-720 (1337)
151 KOG2169 Zn-finger transcriptio 30.5 30 0.00064 36.6 1.8 61 94-157 306-375 (636)
152 cd00065 FYVE FYVE domain; Zinc 30.3 24 0.00053 24.3 0.8 29 96-124 4-35 (57)
153 KOG3576 Ovo and related transc 30.2 14 0.00031 33.3 -0.5 114 90-211 113-240 (267)
154 TIGR00595 priA primosomal prot 29.7 64 0.0014 33.1 4.0 51 83-135 199-262 (505)
155 cd00350 rubredoxin_like Rubred 29.0 47 0.001 20.6 1.9 9 127-135 18-26 (33)
156 KOG0297 TNF receptor-associate 28.5 28 0.00062 34.5 1.2 49 151-204 113-162 (391)
157 KOG0006 E3 ubiquitin-protein l 28.3 28 0.0006 33.5 1.0 31 93-123 220-251 (446)
158 KOG1842 FYVE finger-containing 28.0 14 0.0003 37.0 -1.0 42 84-125 170-214 (505)
159 PF09297 zf-NADH-PPase: NADH p 27.6 17 0.00037 22.4 -0.3 19 115-133 3-28 (32)
160 COG1198 PriA Primosomal protei 27.5 48 0.001 35.7 2.7 51 83-135 421-484 (730)
161 PF06677 Auto_anti-p27: Sjogre 27.1 41 0.00089 22.3 1.4 23 95-121 18-40 (41)
162 TIGR00622 ssl1 transcription f 27.1 46 0.00099 27.2 2.0 38 96-133 57-110 (112)
163 PF13248 zf-ribbon_3: zinc-rib 26.9 28 0.00062 20.4 0.6 6 97-102 5-10 (26)
164 PF06524 NOA36: NOA36 protein; 26.6 45 0.00098 31.2 2.1 99 94-200 51-187 (314)
165 KOG2930 SCF ubiquitin ligase, 25.9 14 0.00031 29.6 -1.1 46 91-136 43-107 (114)
166 COG5242 TFB4 RNA polymerase II 25.6 30 0.00065 31.8 0.7 17 95-111 261-277 (296)
167 KOG1952 Transcription factor N 25.4 43 0.00094 36.3 1.9 41 93-133 190-243 (950)
168 PF14569 zf-UDP: Zinc-binding 25.3 29 0.00063 26.4 0.5 45 93-137 8-62 (80)
169 PHA03096 p28-like protein; Pro 24.9 18 0.00039 34.3 -0.9 38 95-134 179-231 (284)
170 PF02318 FYVE_2: FYVE-type zin 24.7 46 0.001 27.0 1.6 30 95-124 55-88 (118)
171 PF15616 TerY-C: TerY-C metal 24.6 41 0.00089 28.2 1.3 40 94-137 77-116 (131)
172 PF09788 Tmemb_55A: Transmembr 24.4 3.4E+02 0.0074 25.4 7.3 19 150-172 155-173 (256)
173 PF12756 zf-C2H2_2: C2H2 type 24.3 32 0.0007 25.9 0.6 36 173-210 41-78 (100)
174 PLN02436 cellulose synthase A 23.8 41 0.0009 37.5 1.5 44 94-137 36-89 (1094)
175 KOG3268 Predicted E3 ubiquitin 23.5 46 0.00099 29.4 1.4 12 127-138 218-229 (234)
176 PF03854 zf-P11: P-11 zinc fin 22.5 19 0.0004 24.9 -0.9 40 96-137 4-46 (50)
177 TIGR00595 priA primosomal prot 22.4 68 0.0015 32.9 2.7 39 115-167 213-251 (505)
178 PF10272 Tmpp129: Putative tra 21.9 37 0.0008 33.3 0.6 10 128-137 342-351 (358)
179 KOG3799 Rab3 effector RIM1 and 21.7 27 0.00058 29.4 -0.4 34 94-136 65-99 (169)
180 KOG3113 Uncharacterized conser 21.1 43 0.00094 31.2 0.8 42 94-137 111-158 (293)
181 KOG0712 Molecular chaperone (D 21.1 7.8E+02 0.017 24.0 9.5 81 115-209 127-214 (337)
182 PF06750 DiS_P_DiS: Bacterial 20.8 64 0.0014 25.2 1.7 11 127-137 59-69 (92)
183 PRK11595 DNA utilization prote 20.8 49 0.0011 30.0 1.1 35 96-136 7-44 (227)
184 TIGR00373 conserved hypothetic 20.2 70 0.0015 27.5 1.9 15 127-141 129-143 (158)
185 PF01286 XPA_N: XPA protein N- 20.1 70 0.0015 20.4 1.4 31 93-123 2-32 (34)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=100.00 E-value=1.7e-41 Score=317.96 Aligned_cols=227 Identities=37% Similarity=0.735 Sum_probs=194.9
Q ss_pred eecCCCCeeeeccccccccccccccccccEecccccccccCCCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCccc
Q 020290 87 VTLNDPEVLDCPVCYEPLNIPVYQCGNGHVVCHRCCCDLMNKCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEKM 166 (328)
Q Consensus 87 ~~~~~~~~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~ 166 (328)
++..+.++|.||||++.+.+||+||.|||+.|++|..++..+||.|+.+++.+|+++||++++++.|+|+|+.+||++.+
T Consensus 41 ~~~~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~ 120 (299)
T KOG3002|consen 41 VTLLDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSF 120 (299)
T ss_pred ccccchhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHHHHhceecccccccCCceee
Confidence 44557789999999999999999999999999999988889999999999999999999999999999999999999999
Q ss_pred ccchhhhcccccccCCCCCCCC--CCccccccchHhhhhhhccCCCceE-----EEeCcEEEEEEecCC---CEEEEEEe
Q 020290 167 SYSEKYDHGRACHYTPCSCPLA--ACNFVGSFHQIYQHFRGVHKHAAEE-----FVYDKVLRITLSVHH---DLIILQEE 236 (328)
Q Consensus 167 ~~~~~~~He~~C~~~~~~CP~~--gC~~~g~~~~L~~Hl~~~H~~~~~~-----f~y~~~~~l~l~~~~---~~~vl~~~ 236 (328)
+|.+...||+.|.|+++.||.+ .|+|.|..++|..|+...|+..+++ |.|.......+.... ...+..+.
T Consensus 121 ~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (299)
T KOG3002|consen 121 PYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFVATDENLLGAATWTLKTSVCFGR 200 (299)
T ss_pred ccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChhhhhhccccceecccCCccccccchhheeeeecCcE
Confidence 9999999999999999999998 8999999999999999999998763 344332222233221 23345556
Q ss_pred cCCcEEEEecccCCCccEEEEEccCCC--CCCCeeEEEEEeeCCceEEEeeeecccccccCCCCCCcceeEecCCccCC
Q 020290 237 KNGDLFILNNSTEPDGYRISVNCIAPS--CKGGVVYSIVAKSGGAVYEFNSCTKSIQNWDENNPPSVASLLVPSDFFGS 313 (328)
Q Consensus 237 ~d~~lFll~~~~~~~g~~vsV~cIgp~--~a~~f~Y~l~~~~~g~~L~~~s~~~si~~~~~~~~~~~~fL~VP~~l~~~ 313 (328)
..+.+|+++...++.|.+++|++|.|. ++++|+|+|.+.+.+++|+|++.++++.+......|..+||+||.+++..
T Consensus 201 ~~~~~~~~q~~~~~~~~y~tv~~i~~~~~e~~~fsy~L~~~~~~~klt~~s~~~s~~~kvs~~~p~~dfm~ip~~~~~~ 279 (299)
T KOG3002|consen 201 EFGLLFEVQCFREPHGVYVTVNRIAPSAPEAGEFSYSLALGGSGRKLTWQSPPRSIIQKVSKVRPEDDFMLIPRSLLCL 279 (299)
T ss_pred EEeeeeeehhhcCCCceEEEeehhccCCCcccccceeeecCCCCceEeecCCcceeecccceeccCCCceeccHHHhhc
Confidence 677899999999999999999999984 47899999999999999999999988665222367889999999886644
No 2
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=99.96 E-value=8.5e-30 Score=227.98 Aligned_cols=184 Identities=30% Similarity=0.544 Sum_probs=116.1
Q ss_pred CcchhhHHhhhceeeecccCCCCCCcccccchhhhcccccccCCCCCCC--CCCccccccchHhhhhhhccCCCceEEEe
Q 020290 139 SRSTAMEKVIESIQVACENADYGCKEKMSYSEKYDHGRACHYTPCSCPL--AACNFVGSFHQIYQHFRGVHKHAAEEFVY 216 (328)
Q Consensus 139 ~r~~~le~~l~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~--~gC~~~g~~~~L~~Hl~~~H~~~~~~f~y 216 (328)
+||++||++++++++||+|+.+||++.++|.++..||++|+|+|+.||. .+|+|.|+.++|..|+...|.|.+....+
T Consensus 1 iR~~alE~v~~~~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~~~~~~ 80 (198)
T PF03145_consen 1 IRNRALEKVAESIKFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNVTDNGT 80 (198)
T ss_dssp --------------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSEEEESS
T ss_pred CCcHHHHHHHhhceecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCccccCcc
Confidence 4899999999999999999999999999999999999999999999999 79999999999999999999998765332
Q ss_pred Cc-EEEEEEecC---CCEEEEEEecCCcEEEEecc-cCCCcc--EE-EEEccCC-CCCCCeeEEEEEeeCCceEEEeeee
Q 020290 217 DK-VLRITLSVH---HDLIILQEEKNGDLFILNNS-TEPDGY--RI-SVNCIAP-SCKGGVVYSIVAKSGGAVYEFNSCT 287 (328)
Q Consensus 217 ~~-~~~l~l~~~---~~~~vl~~~~d~~lFll~~~-~~~~g~--~v-sV~cIgp-~~a~~f~Y~l~~~~~g~~L~~~s~~ 287 (328)
.. .|....... ..|++++...++.+|+|+.. .+..|. ++ .|++||| .++++|+|+|++.+++++|+||++|
T Consensus 81 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~~~~rkl~~~~~p 160 (198)
T PF03145_consen 81 FSISFLHSDINSVESPDWVLVQFSCFGKLFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVRSNGRKLTWQSFP 160 (198)
T ss_dssp -EEEEEECTTT-SSSEEEEEEE-EETTEEEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEEETTEEEEEEE--
T ss_pred ceEEEeeecccccCCceEEEeecccCCccEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEecCCcEEEEEEcC
Confidence 11 121111111 25666663567899999853 332344 33 4667788 4678999999999999999999999
Q ss_pred cccccccCCCCCCcceeEecC---CccCCCCceEEEEE
Q 020290 288 KSIQNWDENNPPSVASLLVPS---DFFGSYGQLHLGVR 322 (328)
Q Consensus 288 ~si~~~~~~~~~~~~fL~VP~---~l~~~~g~l~l~V~ 322 (328)
+++++.......+.++|++.. .+|.++|.|.++|+
T Consensus 161 ~si~~~~~~~~~~~d~li~~~~~~~~f~~~~~L~~~v~ 198 (198)
T PF03145_consen 161 RSIREDIDDAIESRDCLIINENAAQFFSEDGNLRYRVT 198 (198)
T ss_dssp EETTT-SHHHHHCT-SEEEEHHHHHHHECTTEEEEEEE
T ss_pred cchhhhHHhhccCCcEEEEchHHHHhcCCCCeEEEEeC
Confidence 999873222234456777764 47788899998886
No 3
>cd03829 Sina Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-medi
Probab=99.42 E-value=9.7e-14 Score=112.42 Aligned_cols=97 Identities=18% Similarity=0.243 Sum_probs=78.5
Q ss_pred CCEEEEEEecCCcEEEEeccc-CC-Ccc---EEEEEccCC-CCCCCeeEEEEEeeCCceEEEeeeecccccccCCCCCCc
Q 020290 228 HDLIILQEEKNGDLFILNNST-EP-DGY---RISVNCIAP-SCKGGVVYSIVAKSGGAVYEFNSCTKSIQNWDENNPPSV 301 (328)
Q Consensus 228 ~~~~vl~~~~d~~lFll~~~~-~~-~g~---~vsV~cIgp-~~a~~f~Y~l~~~~~g~~L~~~s~~~si~~~~~~~~~~~ 301 (328)
.+|++++.+.+ +.|+|+..+ +. .+. ++.|+.||+ ++|.+|+|+|++.+++|+|+||++|+||++.......+.
T Consensus 22 ~~w~mv~sCfG-~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~~n~RkL~we~~PRSIrds~~~~~~~~ 100 (127)
T cd03829 22 TDWVMMQSCFG-HHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELNGNRRRLTWEATPRSIREGHASVIDNS 100 (127)
T ss_pred eeeeehhhhcC-ceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEcCCCcEEEeecCCccHHHhhHHHhhcC
Confidence 37888887655 666666544 33 333 367899998 578999999999999999999999999998655557888
Q ss_pred ceeEecC---CccCCCCceEEEEEEec
Q 020290 302 ASLLVPS---DFFGSYGQLHLGVRIQH 325 (328)
Q Consensus 302 ~fL~VP~---~l~~~~g~l~l~V~I~~ 325 (328)
++|++.. .||+++|++.|+|+|+.
T Consensus 101 D~Lii~~~~A~~Fs~~g~l~l~v~It~ 127 (127)
T cd03829 101 DCLVFDTSIAQLFSENGNLGINVTISG 127 (127)
T ss_pred cceEEechHhhhccCCCccEEEEEecC
Confidence 9999984 58889999999999973
No 4
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=99.31 E-value=1.6e-12 Score=127.58 Aligned_cols=116 Identities=26% Similarity=0.581 Sum_probs=101.7
Q ss_pred Ceeeecccccccccccc--ccccccEecccccccc---cCCCCCCCcCCCCC----cchhhHHhhhceeeecccCCCCCC
Q 020290 93 EVLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL---MNKCPSCRLPNGHS----RSTAMEKVIESIQVACENADYGCK 163 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~~----r~~~le~~l~~l~v~C~~~~~GC~ 163 (328)
+++.|++|..++.+|+. +| ||.||..|+..+ ...||.|+..+... ....+.+++.++.+.|.++..||.
T Consensus 20 ~~l~C~~C~~vl~~p~~~~~c--gh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~GC~ 97 (391)
T KOG0297|consen 20 ENLLCPICMSVLRDPVQTTTC--GHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASRGCR 97 (391)
T ss_pred ccccCccccccccCCCCCCCC--CCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCCCcc
Confidence 46999999999999998 89 999999999986 36899998887542 245778999999999999999999
Q ss_pred cccccchhhhcccccccCCCCCCCCCCccccccchHhhhhhhccCCCceE
Q 020290 164 EKMSYSEKYDHGRACHYTPCSCPLAACNFVGSFHQIYQHFRGVHKHAAEE 213 (328)
Q Consensus 164 ~~~~~~~~~~He~~C~~~~~~CP~~gC~~~g~~~~L~~Hl~~~H~~~~~~ 213 (328)
|.+.+..++.|+..| .+++||+ +|+..+.++++..|+...+......
T Consensus 98 ~~~~l~~~~~Hl~~c--~~~~C~~-~C~~~~~~~d~~~hl~~~C~~~~~~ 144 (391)
T KOG0297|consen 98 ADLELEALQGHLSTC--DPLKCPH-RCGVQVPRDDLEDHLEAECPRRSLK 144 (391)
T ss_pred ccccHHHHHhHhccC--CcccCcc-ccccccchHHHHHHHhccccccccc
Confidence 999999999999999 8999996 4999999999999998777665443
No 5
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.54 E-value=2e-08 Score=67.51 Aligned_cols=34 Identities=41% Similarity=1.122 Sum_probs=27.2
Q ss_pred ecccccccccccc-ccccccEeccccccccc-------CCCCCC
Q 020290 97 CPVCYEPLNIPVY-QCGNGHVVCHRCCCDLM-------NKCPSC 132 (328)
Q Consensus 97 CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~~-------~~CP~C 132 (328)
||||+++|++||. .| ||+||..|+.++. ..||.|
T Consensus 1 CpiC~~~~~~Pv~l~C--GH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPC--GHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SS--SSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCC--cCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999998 99 9999999999862 257776
No 6
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.49 E-value=4.9e-08 Score=86.17 Aligned_cols=46 Identities=30% Similarity=0.802 Sum_probs=38.8
Q ss_pred CCCeeeecccccccccccc-ccccccEeccccccccc-------------------CCCCCCCcCCCC
Q 020290 91 DPEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDLM-------------------NKCPSCRLPNGH 138 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~~-------------------~~CP~C~~~~~~ 138 (328)
..+.+.|+||++.+++|+. .| ||+||..|+.+|. ..||.|+..+..
T Consensus 15 ~~~~~~CpICld~~~dPVvT~C--GH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVVTLC--GHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCCccCCccCCCcCCCcEEcCC--CchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 4456899999999999988 89 9999999998751 379999988753
No 7
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.47 E-value=7.3e-08 Score=69.88 Aligned_cols=52 Identities=29% Similarity=0.830 Sum_probs=28.3
Q ss_pred eeeecccccccccccc--ccccccEeccccccc-ccCCCCCCCcCCCC---CcchhhHHh
Q 020290 94 VLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCD-LMNKCPSCRLPNGH---SRSTAMEKV 147 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~-~~~~CP~C~~~~~~---~r~~~le~~ 147 (328)
.|.|++|..+|+.||. .| .|+||+.|+.. +...||+|..+... ..|+.+..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~C--eH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGC--EHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TTS-SSS-S--SS-B---SS--S--B-TTTGGGGTTTB-SSS--B-S-SS----HHHHHH
T ss_pred hcCCcHHHHHhcCCceeccC--ccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhhhhcc
Confidence 5789999999999985 89 99999999987 35679999988632 346666554
No 8
>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=98.44 E-value=1e-07 Score=69.11 Aligned_cols=54 Identities=22% Similarity=0.345 Sum_probs=44.8
Q ss_pred eeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCC---CcchhhHHhhhc
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH---SRSTAMEKVIES 150 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~---~r~~~le~~l~~ 150 (328)
|.||||.+++.+|+. .| ||+||..|+.++ ...||.|++++.. ..+..+++.++.
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~--G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 2 FLCPISLEVMKDPVILPS--GQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred cCCcCCCCcCCCCEECCC--CCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 689999999999988 88 999999999986 3689999998853 456777766653
No 9
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.38 E-value=2.5e-07 Score=83.26 Aligned_cols=45 Identities=31% Similarity=0.842 Sum_probs=39.4
Q ss_pred CCCeeeecccccccccccc-ccccccEecccccccc------cCCCCCCCcCCC
Q 020290 91 DPEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL------MNKCPSCRLPNG 137 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~------~~~CP~C~~~~~ 137 (328)
+-..|.|.||++..++||. .| ||+||..|+.+| ...||+|+..++
T Consensus 44 ~~~~FdCNICLd~akdPVvTlC--GHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLC--GHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccccCCCEEeec--ccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 3446999999999999999 89 999999999998 257999998775
No 10
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=2.5e-07 Score=79.99 Aligned_cols=42 Identities=43% Similarity=1.078 Sum_probs=35.3
Q ss_pred eeeeccccccccc--ccc-ccccccEecccccccc---cCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNI--PVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~--Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
.+.||||++.+.. |+. .| ||+||+.|++.. ..+||+|++.++
T Consensus 131 ~~~CPiCl~~~sek~~vsTkC--GHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVPVSTKC--GHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecchhhcccccccc--chhHHHHHHHHHHHhCCCCCCcccccc
Confidence 5899999999865 453 89 999999999985 479999998665
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.26 E-value=2.5e-07 Score=61.04 Aligned_cols=34 Identities=44% Similarity=1.169 Sum_probs=27.8
Q ss_pred eccccccccccc-c-ccccccEecccccccc---cCCCCCC
Q 020290 97 CPVCYEPLNIPV-Y-QCGNGHVVCHRCCCDL---MNKCPSC 132 (328)
Q Consensus 97 CpiC~~~l~~Pv-~-qC~~GH~~C~~C~~~~---~~~CP~C 132 (328)
|+||++.+.+|+ . .| ||+||..|+.++ ..+||.|
T Consensus 1 C~iC~~~~~~~~~~~~C--GH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPC--GHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTT--SEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCC--CCchhHHHHHHHHHCcCCCcCC
Confidence 899999999994 4 89 999999999986 3678876
No 12
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.26 E-value=3.3e-07 Score=89.75 Aligned_cols=57 Identities=28% Similarity=0.717 Sum_probs=46.5
Q ss_pred Ceeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCC---CcchhhHHhhhce
Q 020290 93 EVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH---SRSTAMEKVIESI 151 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~---~r~~~le~~l~~l 151 (328)
+.+.|+||.+++..|+. .| ||.||..|+..+ ...||.|+..+.. .+|..|+++++.+
T Consensus 25 ~~l~C~IC~d~~~~PvitpC--gH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVLTSC--SHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred cccCCCcCchhhhCccCCCC--CCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence 46899999999999988 89 999999999875 2579999998753 4577777666644
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.18 E-value=4.4e-07 Score=63.18 Aligned_cols=42 Identities=40% Similarity=0.980 Sum_probs=35.5
Q ss_pred eeeecccccccccccc-ccccccE-ecccccccc---cCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHV-VCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~-~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
...|+||++...++++ .| ||. ||..|+.++ ...||.||+++.
T Consensus 2 ~~~C~iC~~~~~~~~~~pC--gH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPC--GHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEETT--CEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeCC--CChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4579999999999887 99 999 999999997 379999998875
No 14
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.14 E-value=1.8e-07 Score=88.08 Aligned_cols=58 Identities=26% Similarity=0.808 Sum_probs=46.5
Q ss_pred CCeeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCC---CcchhhHHhhhce
Q 020290 92 PEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH---SRSTAMEKVIESI 151 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~---~r~~~le~~l~~l 151 (328)
-+.|.|.||+++|+.|+. .| ||.||+-||.+. ...||.|..++.. ..|+.++.++.++
T Consensus 21 D~lLRC~IC~eyf~ip~itpC--sHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMITPC--SHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHHhHHHHHhcCceeccc--cchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 357899999999999988 99 999999999985 4789999988763 3355666666554
No 15
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.04 E-value=1.4e-06 Score=65.64 Aligned_cols=58 Identities=24% Similarity=0.362 Sum_probs=43.6
Q ss_pred CCeeeecccccccccccc-ccccccEeccccccccc----CCCCCCCcCCCC---CcchhhHHhhhce
Q 020290 92 PEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDLM----NKCPSCRLPNGH---SRSTAMEKVIESI 151 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~~----~~CP~C~~~~~~---~r~~~le~~l~~l 151 (328)
|+.|.|||+..+|.+||. .+ ||+|+..|+.++. ..||.|++++.. .+|..|++.+..+
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~--G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~ 67 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPS--GHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETT--SEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcccCCcCcCcHhhCceeCCc--CCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 578999999999999998 78 9999999999872 579999988863 5778888777654
No 16
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.96 E-value=2.1e-06 Score=61.76 Aligned_cols=52 Identities=27% Similarity=0.454 Sum_probs=38.6
Q ss_pred hceeeecccCCCCCCcccccchhhhccc-ccccCCCCCCC--CCCccccccchHhhh
Q 020290 149 ESIQVACENADYGCKEKMSYSEKYDHGR-ACHYTPCSCPL--AACNFVGSFHQIYQH 202 (328)
Q Consensus 149 ~~l~v~C~~~~~GC~~~~~~~~~~~He~-~C~~~~~~CP~--~gC~~~g~~~~L~~H 202 (328)
....|.|+| .+|...+...++.+|++ .|+++++.||+ .||++.+.+.+|..|
T Consensus 6 ~~~~v~C~~--~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 6 PFRPVPCPN--GCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp TTSEEE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCCEeeCCC--CCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 345799997 46678899999999998 99999999998 699999999999988
No 17
>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=97.92 E-value=3.3e-06 Score=55.98 Aligned_cols=34 Identities=47% Similarity=1.229 Sum_probs=29.5
Q ss_pred eccccccccccc-c-ccccccEecccccccc-----cCCCCCC
Q 020290 97 CPVCYEPLNIPV-Y-QCGNGHVVCHRCCCDL-----MNKCPSC 132 (328)
Q Consensus 97 CpiC~~~l~~Pv-~-qC~~GH~~C~~C~~~~-----~~~CP~C 132 (328)
|+||++++..|+ . .| ||.||..|+.++ ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~C--~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPC--GHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTT--SEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecC--CCcchHHHHHHHHHhcCCccCCcC
Confidence 899999999998 4 99 999999999986 2468876
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.89 E-value=2.6e-06 Score=57.74 Aligned_cols=37 Identities=41% Similarity=1.098 Sum_probs=30.6
Q ss_pred eeccccccc---ccccc-ccccccEeccccccccc---CCCCCCCc
Q 020290 96 DCPVCYEPL---NIPVY-QCGNGHVVCHRCCCDLM---NKCPSCRL 134 (328)
Q Consensus 96 ~CpiC~~~l---~~Pv~-qC~~GH~~C~~C~~~~~---~~CP~C~~ 134 (328)
.|++|++.+ ..|++ .| ||+||..|+.++. ..||.|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~C--gH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSC--GHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEccc--CCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999999 23444 99 9999999999874 68999974
No 19
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.83 E-value=5.3e-06 Score=76.14 Aligned_cols=44 Identities=32% Similarity=0.735 Sum_probs=35.5
Q ss_pred Ceeeecccccccccc--------cc-ccccccEecccccccc---cCCCCCCCcCCCC
Q 020290 93 EVLDCPVCYEPLNIP--------VY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH 138 (328)
Q Consensus 93 ~~l~CpiC~~~l~~P--------v~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~ 138 (328)
+...|+||++.+..+ +. .| ||.||..|+.+| ...||.||.++..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C--~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNC--NHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCC--CCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 357899999987643 33 68 999999999987 3689999998753
No 20
>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=97.79 E-value=5e-06 Score=56.15 Aligned_cols=36 Identities=42% Similarity=1.040 Sum_probs=28.7
Q ss_pred eeccccccccc--ccc--ccccccEecccccccc---cCCCCCCC
Q 020290 96 DCPVCYEPLNI--PVY--QCGNGHVVCHRCCCDL---MNKCPSCR 133 (328)
Q Consensus 96 ~CpiC~~~l~~--Pv~--qC~~GH~~C~~C~~~~---~~~CP~C~ 133 (328)
.|+||++.+.+ .++ .| ||.||..|+.+| ..+||.||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C--~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPC--GHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETT--SEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccC--CCeeCHHHHHHHHHhCCcCCccC
Confidence 59999999953 333 67 999999999987 47899995
No 21
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=1.5e-05 Score=74.01 Aligned_cols=44 Identities=30% Similarity=0.751 Sum_probs=38.2
Q ss_pred Ceeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCC
Q 020290 93 EVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH 138 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~ 138 (328)
....|.+|++...+|-- .| ||+||.+|+..| ...||.||..+..
T Consensus 238 a~~kC~LCLe~~~~pSaTpC--GHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 238 ATRKCSLCLENRSNPSATPC--GHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCceEEEecCCCCCCcCcC--cchHHHHHHHHHHccccCCCcccccCCC
Confidence 35799999999999976 89 999999999987 4679999988753
No 22
>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=97.62 E-value=1.6e-05 Score=52.64 Aligned_cols=38 Identities=47% Similarity=1.203 Sum_probs=31.1
Q ss_pred eecccccccccccc--ccccccEecccccccc----cCCCCCCCcC
Q 020290 96 DCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL----MNKCPSCRLP 135 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~----~~~CP~C~~~ 135 (328)
.|+||.+.+..++. .| ||.||..|+..+ ...||.|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C--~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPC--GHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCC--CChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 49999999976655 48 999999999875 2579999865
No 23
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.55 E-value=1.7e-05 Score=53.49 Aligned_cols=26 Identities=46% Similarity=1.240 Sum_probs=18.1
Q ss_pred eccccccccc----ccc-ccccccEecccccccc
Q 020290 97 CPVCYEPLNI----PVY-QCGNGHVVCHRCCCDL 125 (328)
Q Consensus 97 CpiC~~~l~~----Pv~-qC~~GH~~C~~C~~~~ 125 (328)
||||.+ +.. |+. .| ||+||..|+.++
T Consensus 1 CpIc~e-~~~~~n~P~~L~C--GH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPC--GHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE-SS--S-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeC--ccHHHHHHHHHH
Confidence 899999 766 876 99 999999999987
No 24
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.49 E-value=1.8e-05 Score=73.42 Aligned_cols=108 Identities=22% Similarity=0.488 Sum_probs=69.5
Q ss_pred eeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCC----------------CcchhhHHhhhceee
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGH----------------SRSTAMEKVIESIQV 153 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~----------------~r~~~le~~l~~l~v 153 (328)
.+.|-||...++.|+. .| ||.||+-||.+. +..||.|+.+... .+++. .+..-|++
T Consensus 25 ~lrC~IC~~~i~ip~~TtC--gHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~~~ei~es~~~~r~--~l~~~L~~ 100 (391)
T COG5432 25 MLRCRICDCRISIPCETTC--GHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSGSREINESHARNRD--LLRKVLES 100 (391)
T ss_pred HHHhhhhhheeecceeccc--ccchhHHHHHHHhcCCCCCccccccHHhhhcccchhHHHHHHhhhhccH--HHHHHHhc
Confidence 5889999999999988 99 999999999985 4789999987532 12221 12233455
Q ss_pred eccc-----CCCCCCcccccchhhh--------------------------cccccccCCCCCCCCCCccccccchHhhh
Q 020290 154 ACEN-----ADYGCKEKMSYSEKYD--------------------------HGRACHYTPCSCPLAACNFVGSFHQIYQH 202 (328)
Q Consensus 154 ~C~~-----~~~GC~~~~~~~~~~~--------------------------He~~C~~~~~~CP~~gC~~~g~~~~L~~H 202 (328)
.|+- ...-|.|......-.+ -.+.=.-..+.||. |....+.++|..|
T Consensus 101 ~~~~p~p~~ee~p~~~E~v~~~dS~S~~~~~eD~~~~~sS~~~iAKkt~~D~~KrK~E~l~~CP~--C~~~~P~~~i~~H 178 (391)
T COG5432 101 LCRLPRPIKEERPCRWETVIAQDSASGDEEWEDDLASNSSPASIAKKTSRDSKKRKREDLVHCPA--CSNLVPHNQINQH 178 (391)
T ss_pred ccCCCCchhhcCCCchhheeccccccccchhhhhhhhccChHHHHhhhhhHHHHhHHHhhhcCch--hhccCchHHHHHH
Confidence 6632 2334666433221100 00000012478986 9988899999999
Q ss_pred hhhcc
Q 020290 203 FRGVH 207 (328)
Q Consensus 203 l~~~H 207 (328)
|..+-
T Consensus 179 LD~CL 183 (391)
T COG5432 179 LDSCL 183 (391)
T ss_pred HHHHh
Confidence 97763
No 25
>PHA02926 zinc finger-like protein; Provisional
Probab=97.45 E-value=2.5e-05 Score=70.13 Aligned_cols=43 Identities=28% Similarity=0.746 Sum_probs=34.2
Q ss_pred eeeeccccccccc---------ccc-ccccccEeccccccccc---------CCCCCCCcCCCC
Q 020290 94 VLDCPVCYEPLNI---------PVY-QCGNGHVVCHRCCCDLM---------NKCPSCRLPNGH 138 (328)
Q Consensus 94 ~l~CpiC~~~l~~---------Pv~-qC~~GH~~C~~C~~~~~---------~~CP~C~~~~~~ 138 (328)
...|+||++.... ++. .| +|.||..|+.+|. ..||.||..+..
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~C--nHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSC--NHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCccCccccccccccccccccccCCC--CchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 5789999998632 344 78 9999999999984 239999998764
No 26
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.33 E-value=9.8e-05 Score=69.93 Aligned_cols=43 Identities=33% Similarity=0.767 Sum_probs=32.8
Q ss_pred Ceeeeccccc--cccccc--c--ccccccEecccccccc----cCCCCCCCcCCC
Q 020290 93 EVLDCPVCYE--PLNIPV--Y--QCGNGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~--~l~~Pv--~--qC~~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
+...||+|.. ++.+-. + .| ||.||.+|+..+ ...||.|+.++.
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~C--GH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVC--GHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCC--CCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 3468999999 454431 2 58 999999999985 258999998764
No 27
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=5.7e-05 Score=75.13 Aligned_cols=43 Identities=37% Similarity=0.970 Sum_probs=36.3
Q ss_pred eeeecccccccccccc-ccccccEecccccccc--------cCCCCCCCcCCCC
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL--------MNKCPSCRLPNGH 138 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~--------~~~CP~C~~~~~~ 138 (328)
.+.||||++...-|+. .| ||+||..|+-.. ...||.|+..+..
T Consensus 186 ~~~CPICL~~~~~p~~t~C--GHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNC--GHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCccccccc--CceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 5789999999887776 89 999999999873 2589999988764
No 28
>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=97.27 E-value=6.3e-05 Score=47.89 Aligned_cols=34 Identities=47% Similarity=1.195 Sum_probs=28.5
Q ss_pred ecccccccccccc-ccccccEecccccccc----cCCCCCC
Q 020290 97 CPVCYEPLNIPVY-QCGNGHVVCHRCCCDL----MNKCPSC 132 (328)
Q Consensus 97 CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~----~~~CP~C 132 (328)
|+||++....++. .| ||.||..|+..+ ...||.|
T Consensus 1 C~iC~~~~~~~~~~~C--~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPC--GHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecC--CChHHHHHHHHHHHhCcCCCCCC
Confidence 7899999887776 89 999999999875 2568876
No 29
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=1.9e-05 Score=75.14 Aligned_cols=44 Identities=30% Similarity=0.711 Sum_probs=37.8
Q ss_pred eeeecccccccccccc--ccccccEecccccccc----cCCCCCCCcCCCCC
Q 020290 94 VLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL----MNKCPSCRLPNGHS 139 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~----~~~CP~C~~~~~~~ 139 (328)
.+.||||+.+|+.-+. .| +|.||..||.+. .+.||+||+.+...
T Consensus 43 ~v~c~icl~llk~tmttkeC--lhrfc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 43 QVICPICLSLLKKTMTTKEC--LHRFCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred hhccHHHHHHHHhhcccHHH--HHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 5899999999987665 79 999999999874 47999999987654
No 30
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=6.1e-05 Score=69.27 Aligned_cols=62 Identities=31% Similarity=0.730 Sum_probs=46.2
Q ss_pred CCeeeecccccccccccc-ccccccEeccccccccc---CCCCCCCcCC-CCCcchhhHHhhhceeeec
Q 020290 92 PEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDLM---NKCPSCRLPN-GHSRSTAMEKVIESIQVAC 155 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~~---~~CP~C~~~~-~~~r~~~le~~l~~l~v~C 155 (328)
.+.+.||||++.|..|.. .| ||.||..|+..+. ..||.|+... ...+|..+.+++..+....
T Consensus 11 ~~~~~C~iC~~~~~~p~~l~C--~H~~c~~C~~~~~~~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~ 77 (386)
T KOG2177|consen 11 QEELTCPICLEYFREPVLLPC--GHNFCRACLTRSWEGPLSCPVCRPPSRNLRPNVLLANLVERLRQLR 77 (386)
T ss_pred cccccChhhHHHhhcCccccc--cchHhHHHHHHhcCCCcCCcccCCchhccCccHHHHHHHHHHHhcC
Confidence 357899999999999965 79 9999999999864 6899999411 1235666666666554433
No 31
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.11 E-value=0.00011 Score=76.28 Aligned_cols=44 Identities=39% Similarity=0.887 Sum_probs=38.2
Q ss_pred Ceeeecccccccccccc-ccccccEecccccccc----cCCCCCCCcCCCC
Q 020290 93 EVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL----MNKCPSCRLPNGH 138 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~----~~~CP~C~~~~~~ 138 (328)
..|.||+|..=.++-|. .| ||.||..|+.+. ..+||.|..+|+.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~kC--~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITKC--GHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred hceeCCCccCchhhHHHHhc--chHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 36899999988888777 99 999999999874 4799999999874
No 32
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.00 E-value=0.00024 Score=50.90 Aligned_cols=43 Identities=21% Similarity=0.489 Sum_probs=33.9
Q ss_pred cccccccCCCCCCCCCCccccccchHhhhhhhccCCCceEEEe
Q 020290 174 HGRACHYTPCSCPLAACNFVGSFHQIYQHFRGVHKHAAEEFVY 216 (328)
Q Consensus 174 He~~C~~~~~~CP~~gC~~~g~~~~L~~Hl~~~H~~~~~~f~y 216 (328)
|++.|+++++.||+.+|.....+.+|..|+...+....+...|
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 7888999999999877777789999999999888888777666
No 33
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00016 Score=66.49 Aligned_cols=44 Identities=30% Similarity=0.671 Sum_probs=37.1
Q ss_pred CCeeeecccccccccccc-ccccccEeccccccc-cc----CCCCCCCcCCC
Q 020290 92 PEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCD-LM----NKCPSCRLPNG 137 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~-~~----~~CP~C~~~~~ 137 (328)
...+.|+||.++...|.. .| ||+||-.|+-. |. ..||.||+...
T Consensus 213 ~~d~kC~lC~e~~~~ps~t~C--gHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCTPC--GHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCcccccc--cchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 346899999999999988 89 99999999987 51 46999987643
No 34
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.68 E-value=0.0012 Score=67.69 Aligned_cols=106 Identities=20% Similarity=0.416 Sum_probs=67.3
Q ss_pred CCCeeeecccccccccccc-----ccccccEeccc--ccccc-------cCCCCCCCcCCCCCcchhhHHhh--hceeee
Q 020290 91 DPEVLDCPVCYEPLNIPVY-----QCGNGHVVCHR--CCCDL-------MNKCPSCRLPNGHSRSTAMEKVI--ESIQVA 154 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~-----qC~~GH~~C~~--C~~~~-------~~~CP~C~~~~~~~r~~~le~~l--~~l~v~ 154 (328)
+.+...|+-|......--+ .|..--+.|.. |-..+ ...|+.|...+.. ..+++-. -...+.
T Consensus 404 ~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~---s~LekH~~~~Hkpv~ 480 (567)
T PLN03086 404 DVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQ---GEMEKHMKVFHEPLQ 480 (567)
T ss_pred CCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccch---HHHHHHHHhcCCCcc
Confidence 4556789999987643222 46544455652 55443 1479999877642 1122111 135567
Q ss_pred cccCCCCCCcccccchhhhccc-ccccCCCCCCCCCCccccc-----------cchHhhhhhhc
Q 020290 155 CENADYGCKEKMSYSEKYDHGR-ACHYTPCSCPLAACNFVGS-----------FHQIYQHFRGV 206 (328)
Q Consensus 155 C~~~~~GC~~~~~~~~~~~He~-~C~~~~~~CP~~gC~~~g~-----------~~~L~~Hl~~~ 206 (328)
|+ |...+...++..|.. .|+.+++.|++ |+.... ...|..|...+
T Consensus 481 Cp-----Cg~~~~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 481 CP-----CGVVLEKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred CC-----CCCCcchhHHHhhhhccCCCCceeCCC--CCCccccCccccchhhhhhhHHHHHHhc
Confidence 76 777777788888865 79999999976 887664 23688887774
No 35
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.50 E-value=0.0063 Score=62.42 Aligned_cols=37 Identities=19% Similarity=0.372 Sum_probs=18.1
Q ss_pred hhhhcccccccCCCCCCCCCCccccccchHhhhhhhccC
Q 020290 170 EKYDHGRACHYTPCSCPLAACNFVGSFHQIYQHFRGVHK 208 (328)
Q Consensus 170 ~~~~He~~C~~~~~~CP~~gC~~~g~~~~L~~Hl~~~H~ 208 (328)
.+..|+..|.-+++.|. .|+.....++|..|+...|.
T Consensus 529 ~Lt~HE~~CG~rt~~C~--~Cgk~Vrlrdm~~H~~~~h~ 565 (567)
T PLN03086 529 GMSEHESICGSRTAPCD--SCGRSVMLKEMDIHQIAVHQ 565 (567)
T ss_pred hHHHHHHhcCCcceEcc--ccCCeeeehhHHHHHHHhhc
Confidence 44455555555555552 35444444555555554443
No 36
>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=96.40 E-value=0.0019 Score=55.32 Aligned_cols=28 Identities=29% Similarity=0.697 Sum_probs=24.6
Q ss_pred CCCCCCCCCccccccchHhhhhhhccCC
Q 020290 182 PCSCPLAACNFVGSFHQIYQHFRGVHKH 209 (328)
Q Consensus 182 ~~~CP~~gC~~~g~~~~L~~Hl~~~H~~ 209 (328)
+-.|+..+|.|.|.+.+|..|.+..|..
T Consensus 107 ~RsC~~e~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 107 KRSCSQESCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred CccCcccccccccCHHHHHHHHHhhCCC
Confidence 4467778999999999999999999985
No 37
>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=96.25 E-value=0.0024 Score=48.00 Aligned_cols=36 Identities=42% Similarity=1.087 Sum_probs=28.1
Q ss_pred eeccccccccccc------------c--ccccccEecccccccc---cCCCCCCC
Q 020290 96 DCPVCYEPLNIPV------------Y--QCGNGHVVCHRCCCDL---MNKCPSCR 133 (328)
Q Consensus 96 ~CpiC~~~l~~Pv------------~--qC~~GH~~C~~C~~~~---~~~CP~C~ 133 (328)
.|.||++.|.+|. . .| ||.|-..|+.+| ...||.||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C--~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPC--GHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETT--SEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEeccc--CCCEEHHHHHHHHhcCCcCCCCC
Confidence 4999999994332 2 47 999999999986 46899996
No 38
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.14 E-value=0.0013 Score=58.18 Aligned_cols=54 Identities=22% Similarity=0.583 Sum_probs=40.7
Q ss_pred eeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCC--CCcchhhHHhhhc
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNG--HSRSTAMEKVIES 150 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~--~~r~~~le~~l~~ 150 (328)
|.|-||..-+..||. .| ||.||+.|..+- ...|-.|.+.+. ......+.+++..
T Consensus 197 F~C~iCKkdy~spvvt~C--GH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL~~ 256 (259)
T COG5152 197 FLCGICKKDYESPVVTEC--GHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKMLNK 256 (259)
T ss_pred eeehhchhhccchhhhhc--chhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHHhh
Confidence 889999999999998 99 999999998763 368999987653 1223345555543
No 39
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.01 E-value=0.0041 Score=58.21 Aligned_cols=43 Identities=30% Similarity=0.696 Sum_probs=37.0
Q ss_pred eeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCCCC
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNGHS 139 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~~~ 139 (328)
+.|-||...+..||. .| ||.||..|..+- ...|++|.+.+...
T Consensus 242 f~c~icr~~f~~pVvt~c--~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKC--GHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred ccccccccccccchhhcC--CceeehhhhccccccCCcceecccccccc
Confidence 679999999999998 99 999999998763 36899999887543
No 40
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.80 E-value=0.0049 Score=57.12 Aligned_cols=42 Identities=38% Similarity=0.846 Sum_probs=34.9
Q ss_pred eeeecccccccccccc--ccccccEecccccccc-----cCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL-----MNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~-----~~~CP~C~~~~~ 137 (328)
...||+|.+....|.. .| ||++|-.|+.+- .-.||.|..+..
T Consensus 239 ~~~C~~Cg~~PtiP~~~~~C--~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 239 DTECPVCGEPPTIPHVIGKC--GHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CceeeccCCCCCCCeeeccc--cceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4689999999999976 48 999999999873 248999987653
No 41
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.54 E-value=0.0032 Score=45.08 Aligned_cols=30 Identities=30% Similarity=0.722 Sum_probs=22.4
Q ss_pred eeeecccccccccccc--ccccccEecccccccc
Q 020290 94 VLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL 125 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~ 125 (328)
.+.|||...+|.+||. .| ||+|.+..+..+
T Consensus 11 ~~~CPiT~~~~~~PV~s~~C--~H~fek~aI~~~ 42 (57)
T PF11789_consen 11 SLKCPITLQPFEDPVKSKKC--GHTFEKEAILQY 42 (57)
T ss_dssp -SB-TTTSSB-SSEEEESSS----EEEHHHHHHH
T ss_pred ccCCCCcCChhhCCcCcCCC--CCeecHHHHHHH
Confidence 4799999999999987 79 999999888775
No 42
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.19 E-value=0.0061 Score=42.00 Aligned_cols=40 Identities=40% Similarity=1.041 Sum_probs=20.3
Q ss_pred eccccccccc--c-ccccccccEecccccccc----cCCCCCCCcCC
Q 020290 97 CPVCYEPLNI--P-VYQCGNGHVVCHRCCCDL----MNKCPSCRLPN 136 (328)
Q Consensus 97 CpiC~~~l~~--P-v~qC~~GH~~C~~C~~~~----~~~CP~C~~~~ 136 (328)
||+|.+.+.. - ++.|++|+.+|..|+.++ ...||.||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899998832 2 337888999999998875 36899999864
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.13 E-value=0.0022 Score=45.07 Aligned_cols=41 Identities=39% Similarity=0.899 Sum_probs=32.7
Q ss_pred eeecccccccccccc-ccccccE-ecccccccc----cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHV-VCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~-~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
-+|-||.+-..+.|. .| ||. .|..|-.++ ...||.||.++.
T Consensus 8 dECTICye~pvdsVlYtC--GHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTC--GHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHHHHc--chHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 379999998877765 99 995 788887664 368999998753
No 44
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.11 E-value=0.005 Score=60.71 Aligned_cols=44 Identities=34% Similarity=0.709 Sum_probs=38.5
Q ss_pred CCeeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCC
Q 020290 92 PEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
.+.|.|.||...|.+||. .| ||.||..|+.+. ...||.|+..+.
T Consensus 82 ~sef~c~vc~~~l~~pv~tpc--ghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTPC--GHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCCccccc--cccccHHHHHHHhccCCCCcccccccc
Confidence 567999999999999998 88 999999997774 368999998875
No 45
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.11 E-value=0.0049 Score=58.55 Aligned_cols=43 Identities=23% Similarity=0.587 Sum_probs=36.7
Q ss_pred Ceeeecccccccccccc--ccccccEecccccccc---cCCCCCCCcCCC
Q 020290 93 EVLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
....|.+|..+|.++.. .| =|.||++|+.+. ...||.|...+.
T Consensus 14 ~~itC~LC~GYliDATTI~eC--LHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITEC--LHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred cceehhhccceeecchhHHHH--HHHHHHHHHHHHHHHhccCCccceecc
Confidence 35789999999999854 89 999999999884 479999988764
No 46
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=94.78 E-value=0.0097 Score=49.49 Aligned_cols=51 Identities=25% Similarity=0.693 Sum_probs=41.6
Q ss_pred CeeeecCCCCeeeecccccccccccc-----ccccccEeccccccccc------CCCCCCCcCCC
Q 020290 84 PVTVTLNDPEVLDCPVCYEPLNIPVY-----QCGNGHVVCHRCCCDLM------NKCPSCRLPNG 137 (328)
Q Consensus 84 ~~~~~~~~~~~l~CpiC~~~l~~Pv~-----qC~~GH~~C~~C~~~~~------~~CP~C~~~~~ 137 (328)
-+++|+++ ..++|.||.+...+..| -| |-.+|..|...+. +.||.|+..+.
T Consensus 71 vmnvF~d~-~lYeCnIC~etS~ee~FLKPneCC--gY~iCn~Cya~LWK~~~~ypvCPvCkTSFK 132 (140)
T PF05290_consen 71 VMNVFLDP-KLYECNICKETSAEERFLKPNECC--GYSICNACYANLWKFCNLYPVCPVCKTSFK 132 (140)
T ss_pred HheeecCC-CceeccCcccccchhhcCCccccc--chHHHHHHHHHHHHHcccCCCCCccccccc
Confidence 45788855 88999999999877665 36 9999999998852 68999988775
No 47
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.63 E-value=0.0076 Score=57.40 Aligned_cols=46 Identities=35% Similarity=0.941 Sum_probs=36.0
Q ss_pred CCCeeeeccccccccc--ccc-ccccccEecccccccc----cCCCCCCCcCCC
Q 020290 91 DPEVLDCPVCYEPLNI--PVY-QCGNGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~--Pv~-qC~~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
|.+++ ||.|.+++.+ --| .|++|..+|.-|+..+ ...||.||....
T Consensus 12 deed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 12 DEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred ccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 44455 9999999853 344 7888999999999875 579999998653
No 48
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.60 E-value=0.014 Score=54.94 Aligned_cols=41 Identities=34% Similarity=0.780 Sum_probs=35.6
Q ss_pred eeecccccccccccc-ccccccEecccccccc----cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
-+|+||+.-..-|+. .| +|.||.-|++.. ...|++||.++.
T Consensus 8 ~eC~IC~nt~n~Pv~l~C--~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 8 KECLICYNTGNCPVNLYC--FHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred CcceeeeccCCcCccccc--cchhhhhhhcchhhcCCCCCceecCCCC
Confidence 479999999988876 89 999999999874 356999999985
No 49
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.95 E-value=0.014 Score=60.23 Aligned_cols=41 Identities=32% Similarity=0.732 Sum_probs=34.7
Q ss_pred eeeeccccccccc-----c-ccccccccEecccccccc---cCCCCCCCcCC
Q 020290 94 VLDCPVCYEPLNI-----P-VYQCGNGHVVCHRCCCDL---MNKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~l~~-----P-v~qC~~GH~~C~~C~~~~---~~~CP~C~~~~ 136 (328)
.-.|+||.+.|.. | ...| ||+|+..|+.+| ...||.||..+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C--~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPC--GHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred CCeeeeechhhccccccccceeec--ccchHHHHHHHHHHHhCcCCcchhhh
Confidence 4689999999976 3 4499 999999999998 47999999843
No 50
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.82 E-value=0.016 Score=54.27 Aligned_cols=38 Identities=39% Similarity=0.925 Sum_probs=33.3
Q ss_pred eeecccccccccccc--ccccccEecccccccc----cCCCCCCCc
Q 020290 95 LDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL----MNKCPSCRL 134 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~----~~~CP~C~~ 134 (328)
|.||.|..+|+.|+. .| ||.||..|+... -..||.|..
T Consensus 275 LkCplc~~Llrnp~kT~cC--~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCC--GHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcccCccc--cchHHHHHHhhhhhhccccCCCccc
Confidence 899999999999987 46 999999999963 268999976
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.80 E-value=0.018 Score=44.49 Aligned_cols=40 Identities=33% Similarity=0.734 Sum_probs=29.1
Q ss_pred eeccccccccc-ccc--ccccccEecccccccc------cCCCCCCCcCCC
Q 020290 96 DCPVCYEPLNI-PVY--QCGNGHVVCHRCCCDL------MNKCPSCRLPNG 137 (328)
Q Consensus 96 ~CpiC~~~l~~-Pv~--qC~~GH~~C~~C~~~~------~~~CP~C~~~~~ 137 (328)
.||.|..+-.+ |+. +| +|.|=..|+.++ +..||.||++..
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C--~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKC--SHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCccCCCCCCceeeccC--ccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 35566655433 544 67 999999999986 368999998754
No 52
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.58 E-value=0.035 Score=50.73 Aligned_cols=43 Identities=26% Similarity=0.712 Sum_probs=33.2
Q ss_pred Ceeeeccccccc-ccccc--ccccccEecccccccccC-CCCCCCcCCC
Q 020290 93 EVLDCPVCYEPL-NIPVY--QCGNGHVVCHRCCCDLMN-KCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~~l-~~Pv~--qC~~GH~~C~~C~~~~~~-~CP~C~~~~~ 137 (328)
+-..|..|+.-- .+|.| .| +|+||..|...... .||.|++++.
T Consensus 2 ~~VhCn~C~~~~~~~~f~LTaC--~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 2 DFVHCNKCFRFPSQDPFFLTAC--RHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred ceEEeccccccCCCCceeeeec--hhhhhhhhcccCCccccccccceee
Confidence 346899888754 35555 89 99999999887544 8999999864
No 53
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.51 E-value=0.017 Score=54.00 Aligned_cols=40 Identities=35% Similarity=0.865 Sum_probs=34.3
Q ss_pred eeeecccccccccccc-cccccc-EecccccccccCCCCCCCcCC
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGH-VVCHRCCCDLMNKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH-~~C~~C~~~~~~~CP~C~~~~ 136 (328)
...|.||.+...+=++ .| || +.|..|-.++ +.||+||+-+
T Consensus 300 ~~LC~ICmDaP~DCvfLeC--GHmVtCt~CGkrm-~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLEC--GHMVTCTKCGKRM-NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEeec--CcEEeehhhcccc-ccCchHHHHH
Confidence 4569999999999888 99 99 5799998887 5999998754
No 54
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.36 E-value=0.071 Score=37.69 Aligned_cols=41 Identities=32% Similarity=0.655 Sum_probs=31.0
Q ss_pred eeecccccccc-ccccccccccEeccccccccc-CCCCCCCcCCC
Q 020290 95 LDCPVCYEPLN-IPVYQCGNGHVVCHRCCCDLM-NKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~-~Pv~qC~~GH~~C~~C~~~~~-~~CP~C~~~~~ 137 (328)
..|-.|...-. .++.+| ||++|..|+.-.. +-||.|..++.
T Consensus 8 ~~~~~~~~~~~~~~~~pC--gH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 8 QPCVFCGFVGTKGTVLPC--GHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred eeEEEccccccccccccc--cceeeccccChhhccCCCCCCCccc
Confidence 45667777744 445599 9999999998643 67999998875
No 55
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=92.96 E-value=0.025 Score=56.90 Aligned_cols=46 Identities=22% Similarity=0.639 Sum_probs=38.8
Q ss_pred CCCCeeeecccccccccccc-ccccccEecccccccc--------cCCCCCCCcCCC
Q 020290 90 NDPEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL--------MNKCPSCRLPNG 137 (328)
Q Consensus 90 ~~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~--------~~~CP~C~~~~~ 137 (328)
++.....|.+|.++..+++. .| .|.||.-|+... ...||.|...+.
T Consensus 532 enk~~~~C~lc~d~aed~i~s~C--hH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYIESSC--HHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred cccCceeecccCChhhhhHhhhh--hHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 44557899999999999988 99 999999999763 358999988764
No 56
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.29 E-value=0.041 Score=52.97 Aligned_cols=42 Identities=33% Similarity=0.800 Sum_probs=35.7
Q ss_pred eeeecccccccccccc-ccccccE-eccccccccc---CCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHV-VCHRCCCDLM---NKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~-~C~~C~~~~~---~~CP~C~~~~~ 137 (328)
--+|-||+.-.++-+. .| -|. .|+.|.+.+. +.||+||+++.
T Consensus 290 gkeCVIClse~rdt~vLPC--RHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 290 GKECVICLSESRDTVVLPC--RHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCeeEEEecCCcceEEecc--hhhehhHhHHHHHHHhhcCCCccccchH
Confidence 4689999999998765 99 995 8999998863 78999999875
No 57
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.84 E-value=0.025 Score=54.27 Aligned_cols=48 Identities=29% Similarity=0.614 Sum_probs=36.5
Q ss_pred ecCCCCeeeecccccccccccc-ccccccEecccccccc---cCCCCCCCcCCC
Q 020290 88 TLNDPEVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 88 ~~~~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
.+.+.+.-.||||+.--...|+ .| +|.-|..||.+. .+.|-.|+..+.
T Consensus 416 ~lp~sEd~lCpICyA~pi~Avf~PC--~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 416 DLPDSEDNLCPICYAGPINAVFAPC--SHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred CCCCcccccCcceecccchhhccCC--CCchHHHHHHHHHhcCCeeeEecceee
Confidence 3344556789999987666777 89 999999999985 367888876543
No 58
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.44 E-value=0.029 Score=57.52 Aligned_cols=36 Identities=39% Similarity=0.877 Sum_probs=29.9
Q ss_pred Ceeeeccccccc----ccccc-ccccccEecccccccc-cCCCC
Q 020290 93 EVLDCPVCYEPL----NIPVY-QCGNGHVVCHRCCCDL-MNKCP 130 (328)
Q Consensus 93 ~~l~CpiC~~~l----~~Pv~-qC~~GH~~C~~C~~~~-~~~CP 130 (328)
+.|.|+||+..+ ..|++ +| ||++|..|..++ +..||
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl~c--ghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSLQC--GHTICGHCVQLLYNASCP 51 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccccc--cchHHHHHHHhHhhccCC
Confidence 468899997665 35888 99 999999999987 56888
No 59
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=91.22 E-value=0.042 Score=53.51 Aligned_cols=40 Identities=30% Similarity=0.733 Sum_probs=33.2
Q ss_pred eecccccccccc-ccccccccEeccccccccc-----CCCCCCCcCCC
Q 020290 96 DCPVCYEPLNIP-VYQCGNGHVVCHRCCCDLM-----NKCPSCRLPNG 137 (328)
Q Consensus 96 ~CpiC~~~l~~P-v~qC~~GH~~C~~C~~~~~-----~~CP~C~~~~~ 137 (328)
.|-||-+-=++= |-.| ||+.|..|+..|+ ..||.||..+.
T Consensus 371 LCKICaendKdvkIEPC--GHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 371 LCKICAENDKDVKIEPC--GHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHhhccCCCcccccc--cchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 499999987763 3389 9999999999984 68999998774
No 60
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.36 E-value=0.15 Score=48.16 Aligned_cols=41 Identities=29% Similarity=0.678 Sum_probs=33.3
Q ss_pred eeeccccccccc--c--ccccccccEecccccccc----cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNI--P--VYQCGNGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~--P--v~qC~~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
.+|.||..-+.. . +..| .|.|=..|+.+| +.+||+|+.++.
T Consensus 324 veCaICms~fiK~d~~~vlPC--~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 324 VECAICMSNFIKNDRLRVLPC--DHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred ceEEEEhhhhcccceEEEecc--CceechhHHHHHHhhhcccCCccCCCCC
Confidence 789999987742 2 2279 999999999998 479999998763
No 61
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.30 E-value=0.081 Score=52.10 Aligned_cols=30 Identities=37% Similarity=0.906 Sum_probs=27.0
Q ss_pred Ceeeecccccccccccc-ccccccEeccccccc
Q 020290 93 EVLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCD 124 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~ 124 (328)
+.|.||||...+++||. .| ||..|..|...
T Consensus 3 eelkc~vc~~f~~epiil~c--~h~lc~~ca~~ 33 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPIILPC--SHNLCQACARN 33 (699)
T ss_pred ccccCceehhhccCceEeec--ccHHHHHHHHh
Confidence 46899999999999988 99 99999999754
No 62
>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=89.24 E-value=0.23 Score=34.84 Aligned_cols=49 Identities=20% Similarity=0.468 Sum_probs=31.8
Q ss_pred eecccCCCCCCcccccchhhhcccc--cc-cCCCCCCCCCCccccccchHhhhhhhccC
Q 020290 153 VACENADYGCKEKMSYSEKYDHGRA--CH-YTPCSCPLAACNFVGSFHQIYQHFRGVHK 208 (328)
Q Consensus 153 v~C~~~~~GC~~~~~~~~~~~He~~--C~-~~~~~CP~~gC~~~g~~~~L~~Hl~~~H~ 208 (328)
+.||| |...+....|..|... .. -..+.||. |... ...+|..|+...|.
T Consensus 3 f~CP~----C~~~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~-~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPY----CGKGFSESSLVEHCEDEHRSESKNVVCPI--CSSR-VTDNLIRHLNSQHR 54 (54)
T ss_pred cCCCC----CCCccCHHHHHHHHHhHCcCCCCCccCCC--chhh-hhhHHHHHHHHhcC
Confidence 56776 6666666666666432 11 12588987 8764 34699999988874
No 63
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.69 E-value=0.24 Score=46.27 Aligned_cols=44 Identities=34% Similarity=0.638 Sum_probs=36.1
Q ss_pred CCeeeeccccccccc--c-cc--ccccccEeccccccccc--CCCCCCCcCCC
Q 020290 92 PEVLDCPVCYEPLNI--P-VY--QCGNGHVVCHRCCCDLM--NKCPSCRLPNG 137 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~--P-v~--qC~~GH~~C~~C~~~~~--~~CP~C~~~~~ 137 (328)
...|.|||....|.. + |+ .| ||+|+..++..+. ..||.|..++.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~c--G~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPC--GCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCC--CCEeeHHHHHhhcccccccccCCccc
Confidence 346999999999953 2 33 78 9999999999984 47999999986
No 64
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.24 E-value=0.19 Score=48.81 Aligned_cols=44 Identities=30% Similarity=0.858 Sum_probs=36.2
Q ss_pred Ceeeeccccccccccc-----c----ccccccEeccccccccc----------CCCCCCCcCCCC
Q 020290 93 EVLDCPVCYEPLNIPV-----Y----QCGNGHVVCHRCCCDLM----------NKCPSCRLPNGH 138 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv-----~----qC~~GH~~C~~C~~~~~----------~~CP~C~~~~~~ 138 (328)
....|.||.+....+. + .| -|.||..|+.+|. ..||.||.....
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC--~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNC--NHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCc--chhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 3578999999987766 3 58 9999999999983 579999987653
No 65
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.85 E-value=0.21 Score=45.84 Aligned_cols=43 Identities=28% Similarity=0.426 Sum_probs=35.4
Q ss_pred eeeeccccccccccc----c-ccccccEeccccccccc---CCCCCCCcCCCC
Q 020290 94 VLDCPVCYEPLNIPV----Y-QCGNGHVVCHRCCCDLM---NKCPSCRLPNGH 138 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv----~-qC~~GH~~C~~C~~~~~---~~CP~C~~~~~~ 138 (328)
.+.||+|.+.|...+ . .| ||++|..|.+++. ..||+|..++..
T Consensus 221 ryiCpvtrd~LtNt~~ca~Lr~s--g~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 221 RYICPVTRDTLTNTTPCAVLRPS--GHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred ceecccchhhhcCccceEEeccC--CcEeeHHHHHHhccccccccCCCCcCcc
Confidence 589999999998632 2 67 9999999999973 579999988764
No 66
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.07 E-value=0.11 Score=49.83 Aligned_cols=44 Identities=36% Similarity=0.963 Sum_probs=35.2
Q ss_pred CCCeeeeccccccccc-cccccccccEecccccccc-----cCCCCCCCcCC
Q 020290 91 DPEVLDCPVCYEPLNI-PVYQCGNGHVVCHRCCCDL-----MNKCPSCRLPN 136 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~-Pv~qC~~GH~~C~~C~~~~-----~~~CP~C~~~~ 136 (328)
|.+.-.|.||-.-+.- -++.| +|..|.-|--++ .+.||.|+...
T Consensus 58 DEen~~C~ICA~~~TYs~~~PC--~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGSTTYSARYPC--GHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccceeEEecCCceEEEeccC--CchHHHHHHHHHHHHHhccCCCcccccc
Confidence 4456789999998764 35589 999999998875 47899999764
No 67
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.83 E-value=0.26 Score=47.55 Aligned_cols=44 Identities=36% Similarity=0.802 Sum_probs=32.3
Q ss_pred CCCeeeecccccccccccc-ccccccEec-ccccccccCCCCCCCcCCC
Q 020290 91 DPEVLDCPVCYEPLNIPVY-QCGNGHVVC-HRCCCDLMNKCPSCRLPNG 137 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C-~~C~~~~~~~CP~C~~~~~ 137 (328)
.+-...|.||.+-.++-++ .| ||..| ..|...+ .+||.||+.+.
T Consensus 302 ~~~p~lcVVcl~e~~~~~fvpc--Gh~ccct~cs~~l-~~CPvCR~rI~ 347 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSAVFVPC--GHVCCCTLCSKHL-PQCPVCRQRIR 347 (355)
T ss_pred cCCCCceEEecCCccceeeecC--CcEEEchHHHhhC-CCCchhHHHHH
Confidence 3334679999999998888 99 99866 2243344 57999998653
No 68
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=85.42 E-value=0.14 Score=53.89 Aligned_cols=41 Identities=27% Similarity=0.581 Sum_probs=32.6
Q ss_pred eeecccccccccccc----ccccccEecccccccc---cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIPVY----QCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~----qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
-.||+|..-+.+-.. .| +|.||..|+..| ...||.|+..+.
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c--~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHT--AHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhHHHHHHHHHhhcccccc--ccccHHHHhhhhhhhcccCchhhhhhh
Confidence 459999887765432 68 999999999987 378999998764
No 69
>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=85.08 E-value=0.42 Score=35.59 Aligned_cols=38 Identities=34% Similarity=0.765 Sum_probs=23.3
Q ss_pred eeeccccccccccccccccccEecccccccc--cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIPVYQCGNGHVVCHRCCCDL--MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~--~~~CP~C~~~~~ 137 (328)
+.||.|..+|..- +|+..|..|-... ...||.|.+++.
T Consensus 2 ~~CP~C~~~L~~~-----~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQ-----GGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEE-----TTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEe-----CCEEECccccccceecccCCCcccHHH
Confidence 5799999997752 2788999998874 368999988764
No 70
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.65 E-value=0.58 Score=44.16 Aligned_cols=41 Identities=39% Similarity=1.056 Sum_probs=32.8
Q ss_pred eeeecccccccc------cc-ccccccccEeccccccccc----CCCCCCCcCC
Q 020290 94 VLDCPVCYEPLN------IP-VYQCGNGHVVCHRCCCDLM----NKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~l~------~P-v~qC~~GH~~C~~C~~~~~----~~CP~C~~~~ 136 (328)
.+.|-||.+.+. .| +..| ||.+|..|..++. ..||.||.+.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c--~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKC--GHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCccccc--CceehHhHHHHHhcCceeeccCCCCcc
Confidence 467999998874 24 3479 9999999999972 5799999984
No 71
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.37 E-value=0.35 Score=47.79 Aligned_cols=30 Identities=27% Similarity=0.863 Sum_probs=21.5
Q ss_pred eeeecccc-ccccc-ccc---ccccccEecccccccc
Q 020290 94 VLDCPVCY-EPLNI-PVY---QCGNGHVVCHRCCCDL 125 (328)
Q Consensus 94 ~l~CpiC~-~~l~~-Pv~---qC~~GH~~C~~C~~~~ 125 (328)
...|.||. +.... -.+ .| +|.||..|+.+.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C--~H~fC~~C~k~~ 180 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKC--GHRFCKDCVKQH 180 (384)
T ss_pred cccCccCccccccHhhhHHHhcc--cchhhhHHhHHH
Confidence 56899999 44332 122 57 999999999864
No 72
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=83.27 E-value=0.51 Score=45.86 Aligned_cols=42 Identities=26% Similarity=0.744 Sum_probs=33.1
Q ss_pred Ceeeeccccccc-ccc------------c-cccccccEecccccccc---cCCCCCCCcCC
Q 020290 93 EVLDCPVCYEPL-NIP------------V-YQCGNGHVVCHRCCCDL---MNKCPSCRLPN 136 (328)
Q Consensus 93 ~~l~CpiC~~~l-~~P------------v-~qC~~GH~~C~~C~~~~---~~~CP~C~~~~ 136 (328)
++-.|-||.+-+ .+| - ..| ||++=-.|++.| +..||.||.++
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpC--GHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPC--GHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccc--cceeeHHHHHHHHHhccCCCcccCcc
Confidence 346799999874 333 2 268 999999999987 58999999984
No 73
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.07 E-value=0.44 Score=46.61 Aligned_cols=41 Identities=39% Similarity=0.738 Sum_probs=31.7
Q ss_pred Ceeeeccccccc---ccccc-ccccccEeccccccccc------CCCCCCCcC
Q 020290 93 EVLDCPVCYEPL---NIPVY-QCGNGHVVCHRCCCDLM------NKCPSCRLP 135 (328)
Q Consensus 93 ~~l~CpiC~~~l---~~Pv~-qC~~GH~~C~~C~~~~~------~~CP~C~~~ 135 (328)
..|.|||=.+-- .||+. .| ||++|..-+.++. .+||+|-..
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~C--GHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLIC--GHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ceeecccchhhccCCCCCeeeec--cceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 468999976655 36777 99 9999999988872 478888543
No 74
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.93 E-value=0.88 Score=44.18 Aligned_cols=41 Identities=22% Similarity=0.534 Sum_probs=33.1
Q ss_pred eeecccccccccc----ccccccccEecccccccc----cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIP----VYQCGNGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~P----v~qC~~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
..|.||++-+..- +..| .|.|=..|+..| ...||+|+..+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC--~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPC--SHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecC--CCchhhccchhhHhhcCccCCCCCCcCC
Confidence 4899999998642 3489 999999999998 245999998653
No 75
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=82.45 E-value=0.4 Score=45.07 Aligned_cols=39 Identities=31% Similarity=0.849 Sum_probs=29.1
Q ss_pred eecccccc-cccc-cc----ccccccEecccccccc----cCCCCCCCcCC
Q 020290 96 DCPVCYEP-LNIP-VY----QCGNGHVVCHRCCCDL----MNKCPSCRLPN 136 (328)
Q Consensus 96 ~CpiC~~~-l~~P-v~----qC~~GH~~C~~C~~~~----~~~CP~C~~~~ 136 (328)
.||+|..- ...| ++ .| ||..|.+|...+ ...||.|...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C--~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINEC--GHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccc--cchHHHHHHHHHHhcCCCCCCcccchh
Confidence 48888753 3333 22 68 999999999987 36899998765
No 76
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=82.27 E-value=0.32 Score=36.18 Aligned_cols=43 Identities=30% Similarity=0.715 Sum_probs=16.7
Q ss_pred eeecccccccc----ccccccc---cccEecccccccc--------------cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLN----IPVYQCG---NGHVVCHRCCCDL--------------MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~----~Pv~qC~---~GH~~C~~C~~~~--------------~~~CP~C~~~~~ 137 (328)
+.|+||+..+. .|+..|+ +++.|=..|+.+| ...||.|+.++.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 57999998764 3555663 2444445677765 135777776654
No 77
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=81.84 E-value=0.37 Score=41.32 Aligned_cols=28 Identities=39% Similarity=1.013 Sum_probs=23.3
Q ss_pred ccccccE--------------ecccccccccCCCCCCCcCCC
Q 020290 110 QCGNGHV--------------VCHRCCCDLMNKCPSCRLPNG 137 (328)
Q Consensus 110 qC~~GH~--------------~C~~C~~~~~~~CP~C~~~~~ 137 (328)
-|.|||. ||..|-.+....||.|..++.
T Consensus 9 iC~NGH~~t~~~~~~p~~~~~fC~kCG~~tI~~Cp~C~~~Ir 50 (158)
T PF10083_consen 9 ICLNGHVITDSYDKNPELREKFCSKCGAKTITSCPNCSTPIR 50 (158)
T ss_pred HccCccccccccccCchHHHHHHHHhhHHHHHHCcCCCCCCC
Confidence 4888876 899998887678999988874
No 78
>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=81.62 E-value=0.44 Score=33.05 Aligned_cols=39 Identities=38% Similarity=0.882 Sum_probs=19.7
Q ss_pred eeecccccccccccc--ccccccEecccccccc-------cCCCCCCCcC
Q 020290 95 LDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL-------MNKCPSCRLP 135 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~-------~~~CP~C~~~ 135 (328)
|.||+-...+..|+. .| .|.-|-+=..=+ ...||.|.++
T Consensus 3 L~CPls~~~i~~P~Rg~~C--~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNC--KHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT----SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcC--cccceECHHHHHHHhhccCCeECcCCcCc
Confidence 689999999999998 78 998754311101 1469999764
No 79
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.65 E-value=0.4 Score=51.63 Aligned_cols=44 Identities=27% Similarity=0.707 Sum_probs=33.4
Q ss_pred eeeecccccccc-----ccccccc-cccEecccccccc-----cCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLN-----IPVYQCG-NGHVVCHRCCCDL-----MNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~-----~~~CP~C~~~~~ 137 (328)
.-+|+||+.++. -|-..|+ |.|-|=.+|+.+| ...||.||..++
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 347999999985 3544553 3788888999998 368999997664
No 80
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=79.35 E-value=0.59 Score=46.45 Aligned_cols=41 Identities=32% Similarity=0.781 Sum_probs=33.3
Q ss_pred Ceeeeccccccccccc---c--ccccccEeccccccccc-CCCCCCCcC
Q 020290 93 EVLDCPVCYEPLNIPV---Y--QCGNGHVVCHRCCCDLM-NKCPSCRLP 135 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv---~--qC~~GH~~C~~C~~~~~-~~CP~C~~~ 135 (328)
+.-.||||++=|-+-+ . .| .|.|=.+|+.+|. ..||+||--
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c--~Hsfh~~cl~~w~~~scpvcR~~ 220 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILC--NHSFHCSCLMKWWDSSCPVCRYC 220 (493)
T ss_pred cCCCcchhHhhcCccccceeeeec--ccccchHHHhhcccCcChhhhhh
Confidence 4568999999987654 3 69 9999999999984 689999754
No 81
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=78.01 E-value=0.92 Score=36.10 Aligned_cols=40 Identities=38% Similarity=0.834 Sum_probs=14.6
Q ss_pred eecccccccc--cccc-ccccccEecccccccc-------cCCCCCCCcCC
Q 020290 96 DCPVCYEPLN--IPVY-QCGNGHVVCHRCCCDL-------MNKCPSCRLPN 136 (328)
Q Consensus 96 ~CpiC~~~l~--~Pv~-qC~~GH~~C~~C~~~~-------~~~CP~C~~~~ 136 (328)
.|++|...+. ++.. +|.+||.+ .+|.... ...|+.|....
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVW-PRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EE-EB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEE-eeeeeeeeeeccCCeeEcCCCCCEE
Confidence 6999999764 4444 89999987 5565542 15799997653
No 82
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.77 E-value=0.93 Score=41.76 Aligned_cols=29 Identities=17% Similarity=0.293 Sum_probs=25.6
Q ss_pred eeeccccccccccccccccccEeccccccc
Q 020290 95 LDCPVCYEPLNIPVYQCGNGHVVCHRCCCD 124 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~ 124 (328)
-.|+.|+.+..+||. |+.||+||..||..
T Consensus 44 dcCsLtLqPc~dPvi-t~~GylfdrEaILe 72 (303)
T KOG3039|consen 44 DCCSLTLQPCRDPVI-TPDGYLFDREAILE 72 (303)
T ss_pred ceeeeecccccCCcc-CCCCeeeeHHHHHH
Confidence 369999999999986 77799999999976
No 83
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.28 E-value=1.1 Score=47.02 Aligned_cols=40 Identities=35% Similarity=0.821 Sum_probs=31.8
Q ss_pred eecccccccccccc-cccccc-Eeccccccccc---------CCCCCCCcCCC
Q 020290 96 DCPVCYEPLNIPVY-QCGNGH-VVCHRCCCDLM---------NKCPSCRLPNG 137 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~-qC~~GH-~~C~~C~~~~~---------~~CP~C~~~~~ 137 (328)
.|+||..-+.-+.+ .| || .+|..|..++. ..||.|+..+.
T Consensus 2 ~c~ic~~s~~~~~~~s~--~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRGSC--GHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCccccccccc--cccccchhhhhhhhhhcccccccccCccccccee
Confidence 48999988887777 89 99 89999998751 35788987553
No 84
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.17 E-value=0.96 Score=37.42 Aligned_cols=28 Identities=36% Similarity=0.863 Sum_probs=22.7
Q ss_pred ccccccE--------------ecccccccccCCCCCCCcCCC
Q 020290 110 QCGNGHV--------------VCHRCCCDLMNKCPSCRLPNG 137 (328)
Q Consensus 110 qC~~GH~--------------~C~~C~~~~~~~CP~C~~~~~ 137 (328)
-|.|||. ||+.|-......||.|..++.
T Consensus 9 ic~ngh~attaadq~pel~eafcskcgeati~qcp~csasir 50 (160)
T COG4306 9 ICLNGHVATTAADQSPELMEAFCSKCGEATITQCPICSASIR 50 (160)
T ss_pred hcCCCceeeccccCCHHHHHHHHhhhchHHHhcCCccCCccc
Confidence 5888987 799998775568999988763
No 85
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.93 E-value=1.2 Score=41.91 Aligned_cols=31 Identities=32% Similarity=0.729 Sum_probs=27.5
Q ss_pred eeeecccccccccccc-ccc--cccEeccccccc
Q 020290 94 VLDCPVCYEPLNIPVY-QCG--NGHVVCHRCCCD 124 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~--~GH~~C~~C~~~ 124 (328)
-|.|-+|.+-|.+-.| ||+ +.|.||..|-..
T Consensus 268 pLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred ceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 4999999999999988 998 689999999654
No 86
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=75.03 E-value=1.9 Score=41.03 Aligned_cols=75 Identities=27% Similarity=0.491 Sum_probs=51.3
Q ss_pred eeeecccccccccc--ccccccccEecccccccc-cCCCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCcc-cccc
Q 020290 94 VLDCPVCYEPLNIP--VYQCGNGHVVCHRCCCDL-MNKCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEK-MSYS 169 (328)
Q Consensus 94 ~l~CpiC~~~l~~P--v~qC~~GH~~C~~C~~~~-~~~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~-~~~~ 169 (328)
+-.|--|..++..- +..| .|+||-.|...- .+.||.|...+ ..+|.....-.+-|. ...||.-+ +.-.
T Consensus 90 VHfCd~Cd~PI~IYGRmIPC--kHvFCl~CAr~~~dK~Cp~C~d~V-----qrIeq~~~g~iFmC~-~~~GC~RTyLsqr 161 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPC--KHVFCLECARSDSDKICPLCDDRV-----QRIEQIMMGGIFMCA-APHGCLRTYLSQR 161 (389)
T ss_pred eEeecccCCcceeeeccccc--chhhhhhhhhcCccccCcCcccHH-----HHHHHhcccceEEee-cchhHHHHHhhHH
Confidence 56799999988742 2379 999999996543 26899996543 345555555567787 56788754 4455
Q ss_pred hhhhccc
Q 020290 170 EKYDHGR 176 (328)
Q Consensus 170 ~~~~He~ 176 (328)
+++.|..
T Consensus 162 DlqAHIn 168 (389)
T KOG2932|consen 162 DLQAHIN 168 (389)
T ss_pred HHHHHhh
Confidence 6666653
No 87
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.09 E-value=0.98 Score=44.42 Aligned_cols=39 Identities=28% Similarity=0.759 Sum_probs=31.7
Q ss_pred eeeccccccccccc------cccccccEecccccccc-----cCCCCCCCcC
Q 020290 95 LDCPVCYEPLNIPV------YQCGNGHVVCHRCCCDL-----MNKCPSCRLP 135 (328)
Q Consensus 95 l~CpiC~~~l~~Pv------~qC~~GH~~C~~C~~~~-----~~~CP~C~~~ 135 (328)
-.||||++-..-|. .+| ||.|=++|+++| ...||.|...
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~c--ghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQC--GHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred ccCceeeeeeeecCceEEeeecc--cccccHHHHHHHHhhhhhhhCcccCCh
Confidence 47999999876552 289 999999999997 2589999764
No 88
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=73.72 E-value=1.3 Score=41.18 Aligned_cols=23 Identities=30% Similarity=0.842 Sum_probs=18.8
Q ss_pred eeecccccccc--ccccccccccEe
Q 020290 95 LDCPVCYEPLN--IPVYQCGNGHVV 117 (328)
Q Consensus 95 l~CpiC~~~l~--~Pv~qC~~GH~~ 117 (328)
|.||+|..+|. ...+.|.+||.|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 78999999996 334589999987
No 89
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=73.07 E-value=0.88 Score=48.17 Aligned_cols=39 Identities=31% Similarity=0.690 Sum_probs=31.8
Q ss_pred eeecccccccccccc-ccccccEecccccccc-----cCCCCCCCcCC
Q 020290 95 LDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL-----MNKCPSCRLPN 136 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~-----~~~CP~C~~~~ 136 (328)
+.|++|.+ +..++. .| ||.+|..|+.+. ...||.|+..+
T Consensus 455 ~~c~ic~~-~~~~~it~c--~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRC--GHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-cccceeecc--cchHHHHHHHhccccccCCCCcHHHHHH
Confidence 79999999 666666 89 999999999885 24699997543
No 90
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.42 E-value=1.5 Score=43.16 Aligned_cols=84 Identities=25% Similarity=0.549 Sum_probs=49.9
Q ss_pred eeeecccccccccc---cc-ccccccEecccccccc-----------cCCCCCCCcCCCCC--------------c--ch
Q 020290 94 VLDCPVCYEPLNIP---VY-QCGNGHVVCHRCCCDL-----------MNKCPSCRLPNGHS--------------R--ST 142 (328)
Q Consensus 94 ~l~CpiC~~~l~~P---v~-qC~~GH~~C~~C~~~~-----------~~~CP~C~~~~~~~--------------r--~~ 142 (328)
.+.|.||++-..-. ++ .| +|+||..|.... .-+||.+.-.-... | ..
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC--~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPC--SHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred cccceeeehhhcCcceeeeccc--chHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 58999999987653 22 79 999999998863 14788754332110 1 12
Q ss_pred hhHHhhhcee--eecccCCCCCCcccccchhhhccc---ccccCC
Q 020290 143 AMEKVIESIQ--VACENADYGCKEKMSYSEKYDHGR---ACHYTP 182 (328)
Q Consensus 143 ~le~~l~~l~--v~C~~~~~GC~~~~~~~~~~~He~---~C~~~~ 182 (328)
.+++.++.+. +.||++ -|.... ..+...-.. .|.|+-
T Consensus 262 ~lqk~l~~msdv~yCPr~--~Cq~p~-~~d~~~~l~~CskCnFaF 303 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRA--CCQLPV-KQDPGRALAICSKCNFAF 303 (445)
T ss_pred HHHHHHHhhcccccCChh--hccCcc-ccCchhhhhhhccCccHH
Confidence 3344555555 899985 465544 334343333 444543
No 91
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=72.13 E-value=1 Score=34.38 Aligned_cols=44 Identities=18% Similarity=0.308 Sum_probs=30.7
Q ss_pred eeecccccccccccccccc---------------ccEecccccccc---cCCCCCCCcCCCC
Q 020290 95 LDCPVCYEPLNIPVYQCGN---------------GHVVCHRCCCDL---MNKCPSCRLPNGH 138 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~---------------GH~~C~~C~~~~---~~~CP~C~~~~~~ 138 (328)
-.|.||...+..+-.+|.+ .|.|=..|+.++ ++.||.++++...
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 4588888777665445543 466767788886 4789999987643
No 92
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=72.02 E-value=1.1 Score=25.57 Aligned_cols=23 Identities=26% Similarity=0.687 Sum_probs=16.6
Q ss_pred CCCCCCCccccccchHhhhhhhccC
Q 020290 184 SCPLAACNFVGSFHQIYQHFRGVHK 208 (328)
Q Consensus 184 ~CP~~gC~~~g~~~~L~~Hl~~~H~ 208 (328)
.|+. |+|......|..|+...|.
T Consensus 2 ~C~~--C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCPH--CSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp E-SS--SS-EESHHHHHHHHHHHHS
T ss_pred CCCC--CCCcCCHHHHHHHHHhhCc
Confidence 4764 8888877889999988774
No 93
>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=71.76 E-value=2.1 Score=29.93 Aligned_cols=37 Identities=27% Similarity=0.721 Sum_probs=19.0
Q ss_pred ecccccccccc--------ccccc-cccEeccccccc---ccCCCCCCC
Q 020290 97 CPVCYEPLNIP--------VYQCG-NGHVVCHRCCCD---LMNKCPSCR 133 (328)
Q Consensus 97 CpiC~~~l~~P--------v~qC~-~GH~~C~~C~~~---~~~~CP~C~ 133 (328)
|--|..+|..+ +|+|+ +++.||..|=.= ....||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 66677777664 46665 388999998432 236799883
No 94
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=70.15 E-value=1.8 Score=25.53 Aligned_cols=22 Identities=27% Similarity=0.614 Sum_probs=13.0
Q ss_pred eecccCCCCCCcccccchhhhccccc
Q 020290 153 VACENADYGCKEKMSYSEKYDHGRAC 178 (328)
Q Consensus 153 v~C~~~~~GC~~~~~~~~~~~He~~C 178 (328)
++|++ |.-++....+..|++.|
T Consensus 3 ~~C~~----CgR~F~~~~l~~H~~~C 24 (25)
T PF13913_consen 3 VPCPI----CGRKFNPDRLEKHEKIC 24 (25)
T ss_pred CcCCC----CCCEECHHHHHHHHHhc
Confidence 45554 66666666666666655
No 95
>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=68.67 E-value=2.9 Score=32.77 Aligned_cols=29 Identities=38% Similarity=0.689 Sum_probs=22.5
Q ss_pred eecccccccccccc-ccccccEeccccccc
Q 020290 96 DCPVCYEPLNIPVY-QCGNGHVVCHRCCCD 124 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~ 124 (328)
.|++|...|....+ -.++||++-..|+.+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 49999999987655 344499999988753
No 96
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.40 E-value=1.2 Score=41.48 Aligned_cols=41 Identities=29% Similarity=0.726 Sum_probs=31.0
Q ss_pred eeeccccccccccc---------c--ccccccEecccccccc-----cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLNIPV---------Y--QCGNGHVVCHRCCCDL-----MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~~Pv---------~--qC~~GH~~C~~C~~~~-----~~~CP~C~~~~~ 137 (328)
-.|.||..-+...+ + .| +|+|=..|+.-| ++.||.|++.+.
T Consensus 225 ~vCaVCg~~~~~s~~eegvienty~LsC--nHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 225 SVCAVCGQQIDVSVDEEGVIENTYKLSC--NHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred chhHhhcchheeecchhhhhhhheeeec--ccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 46999988765333 3 68 999888888775 478999998764
No 97
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.90 E-value=2.5 Score=45.24 Aligned_cols=38 Identities=34% Similarity=0.826 Sum_probs=33.2
Q ss_pred eeecccccccccccc--ccccccEecccccccccCCCCCCCc
Q 020290 95 LDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDLMNKCPSCRL 134 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~~~~CP~C~~ 134 (328)
-.|..|...|..|++ .| ||.|=..|...-...||.|+.
T Consensus 841 skCs~C~~~LdlP~VhF~C--gHsyHqhC~e~~~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLC--GHSYHQHCLEDKEDKCPKCLP 880 (933)
T ss_pred eeecccCCccccceeeeec--ccHHHHHhhccCcccCCccch
Confidence 479999999999965 89 999999999865578999976
No 98
>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=64.61 E-value=3.7 Score=28.61 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=23.0
Q ss_pred CCCCCCCCccccccchHhhhhhhccCCCce
Q 020290 183 CSCPLAACNFVGSFHQIYQHFRGVHKHAAE 212 (328)
Q Consensus 183 ~~CP~~gC~~~g~~~~L~~Hl~~~H~~~~~ 212 (328)
+.||+ |+.......|..|+...|.....
T Consensus 3 f~CP~--C~~~~~~~~L~~H~~~~H~~~~~ 30 (54)
T PF05605_consen 3 FTCPY--CGKGFSESSLVEHCEDEHRSESK 30 (54)
T ss_pred cCCCC--CCCccCHHHHHHHHHhHCcCCCC
Confidence 57987 88866778999999999997644
No 99
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=64.19 E-value=14 Score=29.37 Aligned_cols=38 Identities=16% Similarity=0.556 Sum_probs=26.8
Q ss_pred Ceeeec--CCCCeeeecccccccccccc-ccccccEecccc
Q 020290 84 PVTVTL--NDPEVLDCPVCYEPLNIPVY-QCGNGHVVCHRC 121 (328)
Q Consensus 84 ~~~~~~--~~~~~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C 121 (328)
+++|.+ ...+.|.|..|+.|-..-.. .=.+|+.+|..|
T Consensus 58 EL~V~ViP~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 58 ELSVRVIPKQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eEEEEEecCCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 455554 45578999999998754333 334589999998
No 100
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=64.18 E-value=3.9 Score=39.11 Aligned_cols=53 Identities=9% Similarity=0.192 Sum_probs=41.3
Q ss_pred ceeeecccCCCCCCcccccchhhhcccccccCCCCCCC--CCCccccccchHhhhhhhc
Q 020290 150 SIQVACENADYGCKEKMSYSEKYDHGRACHYTPCSCPL--AACNFVGSFHQIYQHFRGV 206 (328)
Q Consensus 150 ~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~--~gC~~~g~~~~L~~Hl~~~ 206 (328)
++...||. |...++...-..=|+.+.-..++||+ .||.+..++..-..|.+.+
T Consensus 78 ~~~~~CP~----Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~~~HE~~C 132 (299)
T KOG3002|consen 78 KVSNKCPT----CRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEKSKHEKVC 132 (299)
T ss_pred hhcccCCc----cccccccHHHHHHHHHHHhceecccccccCCceeecccccccccccc
Confidence 56778886 88887744334456789999999998 5999999888888887665
No 101
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=62.73 E-value=5.5 Score=28.68 Aligned_cols=34 Identities=32% Similarity=0.723 Sum_probs=19.8
Q ss_pred eeeecccCCCCCCcccccchh--hhcccccccCCCCCCCCCCccccc
Q 020290 151 IQVACENADYGCKEKMSYSEK--YDHGRACHYTPCSCPLAACNFVGS 195 (328)
Q Consensus 151 l~v~C~~~~~GC~~~~~~~~~--~~He~~C~~~~~~CP~~gC~~~g~ 195 (328)
..++||| |...+.+.-. +.| -.++.||. |+|.|+
T Consensus 26 v~F~CPn----CGe~~I~Rc~~CRk~-----g~~Y~Cp~--CGF~GP 61 (61)
T COG2888 26 VKFPCPN----CGEVEIYRCAKCRKL-----GNPYRCPK--CGFEGP 61 (61)
T ss_pred eEeeCCC----CCceeeehhhhHHHc-----CCceECCC--cCccCC
Confidence 4678887 7744333221 111 23678875 998874
No 102
>PHA00616 hypothetical protein
Probab=60.87 E-value=7.4 Score=26.33 Aligned_cols=33 Identities=21% Similarity=0.369 Sum_probs=24.8
Q ss_pred CCCCCCCCCcccc-ccchHhhhhhhccCCCceEEEe
Q 020290 182 PCSCPLAACNFVG-SFHQIYQHFRGVHKHAAEEFVY 216 (328)
Q Consensus 182 ~~~CP~~gC~~~g-~~~~L~~Hl~~~H~~~~~~f~y 216 (328)
|+.||. |+... .+++|..|+...|.....+..|
T Consensus 1 pYqC~~--CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLR--CGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccch--hhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 467875 88655 4578999999999887666555
No 103
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.73 E-value=4.5 Score=30.25 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=23.6
Q ss_pred ccccccEeccccccc-ccCCCCCCCcCCCC
Q 020290 110 QCGNGHVVCHRCCCD-LMNKCPSCRLPNGH 138 (328)
Q Consensus 110 qC~~GH~~C~~C~~~-~~~~CP~C~~~~~~ 138 (328)
.|+.-+.||..|... +...||.|...+..
T Consensus 24 ICtfEcTFCadCae~~l~g~CPnCGGelv~ 53 (84)
T COG3813 24 ICTFECTFCADCAENRLHGLCPNCGGELVA 53 (84)
T ss_pred EEEEeeehhHhHHHHhhcCcCCCCCchhhc
Confidence 577678999999984 56899999987754
No 104
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=60.54 E-value=4.1 Score=24.32 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=4.8
Q ss_pred ecccccccc
Q 020290 97 CPVCYEPLN 105 (328)
Q Consensus 97 CpiC~~~l~ 105 (328)
||.|...+.
T Consensus 3 CP~C~~~V~ 11 (26)
T PF10571_consen 3 CPECGAEVP 11 (26)
T ss_pred CCCCcCCch
Confidence 555555543
No 105
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.17 E-value=10 Score=41.67 Aligned_cols=43 Identities=23% Similarity=0.553 Sum_probs=32.3
Q ss_pred Ceeeeccccccccccccccc-cc-----cEecccccccc-cCCCCCCCcCCC
Q 020290 93 EVLDCPVCYEPLNIPVYQCG-NG-----HVVCHRCCCDL-MNKCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~qC~-~G-----H~~C~~C~~~~-~~~CP~C~~~~~ 137 (328)
....||-|.... +.+.|+ || ..+|..|.... ...||.|.....
T Consensus 625 g~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 625 GRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred cCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCC
Confidence 346899999985 344676 57 35999997765 367999988764
No 106
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=60.06 E-value=4.7 Score=31.56 Aligned_cols=36 Identities=22% Similarity=0.621 Sum_probs=29.7
Q ss_pred eeccccccccccccccccccEecccccccccCCCCCCCcCCCC
Q 020290 96 DCPVCYEPLNIPVYQCGNGHVVCHRCCCDLMNKCPSCRLPNGH 138 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~~~ 138 (328)
.|-||..-+..+ ||.+|..|-.+. ..|..|.+.+..
T Consensus 46 ~C~~CK~~v~q~------g~~YCq~CAYkk-GiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKVHQP------GAKYCQTCAYKK-GICAMCGKKILD 81 (90)
T ss_pred cccccccccccC------CCccChhhhccc-CcccccCCeecc
Confidence 699998877665 999999998775 689999988743
No 107
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=59.78 E-value=1.5 Score=33.17 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=19.6
Q ss_pred ccccccEecccccccc------cCCCCCCCcCCC
Q 020290 110 QCGNGHVVCHRCCCDL------MNKCPSCRLPNG 137 (328)
Q Consensus 110 qC~~GH~~C~~C~~~~------~~~CP~C~~~~~ 137 (328)
.| -|.|=..|+.++ +..||.||+...
T Consensus 50 ~C--~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YC--LHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HH--HHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 56 677777888886 368999998653
No 108
>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=59.20 E-value=5.1 Score=29.10 Aligned_cols=33 Identities=27% Similarity=0.709 Sum_probs=15.7
Q ss_pred CCeeeecccccccccccc--ccc-cccEeccccccc
Q 020290 92 PEVLDCPVCYEPLNIPVY--QCG-NGHVVCHRCCCD 124 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~Pv~--qC~-~GH~~C~~C~~~ 124 (328)
.+.-.|.+|...|..-.. .|. +|++||..|...
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 345679999999853221 343 399999999875
No 109
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=58.66 E-value=3.7 Score=39.91 Aligned_cols=112 Identities=21% Similarity=0.502 Sum_probs=68.4
Q ss_pred Ceeeecccccccccc--cc-ccc------cccEecccccccc---------------cCCCCCCCcCCCCC---cchhhH
Q 020290 93 EVLDCPVCYEPLNIP--VY-QCG------NGHVVCHRCCCDL---------------MNKCPSCRLPNGHS---RSTAME 145 (328)
Q Consensus 93 ~~l~CpiC~~~l~~P--v~-qC~------~GH~~C~~C~~~~---------------~~~CP~C~~~~~~~---r~~~le 145 (328)
.++-||-|.++|..- .+ .|. ..|-.|+.|.++. ..+||.|....... ++..+-
T Consensus 206 KvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~ 285 (467)
T KOG3608|consen 206 KVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRY 285 (467)
T ss_pred eEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHh
Confidence 358899999998642 22 331 2366788998763 14899998766532 112222
Q ss_pred HhhhceeeecccCCCCCCcc-cccchhhhcccccccCCCCCCCCCCcccc-ccchHhhhhhhccC
Q 020290 146 KVIESIQVACENADYGCKEK-MSYSEKYDHGRACHYTPCSCPLAACNFVG-SFHQIYQHFRGVHK 208 (328)
Q Consensus 146 ~~l~~l~v~C~~~~~GC~~~-~~~~~~~~He~~C~~~~~~CP~~gC~~~g-~~~~L~~Hl~~~H~ 208 (328)
+-..+-.+.|. -|... +...++.+|...=.-..+.|..+.|.+.. .+.+|..|+...|.
T Consensus 286 rHs~dkpfKCd----~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 286 RHSKDKPFKCD----ECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred hhccCCCcccc----chhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 33344556665 35543 45667777765222334677777787755 45678888888774
No 110
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=58.33 E-value=4.3 Score=27.60 Aligned_cols=39 Identities=18% Similarity=0.483 Sum_probs=27.9
Q ss_pred CCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCccccc
Q 020290 128 KCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEKMSY 168 (328)
Q Consensus 128 ~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~~~ 168 (328)
.||.|...........+...+..+-..|.|. -|.+.+..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~--~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNP--ECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCC--cCCCEEEE
Confidence 4999988765545566777788888999986 46555443
No 111
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=56.79 E-value=4.6 Score=24.17 Aligned_cols=24 Identities=25% Similarity=0.409 Sum_probs=13.7
Q ss_pred eecccCCCCCCcccccchhhhcccccc
Q 020290 153 VACENADYGCKEKMSYSEKYDHGRACH 179 (328)
Q Consensus 153 v~C~~~~~GC~~~~~~~~~~~He~~C~ 179 (328)
+.||| --.-.++..+|..|+..|+
T Consensus 3 v~CPy---n~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 3 VRCPY---NPSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EE-TT---TSS-EEEGGGHHHHHHHHH
T ss_pred eeCCC---CCCcCcCHHHHHHHHHHcC
Confidence 45665 3455666667777766664
No 112
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=53.29 E-value=8 Score=22.97 Aligned_cols=21 Identities=24% Similarity=0.447 Sum_probs=15.3
Q ss_pred CCCCCCCCccccccchHhhhhhh
Q 020290 183 CSCPLAACNFVGSFHQIYQHFRG 205 (328)
Q Consensus 183 ~~CP~~gC~~~g~~~~L~~Hl~~ 205 (328)
+.||. |++..+...+..|+..
T Consensus 2 v~CPi--C~~~v~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLDS 22 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHHH
Confidence 56875 8777777778888764
No 113
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=53.11 E-value=13 Score=34.91 Aligned_cols=15 Identities=20% Similarity=0.523 Sum_probs=11.2
Q ss_pred CCeeeeccccccccc
Q 020290 92 PEVLDCPVCYEPLNI 106 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~ 106 (328)
...+.|+-|...+..
T Consensus 128 ~~r~~c~eCgk~ysT 142 (279)
T KOG2462|consen 128 HPRYKCPECGKSYST 142 (279)
T ss_pred CCceecccccccccc
Confidence 346889999988753
No 114
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=52.16 E-value=7.4 Score=36.77 Aligned_cols=41 Identities=32% Similarity=0.649 Sum_probs=20.1
Q ss_pred eeeccccccccccccccc----cccEeccccccccc---CCCCCCCcC
Q 020290 95 LDCPVCYEPLNIPVYQCG----NGHVVCHRCCCDLM---NKCPSCRLP 135 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~----~GH~~C~~C~~~~~---~~CP~C~~~ 135 (328)
-.||||...-.--+..=. .-+.+|+-|-..|. ..||.|...
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 479999987543333111 13679999999883 689999764
No 115
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=51.76 E-value=7.5 Score=37.19 Aligned_cols=40 Identities=38% Similarity=0.708 Sum_probs=28.1
Q ss_pred Ceeeecccccccc---cccc-ccccccEeccccccccc------CCCCCCCc
Q 020290 93 EVLDCPVCYEPLN---IPVY-QCGNGHVVCHRCCCDLM------NKCPSCRL 134 (328)
Q Consensus 93 ~~l~CpiC~~~l~---~Pv~-qC~~GH~~C~~C~~~~~------~~CP~C~~ 134 (328)
..|.||+=.+.-. +|+. .| ||++=..-...++ .+||+|-.
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~C--gHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLEC--GHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred ceeeccccHhhhcccCCCeeeec--cceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 4799999776653 6776 89 9998766655542 46888843
No 116
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=51.19 E-value=3.7 Score=43.24 Aligned_cols=41 Identities=29% Similarity=0.826 Sum_probs=34.5
Q ss_pred eeeecccccccccccc-ccccccEecccccccc------cCCCCCCCcCC
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHVVCHRCCCDL------MNKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~~C~~C~~~~------~~~CP~C~~~~ 136 (328)
.+.||||......|+. .| -|.||..|+... ...||.|+..+
T Consensus 21 ~lEc~ic~~~~~~p~~~kc--~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 21 ILECPICLEHVKEPSLLKC--DHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hccCCceeEEeeccchhhh--hHHHHhhhhhceeeccCccccchhhhhhh
Confidence 4789999999999966 99 999999999874 25799998554
No 117
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=49.74 E-value=7.6 Score=24.60 Aligned_cols=24 Identities=29% Similarity=0.492 Sum_probs=14.1
Q ss_pred eeecccCCCCCCcccccchhhhcccccc
Q 020290 152 QVACENADYGCKEKMSYSEKYDHGRACH 179 (328)
Q Consensus 152 ~v~C~~~~~GC~~~~~~~~~~~He~~C~ 179 (328)
.+.|+| |.-.+.-..+..|++.|.
T Consensus 4 ~~~C~n----C~R~v~a~RfA~HLekCm 27 (33)
T PF08209_consen 4 YVECPN----CGRPVAASRFAPHLEKCM 27 (33)
T ss_dssp EEE-TT----TSSEEEGGGHHHHHHHHT
T ss_pred eEECCC----CcCCcchhhhHHHHHHHH
Confidence 456665 666666666666666553
No 118
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=49.74 E-value=11 Score=39.85 Aligned_cols=10 Identities=30% Similarity=0.511 Sum_probs=6.4
Q ss_pred eecccccccc
Q 020290 96 DCPVCYEPLN 105 (328)
Q Consensus 96 ~CpiC~~~l~ 105 (328)
.||-|.....
T Consensus 3 ~Cp~Cg~~n~ 12 (645)
T PRK14559 3 ICPQCQFENP 12 (645)
T ss_pred cCCCCCCcCC
Confidence 5777776643
No 119
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.52 E-value=13 Score=33.66 Aligned_cols=38 Identities=34% Similarity=0.771 Sum_probs=27.2
Q ss_pred ecccccccccccc-cccccc-EecccccccccCCCCCCCcCCC
Q 020290 97 CPVCYEPLNIPVY-QCGNGH-VVCHRCCCDLMNKCPSCRLPNG 137 (328)
Q Consensus 97 CpiC~~~l~~Pv~-qC~~GH-~~C~~C~~~~~~~CP~C~~~~~ 137 (328)
|-.|.+-=..=+. +| -| .+|..|-..+ ..||+|+.+..
T Consensus 161 Cr~C~~~~~~VlllPC--rHl~lC~~C~~~~-~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGEREATVLLLPC--RHLCLCGICDESL-RICPICRSPKT 200 (207)
T ss_pred ceecCcCCceEEeecc--cceEecccccccC-ccCCCCcChhh
Confidence 8888875444222 79 66 6999998763 57999987643
No 120
>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=47.11 E-value=12 Score=26.68 Aligned_cols=42 Identities=24% Similarity=0.580 Sum_probs=29.6
Q ss_pred eecccccccccc---ccccccccEecccccccc-cCCCCCCCcCCC
Q 020290 96 DCPVCYEPLNIP---VYQCGNGHVVCHRCCCDL-MNKCPSCRLPNG 137 (328)
Q Consensus 96 ~CpiC~~~l~~P---v~qC~~GH~~C~~C~~~~-~~~CP~C~~~~~ 137 (328)
.|-.|..-|-+. .+-|.--..||..|...+ ...||.|...+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 366666666432 235654558999999986 789999988764
No 121
>PF12773 DZR: Double zinc ribbon
Probab=46.83 E-value=13 Score=25.05 Aligned_cols=9 Identities=56% Similarity=1.302 Sum_probs=3.5
Q ss_pred ecccccccc
Q 020290 97 CPVCYEPLN 105 (328)
Q Consensus 97 CpiC~~~l~ 105 (328)
|+.|...|.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444443333
No 122
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=46.42 E-value=15 Score=26.37 Aligned_cols=35 Identities=34% Similarity=0.814 Sum_probs=19.6
Q ss_pred eeeecccCCCCCCcc-cccchhhhcccccccCCCCCCCCCCccccc
Q 020290 151 IQVACENADYGCKEK-MSYSEKYDHGRACHYTPCSCPLAACNFVGS 195 (328)
Q Consensus 151 l~v~C~~~~~GC~~~-~~~~~~~~He~~C~~~~~~CP~~gC~~~g~ 195 (328)
..+.||| |... |..-..=.- ...++.||. |+|.|+
T Consensus 24 ~~F~CPn----CG~~~I~RC~~CRk----~~~~Y~CP~--CGF~GP 59 (59)
T PRK14890 24 VKFLCPN----CGEVIIYRCEKCRK----QSNPYTCPK--CGFEGP 59 (59)
T ss_pred CEeeCCC----CCCeeEeechhHHh----cCCceECCC--CCCcCc
Confidence 4677877 7665 333221000 124678975 998874
No 123
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.61 E-value=5.6 Score=39.06 Aligned_cols=37 Identities=27% Similarity=0.804 Sum_probs=27.7
Q ss_pred eeecccccccc-----ccccccccccEecccccccc-----c-CCCCCCC
Q 020290 95 LDCPVCYEPLN-----IPVYQCGNGHVVCHRCCCDL-----M-NKCPSCR 133 (328)
Q Consensus 95 l~CpiC~~~l~-----~Pv~qC~~GH~~C~~C~~~~-----~-~~CP~C~ 133 (328)
..|.||-+..- .||-.| ||+|=..|+..| + ..||.|+
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~c--Ghifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTC--GHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred ceeeEeccCCccccccccccch--hhHHHHHHHHHHHccCCccCCCCcee
Confidence 47999955431 244469 999999999987 2 4799998
No 124
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=44.85 E-value=16 Score=34.97 Aligned_cols=41 Identities=27% Similarity=0.601 Sum_probs=28.0
Q ss_pred eeecccccccccccc-cc--ccc--cEeccccccccc---CCCCCCCcC
Q 020290 95 LDCPVCYEPLNIPVY-QC--GNG--HVVCHRCCCDLM---NKCPSCRLP 135 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~-qC--~~G--H~~C~~C~~~~~---~~CP~C~~~ 135 (328)
-.||||...-.--+. .- ..| +..|+-|-..|. .+||.|...
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 479999987543222 22 235 568999998873 689999753
No 125
>smart00301 DM Doublesex DNA-binding motif.
Probab=44.58 E-value=13 Score=26.34 Aligned_cols=39 Identities=18% Similarity=0.491 Sum_probs=28.7
Q ss_pred CCcccccchhhhcccccccCCCCCCCCCCccccccchHhhh
Q 020290 162 CKEKMSYSEKYDHGRACHYTPCSCPLAACNFVGSFHQIYQH 202 (328)
Q Consensus 162 C~~~~~~~~~~~He~~C~~~~~~CP~~gC~~~g~~~~L~~H 202 (328)
|.-......++-|-..|+|+.|.|+ .|.....+..+...
T Consensus 8 CrnHg~~~~lKGHKr~C~~r~C~C~--kC~Li~~Rq~vma~ 46 (54)
T smart00301 8 CENHGVKVPLKGHKPECPFRDCECE--KCTLVEKRRALMAL 46 (54)
T ss_pred HhcCCCeeccCCcCCCCCCCCCcCC--CCcChHHHHHHHHH
Confidence 4444556678899999999999996 59877766655543
No 126
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.85 E-value=5.3 Score=40.38 Aligned_cols=26 Identities=35% Similarity=0.815 Sum_probs=21.4
Q ss_pred ccccccEeccccccccc----CCCCCCCcCCC
Q 020290 110 QCGNGHVVCHRCCCDLM----NKCPSCRLPNG 137 (328)
Q Consensus 110 qC~~GH~~C~~C~~~~~----~~CP~C~~~~~ 137 (328)
.| .|+|=..|+.+|. -.||.||.++.
T Consensus 605 PC--~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 605 PC--HHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred ch--HHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 47 8999999999874 37999998764
No 127
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=42.53 E-value=27 Score=27.78 Aligned_cols=38 Identities=16% Similarity=0.473 Sum_probs=22.1
Q ss_pred eeeecCCCCeeeecccccccc-ccccccccccEecccccc
Q 020290 85 VTVTLNDPEVLDCPVCYEPLN-IPVYQCGNGHVVCHRCCC 123 (328)
Q Consensus 85 ~~~~~~~~~~l~CpiC~~~l~-~Pv~qC~~GH~~C~~C~~ 123 (328)
+......+..+.||-|..... .++-. ..+|+.|..|-.
T Consensus 12 ~k~k~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~ 50 (99)
T PRK14892 12 IRPKPKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCGL 50 (99)
T ss_pred cccccCCCcEeECCCCCCeEeeeecCC-CcceEECCCCCC
Confidence 333455667899999996322 22223 346777666644
No 128
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=42.39 E-value=14 Score=27.77 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=30.1
Q ss_pred CCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCcccccchhhhcc
Q 020290 128 KCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEKMSYSEKYDHG 175 (328)
Q Consensus 128 ~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~~~~~~~~He 175 (328)
.||.|+........+.+...+..+.-.|.|. .|..++...+--.|.
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~--eCg~tF~t~es~s~t 48 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNV--NCSATFITYESVQRY 48 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCC--CCCCEEEEEEEEEEE
Confidence 6999987763334455555677788889874 466666665555553
No 129
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=41.39 E-value=11 Score=36.25 Aligned_cols=46 Identities=28% Similarity=0.600 Sum_probs=33.5
Q ss_pred CCCeeeeccccccccccccccccccEecccccccc---cCCCCCCCcCC
Q 020290 91 DPEVLDCPVCYEPLNIPVYQCGNGHVVCHRCCCDL---MNKCPSCRLPN 136 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~---~~~CP~C~~~~ 136 (328)
.++.-.||+|..--..|..-=..|-+||-.|+-.. -+.||+-..+.
T Consensus 297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred CCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 34456799999988888541123999999999874 26899865554
No 130
>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 PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.46 E-value=13 Score=21.40 Aligned_cols=7 Identities=43% Similarity=1.231 Sum_probs=3.1
Q ss_pred CCCCCCc
Q 020290 128 KCPSCRL 134 (328)
Q Consensus 128 ~CP~C~~ 134 (328)
.||.|..
T Consensus 15 fC~~CG~ 21 (23)
T PF13240_consen 15 FCPNCGT 21 (23)
T ss_pred chhhhCC
Confidence 3444443
No 132
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=39.27 E-value=23 Score=24.78 Aligned_cols=33 Identities=24% Similarity=0.617 Sum_probs=22.4
Q ss_pred Ceeeec--ccccccccc------cccc-ccccEecccccccc
Q 020290 93 EVLDCP--VCYEPLNIP------VYQC-GNGHVVCHRCCCDL 125 (328)
Q Consensus 93 ~~l~Cp--iC~~~l~~P------v~qC-~~GH~~C~~C~~~~ 125 (328)
+...|| -|..++..+ ...| .+|+.||..|...+
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 344588 787765432 3367 46999999998765
No 133
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=39.26 E-value=20 Score=36.60 Aligned_cols=34 Identities=21% Similarity=0.447 Sum_probs=19.6
Q ss_pred CCCCCCcCCCCCcch--------hhHHhhhceeeecccCCCCCCcc
Q 020290 128 KCPSCRLPNGHSRST--------AMEKVIESIQVACENADYGCKEK 165 (328)
Q Consensus 128 ~CP~C~~~~~~~r~~--------~le~~l~~l~v~C~~~~~GC~~~ 165 (328)
.||.|..++...... .-...-..+.+.|.| |.|.
T Consensus 54 ~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~----C~Ws 95 (483)
T PF05502_consen 54 DCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSY----CRWS 95 (483)
T ss_pred cCCCCCCcceeEecccccccccccccCCCCCEEEECCC----ceee
Confidence 699998876532110 111223356678987 8885
No 134
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=38.82 E-value=5 Score=44.97 Aligned_cols=43 Identities=30% Similarity=0.729 Sum_probs=34.6
Q ss_pred Ceeeeccccccccc--cccccccccEecccccccc---cCCCCCCCcCCC
Q 020290 93 EVLDCPVCYEPLNI--PVYQCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~~l~~--Pv~qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
+...|+||++++.. -|++| ||.+|..|...+ +..||.|.....
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~c--gh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGC--GHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred cccchHHHHHHHHhcCCeeee--chhHhhhHHHHHHHHhccCcchhhhhh
Confidence 34689999999983 46699 999999999876 468999975443
No 135
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.56 E-value=14 Score=26.06 Aligned_cols=37 Identities=22% Similarity=0.457 Sum_probs=21.6
Q ss_pred eeeeccccccc--cccccccc-cccEecccccccccCCCCC
Q 020290 94 VLDCPVCYEPL--NIPVYQCG-NGHVVCHRCCCDLMNKCPS 131 (328)
Q Consensus 94 ~l~CpiC~~~l--~~Pv~qC~-~GH~~C~~C~~~~~~~CP~ 131 (328)
.-.|++|.+.| .+.|.+|+ +|-.+=+.|+.+. ..|-.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~-g~C~~ 44 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA-GGCIN 44 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC-CceEe
Confidence 35799999999 56666554 2533334455543 34544
No 136
>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=38.34 E-value=25 Score=24.50 Aligned_cols=35 Identities=26% Similarity=0.571 Sum_probs=18.5
Q ss_pred CCCeeeecc--cccccccc----c--cccc-cccEecccccccc
Q 020290 91 DPEVLDCPV--CYEPLNIP----V--YQCG-NGHVVCHRCCCDL 125 (328)
Q Consensus 91 ~~~~l~Cpi--C~~~l~~P----v--~qC~-~GH~~C~~C~~~~ 125 (328)
+++...||- |..++... . +.|+ +++.||..|...+
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 334457988 99988532 1 4566 5999999998765
No 137
>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=37.74 E-value=5.1 Score=36.88 Aligned_cols=40 Identities=33% Similarity=0.774 Sum_probs=28.6
Q ss_pred eeeecccccc--cccccc-----ccccccEecccccccc----cCCCC--CCCcC
Q 020290 94 VLDCPVCYEP--LNIPVY-----QCGNGHVVCHRCCCDL----MNKCP--SCRLP 135 (328)
Q Consensus 94 ~l~CpiC~~~--l~~Pv~-----qC~~GH~~C~~C~~~~----~~~CP--~C~~~ 135 (328)
.-.||+|..- |.|-+. .| =|..|.+|..++ +..|| -|.+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPEC--yHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPEC--YHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHH--HHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 3479999863 333332 48 999999999986 36899 47653
No 138
>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=37.17 E-value=5.7 Score=33.38 Aligned_cols=32 Identities=19% Similarity=0.630 Sum_probs=24.1
Q ss_pred eeeeccccccccc--ccc--cccc----ccEecccccccc
Q 020290 94 VLDCPVCYEPLNI--PVY--QCGN----GHVVCHRCCCDL 125 (328)
Q Consensus 94 ~l~CpiC~~~l~~--Pv~--qC~~----GH~~C~~C~~~~ 125 (328)
..+|.||++-+.. -|. .|.. -|.||..|+.+|
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 4789999998876 333 6621 177999999998
No 139
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=37.10 E-value=15 Score=34.62 Aligned_cols=103 Identities=16% Similarity=0.295 Sum_probs=58.3
Q ss_pred CCeeeeccccccccc-cccccccccEecccccccccCCCCCCCcCCCCCcchh----hHHhhhceeeecccCCCCCCccc
Q 020290 92 PEVLDCPVCYEPLNI-PVYQCGNGHVVCHRCCCDLMNKCPSCRLPNGHSRSTA----MEKVIESIQVACENADYGCKEKM 166 (328)
Q Consensus 92 ~~~l~CpiC~~~l~~-Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~~~~r~~~----le~~l~~l~v~C~~~~~GC~~~~ 166 (328)
...+.|++|..++.. |-+. .|+.= ..+.-.|++|.+.+. |... ++.-..+-++.|+. |...+
T Consensus 159 ~ka~~C~~C~K~YvSmpALk---MHirT----H~l~c~C~iCGKaFS--RPWLLQGHiRTHTGEKPF~C~h----C~kAF 225 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALK---MHIRT----HTLPCECGICGKAFS--RPWLLQGHIRTHTGEKPFSCPH----CGKAF 225 (279)
T ss_pred cccccCCCCCceeeehHHHh---hHhhc----cCCCccccccccccc--chHHhhcccccccCCCCccCCc----ccchh
Confidence 346889999988653 3221 22210 012336777877664 2222 22333344667775 66544
Q ss_pred c-cchhhhccc-ccccCCCCCCCCCCccccccc-hHhhhhhhccCC
Q 020290 167 S-YSEKYDHGR-ACHYTPCSCPLAACNFVGSFH-QIYQHFRGVHKH 209 (328)
Q Consensus 167 ~-~~~~~~He~-~C~~~~~~CP~~gC~~~g~~~-~L~~Hl~~~H~~ 209 (328)
. ..+|+.|+. .=....+.|+. |+....++ .|..|++..+..
T Consensus 226 ADRSNLRAHmQTHS~~K~~qC~~--C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 226 ADRSNLRAHMQTHSDVKKHQCPR--CGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred cchHHHHHHHHhhcCCccccCcc--hhhHHHHHHHHHHhhhhcccc
Confidence 3 667777764 34556778854 88766554 477787766543
No 140
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=36.67 E-value=12 Score=20.33 Aligned_cols=22 Identities=36% Similarity=0.664 Sum_probs=13.8
Q ss_pred CCCCCCCcccc-ccchHhhhhhhcc
Q 020290 184 SCPLAACNFVG-SFHQIYQHFRGVH 207 (328)
Q Consensus 184 ~CP~~gC~~~g-~~~~L~~Hl~~~H 207 (328)
.|+. |+... ...+|..|+...|
T Consensus 2 ~C~~--C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCPI--CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-SS--TS-EESSHHHHHHHHHHHS
T ss_pred CCcC--CCCcCCcHHHHHHHHHhhC
Confidence 4655 77655 4467899988766
No 141
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=36.50 E-value=3 Score=28.99 Aligned_cols=43 Identities=28% Similarity=0.540 Sum_probs=29.7
Q ss_pred eeeeccccccccccc-cccc-cccEecccccccccCCCCCCCcCC
Q 020290 94 VLDCPVCYEPLNIPV-YQCG-NGHVVCHRCCCDLMNKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv-~qC~-~GH~~C~~C~~~~~~~CP~C~~~~ 136 (328)
.+.|..|.......- .||. +|...|.+|+..--..|..|...+
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~Gii 51 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNGII 51 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhchh
Confidence 477999988764432 3654 499999999987434677775543
No 142
>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=35.54 E-value=14 Score=25.46 Aligned_cols=32 Identities=28% Similarity=0.613 Sum_probs=23.1
Q ss_pred CeeeeccccccccccccccccccEeccccccc
Q 020290 93 EVLDCPVCYEPLNIPVYQCGNGHVVCHRCCCD 124 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~ 124 (328)
+=|.|..|...|.+..+.=.+|..+|..|..+
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 44889999988877644344578888888654
No 143
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=35.03 E-value=4 Score=27.98 Aligned_cols=31 Identities=19% Similarity=0.526 Sum_probs=17.3
Q ss_pred ccccchhhhcccccccCCCCCCCCCCccccccc
Q 020290 165 KMSYSEKYDHGRACHYTPCSCPLAACNFVGSFH 197 (328)
Q Consensus 165 ~~~~~~~~~He~~C~~~~~~CP~~gC~~~g~~~ 197 (328)
.+....++.|...|+|+.+.|. .|.....+.
T Consensus 11 HG~~~~lKgHk~~C~~~~C~C~--kC~li~eRq 41 (47)
T PF00751_consen 11 HGVIVPLKGHKRYCPFRDCQCD--KCALIAERQ 41 (47)
T ss_dssp TT---TTTT-GGG-TTTT--SH--HHHHHHHHH
T ss_pred CCcccchhhhccccCcCCCcCC--CCcCcHHHH
Confidence 3446667899999999999995 487654443
No 144
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=35.01 E-value=25 Score=33.90 Aligned_cols=43 Identities=35% Similarity=0.899 Sum_probs=33.4
Q ss_pred eeecccccccc---ccccccccccEecccccccc---cCCCCCCCcCCC
Q 020290 95 LDCPVCYEPLN---IPVYQCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 95 l~CpiC~~~l~---~Pv~qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
-.||+|..++. .+...|++|+..|..|+..+ ...||.|+++..
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 46999999873 23347888999999998886 368999997653
No 145
>PRK00420 hypothetical protein; Validated
Probab=34.01 E-value=24 Score=28.80 Aligned_cols=25 Identities=40% Similarity=0.616 Sum_probs=16.5
Q ss_pred eeeccccccccccccccccccEecccccc
Q 020290 95 LDCPVCYEPLNIPVYQCGNGHVVCHRCCC 123 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~ 123 (328)
-.||+|..+|... .+|+.+|..|-.
T Consensus 24 ~~CP~Cg~pLf~l----k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL----KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec----CCCceECCCCCC
Confidence 4799999877642 337767655544
No 146
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=33.75 E-value=22 Score=29.83 Aligned_cols=24 Identities=38% Similarity=0.808 Sum_probs=18.2
Q ss_pred eeeccccccccccccccccccEecccccc
Q 020290 95 LDCPVCYEPLNIPVYQCGNGHVVCHRCCC 123 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~ 123 (328)
.+||.|..||-. ..|-+||..|-.
T Consensus 29 ~hCp~Cg~PLF~-----KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFR-----KDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCccee-----eCCeEECCCCCc
Confidence 589999997653 449888877763
No 147
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=33.17 E-value=18 Score=32.06 Aligned_cols=47 Identities=26% Similarity=0.272 Sum_probs=26.7
Q ss_pred CCcCCCCCcchhhHHhhhceeeecccCCCCCCcccccchhhhccccc
Q 020290 132 CRLPNGHSRSTAMEKVIESIQVACENADYGCKEKMSYSEKYDHGRAC 178 (328)
Q Consensus 132 C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~~~~~~~~He~~C 178 (328)
|...+.+..-..-|+...-.+..||....||.|.+.+.++..|....
T Consensus 24 C~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~ 70 (198)
T PF03145_consen 24 CTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDK 70 (198)
T ss_dssp ---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHH
T ss_pred CcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHH
Confidence 44433333333445556667889998778999999999999998653
No 148
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.78 E-value=34 Score=32.90 Aligned_cols=41 Identities=27% Similarity=0.488 Sum_probs=27.6
Q ss_pred eeeecccccccccccc-cc-ccc--cEeccccccccc---CCCCCCCc
Q 020290 94 VLDCPVCYEPLNIPVY-QC-GNG--HVVCHRCCCDLM---NKCPSCRL 134 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC-~~G--H~~C~~C~~~~~---~~CP~C~~ 134 (328)
.-.||||...-.--+. .- ..| +..|+-|-..|. ..||.|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 3579999987532222 11 235 568999988873 68999975
No 149
>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=32.31 E-value=16 Score=22.59 Aligned_cols=22 Identities=23% Similarity=0.535 Sum_probs=9.6
Q ss_pred CCCCCCCCccccccchHhhhhh
Q 020290 183 CSCPLAACNFVGSFHQIYQHFR 204 (328)
Q Consensus 183 ~~CP~~gC~~~g~~~~L~~Hl~ 204 (328)
+.||..+|...........|++
T Consensus 3 vrCPvkdC~EEv~lgKY~~H~s 24 (30)
T PF10426_consen 3 VRCPVKDCDEEVSLGKYSHHLS 24 (30)
T ss_dssp EE--STT---EEEHHHHHHHHH
T ss_pred cccccccCcchhhhhhhccccc
Confidence 3566666666665555555554
No 150
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.25 E-value=44 Score=37.90 Aligned_cols=42 Identities=26% Similarity=0.635 Sum_probs=30.3
Q ss_pred eeeeccccccccccccccc-cccE-----eccccccccc------CCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPVYQCG-NGHV-----VCHRCCCDLM------NKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~qC~-~GH~-----~C~~C~~~~~------~~CP~C~~~~~ 137 (328)
.+.||-|....... .|+ ||.. .|..|-.++. ..||.|..++.
T Consensus 667 ~rkCPkCG~~t~~~--fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYEN--RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCccccc--cCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 68999999965332 444 4754 5999988752 27999998764
No 151
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=30.46 E-value=30 Score=36.63 Aligned_cols=61 Identities=21% Similarity=0.563 Sum_probs=40.5
Q ss_pred eeeecccccccccccc--ccccccEecccccccc-------cCCCCCCCcCCCCCcchhhHHhhhceeeeccc
Q 020290 94 VLDCPVCYEPLNIPVY--QCGNGHVVCHRCCCDL-------MNKCPSCRLPNGHSRSTAMEKVIESIQVACEN 157 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~--qC~~GH~~C~~C~~~~-------~~~CP~C~~~~~~~r~~~le~~l~~l~v~C~~ 157 (328)
-|.||+++.-++-|.. .| .|+-|.+=..-+ ...||+|.+...+. ...+...+..+...|+.
T Consensus 306 SL~CPl~~~Rm~~P~r~~~C--kHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e-~l~iD~~~~~iL~~~~~ 375 (636)
T KOG2169|consen 306 SLNCPLSKMRMSLPARGHTC--KHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFE-GLIIDGYFLNILQSCQA 375 (636)
T ss_pred EecCCcccceeecCCccccc--ccceecchhhhHHhccCCCeeeCccCCcccccc-chhhhHHHHHHHhhccC
Confidence 3899999999998876 67 887765543322 14799998876542 34445555555566654
No 152
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=30.29 E-value=24 Score=24.27 Aligned_cols=29 Identities=24% Similarity=0.827 Sum_probs=19.3
Q ss_pred eeccccccccccc--cccc-cccEeccccccc
Q 020290 96 DCPVCYEPLNIPV--YQCG-NGHVVCHRCCCD 124 (328)
Q Consensus 96 ~CpiC~~~l~~Pv--~qC~-~GH~~C~~C~~~ 124 (328)
.|++|...|..-. ..|. +|++||..|...
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~ 35 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSN 35 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCC
Confidence 5888887665321 1332 299999999775
No 153
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=30.23 E-value=14 Score=33.33 Aligned_cols=114 Identities=16% Similarity=0.327 Sum_probs=57.4
Q ss_pred CCCCeeeeccccccccccccccccccEecccccccccCCCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCcccc-c
Q 020290 90 NDPEVLDCPVCYEPLNIPVYQCGNGHVVCHRCCCDLMNKCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEKMS-Y 168 (328)
Q Consensus 90 ~~~~~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~~-~ 168 (328)
++.+.+.|-||..-|.-..+. |.|+-|.+=+.+ ..|..|.+.+... ..|.+-+..-.--=||+-.-|...++ .
T Consensus 113 sd~d~ftCrvCgK~F~lQRml--nrh~kch~~vkr--~lct~cgkgfndt--fdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRML--NRHLKCHSDVKR--HLCTFCGKGFNDT--FDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHH--HHHhhhccHHHH--HHHhhccCcccch--hhhhhhhccccCccccchhhhhHHHHhh
Confidence 356789999999988643222 256555443333 3566777665432 11111111111111222122443332 2
Q ss_pred chhhhccccc-----cc-------CCCCCCCCCCcccccc-chHhhhhhhccCCCc
Q 020290 169 SEKYDHGRAC-----HY-------TPCSCPLAACNFVGSF-HQIYQHFRGVHKHAA 211 (328)
Q Consensus 169 ~~~~~He~~C-----~~-------~~~~CP~~gC~~~g~~-~~L~~Hl~~~H~~~~ 211 (328)
-.++.|.+.= .| ..+-| ..|++...+ ..++.|+...|....
T Consensus 187 csleshl~kvhgv~~~yaykerr~kl~vc--edcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAKLYVC--EDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhheeee--cccCCCCCChhHHHHHHHhcCCCCH
Confidence 2334443211 11 13567 358887755 568899999898754
No 154
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.67 E-value=64 Score=33.09 Aligned_cols=51 Identities=29% Similarity=0.600 Sum_probs=33.4
Q ss_pred CCeeeecCCC---Ceeeeccccccccccccccc--------cccEecccccccc--cCCCCCCCcC
Q 020290 83 GPVTVTLNDP---EVLDCPVCYEPLNIPVYQCG--------NGHVVCHRCCCDL--MNKCPSCRLP 135 (328)
Q Consensus 83 ~~~~~~~~~~---~~l~CpiC~~~l~~Pv~qC~--------~GH~~C~~C~~~~--~~~CP~C~~~ 135 (328)
..+.+|++.. ..+.|..|..+++=| .|. .+...|..|-... ...||.|...
T Consensus 199 ~qvLvflnrrGya~~~~C~~Cg~~~~C~--~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 199 EQSILFLNRRGYSKNLLCRSCGYILCCP--NCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CcEEEEEeCCcCCCeeEhhhCcCccCCC--CCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3455565433 246788888887655 342 2356799997764 4689999764
No 155
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=29.01 E-value=47 Score=20.61 Aligned_cols=9 Identities=44% Similarity=1.099 Sum_probs=6.1
Q ss_pred CCCCCCCcC
Q 020290 127 NKCPSCRLP 135 (328)
Q Consensus 127 ~~CP~C~~~ 135 (328)
..||.|..+
T Consensus 18 ~~CP~Cg~~ 26 (33)
T cd00350 18 WVCPVCGAP 26 (33)
T ss_pred CcCcCCCCc
Confidence 478888653
No 156
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=28.49 E-value=28 Score=34.47 Aligned_cols=49 Identities=16% Similarity=0.328 Sum_probs=35.5
Q ss_pred eeeecccCCCCCCcccccchhhhcc-cccccCCCCCCCCCCccccccchHhhhhh
Q 020290 151 IQVACENADYGCKEKMSYSEKYDHG-RACHYTPCSCPLAACNFVGSFHQIYQHFR 204 (328)
Q Consensus 151 l~v~C~~~~~GC~~~~~~~~~~~He-~~C~~~~~~CP~~gC~~~g~~~~L~~Hl~ 204 (328)
-.+.|+| +|...++..++.+|. +.|+++...|....+. .....+..|..
T Consensus 113 ~~~~C~~---~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~--~~~~~~~~h~~ 162 (391)
T KOG0297|consen 113 DPLKCPH---RCGVQVPRDDLEDHLEAECPRRSLKCSLCQSD--SILILLEAHEE 162 (391)
T ss_pred CcccCcc---ccccccchHHHHHHHhcccccccccchhhcCc--cchhhhhhcCC
Confidence 4688987 499999999999996 6999999988763333 23345555543
No 157
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=28.26 E-value=28 Score=33.51 Aligned_cols=31 Identities=29% Similarity=0.698 Sum_probs=24.2
Q ss_pred Ceeeecccccccccc-ccccccccEecccccc
Q 020290 93 EVLDCPVCYEPLNIP-VYQCGNGHVVCHRCCC 123 (328)
Q Consensus 93 ~~l~CpiC~~~l~~P-v~qC~~GH~~C~~C~~ 123 (328)
....|-.|-++-.+- +++|+..|+.|..|+.
T Consensus 220 ~ni~C~~Ctdv~~~vlvf~Cns~HvtC~dCFr 251 (446)
T KOG0006|consen 220 RNITCITCTDVRSPVLVFQCNSRHVTCLDCFR 251 (446)
T ss_pred ccceeEEecCCccceEEEecCCceeehHHhhh
Confidence 457899999876532 3499888999999987
No 158
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=27.95 E-value=14 Score=37.01 Aligned_cols=42 Identities=29% Similarity=0.616 Sum_probs=30.2
Q ss_pred CeeeecCCCCeeeecccccccccccc--ccc-cccEecccccccc
Q 020290 84 PVTVTLNDPEVLDCPVCYEPLNIPVY--QCG-NGHVVCHRCCCDL 125 (328)
Q Consensus 84 ~~~~~~~~~~~l~CpiC~~~l~~Pv~--qC~-~GH~~C~~C~~~~ 125 (328)
++-..++|.++..||+|...|..-.. .|. +|-+.|..|..-+
T Consensus 170 svVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~i 214 (505)
T KOG1842|consen 170 SVVPWLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFI 214 (505)
T ss_pred ccccccCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHhc
Confidence 33445678889999999999975433 333 3999999997643
No 159
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=27.61 E-value=17 Score=22.41 Aligned_cols=19 Identities=42% Similarity=1.069 Sum_probs=8.8
Q ss_pred cEecccccccc-------cCCCCCCC
Q 020290 115 HVVCHRCCCDL-------MNKCPSCR 133 (328)
Q Consensus 115 H~~C~~C~~~~-------~~~CP~C~ 133 (328)
|.||..|-... ...||.|.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 56676665543 13566664
No 160
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.51 E-value=48 Score=35.70 Aligned_cols=51 Identities=29% Similarity=0.648 Sum_probs=34.5
Q ss_pred CCeeeecCCC---Ceeeeccccccccccccccc--------cccEeccccccc--ccCCCCCCCcC
Q 020290 83 GPVTVTLNDP---EVLDCPVCYEPLNIPVYQCG--------NGHVVCHRCCCD--LMNKCPSCRLP 135 (328)
Q Consensus 83 ~~~~~~~~~~---~~l~CpiC~~~l~~Pv~qC~--------~GH~~C~~C~~~--~~~~CP~C~~~ 135 (328)
...-+|++.. ..+.|..|..+++=| .|. .+...|..|-.. ....||.|...
T Consensus 421 eQ~llflnRRGys~~l~C~~Cg~v~~Cp--~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 421 EQVLLFLNRRGYAPLLLCRDCGYIAECP--NCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CeEEEEEccCCccceeecccCCCcccCC--CCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3345555433 257899998888755 341 246789999776 34789999876
No 161
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=27.08 E-value=41 Score=22.31 Aligned_cols=23 Identities=35% Similarity=0.849 Sum_probs=15.1
Q ss_pred eeeccccccccccccccccccEecccc
Q 020290 95 LDCPVCYEPLNIPVYQCGNGHVVCHRC 121 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC~~GH~~C~~C 121 (328)
-.||.|..||-.. .+|.++|-.|
T Consensus 18 ~~Cp~C~~PL~~~----k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMRD----KDGKIYCVSC 40 (41)
T ss_pred CccCCCCCeeEEe----cCCCEECCCC
Confidence 3699997665442 2477777766
No 162
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.07 E-value=46 Score=27.15 Aligned_cols=38 Identities=32% Similarity=0.752 Sum_probs=23.5
Q ss_pred eecccccccccc------------ccccc-cccEecccccccc---cCCCCCCC
Q 020290 96 DCPVCYEPLNIP------------VYQCG-NGHVVCHRCCCDL---MNKCPSCR 133 (328)
Q Consensus 96 ~CpiC~~~l~~P------------v~qC~-~GH~~C~~C~~~~---~~~CP~C~ 133 (328)
.|-.|...|..+ .|+|+ +.+.||.+|-.-+ ...||.|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 488888776533 24554 3777888884432 25688774
No 163
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.90 E-value=28 Score=20.41 Aligned_cols=6 Identities=50% Similarity=1.353 Sum_probs=2.5
Q ss_pred eccccc
Q 020290 97 CPVCYE 102 (328)
Q Consensus 97 CpiC~~ 102 (328)
||-|..
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444444
No 164
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=26.60 E-value=45 Score=31.22 Aligned_cols=99 Identities=19% Similarity=0.517 Sum_probs=60.5
Q ss_pred eeeecccccccccccc-ccccccEecc----ccccccc-----------CCCCCCCc----------------CCCCCcc
Q 020290 94 VLDCPVCYEPLNIPVY-QCGNGHVVCH----RCCCDLM-----------NKCPSCRL----------------PNGHSRS 141 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~-qC~~GH~~C~----~C~~~~~-----------~~CP~C~~----------------~~~~~r~ 141 (328)
...|-.|..+-+-|+- +| |.+-|- .|+.+.. ..|-.|-. |+....+
T Consensus 51 RAFCYFC~s~qrlp~Ca~C--gk~KCm~k~gdCvvkH~g~~~tGl~mvGaiCDfCEawvCHgrkCl~~HaC~Cpl~da~C 128 (314)
T PF06524_consen 51 RAFCYFCQSVQRLPMCAHC--GKTKCMLKTGDCVVKHPGVFTTGLGMVGAICDFCEAWVCHGRKCLSTHACTCPLQDAVC 128 (314)
T ss_pred cceeehhhhhhcCchhhhc--CCeeeeccCCCeEEecCceeecccchhhhhhccchhheeccccccccccccCcCCCcEe
Confidence 3568889999888987 88 877664 4766531 23333322 2221111
Q ss_pred hhhHHhhh---ceeeecccCCCCCCcccccchhhhcccccccC---CCCCCCCCCccccccchHh
Q 020290 142 TAMEKVIE---SIQVACENADYGCKEKMSYSEKYDHGRACHYT---PCSCPLAACNFVGSFHQIY 200 (328)
Q Consensus 142 ~~le~~l~---~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~---~~~CP~~gC~~~g~~~~L~ 200 (328)
.--++-+. --.+.|.+ |...+.-.+--.|+.+|+.. .++| ..|+-.|...=|.
T Consensus 129 ~EC~R~vw~hGGrif~Csf----C~~flCEDDQFEHQAsCQvLe~E~~KC--~SCNrlGq~sCLR 187 (314)
T PF06524_consen 129 IECERGVWDHGGRIFKCSF----CDNFLCEDDQFEHQASCQVLESETFKC--QSCNRLGQYSCLR 187 (314)
T ss_pred eeeecccccCCCeEEEeec----CCCeeeccchhhhhhhhhhhhcccccc--cccccccchhhhh
Confidence 11122222 22467776 88888888888999999875 4778 4587777655543
No 165
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=25.85 E-value=14 Score=29.57 Aligned_cols=46 Identities=22% Similarity=0.403 Sum_probs=31.0
Q ss_pred CCCeeeecccccccccccccccc----------------ccEecccccccc---cCCCCCCCcCC
Q 020290 91 DPEVLDCPVCYEPLNIPVYQCGN----------------GHVVCHRCCCDL---MNKCPSCRLPN 136 (328)
Q Consensus 91 ~~~~l~CpiC~~~l~~Pv~qC~~----------------GH~~C~~C~~~~---~~~CP~C~~~~ 136 (328)
|...-.|.||..-+-++-..|.. .|.|=..|+.++ .+.||.|.+.-
T Consensus 43 Di~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 43 DIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred eeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 44556799999877665444422 466656688876 47899997754
No 166
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=25.63 E-value=30 Score=31.77 Aligned_cols=17 Identities=35% Similarity=0.784 Sum_probs=11.7
Q ss_pred eeecccccccccccccc
Q 020290 95 LDCPVCYEPLNIPVYQC 111 (328)
Q Consensus 95 l~CpiC~~~l~~Pv~qC 111 (328)
|.|+||+.+|.+|+-.|
T Consensus 261 fvCsVCLsvfc~p~~~C 277 (296)
T COG5242 261 FVCSVCLSVFCRPVPVC 277 (296)
T ss_pred eehhhhheeecCCcCcC
Confidence 67888888887665433
No 167
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=25.38 E-value=43 Score=36.29 Aligned_cols=41 Identities=29% Similarity=0.743 Sum_probs=31.5
Q ss_pred Ceeeecccccccc--ccccccc-cccEecccccccc----------cCCCCCCC
Q 020290 93 EVLDCPVCYEPLN--IPVYQCG-NGHVVCHRCCCDL----------MNKCPSCR 133 (328)
Q Consensus 93 ~~l~CpiC~~~l~--~Pv~qC~-~GH~~C~~C~~~~----------~~~CP~C~ 133 (328)
+.+.|.||.+-++ .||..|. +=|+|=-.||.+| ...||.|.
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cq 243 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQ 243 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCccc
Confidence 4699999999986 5788774 2467766788887 14799998
No 168
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.28 E-value=29 Score=26.40 Aligned_cols=45 Identities=22% Similarity=0.581 Sum_probs=16.9
Q ss_pred Ceeeeccccccccc----ccc-ccc-cccEecccccccc----cCCCCCCCcCCC
Q 020290 93 EVLDCPVCYEPLNI----PVY-QCG-NGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 93 ~~l~CpiC~~~l~~----Pv~-qC~-~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
..-.|.||.+-+-. -+| .|. ++-.+|+.|..-- ...||.|+.+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 34579999987631 233 443 2788999998631 368999986653
No 169
>PHA03096 p28-like protein; Provisional
Probab=24.91 E-value=18 Score=34.33 Aligned_cols=38 Identities=21% Similarity=0.309 Sum_probs=26.7
Q ss_pred eeeccccccccc--cc------c-ccccccEeccccccccc------CCCCCCCc
Q 020290 95 LDCPVCYEPLNI--PV------Y-QCGNGHVVCHRCCCDLM------NKCPSCRL 134 (328)
Q Consensus 95 l~CpiC~~~l~~--Pv------~-qC~~GH~~C~~C~~~~~------~~CP~C~~ 134 (328)
-.|.||.+.... +. . .| -|.||..|+..|. ..||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c--~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEI--KHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccC--CcHHHHHHHHHHHHhhhhcccCccccc
Confidence 569999998642 21 1 48 8999999999772 35666654
No 170
>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=24.73 E-value=46 Score=27.03 Aligned_cols=30 Identities=27% Similarity=0.589 Sum_probs=17.9
Q ss_pred eeecccccccccc---ccccc-cccEeccccccc
Q 020290 95 LDCPVCYEPLNIP---VYQCG-NGHVVCHRCCCD 124 (328)
Q Consensus 95 l~CpiC~~~l~~P---v~qC~-~GH~~C~~C~~~ 124 (328)
-.|.+|..+|.-. -..|. ++|.+|+.|...
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred cchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 3799998876421 11333 388899988765
No 171
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.64 E-value=41 Score=28.21 Aligned_cols=40 Identities=25% Similarity=0.569 Sum_probs=27.4
Q ss_pred eeeeccccccccccccccccccEecccccccccCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPVYQCGNGHVVCHRCCCDLMNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~~ 137 (328)
.--||-|...+---+-.| |+++|-.=-. ...||.|.+...
T Consensus 77 ~PgCP~CGn~~~fa~C~C--Gkl~Ci~g~~--~~~CPwCg~~g~ 116 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVCGC--GKLFCIDGEG--EVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCcChhcEEEecC--CCEEEeCCCC--CEECCCCCCeee
Confidence 367999998765433355 9999844322 258999987654
No 172
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=24.36 E-value=3.4e+02 Score=25.35 Aligned_cols=19 Identities=21% Similarity=0.546 Sum_probs=9.4
Q ss_pred ceeeecccCCCCCCcccccchhh
Q 020290 150 SIQVACENADYGCKEKMSYSEKY 172 (328)
Q Consensus 150 ~l~v~C~~~~~GC~~~~~~~~~~ 172 (328)
..+|.|.+ |..++-+..+.
T Consensus 155 ~~rv~Cgh----C~~~Fl~~~~~ 173 (256)
T PF09788_consen 155 SCRVICGH----CSNTFLFNTLT 173 (256)
T ss_pred ceeEECCC----CCCcEeccCCC
Confidence 34455554 55555444443
No 173
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=24.33 E-value=32 Score=25.93 Aligned_cols=36 Identities=28% Similarity=0.375 Sum_probs=18.9
Q ss_pred hcccccccCCCCCCCCCCcccc-ccchHhhhhhhc-cCCC
Q 020290 173 DHGRACHYTPCSCPLAACNFVG-SFHQIYQHFRGV-HKHA 210 (328)
Q Consensus 173 ~He~~C~~~~~~CP~~gC~~~g-~~~~L~~Hl~~~-H~~~ 210 (328)
.+...-......|+. |+... +...|..|+... |...
T Consensus 41 ~~~~~~~~~~~~C~~--C~~~f~s~~~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 41 NYLRKKVKESFRCPY--CNKTFRSREALQEHMRSKHHKKR 78 (100)
T ss_dssp --------SSEEBSS--SS-EESSHHHHHHHHHHTTTTC-
T ss_pred cccccccCCCCCCCc--cCCCCcCHHHHHHHHcCccCCCc
Confidence 333333333577865 77654 568899999876 6553
No 174
>PLN02436 cellulose synthase A
Probab=23.77 E-value=41 Score=37.50 Aligned_cols=44 Identities=23% Similarity=0.600 Sum_probs=31.4
Q ss_pred eeeecccccccc-----ccccccc-cccEecccccccc----cCCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLN-----IPVYQCG-NGHVVCHRCCCDL----MNKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~C~~~~~ 137 (328)
.-.|.||.+-+- .|-.-|. ||--+|..|.+-- +..||.|+....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 347999999763 2323554 4888999998642 478999988654
No 175
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.51 E-value=46 Score=29.42 Aligned_cols=12 Identities=33% Similarity=0.819 Sum_probs=8.5
Q ss_pred CCCCCCCcCCCC
Q 020290 127 NKCPSCRLPNGH 138 (328)
Q Consensus 127 ~~CP~C~~~~~~ 138 (328)
..||+|..++..
T Consensus 218 GeCPYCS~Pial 229 (234)
T KOG3268|consen 218 GECPYCSDPIAL 229 (234)
T ss_pred ccCCCCCCccee
Confidence 468888877653
No 176
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=22.46 E-value=19 Score=24.85 Aligned_cols=40 Identities=25% Similarity=0.742 Sum_probs=21.3
Q ss_pred eeccccccccccccccccccEecccccccc---cCCCCCCCcCCC
Q 020290 96 DCPVCYEPLNIPVYQCGNGHVVCHRCCCDL---MNKCPSCRLPNG 137 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~---~~~CP~C~~~~~ 137 (328)
.|--|-..-+. ...|. .|-.|-.|+..+ +..||+|..++.
T Consensus 4 nCKsCWf~~k~-Li~C~-dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 4 NCKSCWFANKG-LIKCS-DHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ---SS-S--SS-EEE-S-S-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cChhhhhcCCC-eeeec-chhHHHHHHHHHhccccCCCcccCcCc
Confidence 34455443333 23573 588999998875 478999988764
No 177
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.43 E-value=68 Score=32.88 Aligned_cols=39 Identities=21% Similarity=0.590 Sum_probs=25.2
Q ss_pred cEecccccccccCCCCCCCcCCCCCcchhhHHhhhceeeecccCCCCCCcccc
Q 020290 115 HVVCHRCCCDLMNKCPSCRLPNGHSRSTAMEKVIESIQVACENADYGCKEKMS 167 (328)
Q Consensus 115 H~~C~~C~~~~~~~CP~C~~~~~~~r~~~le~~l~~l~v~C~~~~~GC~~~~~ 167 (328)
.+.|..|-... .||.|..++++.... -.+.|.+ |....+
T Consensus 213 ~~~C~~Cg~~~--~C~~C~~~l~~h~~~--------~~l~Ch~----Cg~~~~ 251 (505)
T TIGR00595 213 NLLCRSCGYIL--CCPNCDVSLTYHKKE--------GKLRCHY----CGYQEP 251 (505)
T ss_pred eeEhhhCcCcc--CCCCCCCceEEecCC--------CeEEcCC----CcCcCC
Confidence 45899997754 799998877653221 1467776 665543
No 178
>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=21.91 E-value=37 Score=33.32 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=7.2
Q ss_pred CCCCCCcCCC
Q 020290 128 KCPSCRLPNG 137 (328)
Q Consensus 128 ~CP~C~~~~~ 137 (328)
.||+||+.+.
T Consensus 342 ~CPtCRa~FC 351 (358)
T PF10272_consen 342 PCPTCRAKFC 351 (358)
T ss_pred CCCCCcccce
Confidence 6888887653
No 179
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.68 E-value=27 Score=29.44 Aligned_cols=34 Identities=26% Similarity=0.661 Sum_probs=19.3
Q ss_pred eeeecccccc-ccccccccccccEecccccccccCCCCCCCcCC
Q 020290 94 VLDCPVCYEP-LNIPVYQCGNGHVVCHRCCCDLMNKCPSCRLPN 136 (328)
Q Consensus 94 ~l~CpiC~~~-l~~Pv~qC~~GH~~C~~C~~~~~~~CP~C~~~~ 136 (328)
...|.||+.. |.+ -| ||. |+.|-.+ .|-.|....
T Consensus 65 datC~IC~KTKFAD---G~--GH~-C~YCq~r---~CARCGGrv 99 (169)
T KOG3799|consen 65 DATCGICHKTKFAD---GC--GHN-CSYCQTR---FCARCGGRV 99 (169)
T ss_pred Ccchhhhhhccccc---cc--Ccc-cchhhhh---HHHhcCCee
Confidence 4589999875 344 46 773 5555432 344454433
No 180
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.11 E-value=43 Score=31.21 Aligned_cols=42 Identities=24% Similarity=0.388 Sum_probs=32.9
Q ss_pred eeeeccccccccccc-----cccccccEeccccccccc-CCCCCCCcCCC
Q 020290 94 VLDCPVCYEPLNIPV-----YQCGNGHVVCHRCCCDLM-NKCPSCRLPNG 137 (328)
Q Consensus 94 ~l~CpiC~~~l~~Pv-----~qC~~GH~~C~~C~~~~~-~~CP~C~~~~~ 137 (328)
.|+|||=...|..-. .+| ||+|=.+-+..+. ..|+.|...+.
T Consensus 111 ~fiCPvtgleMng~~~F~~l~~C--GcV~SerAlKeikas~C~~C~a~y~ 158 (293)
T KOG3113|consen 111 RFICPVTGLEMNGKYRFCALRCC--GCVFSERALKEIKASVCHVCGAAYQ 158 (293)
T ss_pred eeecccccceecceEEEEEEecc--ceeccHHHHHHhhhccccccCCccc
Confidence 599999999887532 168 9999877777663 68999998875
No 181
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.09 E-value=7.8e+02 Score=24.02 Aligned_cols=81 Identities=21% Similarity=0.432 Sum_probs=45.2
Q ss_pred cEecccccccc-----cCCCCCCCcCCCCCcchhhHH-hhhceeeecccCCCCCCcccccchhhhcccccccCCCCCCC-
Q 020290 115 HVVCHRCCCDL-----MNKCPSCRLPNGHSRSTAMEK-VIESIQVACENADYGCKEKMSYSEKYDHGRACHYTPCSCPL- 187 (328)
Q Consensus 115 H~~C~~C~~~~-----~~~CP~C~~~~~~~r~~~le~-~l~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~- 187 (328)
..+|+.|-..- ...|+.|+..-...+-+.+.- ++.+....|. .|.-........+ .||.
T Consensus 127 ~~iCs~C~GsGgksg~~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~----~C~G~G~~~~~kd----------~C~~C 192 (337)
T KOG0712|consen 127 NFICSKCSGSGGKSGSAPKCTTCRGSGVQTRTRQMGPGMVQSPQLVCD----SCNGSGETISLKD----------RCKTC 192 (337)
T ss_pred CccCCcCCCCCCCCCCCCCCCCCCCCCceeEEEeccccccccceeEec----cCCCccccccccc----------cCccc
Confidence 34667776542 246899987644444444444 6677788886 3665544311111 4643
Q ss_pred CCCccccccchHhhhhhhccCC
Q 020290 188 AACNFVGSFHQIYQHFRGVHKH 209 (328)
Q Consensus 188 ~gC~~~g~~~~L~~Hl~~~H~~ 209 (328)
.|=.++-..+.|..|....|..
T Consensus 193 ~G~~~v~~kkil~v~V~~g~~~ 214 (337)
T KOG0712|consen 193 SGAKVVREKKILEVHVEPGMPH 214 (337)
T ss_pred ccchhhhhhheeeccccCCCcc
Confidence 2223444556788887766554
No 182
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=20.84 E-value=64 Score=25.16 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=8.1
Q ss_pred CCCCCCCcCCC
Q 020290 127 NKCPSCRLPNG 137 (328)
Q Consensus 127 ~~CP~C~~~~~ 137 (328)
.+|..|++++.
T Consensus 59 GrCr~C~~~I~ 69 (92)
T PF06750_consen 59 GRCRYCGAPIP 69 (92)
T ss_pred CCCcccCCCCC
Confidence 57888877765
No 183
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.79 E-value=49 Score=29.99 Aligned_cols=35 Identities=34% Similarity=0.796 Sum_probs=22.7
Q ss_pred eeccccccccccccccccccEeccccccccc---CCCCCCCcCC
Q 020290 96 DCPVCYEPLNIPVYQCGNGHVVCHRCCCDLM---NKCPSCRLPN 136 (328)
Q Consensus 96 ~CpiC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~C~~~~ 136 (328)
.|.+|..++..+ ...+|..|...+. ..||.|..++
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCcC
Confidence 488888876432 2236788877652 4688887653
No 184
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.19 E-value=70 Score=27.47 Aligned_cols=15 Identities=20% Similarity=0.361 Sum_probs=11.0
Q ss_pred CCCCCCCcCCCCCcc
Q 020290 127 NKCPSCRLPNGHSRS 141 (328)
Q Consensus 127 ~~CP~C~~~~~~~r~ 141 (328)
..||.|+..+...-|
T Consensus 129 F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 129 FTCPRCGAMLDYLDN 143 (158)
T ss_pred CcCCCCCCEeeeccC
Confidence 689999888765444
No 185
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.10 E-value=70 Score=20.39 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=13.6
Q ss_pred CeeeeccccccccccccccccccEecccccc
Q 020290 93 EVLDCPVCYEPLNIPVYQCGNGHVVCHRCCC 123 (328)
Q Consensus 93 ~~l~CpiC~~~l~~Pv~qC~~GH~~C~~C~~ 123 (328)
+...|--|..+|.+..+.=.-++.+|-.|..
T Consensus 2 ~~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD 32 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLNNFDLPVCDKCRD 32 (34)
T ss_dssp S-EE-TTT--EES-SSCCCCTS-S--TTT-S
T ss_pred CCchHhHhCCHHHHHHHHHhCCccccccccC
Confidence 3457888888887754433336677777754
Done!