Query 038068
Match_columns 269
No_of_seqs 271 out of 1889
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:15:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038068.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038068hhsearch_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 5.5E-38 1.2E-42 277.0 13.3 219 47-269 41-270 (299)
2 PF03145 Sina: Seven in absent 99.9 8.7E-28 1.9E-32 203.1 11.0 159 99-261 1-168 (198)
3 KOG0297 TNF receptor-associate 99.5 6E-14 1.3E-18 129.8 6.0 123 53-178 20-149 (391)
4 cd03829 Sina Seven in absentia 99.1 3E-11 6.5E-16 91.7 2.0 77 183-261 11-94 (127)
5 PF15227 zf-C3HC4_4: zinc fing 98.8 2.4E-09 5.2E-14 67.5 2.4 35 57-92 1-42 (42)
6 KOG0823 Predicted E3 ubiquitin 98.8 4.8E-09 1E-13 88.4 4.6 46 51-97 44-95 (230)
7 KOG0320 Predicted E3 ubiquitin 98.7 8.1E-09 1.7E-13 83.5 3.7 45 53-97 130-178 (187)
8 PF14835 zf-RING_6: zf-RING of 98.7 7.7E-09 1.7E-13 69.9 2.4 56 53-108 6-65 (65)
9 PLN03208 E3 ubiquitin-protein 98.7 1.2E-08 2.5E-13 84.6 3.6 46 52-98 16-80 (193)
10 smart00504 Ubox Modified RING 98.7 2.7E-08 5.9E-13 68.1 4.4 56 54-110 1-62 (63)
11 PF13923 zf-C3HC4_2: Zinc fing 98.7 1.5E-08 3.2E-13 62.8 2.5 36 57-92 1-39 (39)
12 KOG0287 Postreplication repair 98.6 1.2E-08 2.5E-13 90.1 -0.2 68 45-113 14-87 (442)
13 PF13920 zf-C3HC4_3: Zinc fing 98.5 5.4E-08 1.2E-12 63.7 2.5 43 54-97 2-48 (50)
14 PF02176 zf-TRAF: TRAF-type zi 98.5 7E-08 1.5E-12 65.5 2.7 53 108-162 5-60 (60)
15 KOG0317 Predicted E3 ubiquitin 98.5 5.1E-08 1.1E-12 84.6 2.1 47 52-99 237-286 (293)
16 TIGR00599 rad18 DNA repair pro 98.5 7E-08 1.5E-12 88.9 2.5 59 53-112 25-89 (397)
17 PF13639 zf-RING_2: Ring finge 98.4 1.3E-07 2.8E-12 60.2 1.5 38 56-93 2-44 (44)
18 PF00097 zf-C3HC4: Zinc finger 98.4 3.3E-07 7.2E-12 57.2 2.8 36 57-92 1-41 (41)
19 PF04564 U-box: U-box domain; 98.3 4.7E-07 1E-11 64.1 3.1 59 52-111 2-67 (73)
20 PHA02929 N1R/p28-like protein; 98.3 5E-07 1.1E-11 77.9 2.9 46 53-98 173-228 (238)
21 PF14634 zf-RING_5: zinc-RING 98.2 7.1E-07 1.5E-11 56.8 2.1 39 56-94 1-44 (44)
22 cd00162 RING RING-finger (Real 98.1 1.5E-06 3.2E-11 54.6 2.5 40 56-95 1-44 (45)
23 COG5432 RAD18 RING-finger-cont 98.0 2.4E-06 5.1E-11 74.3 2.2 44 53-97 24-70 (391)
24 PF13445 zf-RING_UBOX: RING-ty 97.9 3.9E-06 8.5E-11 52.9 1.5 27 57-85 1-31 (43)
25 COG5574 PEX10 RING-finger-cont 97.8 6E-06 1.3E-10 71.1 1.5 45 52-97 213-262 (271)
26 KOG2164 Predicted E3 ubiquitin 97.8 6.5E-06 1.4E-10 76.9 1.7 44 54-98 186-237 (513)
27 PHA02926 zinc finger-like prot 97.8 7.2E-06 1.6E-10 69.0 1.3 45 53-98 169-231 (242)
28 smart00184 RING Ring finger. E 97.7 1.8E-05 3.8E-10 47.7 2.0 35 57-92 1-39 (39)
29 PF02176 zf-TRAF: TRAF-type zi 97.6 2.8E-05 6E-10 52.6 1.6 43 134-176 1-43 (60)
30 TIGR00570 cdk7 CDK-activating 97.6 4.3E-05 9.3E-10 68.0 2.8 45 53-97 2-54 (309)
31 KOG0311 Predicted E3 ubiquitin 97.5 6.7E-06 1.4E-10 73.4 -3.8 59 53-111 42-108 (381)
32 PF12678 zf-rbx1: RING-H2 zinc 97.4 0.00011 2.4E-09 51.9 2.7 38 56-93 21-73 (73)
33 KOG2177 Predicted E3 ubiquitin 97.4 4.6E-05 1E-09 67.2 0.3 62 53-115 12-77 (386)
34 KOG0978 E3 ubiquitin ligase in 97.3 5.5E-05 1.2E-09 73.9 0.3 45 53-98 642-690 (698)
35 PF07800 DUF1644: Protein of u 97.2 0.00067 1.5E-08 54.3 5.4 27 143-169 108-134 (162)
36 PLN03086 PRLI-interacting fact 96.9 0.00095 2.1E-08 64.4 4.4 117 52-177 405-547 (567)
37 PLN03086 PRLI-interacting fact 96.9 0.0012 2.6E-08 63.7 4.6 53 122-178 459-511 (567)
38 COG5152 Uncharacterized conser 96.7 0.00051 1.1E-08 56.9 0.8 56 54-110 196-256 (259)
39 PF11789 zf-Nse: Zinc-finger o 96.7 0.00095 2.1E-08 44.8 1.6 33 53-85 10-42 (57)
40 KOG2879 Predicted E3 ubiquitin 96.6 0.0017 3.7E-08 56.4 3.1 45 53-97 238-287 (298)
41 KOG1813 Predicted E3 ubiquitin 96.5 0.0017 3.7E-08 57.0 2.5 46 55-101 242-290 (313)
42 KOG4159 Predicted E3 ubiquitin 96.5 0.00093 2E-08 62.0 0.9 45 52-97 82-129 (398)
43 KOG2660 Locus-specific chromos 96.4 0.00066 1.4E-08 60.5 -0.4 45 53-97 14-61 (331)
44 PF12861 zf-Apc11: Anaphase-pr 96.4 0.0023 4.9E-08 46.2 2.1 43 55-97 33-82 (85)
45 KOG4265 Predicted E3 ubiquitin 96.3 0.0026 5.6E-08 57.4 2.8 44 53-97 289-336 (349)
46 KOG4739 Uncharacterized protei 96.1 0.0032 7E-08 53.9 2.2 43 55-97 4-48 (233)
47 KOG0802 E3 ubiquitin ligase [P 95.9 0.0025 5.4E-08 62.0 0.6 43 53-96 290-340 (543)
48 PF14570 zf-RING_4: RING/Ubox 95.9 0.0044 9.5E-08 39.8 1.5 40 57-96 1-47 (48)
49 KOG4172 Predicted E3 ubiquitin 95.7 0.0012 2.6E-08 43.1 -1.6 42 55-97 8-54 (62)
50 COG5540 RING-finger-containing 95.6 0.0068 1.5E-07 53.5 2.1 44 54-97 323-372 (374)
51 COG5222 Uncharacterized conser 95.3 0.0059 1.3E-07 53.7 0.7 40 55-94 275-318 (427)
52 KOG0824 Predicted E3 ubiquitin 95.3 0.0074 1.6E-07 53.2 1.2 43 54-97 7-53 (324)
53 KOG1785 Tyrosine kinase negati 95.1 0.0056 1.2E-07 55.9 0.0 41 56-97 371-416 (563)
54 COG5236 Uncharacterized conser 95.1 0.015 3.2E-07 52.3 2.5 46 50-96 57-107 (493)
55 COG5175 MOT2 Transcriptional r 95.0 0.0072 1.6E-07 54.1 0.4 46 51-97 12-64 (480)
56 PF05290 Baculo_IE-1: Baculovi 94.6 0.02 4.3E-07 44.6 1.8 53 45-98 72-133 (140)
57 KOG4275 Predicted E3 ubiquitin 94.6 0.0095 2.1E-07 52.3 -0.1 41 54-96 300-341 (350)
58 COG5243 HRD1 HRD ubiquitin lig 94.1 0.029 6.4E-07 50.9 1.9 44 53-97 286-345 (491)
59 PF14447 Prok-RING_4: Prokaryo 93.6 0.052 1.1E-06 35.8 1.9 43 54-97 7-50 (55)
60 KOG4692 Predicted E3 ubiquitin 93.5 0.029 6.2E-07 50.6 0.8 47 50-97 418-467 (489)
61 KOG1002 Nucleotide excision re 93.4 0.025 5.4E-07 53.6 0.3 45 52-97 534-586 (791)
62 KOG1039 Predicted E3 ubiquitin 93.2 0.037 7.9E-07 50.5 1.1 45 53-97 160-221 (344)
63 KOG4628 Predicted E3 ubiquitin 92.9 0.063 1.4E-06 48.9 2.0 43 55-97 230-278 (348)
64 PF11793 FANCL_C: FANCL C-term 91.9 0.06 1.3E-06 37.6 0.6 44 54-97 2-66 (70)
65 KOG4367 Predicted Zn-finger pr 91.8 0.053 1.1E-06 50.3 0.2 32 53-85 3-34 (699)
66 PF05605 zf-Di19: Drought indu 91.3 0.14 3.1E-06 33.6 1.9 49 113-168 3-54 (54)
67 KOG3039 Uncharacterized conser 91.3 0.15 3.3E-06 43.9 2.4 45 53-97 220-270 (303)
68 PF04641 Rtf2: Rtf2 RING-finge 90.9 0.27 5.8E-06 43.3 3.8 46 52-97 111-161 (260)
69 KOG1571 Predicted E3 ubiquitin 90.9 0.11 2.5E-06 47.0 1.4 44 52-97 303-347 (355)
70 KOG0825 PHD Zn-finger protein 89.9 0.094 2E-06 52.0 0.0 45 53-97 122-171 (1134)
71 KOG0804 Cytoplasmic Zn-finger 89.7 0.14 3E-06 47.7 0.9 44 53-96 174-221 (493)
72 KOG2932 E3 ubiquitin ligase in 89.3 0.24 5.2E-06 44.1 2.1 77 53-135 89-167 (389)
73 PF10571 UPF0547: Uncharacteri 89.0 0.18 4E-06 28.0 0.8 22 56-77 2-24 (26)
74 COG5219 Uncharacterized conser 89.0 0.083 1.8E-06 53.4 -1.1 45 53-97 1468-1523(1525)
75 KOG1814 Predicted E3 ubiquitin 88.7 0.32 6.9E-06 45.0 2.5 100 53-155 183-322 (445)
76 KOG1645 RING-finger-containing 88.0 0.23 4.9E-06 45.8 1.1 42 55-96 5-55 (463)
77 KOG0826 Predicted E3 ubiquitin 87.4 0.75 1.6E-05 41.4 3.9 45 53-97 299-346 (357)
78 KOG1734 Predicted RING-contain 86.9 0.17 3.6E-06 44.2 -0.4 45 53-97 223-281 (328)
79 PF13909 zf-H2C2_5: C2H2-type 86.4 0.46 9.9E-06 25.4 1.4 24 143-168 1-24 (24)
80 PF07191 zinc-ribbons_6: zinc- 86.1 0.2 4.3E-06 34.8 -0.3 38 55-97 2-41 (70)
81 KOG2817 Predicted E3 ubiquitin 85.7 0.6 1.3E-05 43.0 2.5 42 53-95 333-383 (394)
82 KOG3608 Zn finger proteins [Ge 85.1 0.59 1.3E-05 42.5 2.1 114 51-168 204-346 (467)
83 PF07975 C1_4: TFIIH C1-like d 84.6 0.88 1.9E-05 29.6 2.2 37 57-93 2-50 (51)
84 COG5194 APC11 Component of SCF 84.6 0.41 8.9E-06 34.0 0.7 27 72-98 53-82 (88)
85 KOG0828 Predicted E3 ubiquitin 84.2 0.35 7.5E-06 45.7 0.3 45 53-97 570-634 (636)
86 PF02891 zf-MIZ: MIZ/SP-RING z 84.1 0.64 1.4E-05 30.1 1.5 42 54-95 2-50 (50)
87 KOG3161 Predicted E3 ubiquitin 83.9 0.22 4.7E-06 48.5 -1.2 37 53-90 10-51 (861)
88 KOG1001 Helicase-like transcri 82.0 0.53 1.2E-05 47.0 0.6 40 55-96 455-499 (674)
89 KOG4185 Predicted E3 ubiquitin 81.8 1.3 2.8E-05 39.6 3.0 57 54-111 3-77 (296)
90 COG2888 Predicted Zn-ribbon RN 80.8 1.8 3.8E-05 29.0 2.6 37 110-155 25-61 (61)
91 PF13913 zf-C2HC_2: zinc-finge 80.5 0.75 1.6E-05 25.2 0.6 17 122-138 8-24 (25)
92 PF05605 zf-Di19: Drought indu 80.0 1.9 4.1E-05 28.2 2.5 27 143-171 3-29 (54)
93 KOG3800 Predicted E3 ubiquitin 79.8 0.97 2.1E-05 40.0 1.4 41 56-96 2-50 (300)
94 PHA00616 hypothetical protein 79.5 1.9 4.1E-05 27.2 2.3 34 142-177 1-35 (44)
95 KOG1812 Predicted E3 ubiquitin 78.2 0.69 1.5E-05 43.1 0.1 33 53-85 145-180 (384)
96 KOG3039 Uncharacterized conser 77.6 1.2 2.7E-05 38.4 1.4 30 55-85 44-73 (303)
97 smart00647 IBR In Between Ring 75.9 2 4.3E-05 28.6 1.8 31 55-85 19-58 (64)
98 KOG2231 Predicted E3 ubiquitin 73.5 2.1 4.6E-05 42.4 2.0 41 56-97 2-52 (669)
99 PF04216 FdhE: Protein involve 73.5 1.6 3.4E-05 39.0 1.1 43 53-95 171-220 (290)
100 PF05253 zf-U11-48K: U11-48K-l 71.8 1.3 2.9E-05 24.7 0.1 24 113-139 3-26 (27)
101 PRK04023 DNA polymerase II lar 69.1 4.5 9.7E-05 41.9 3.2 44 52-97 624-674 (1121)
102 PF03145 Sina: Seven in absent 68.9 3.7 8E-05 34.4 2.2 48 92-139 24-71 (198)
103 smart00301 DM Doublesex DNA-bi 68.1 2.9 6.4E-05 27.5 1.1 39 122-162 8-46 (54)
104 PRK11088 rrmA 23S rRNA methylt 67.8 3 6.5E-05 36.7 1.5 24 54-77 2-27 (272)
105 COG3813 Uncharacterized protei 67.5 4.5 9.7E-05 28.2 2.0 29 70-98 24-53 (84)
106 smart00154 ZnF_AN1 AN1-like Zi 67.4 4 8.7E-05 24.9 1.6 23 57-80 1-25 (39)
107 PF01428 zf-AN1: AN1-like Zinc 65.9 6.7 0.00015 24.3 2.5 33 57-90 1-36 (43)
108 TIGR01562 FdhE formate dehydro 64.9 4.2 9E-05 36.7 1.9 41 54-94 184-232 (305)
109 PF14446 Prok-RING_1: Prokaryo 64.8 7.4 0.00016 25.6 2.5 38 53-91 4-44 (54)
110 PF01363 FYVE: FYVE zinc finge 64.5 4 8.6E-05 27.9 1.3 33 53-85 8-43 (69)
111 PF10367 Vps39_2: Vacuolar sor 64.2 5.1 0.00011 29.6 2.0 30 54-83 78-108 (109)
112 PF01485 IBR: IBR domain; Int 62.6 3.8 8.3E-05 27.1 1.0 33 53-85 17-58 (64)
113 PF06906 DUF1272: Protein of u 61.2 8.4 0.00018 25.5 2.3 41 57-97 8-52 (57)
114 PF04606 Ogr_Delta: Ogr/Delta- 61.1 3 6.4E-05 26.5 0.2 38 88-127 1-38 (47)
115 PF13894 zf-C2H2_4: C2H2-type 61.0 9.1 0.0002 19.5 2.1 22 144-167 2-24 (24)
116 PF15616 TerY-C: TerY-C metal 60.1 6.6 0.00014 30.9 2.0 41 53-97 76-116 (131)
117 PRK03564 formate dehydrogenase 58.8 8.2 0.00018 34.9 2.6 42 53-94 186-234 (309)
118 COG5109 Uncharacterized conser 57.9 7.6 0.00016 34.9 2.2 40 53-93 335-383 (396)
119 KOG4362 Transcriptional regula 57.9 2.4 5.1E-05 42.1 -1.0 44 53-97 20-69 (684)
120 COG4647 AcxC Acetone carboxyla 57.8 4.7 0.0001 31.4 0.8 51 59-117 62-114 (165)
121 PF08209 Sgf11: Sgf11 (transcr 57.3 4.9 0.00011 23.7 0.6 15 150-164 10-24 (33)
122 KOG3579 Predicted E3 ubiquitin 57.0 29 0.00063 30.9 5.5 33 52-84 266-301 (352)
123 smart00734 ZnF_Rad18 Rad18-lik 56.7 9.2 0.0002 21.1 1.7 21 143-165 2-22 (26)
124 PRK14714 DNA polymerase II lar 55.8 10 0.00022 40.3 3.0 43 53-97 666-720 (1337)
125 KOG1493 Anaphase-promoting com 55.5 2.1 4.7E-05 30.1 -1.3 42 56-97 33-81 (84)
126 TIGR00622 ssl1 transcription f 55.4 11 0.00024 28.7 2.5 39 55-93 56-110 (112)
127 KOG0827 Predicted E3 ubiquitin 54.4 5 0.00011 37.1 0.5 38 55-93 5-52 (465)
128 KOG0297 TNF receptor-associate 54.0 10 0.00022 35.5 2.5 34 111-147 113-147 (391)
129 PRK14890 putative Zn-ribbon RN 53.6 19 0.00042 24.1 3.1 17 78-94 39-56 (59)
130 PF00412 LIM: LIM domain; Int 53.5 10 0.00022 24.5 1.8 32 53-84 25-56 (58)
131 PF13719 zinc_ribbon_5: zinc-r 51.2 15 0.00033 21.9 2.2 13 55-67 3-15 (37)
132 PF03854 zf-P11: P-11 zinc fin 50.5 5.1 0.00011 25.6 -0.0 40 56-97 4-46 (50)
133 PF10272 Tmpp129: Putative tra 50.0 8.9 0.00019 35.4 1.4 28 70-97 308-351 (358)
134 KOG2114 Vacuolar assembly/sort 50.0 8.6 0.00019 39.0 1.4 43 53-95 839-881 (933)
135 PF08882 Acetone_carb_G: Aceto 49.4 9.4 0.0002 29.0 1.2 17 68-85 24-40 (112)
136 KOG1100 Predicted E3 ubiquitin 48.8 15 0.00032 31.3 2.5 39 57-97 161-200 (207)
137 PF05883 Baculo_RING: Baculovi 48.7 5.2 0.00011 31.5 -0.3 32 54-85 26-65 (134)
138 COG5220 TFB3 Cdk activating ki 48.4 6 0.00013 34.2 0.1 42 53-94 9-61 (314)
139 KOG1812 Predicted E3 ubiquitin 48.3 10 0.00022 35.4 1.5 32 54-85 306-341 (384)
140 PF13717 zinc_ribbon_4: zinc-r 47.8 18 0.0004 21.5 2.1 11 55-65 3-13 (36)
141 PF14569 zf-UDP: Zinc-binding 47.8 14 0.0003 26.2 1.8 45 53-97 8-62 (80)
142 KOG2807 RNA polymerase II tran 47.2 13 0.00027 33.7 1.9 38 56-93 332-374 (378)
143 PF10083 DUF2321: Uncharacteri 47.2 6.2 0.00014 31.8 -0.0 22 76-97 29-50 (158)
144 PHA03096 p28-like protein; Pro 46.3 7.3 0.00016 34.8 0.3 40 55-94 179-231 (284)
145 cd00065 FYVE FYVE domain; Zinc 45.8 11 0.00023 24.5 1.0 30 56-85 4-36 (57)
146 KOG1952 Transcription factor N 45.5 25 0.00054 35.9 3.8 42 53-94 190-244 (950)
147 PF01286 XPA_N: XPA protein N- 44.0 10 0.00023 22.4 0.6 30 54-83 3-32 (34)
148 PF10426 zf-RAG1: Recombinatio 43.8 12 0.00025 21.5 0.7 22 143-164 3-24 (30)
149 KOG3576 Ovo and related transc 43.5 25 0.00054 29.8 3.0 114 51-172 114-241 (267)
150 PRK09678 DNA-binding transcrip 42.9 12 0.00025 26.3 0.8 45 88-134 3-47 (72)
151 KOG3002 Zn finger protein [Gen 42.9 12 0.00026 33.7 1.1 74 87-164 49-130 (299)
152 PLN02189 cellulose synthase 42.6 19 0.0004 37.8 2.5 45 53-97 33-87 (1040)
153 KOG2462 C2H2-type Zn-finger pr 41.7 13 0.00028 32.8 1.1 76 86-169 187-269 (279)
154 PF00751 DM: DM DNA binding do 40.2 9.9 0.00021 24.3 0.1 31 123-155 9-39 (47)
155 PF09297 zf-NADH-PPase: NADH p 40.2 6.9 0.00015 22.5 -0.6 19 75-93 3-28 (32)
156 PF05502 Dynactin_p62: Dynacti 39.3 21 0.00046 34.4 2.2 35 88-126 54-96 (483)
157 KOG3113 Uncharacterized conser 38.7 28 0.0006 30.5 2.6 45 53-97 110-158 (293)
158 COG1645 Uncharacterized Zn-fin 38.6 16 0.00034 28.7 1.0 25 53-82 27-51 (131)
159 PF13248 zf-ribbon_3: zinc-rib 38.4 12 0.00027 20.4 0.3 6 57-62 5-10 (26)
160 KOG0298 DEAD box-containing he 37.8 5 0.00011 42.5 -2.3 44 53-96 1152-1198(1394)
161 smart00744 RINGv The RING-vari 37.6 24 0.00053 22.5 1.6 37 56-93 1-49 (49)
162 smart00064 FYVE Protein presen 37.5 21 0.00046 24.0 1.5 33 53-85 9-44 (68)
163 PF00096 zf-C2H2: Zinc finger, 37.4 22 0.00049 18.2 1.2 20 144-165 2-22 (23)
164 PF09292 Neil1-DNA_bind: Endon 37.2 31 0.00066 20.8 1.8 15 239-253 20-34 (39)
165 PF10497 zf-4CXXC_R1: Zinc-fin 37.0 30 0.00064 26.0 2.3 40 55-94 8-69 (105)
166 KOG1815 Predicted E3 ubiquitin 35.4 18 0.00039 34.4 1.1 27 65-92 177-205 (444)
167 PLN02436 cellulose synthase A 35.4 28 0.00062 36.6 2.5 45 53-97 35-89 (1094)
168 COG1592 Rubrerythrin [Energy p 35.2 27 0.00059 28.6 1.9 10 86-95 149-158 (166)
169 KOG1356 Putative transcription 34.4 14 0.00031 37.5 0.2 32 54-85 229-261 (889)
170 PRK14559 putative protein seri 34.1 25 0.00055 35.1 1.9 42 56-97 3-52 (645)
171 KOG2857 Predicted MYND Zn-fing 33.9 26 0.00055 27.9 1.5 33 71-104 2-35 (157)
172 smart00661 RPOL9 RNA polymeras 33.7 38 0.00082 21.4 2.1 12 56-67 2-13 (52)
173 PLN02195 cellulose synthase A 33.0 37 0.00079 35.4 2.9 43 55-97 7-59 (977)
174 COG5242 TFB4 RNA polymerase II 32.9 18 0.00038 31.2 0.5 16 54-69 260-275 (296)
175 PF09237 GAGA: GAGA factor; I 32.9 34 0.00075 22.3 1.7 27 141-169 23-50 (54)
176 PF08746 zf-RING-like: RING-li 32.2 48 0.001 20.5 2.3 35 57-92 1-43 (43)
177 PF12756 zf-C2H2_2: C2H2 type 32.1 36 0.00079 24.2 2.1 35 133-169 41-77 (100)
178 PRK00420 hypothetical protein; 31.7 32 0.00069 26.3 1.7 26 55-84 24-49 (112)
179 PRK00398 rpoP DNA-directed RNA 31.5 10 0.00022 23.7 -0.9 11 88-98 23-33 (46)
180 PLN02638 cellulose synthase A 31.4 37 0.0008 35.8 2.6 44 54-97 17-70 (1079)
181 PF06677 Auto_anti-p27: Sjogre 31.2 44 0.00094 20.6 1.9 23 55-81 18-40 (41)
182 cd00350 rubredoxin_like Rubred 31.2 42 0.0009 19.4 1.8 9 87-95 18-26 (33)
183 KOG2462 C2H2-type Zn-finger pr 30.7 62 0.0013 28.7 3.5 75 86-166 161-238 (279)
184 KOG0006 E3 ubiquitin-protein l 30.5 61 0.0013 29.4 3.5 99 50-160 217-352 (446)
185 KOG4471 Phosphatidylinositol 3 30.2 67 0.0015 31.7 3.9 45 206-253 75-120 (717)
186 PF02318 FYVE_2: FYVE-type zin 29.6 46 0.00099 25.4 2.3 32 53-85 53-89 (118)
187 PRK11595 DNA utilization prote 29.4 43 0.00093 28.6 2.3 34 56-95 7-43 (227)
188 PTZ00303 phosphatidylinositol 29.3 43 0.00094 34.1 2.5 31 55-85 461-499 (1374)
189 COG1198 PriA Primosomal protei 29.2 51 0.0011 33.5 3.1 48 67-151 434-482 (730)
190 TIGR00373 conserved hypothetic 28.9 36 0.00077 27.5 1.7 16 86-101 128-143 (158)
191 PF14445 Prok-RING_2: Prokaryo 28.3 5 0.00011 25.9 -2.6 42 53-94 6-49 (57)
192 cd02249 ZZ Zinc finger, ZZ typ 27.6 49 0.0011 20.6 1.8 30 55-84 1-32 (46)
193 smart00132 LIM Zinc-binding do 27.4 65 0.0014 18.3 2.3 35 57-96 2-37 (39)
194 PLN02400 cellulose synthase 27.3 48 0.001 35.0 2.6 45 53-97 35-89 (1085)
195 PF03833 PolC_DP2: DNA polymer 27.1 21 0.00045 36.5 0.0 44 52-97 653-703 (900)
196 PRK06266 transcription initiat 27.0 47 0.001 27.4 2.1 14 86-99 136-149 (178)
197 KOG3815 Transcription factor D 27.0 24 0.00051 32.1 0.3 36 122-159 42-77 (322)
198 PF07649 C1_3: C1-like domain; 27.0 45 0.00098 18.7 1.4 22 56-77 2-25 (30)
199 KOG2272 Focal adhesion protein 25.9 32 0.0007 30.1 0.9 44 53-97 162-206 (332)
200 COG4306 Uncharacterized protei 25.7 24 0.00052 27.4 0.1 22 76-97 29-50 (160)
201 KOG3899 Uncharacterized conser 24.6 26 0.00056 31.3 0.1 27 71-97 323-365 (381)
202 KOG2068 MOT2 transcription fac 24.5 60 0.0013 29.5 2.4 43 55-97 250-298 (327)
203 PF02148 zf-UBP: Zn-finger in 24.0 59 0.0013 21.7 1.8 23 57-80 1-24 (63)
204 KOG3970 Predicted E3 ubiquitin 23.6 46 0.001 28.6 1.4 45 53-98 49-106 (299)
205 PF10235 Cript: Microtubule-as 23.4 51 0.0011 24.1 1.5 37 55-98 45-81 (90)
206 COG4357 Zinc finger domain con 23.1 60 0.0013 24.0 1.8 23 76-98 63-92 (105)
207 PF12907 zf-met2: Zinc-binding 22.8 43 0.00092 20.6 0.8 17 154-170 15-31 (40)
208 PF03107 C1_2: C1 domain; Int 22.7 93 0.002 17.4 2.2 21 56-76 2-24 (30)
209 cd02340 ZZ_NBR1_like Zinc fing 22.5 70 0.0015 19.8 1.8 29 56-84 2-32 (43)
210 KOG1819 FYVE finger-containing 22.0 62 0.0013 31.2 2.1 34 50-83 897-933 (990)
211 PLN02915 cellulose synthase A 21.7 68 0.0015 33.8 2.4 43 55-97 16-68 (1044)
212 PF08271 TF_Zn_Ribbon: TFIIB z 21.1 82 0.0018 19.2 1.9 25 56-82 2-26 (43)
213 PF01754 zf-A20: A20-like zinc 21.0 55 0.0012 17.9 0.9 14 143-157 2-15 (25)
214 PF04438 zf-HIT: HIT zinc fing 20.9 70 0.0015 18.2 1.4 21 56-79 4-25 (30)
215 KOG4621 Uncharacterized conser 20.9 35 0.00076 26.7 0.2 35 44-79 71-106 (167)
216 KOG1815 Predicted E3 ubiquitin 20.7 42 0.00092 31.9 0.7 34 52-85 68-101 (444)
217 PF14205 Cys_rich_KTR: Cystein 20.5 83 0.0018 20.7 1.8 12 106-117 22-33 (55)
218 COG2816 NPY1 NTP pyrophosphohy 20.5 40 0.00086 30.0 0.5 25 73-97 109-140 (279)
219 PF14319 Zn_Tnp_IS91: Transpos 20.4 47 0.001 25.1 0.8 26 53-81 41-66 (111)
220 PRK14892 putative transcriptio 20.2 71 0.0015 23.8 1.7 32 51-83 18-50 (99)
221 PHA00626 hypothetical protein 20.1 71 0.0015 21.2 1.4 10 87-96 24-33 (59)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=100.00 E-value=5.5e-38 Score=277.00 Aligned_cols=219 Identities=33% Similarity=0.607 Sum_probs=183.3
Q ss_pred eecCCCCeeeccCCCCCCcCceeeccCCceechhchhhcCCCCCCCCCCCccccchhHHHHhhcceecccCCCCCccccc
Q 038068 47 LTITDQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKM 126 (269)
Q Consensus 47 ~~~~~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~ 126 (269)
+...+.+.|.||||.+++.+|++||..||+.|+.|..++...||.|+.+++.+|+++||++++++.|+|+|..+||++.+
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 44556699999999999999999999999999999988888999999999999999999999999999999999999999
Q ss_pred cccchhhhhccCCCeeeeCCCC--CCCCccChhHHhhhhhhhCCCCcc-----ceeecceEEEEeeccCCCCCCceEEEE
Q 038068 127 SFSKKRGHEKTCQHSPLPCPLS--DCSFLGCSSQFVRHFMAKHNISAV-----PFKYNSLLNVNLNVNDINIDGKFSVLQ 199 (269)
Q Consensus 127 ~~~~~~~He~~C~~~p~~Cp~~--~C~~~g~~~~l~~Hl~~~H~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~~~~ 199 (269)
+|.+...||+.|.|+|+.||.+ .|+|.|..++|..|++..|+..++ .+.|.......+....- --++. +.
T Consensus 121 ~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~ 197 (299)
T KOG3002|consen 121 PYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFVATDENLLGAATW--TLKTS-VC 197 (299)
T ss_pred ccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChhhhhhccccceecccCCccccccchh--heeee-ec
Confidence 9999999999999999999998 999999999999999999999776 33333322222221100 00211 12
Q ss_pred eeeCCCeEEEEEcCccCccceEEEEEeecCC---CCCeEEEEEEecCCeEEEEeeeeeeecc-ccCCCCCCCCC
Q 038068 200 EEKNDDVLFILNNNTGSLGNLVSVCCIASVR---KDLYYDIVARCVTGTTLKIQSSTWSSKV-RSDIPSPFGFF 269 (269)
Q Consensus 200 ~~~~~~~lF~l~~~~~~~g~~v~v~ci~~~~---~~f~Y~l~~~~~~~~~l~~~s~~~~~~~-~~~~~~~~~~~ 269 (269)
.+..++.+|.++...++.|.+++|++|.|.+ .+|+|+|.+. +++++|+|||.++|+.+ ++...|..+|+
T Consensus 198 ~~~~~~~~~~~q~~~~~~~~y~tv~~i~~~~~e~~~fsy~L~~~-~~~~klt~~s~~~s~~~kvs~~~p~~dfm 270 (299)
T KOG3002|consen 198 FGREFGLLFEVQCFREPHGVYVTVNRIAPSAPEAGEFSYSLALG-GSGRKLTWQSPPRSIIQKVSKVRPEDDFM 270 (299)
T ss_pred CcEEEeeeeeehhhcCCCceEEEeehhccCCCcccccceeeecC-CCCceEeecCCcceeecccceeccCCCce
Confidence 3346678888888888889999999998876 8899999999 89999999999999975 55466666654
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=99.95 E-value=8.7e-28 Score=203.14 Aligned_cols=159 Identities=31% Similarity=0.524 Sum_probs=98.9
Q ss_pred ccchhHHHHhhcceecccCCCCCccccccccchhhhhccCCCeeeeCCC--CCCCCccChhHHhhhhhhhCCCCccceee
Q 038068 99 VRNWAIEKVIELVQVNCKNAEYGCQQKMSFSKKRGHEKTCQHSPLPCPL--SDCSFLGCSSQFVRHFMAKHNISAVPFKY 176 (269)
Q Consensus 99 ~~~~~l~~~i~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~p~~Cp~--~~C~~~g~~~~l~~Hl~~~H~~~~~~~~~ 176 (269)
+||++||++++++++||+|+.+||.+.++|.++.+||++|+|+|+.||. .+|+|.|..++|..|+...|.|.++...+
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 4789999999999999999999999999999999999999999999999 79999999999999999999997754322
Q ss_pred cceEEEEeeccCCCCCCceEEEEee-eCCCeEEEEEcCccC-ccceE---EEEEeecCC--CCCeEEEEEEecCCeEEEE
Q 038068 177 NSLLNVNLNVNDINIDGKFSVLQEE-KNDDVLFILNNNTGS-LGNLV---SVCCIASVR--KDLYYDIVARCVTGTTLKI 249 (269)
Q Consensus 177 ~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~lF~l~~~~~~-~g~~v---~v~ci~~~~--~~f~Y~l~~~~~~~~~l~~ 249 (269)
+.+.+........+...|++.. .+++.+|+|++.... .|..+ .|++||+.+ .+|+|+|++. +++++|+|
T Consensus 81 ---~~~~f~~~~~~~~~~~~~~~~~~~~~~~~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~-~~~rkl~~ 156 (198)
T PF03145_consen 81 ---FSISFLHSDINSVESPDWVLVQFSCFGKLFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVR-SNGRKLTW 156 (198)
T ss_dssp ----EEEEEECTTT-SSSEEEEEEE-EETTEEEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEE-ETTEEEEE
T ss_pred ---ceEEEeeecccccCCceEEEeecccCCccEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEe-cCCcEEEE
Confidence 1111111111212244555544 689999999965432 34443 355567765 9999999999 89999999
Q ss_pred eeeeeeeccccC
Q 038068 250 QSSTWSSKVRSD 261 (269)
Q Consensus 250 ~s~~~~~~~~~~ 261 (269)
|+.++||++..+
T Consensus 157 ~~~p~si~~~~~ 168 (198)
T PF03145_consen 157 QSFPRSIREDID 168 (198)
T ss_dssp EE--EETTT-SH
T ss_pred EEcCcchhhhHH
Confidence 999999987544
No 3
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=99.46 E-value=6e-14 Score=129.83 Aligned_cols=123 Identities=24% Similarity=0.533 Sum_probs=109.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCccc----cchhHHHHhhcceecccCCCCCcccc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVIV----RNWAIEKVIELVQVNCKNAEYGCQQK 125 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~~----~~~~l~~~i~~l~v~C~~~~~GC~~~ 125 (269)
+++.|++|..++.+|+....|||.||..|+..+ ...||.|+..+... ....+.+.+.++.+.|.+...||.|.
T Consensus 20 ~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~GC~~~ 99 (391)
T KOG0297|consen 20 ENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASRGCRAD 99 (391)
T ss_pred ccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCCCcccc
Confidence 679999999999999832489999999999998 46899998877642 24678889999999999999999999
Q ss_pred ccccchhhhhccCCCeeeeCCCCCCCCccChhHHhhhhhhhCCCCccceeecc
Q 038068 126 MSFSKKRGHEKTCQHSPLPCPLSDCSFLGCSSQFVRHFMAKHNISAVPFKYNS 178 (269)
Q Consensus 126 ~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~~~~l~~Hl~~~H~~~~~~~~~~~ 178 (269)
+....++.|+..| .++.||+ +|+..+.+.++.+|+...+......+.+.+
T Consensus 100 ~~l~~~~~Hl~~c--~~~~C~~-~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~ 149 (391)
T KOG0297|consen 100 LELEALQGHLSTC--DPLKCPH-RCGVQVPRDDLEDHLEAECPRRSLKCSLCQ 149 (391)
T ss_pred ccHHHHHhHhccC--CcccCcc-ccccccchHHHHHHHhcccccccccchhhc
Confidence 9999999999999 8999998 599999999999999999988887776664
No 4
>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=99.10 E-value=3e-11 Score=91.73 Aligned_cols=77 Identities=16% Similarity=0.151 Sum_probs=62.0
Q ss_pred EeeccCCCCCCceEEEEeeeCCCeEEEEEcCccCc-cc----eEEEEEeecCC--CCCeEEEEEEecCCeEEEEeeeeee
Q 038068 183 NLNVNDINIDGKFSVLQEEKNDDVLFILNNNTGSL-GN----LVSVCCIASVR--KDLYYDIVARCVTGTTLKIQSSTWS 255 (269)
Q Consensus 183 ~l~~~~~~~~~~~~~~~~~~~~~~lF~l~~~~~~~-g~----~v~v~ci~~~~--~~f~Y~l~~~~~~~~~l~~~s~~~~ 255 (269)
.|.+| +++.|...|++...++|+.|+|+..+..+ +. .+.|+.||+.. .+|+|.|++. ++||+|+|||+|||
T Consensus 11 fl~t~-~~~~~a~~w~mv~sCfG~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~-~n~RkL~we~~PRS 88 (127)
T cd03829 11 FLATD-INLPGATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELN-GNRRRLTWEATPRS 88 (127)
T ss_pred EEecC-CCCccceeeeehhhhcCceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEc-CCCcEEEeecCCcc
Confidence 34444 45555666777778999999999987766 32 36788999987 9999999999 99999999999999
Q ss_pred eccccC
Q 038068 256 SKVRSD 261 (269)
Q Consensus 256 ~~~~~~ 261 (269)
||+...
T Consensus 89 Irds~~ 94 (127)
T cd03829 89 IREGHA 94 (127)
T ss_pred HHHhhH
Confidence 997543
No 5
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.81 E-value=2.4e-09 Score=67.49 Aligned_cols=35 Identities=37% Similarity=0.970 Sum_probs=27.1
Q ss_pred ccCCCCCCcCceeeccCCceechhchhhc-----C--CCCCCC
Q 038068 57 CPICFEPLTVPVFQCVNGHLACSDCCAKI-----K--RNCPTC 92 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~--~~Cp~C 92 (269)
||||+++|++||. .+|||+||..|+.++ . ..||.|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999996 599999999999987 1 357766
No 6
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=4.8e-09 Score=88.44 Aligned_cols=46 Identities=35% Similarity=0.832 Sum_probs=40.8
Q ss_pred CCCeeeccCCCCCCcCceeeccCCceechhchhhc------CCCCCCCCCCCc
Q 038068 51 DQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI------KRNCPTCSSPTV 97 (269)
Q Consensus 51 ~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~~~~~ 97 (269)
+-..+.|.||++..++||. +.|||+||+.|+.+| +..||+|+..++
T Consensus 44 ~~~~FdCNICLd~akdPVv-TlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVV-TLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccccCCCEE-eecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 3478999999999999995 689999999999999 467999998775
No 7
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=8.1e-09 Score=83.55 Aligned_cols=45 Identities=31% Similarity=0.849 Sum_probs=38.0
Q ss_pred CeeeccCCCCCCcCce-eeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPV-FQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv-~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
..+.||||++.+..-+ +-+.|||+||+.|+... ...||+|+..++
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 6799999999987554 34789999999999987 678999998665
No 8
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.71 E-value=7.7e-09 Score=69.92 Aligned_cols=56 Identities=30% Similarity=0.697 Sum_probs=30.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc-CCCCCCCCCCCc--c-ccchhHHHHh
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-KRNCPTCSSPTV--I-VRNWAIEKVI 108 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~--~-~~~~~l~~~i 108 (269)
+.|.|++|.++++.||....|.|+||+.|+..- ...||.|..+.- . ..|+.++.+|
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HHHHHHH
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhhhhccC
Confidence 468999999999999977789999999999875 557999998763 2 3466666553
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.69 E-value=1.2e-08 Score=84.57 Aligned_cols=46 Identities=37% Similarity=0.779 Sum_probs=39.6
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc-------------------CCCCCCCCCCCcc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-------------------KRNCPTCSSPTVI 98 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-------------------~~~Cp~C~~~~~~ 98 (269)
.+.+.|+||++.+++|+. +.|||.||..|+.+| ...||.|+.++..
T Consensus 16 ~~~~~CpICld~~~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCCCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 367999999999999995 699999999999887 1369999998763
No 10
>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=98.67 E-value=2.7e-08 Score=68.12 Aligned_cols=56 Identities=25% Similarity=0.370 Sum_probs=46.4
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCcc---ccchhHHHHhhc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVI---VRNWAIEKVIEL 110 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~---~~~~~l~~~i~~ 110 (269)
+|.||||.+++.+|+. .+|||+||..|+.++ ...||.|+.++.. ..+..+.+.++.
T Consensus 1 ~~~Cpi~~~~~~~Pv~-~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 1 EFLCPISLEVMKDPVI-LPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CcCCcCCCCcCCCCEE-CCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 3789999999999985 699999999999988 5689999998853 466777776653
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=98.66 E-value=1.5e-08 Score=62.82 Aligned_cols=36 Identities=42% Similarity=1.035 Sum_probs=30.3
Q ss_pred ccCCCCCCcCceeeccCCceechhchhhc---CCCCCCC
Q 038068 57 CPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTC 92 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C 92 (269)
|+||.+.+.+|+...+|||+||..|+.++ ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999999999767899999999999988 5678876
No 12
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.55 E-value=1.2e-08 Score=90.09 Aligned_cols=68 Identities=28% Similarity=0.582 Sum_probs=52.7
Q ss_pred ceeecCCCCeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCcc---ccchhHHHHhhccee
Q 038068 45 EALTITDQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVI---VRNWAIEKVIELVQV 113 (269)
Q Consensus 45 ~~~~~~~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~---~~~~~l~~~i~~l~v 113 (269)
........+.|.|-||.++|..|+. ++|||+||+-||-.. ...||.|+.++.. ..|+.++++++++.+
T Consensus 14 ipslk~lD~lLRC~IC~eyf~ip~i-tpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~~ 87 (442)
T KOG0287|consen 14 IPSLKTLDDLLRCGICFEYFNIPMI-TPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSLNF 87 (442)
T ss_pred CchhhhhHHHHHHhHHHHHhcCcee-ccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHHHH
Confidence 3333344478999999999999995 699999999999876 6789999988763 346667777766543
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=98.53 E-value=5.4e-08 Score=63.69 Aligned_cols=43 Identities=40% Similarity=0.932 Sum_probs=36.6
Q ss_pred eeeccCCCCCCcCceeeccCCce-echhchhhc---CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHL-ACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~-fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
+..|+||++...++++. +|||. ||..|..++ ...||+||.++.
T Consensus 2 ~~~C~iC~~~~~~~~~~-pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLL-PCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEE-TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEe-CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 56899999999998864 99999 999999998 578999999875
No 14
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.51 E-value=7e-08 Score=65.51 Aligned_cols=53 Identities=23% Similarity=0.516 Sum_probs=40.5
Q ss_pred hhcceecccCCCCCccccccccchhhhhc-cCCCeeeeCCC--CCCCCccChhHHhhh
Q 038068 108 IELVQVNCKNAEYGCQQKMSFSKKRGHEK-TCQHSPLPCPL--SDCSFLGCSSQFVRH 162 (269)
Q Consensus 108 i~~l~v~C~~~~~GC~~~~~~~~~~~He~-~C~~~p~~Cp~--~~C~~~g~~~~l~~H 162 (269)
.....|.|||. ||...+...++.+|++ +|+++++.||+ .||++.+.+.+|.+|
T Consensus 5 C~~~~v~C~~~--cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 5 CPFRPVPCPNG--CCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp STTSEEE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCCCEeeCCCC--CcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 56678999986 7788899999999988 99999999999 499999999999988
No 15
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.49 E-value=5.1e-08 Score=84.65 Aligned_cols=47 Identities=26% Similarity=0.594 Sum_probs=41.2
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCccc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVIV 99 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~~ 99 (269)
.....|.+|++...+|- .++|||+||+.|+..| +..||.||..+...
T Consensus 237 ~a~~kC~LCLe~~~~pS-aTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNPS-ATPCGHIFCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CCCCceEEEecCCCCCC-cCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence 36689999999999997 6799999999999999 56899999987643
No 16
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.47 E-value=7e-08 Score=88.86 Aligned_cols=59 Identities=27% Similarity=0.654 Sum_probs=48.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCcc---ccchhHHHHhhcce
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVI---VRNWAIEKVIELVQ 112 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~---~~~~~l~~~i~~l~ 112 (269)
+.+.|+||.+++..|+. .+|||.||..|+..+ ...||.|+..+.. .+|..++++++.++
T Consensus 25 ~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred cccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHHH
Confidence 67999999999999984 699999999999977 4579999998753 35666666666543
No 17
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.39 E-value=1.3e-07 Score=60.15 Aligned_cols=38 Identities=32% Similarity=0.829 Sum_probs=31.8
Q ss_pred eccCCCCCCc--CceeeccCCceechhchhhc---CCCCCCCC
Q 038068 56 DCPICFEPLT--VPVFQCVNGHLACSDCCAKI---KRNCPTCS 93 (269)
Q Consensus 56 ~C~iC~~~l~--~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~ 93 (269)
.|+||++.+. ..++..+|||.||..|+..| +..||.||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 5999999984 45667789999999999999 67899996
No 18
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.35 E-value=3.3e-07 Score=57.21 Aligned_cols=36 Identities=47% Similarity=1.066 Sum_probs=31.4
Q ss_pred ccCCCCCCcCceeeccCCceechhchhhc-----CCCCCCC
Q 038068 57 CPICFEPLTVPVFQCVNGHLACSDCCAKI-----KRNCPTC 92 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~~~Cp~C 92 (269)
|+||.+++..|++..+|||.||..|+.++ ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999999999966799999999999987 3468776
No 19
>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=98.31 E-value=4.7e-07 Score=64.11 Aligned_cols=59 Identities=27% Similarity=0.314 Sum_probs=44.9
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCCCCcc---ccchhHHHHhhcc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTVI---VRNWAIEKVIELV 111 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~~---~~~~~l~~~i~~l 111 (269)
|+.|.|||+.+++.+||. .++||+|+..++.+| ...||.++.++.. ..|..|.+.|+.+
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 PDEFLCPITGELMRDPVI-LPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp SGGGB-TTTSSB-SSEEE-ETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcccCCcCcCcHhhCcee-CCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 578999999999999995 599999999999998 3679999998863 4788888877765
No 20
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.27 E-value=5e-07 Score=77.91 Aligned_cols=46 Identities=26% Similarity=0.607 Sum_probs=37.7
Q ss_pred CeeeccCCCCCCcCc-------eeeccCCceechhchhhc---CCCCCCCCCCCcc
Q 038068 53 DIFDCPICFEPLTVP-------VFQCVNGHLACSDCCAKI---KRNCPTCSSPTVI 98 (269)
Q Consensus 53 ~~l~C~iC~~~l~~P-------v~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~ 98 (269)
+...|+||++.+..+ ....+|||.||..|+.+| ...||.||.++..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 567999999987653 124689999999999999 5789999998763
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.22 E-value=7.1e-07 Score=56.76 Aligned_cols=39 Identities=36% Similarity=0.824 Sum_probs=31.9
Q ss_pred eccCCCCCC--cCceeeccCCceechhchhhcC---CCCCCCCC
Q 038068 56 DCPICFEPL--TVPVFQCVNGHLACSDCCAKIK---RNCPTCSS 94 (269)
Q Consensus 56 ~C~iC~~~l--~~Pv~~c~cgH~fC~~C~~~~~---~~Cp~C~~ 94 (269)
.|++|.+.+ ..+.+..+|||+||..|+..+. ..||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 489999998 3344567999999999999884 68999974
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=98.15 E-value=1.5e-06 Score=54.57 Aligned_cols=40 Identities=43% Similarity=1.035 Sum_probs=33.7
Q ss_pred eccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCCC
Q 038068 56 DCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSSP 95 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~ 95 (269)
.|+||.+.+..++...+|||.||..|+..| ...||.|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 489999999888766569999999999877 3579999875
No 23
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.03 E-value=2.4e-06 Score=74.29 Aligned_cols=44 Identities=27% Similarity=0.707 Sum_probs=39.2
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
..+.|-||.+.++.|+ .++|||.||+-||... +..||.|+.+..
T Consensus 24 s~lrC~IC~~~i~ip~-~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRISIPC-ETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hHHHhhhhhheeecce-ecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 5689999999999999 5799999999999876 678999998764
No 24
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.94 E-value=3.9e-06 Score=52.92 Aligned_cols=27 Identities=44% Similarity=1.069 Sum_probs=18.4
Q ss_pred ccCCCCCCcC----ceeeccCCceechhchhhc
Q 038068 57 CPICFEPLTV----PVFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 57 C~iC~~~l~~----Pv~~c~cgH~fC~~C~~~~ 85 (269)
||||.+ +.. |+.+ +|||+||..|+.++
T Consensus 1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHH
Confidence 899999 877 8865 79999999999987
No 25
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=6e-06 Score=71.09 Aligned_cols=45 Identities=29% Similarity=0.611 Sum_probs=38.8
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhh-c----CCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAK-I----KRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~-~----~~~Cp~C~~~~~ 97 (269)
..++.|++|.+....|.. ++|||+||..|+.. | ...||.||+...
T Consensus 213 ~~d~kC~lC~e~~~~ps~-t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPSC-TPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCccc-ccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 478999999999999984 69999999999988 6 245999998654
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.84 E-value=6.5e-06 Score=76.85 Aligned_cols=44 Identities=39% Similarity=0.902 Sum_probs=37.7
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc--------CCCCCCCCCCCcc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI--------KRNCPTCSSPTVI 98 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~--------~~~Cp~C~~~~~~ 98 (269)
...||||+++..-|+. +.|||+||..|+.+. -..||+|+..+..
T Consensus 186 ~~~CPICL~~~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCcccc-cccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 7899999999999985 589999999999874 2579999987764
No 27
>PHA02926 zinc finger-like protein; Provisional
Probab=97.80 E-value=7.2e-06 Score=69.05 Aligned_cols=45 Identities=24% Similarity=0.529 Sum_probs=35.8
Q ss_pred CeeeccCCCCCCcC---------ceeeccCCceechhchhhcC---------CCCCCCCCCCcc
Q 038068 53 DIFDCPICFEPLTV---------PVFQCVNGHLACSDCCAKIK---------RNCPTCSSPTVI 98 (269)
Q Consensus 53 ~~l~C~iC~~~l~~---------Pv~~c~cgH~fC~~C~~~~~---------~~Cp~C~~~~~~ 98 (269)
++..|+||++.... ++ .-+|+|.||..|+.+|. ..||.||..+..
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGI-L~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGL-LDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCCccCccccccccccccccccc-cCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 67899999998643 34 35899999999999992 239999998764
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=97.74 E-value=1.8e-05 Score=47.74 Aligned_cols=35 Identities=46% Similarity=1.051 Sum_probs=29.3
Q ss_pred ccCCCCCCcCceeeccCCceechhchhhc----CCCCCCC
Q 038068 57 CPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTC 92 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C 92 (269)
|+||.+....++. .+|||.||..|+..| ...||.|
T Consensus 1 C~iC~~~~~~~~~-~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVV-LPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEE-ecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899999888875 599999999999877 3568876
No 29
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.61 E-value=2.8e-05 Score=52.59 Aligned_cols=43 Identities=28% Similarity=0.591 Sum_probs=35.0
Q ss_pred hhccCCCeeeeCCCCCCCCccChhHHhhhhhhhCCCCccceee
Q 038068 134 HEKTCQHSPLPCPLSDCSFLGCSSQFVRHFMAKHNISAVPFKY 176 (269)
Q Consensus 134 He~~C~~~p~~Cp~~~C~~~g~~~~l~~Hl~~~H~~~~~~~~~ 176 (269)
|+++|+++++.||+.+|.....+.+|.+|+...+....+.+.|
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 8889999999999866777789999999999999998888887
No 30
>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=97.58 E-value=4.3e-05 Score=68.01 Aligned_cols=45 Identities=29% Similarity=0.665 Sum_probs=34.6
Q ss_pred CeeeccCCCC--CCcCce--eeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFE--PLTVPV--FQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~--~l~~Pv--~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
++..||+|.. ++.+-+ +.-+|||.||.+|+..+ ...||.|+.++.
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 4578999999 555542 22379999999999985 457999988764
No 31
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=6.7e-06 Score=73.42 Aligned_cols=59 Identities=27% Similarity=0.442 Sum_probs=46.6
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCCCCccc----cchhHHHHhhcc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTVIV----RNWAIEKVIELV 111 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~~~----~~~~l~~~i~~l 111 (269)
..+.|+||+++|+..+..-.|+|.||..||... .+.||.||+.+... .+.+...+|..+
T Consensus 42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 679999999999999865569999999999875 57899999987642 344555565554
No 32
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=97.42 E-value=0.00011 Score=51.94 Aligned_cols=38 Identities=34% Similarity=0.809 Sum_probs=30.0
Q ss_pred eccCCCCCCcC------------ceeeccCCceechhchhhc---CCCCCCCC
Q 038068 56 DCPICFEPLTV------------PVFQCVNGHLACSDCCAKI---KRNCPTCS 93 (269)
Q Consensus 56 ~C~iC~~~l~~------------Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~ 93 (269)
.|.||++.+.+ ++....|||.|-..|+.+| ...||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 49999999933 3444579999999999999 56899997
No 33
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=4.6e-05 Score=67.17 Aligned_cols=62 Identities=27% Similarity=0.606 Sum_probs=46.8
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhcC---CCCCCCCCCCc-cccchhHHHHhhcceecc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKIK---RNCPTCSSPTV-IVRNWAIEKVIELVQVNC 115 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~---~~Cp~C~~~~~-~~~~~~l~~~i~~l~v~C 115 (269)
+.+.|+||++.+..|. ..+|||.||..|+..+. ..||.|+.... ..+|..+.+++..+....
T Consensus 12 ~~~~C~iC~~~~~~p~-~l~C~H~~c~~C~~~~~~~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~ 77 (386)
T KOG2177|consen 12 EELTCPICLEYFREPV-LLPCGHNFCRACLTRSWEGPLSCPVCRPPSRNLRPNVLLANLVERLRQLR 77 (386)
T ss_pred ccccChhhHHHhhcCc-cccccchHhHHHHHHhcCCCcCCcccCCchhccCccHHHHHHHHHHHhcC
Confidence 7899999999999995 55899999999999873 68999994111 124566666666655443
No 34
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=5.5e-05 Score=73.88 Aligned_cols=45 Identities=24% Similarity=0.717 Sum_probs=40.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCCCCcc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTVI 98 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~~ 98 (269)
..|.||+|..-.++.|. ..|||.||..|+... ..+||.|..+|+.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred hceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 68999999998999884 699999999999876 5789999999874
No 35
>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=97.23 E-value=0.00067 Score=54.35 Aligned_cols=27 Identities=30% Similarity=0.571 Sum_probs=23.5
Q ss_pred eeCCCCCCCCccChhHHhhhhhhhCCC
Q 038068 143 LPCPLSDCSFLGCSSQFVRHFMAKHNI 169 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~~l~~Hl~~~H~~ 169 (269)
=.|+..+|.|.|.+.+|..|.+.+|+.
T Consensus 108 RsC~~e~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 108 RSCSQESCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred ccCcccccccccCHHHHHHHHHhhCCC
Confidence 356666999999999999999999975
No 36
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.93 E-value=0.00095 Score=64.37 Aligned_cols=117 Identities=16% Similarity=0.337 Sum_probs=69.8
Q ss_pred CCeeeccCCCCCCcCceee-----ccCCceech--hchhhc-------CCCCCCCCCCCccccchhHHHHhhcceecccC
Q 038068 52 QDIFDCPICFEPLTVPVFQ-----CVNGHLACS--DCCAKI-------KRNCPTCSSPTVIVRNWAIEKVIELVQVNCKN 117 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~-----c~cgH~fC~--~C~~~~-------~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~ 117 (269)
.+...|+-|......--++ |.---+.|. .|-..+ ...|+.|...+....-....+.. ..++.|+
T Consensus 405 ~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~~~~-Hkpv~Cp- 482 (567)
T PLN03086 405 VDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHMKVF-HEPLQCP- 482 (567)
T ss_pred CCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccchHHHHHHHHhc-CCCccCC-
Confidence 4667899998765433111 211112232 132222 24699998776522112222222 4667886
Q ss_pred CCCCccccccccchhhhhc-cCCCeeeeCCCCCCCCccCh-----------hHHhhhhhhhCCCCccceeec
Q 038068 118 AEYGCQQKMSFSKKRGHEK-TCQHSPLPCPLSDCSFLGCS-----------SQFVRHFMAKHNISAVPFKYN 177 (269)
Q Consensus 118 ~~~GC~~~~~~~~~~~He~-~C~~~p~~Cp~~~C~~~g~~-----------~~l~~Hl~~~H~~~~~~~~~~ 177 (269)
|...+...++..|.. .|+.+++.|++ |+..+.. ..|..|... |....+.|..|
T Consensus 483 ----Cg~~~~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~C 547 (567)
T PLN03086 483 ----CGVVLEKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRTAPCDSC 547 (567)
T ss_pred ----CCCCcchhHHHhhhhccCCCCceeCCC--CCCccccCccccchhhhhhhHHHHHHh-cCCcceEcccc
Confidence 777777888889965 69999999996 9887642 378888776 44555566544
No 37
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.88 E-value=0.0012 Score=63.72 Aligned_cols=53 Identities=25% Similarity=0.519 Sum_probs=32.5
Q ss_pred ccccccccchhhhhccCCCeeeeCCCCCCCCccChhHHhhhhhhhCCCCccceeecc
Q 038068 122 CQQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGCSSQFVRHFMAKHNISAVPFKYNS 178 (269)
Q Consensus 122 C~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~~~~l~~Hl~~~H~~~~~~~~~~~ 178 (269)
|...+...+++.|.+.| +.++.|| |+....+.+|..|....++...+.|.||.
T Consensus 459 Cgk~f~~s~LekH~~~~-Hkpv~Cp---Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~ 511 (567)
T PLN03086 459 CGQAFQQGEMEKHMKVF-HEPLQCP---CGVVLEKEQMVQHQASTCPLRLITCRFCG 511 (567)
T ss_pred CCCccchHHHHHHHHhc-CCCccCC---CCCCcchhHHHhhhhccCCCCceeCCCCC
Confidence 44444455555565555 4666666 66656666777776666666666666664
No 38
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.73 E-value=0.00051 Score=56.86 Aligned_cols=56 Identities=27% Similarity=0.495 Sum_probs=42.5
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc--cccchhHHHHhhc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV--IVRNWAIEKVIEL 110 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~--~~~~~~l~~~i~~ 110 (269)
-|.|-||..-+..||. +.|||.||+.|..+- ...|-.|..... ......+++++..
T Consensus 196 PF~C~iCKkdy~spvv-t~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL~~ 256 (259)
T COG5152 196 PFLCGICKKDYESPVV-TECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKMLNK 256 (259)
T ss_pred ceeehhchhhccchhh-hhcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHHhh
Confidence 4789999999999995 699999999997754 568999987653 1233445666554
No 39
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.66 E-value=0.00095 Score=44.75 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=24.1
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~ 85 (269)
-.+.|||...+|.+||....|||+|....+..+
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~ 42 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQY 42 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--EEEHHHHHHH
T ss_pred eccCCCCcCChhhCCcCcCCCCCeecHHHHHHH
Confidence 568999999999999976689999998888776
No 40
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.59 E-value=0.0017 Score=56.40 Aligned_cols=45 Identities=33% Similarity=0.697 Sum_probs=37.8
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc-----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~~ 97 (269)
..-+||+|.+....|...-+|||++|-.|+... +..||.|..+..
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 557999999999999866569999999999864 368999987653
No 41
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.0017 Score=57.00 Aligned_cols=46 Identities=35% Similarity=0.574 Sum_probs=38.4
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCccccc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTVIVRN 101 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~~~~~ 101 (269)
+.|-||..++..||. +.|||.||..|...- ...|.+|.+++...-|
T Consensus 242 f~c~icr~~f~~pVv-t~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVV-TKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFN 290 (313)
T ss_pred ccccccccccccchh-hcCCceeehhhhccccccCCcceecccccccccc
Confidence 569999999999995 699999999997765 4689999988764433
No 42
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.00093 Score=61.96 Aligned_cols=45 Identities=31% Similarity=0.750 Sum_probs=39.8
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
...|.|.||...|.+|+. ++|||.||..|+.+. ...||.|+.++.
T Consensus 82 ~sef~c~vc~~~l~~pv~-tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVV-TPCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCCcc-ccccccccHHHHHHHhccCCCCcccccccc
Confidence 478999999999999996 599999999998876 568999998775
No 43
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.43 E-value=0.00066 Score=60.46 Aligned_cols=45 Identities=24% Similarity=0.433 Sum_probs=39.5
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
....|.+|..+|.++-....|-|+||.+|+.+. ...||.|...+.
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 567899999999999877789999999999876 678999987664
No 44
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.37 E-value=0.0023 Score=46.22 Aligned_cols=43 Identities=30% Similarity=0.447 Sum_probs=33.6
Q ss_pred eeccCCCCCCcC-ceeeccCCceechhchhhc------CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLTV-PVFQCVNGHLACSDCCAKI------KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~~-Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~~~~~ 97 (269)
-.||.|..+-.+ |+....|+|.|=..||.+| +..||+||++..
T Consensus 33 g~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 33 GCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred cCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 346777766543 6656789999999999998 368999998764
No 45
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0026 Score=57.39 Aligned_cols=44 Identities=32% Similarity=0.689 Sum_probs=38.2
Q ss_pred CeeeccCCCCCCcCceeeccCCce-echhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHL-ACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~-fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
.--+|-||+.-.++-+.. +|.|+ .|+.|.+.+ .+.||+||+++.
T Consensus 289 ~gkeCVIClse~rdt~vL-PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICLSESRDTVVL-PCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCCeeEEEecCCcceEEe-cchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 356899999999999865 99997 999999877 578999999875
No 46
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.14 E-value=0.0032 Score=53.92 Aligned_cols=43 Identities=26% Similarity=0.599 Sum_probs=35.0
Q ss_pred eeccCCCCC-CcCceeeccCCceechhchhhcCC-CCCCCCCCCc
Q 038068 55 FDCPICFEP-LTVPVFQCVNGHLACSDCCAKIKR-NCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~-l~~Pv~~c~cgH~fC~~C~~~~~~-~Cp~C~~~~~ 97 (269)
..|..|..- -.+|.+.+.|+|+||..|...... .||.|+.++.
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 568877653 368889999999999999987744 8999999864
No 47
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0025 Score=61.96 Aligned_cols=43 Identities=30% Similarity=0.573 Sum_probs=36.9
Q ss_pred CeeeccCCCCCCcC-----ceeeccCCceechhchhhc---CCCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTV-----PVFQCVNGHLACSDCCAKI---KRNCPTCSSPT 96 (269)
Q Consensus 53 ~~l~C~iC~~~l~~-----Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~ 96 (269)
.+..|+||.+.+.. |.. -+|||.|+..|+..| +..||.||..+
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~r-L~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKR-LPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccce-eecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 46789999999988 554 499999999999999 67999999844
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.88 E-value=0.0044 Score=39.80 Aligned_cols=40 Identities=35% Similarity=0.876 Sum_probs=20.0
Q ss_pred ccCCCCCCcC---ceeeccCCceechhchhhc----CCCCCCCCCCC
Q 038068 57 CPICFEPLTV---PVFQCVNGHLACSDCCAKI----KRNCPTCSSPT 96 (269)
Q Consensus 57 C~iC~~~l~~---Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~ 96 (269)
||+|.+.+.. -++=|+||..+|..|+.++ ...||.||.+.
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 6888887732 2345899999999998876 46899999864
No 49
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.0012 Score=43.14 Aligned_cols=42 Identities=31% Similarity=0.817 Sum_probs=33.8
Q ss_pred eeccCCCCCCcCceeeccCCce-echhchhhc----CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHL-ACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~-fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
-+|.||.+-..+.|. =.|||. .|-.|-.++ ...||+||.++.
T Consensus 8 dECTICye~pvdsVl-YtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVL-YTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHH-HHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 589999998888874 379997 888886654 568999998764
No 50
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.62 E-value=0.0068 Score=53.48 Aligned_cols=44 Identities=20% Similarity=0.449 Sum_probs=37.0
Q ss_pred eeeccCCCCCCc--CceeeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLT--VPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~--~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
-.+|.||++-+. +.+...+|.|.|=..|+++| +..||.||.++.
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 478999999774 44556799999999999999 689999998764
No 51
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.34 E-value=0.0059 Score=53.74 Aligned_cols=40 Identities=33% Similarity=0.818 Sum_probs=35.0
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCC
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSS 94 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~ 94 (269)
|.|+.|..+++.|+..-.|||.||..|+... ...||.|..
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 8999999999999964359999999999864 578999976
No 52
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.0074 Score=53.23 Aligned_cols=43 Identities=28% Similarity=0.526 Sum_probs=37.0
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
+-+|+||+.-..-|+. -.|+|.||--|++.. ...|++||.++.
T Consensus 7 ~~eC~IC~nt~n~Pv~-l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVN-LYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred CCcceeeeccCCcCcc-ccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 4589999999999985 499999999999976 456999999885
No 53
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.15 E-value=0.0056 Score=55.90 Aligned_cols=41 Identities=32% Similarity=0.566 Sum_probs=34.5
Q ss_pred eccCCCCCCcCceeeccCCceechhchhhc-----CCCCCCCCCCCc
Q 038068 56 DCPICFEPLTVPVFQCVNGHLACSDCCAKI-----KRNCPTCSSPTV 97 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~~ 97 (269)
.|-||-+--++-- .=+|||..|..|+..| ...||.||..|.
T Consensus 371 LCKICaendKdvk-IEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 371 LCKICAENDKDVK-IEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHhhccCCCcc-cccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 5999999777654 3489999999999999 367999998875
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.10 E-value=0.015 Score=52.28 Aligned_cols=46 Identities=30% Similarity=0.802 Sum_probs=36.8
Q ss_pred CCCCeeeccCCCCCCcCceeeccCCceechhchhhc-----CCCCCCCCCCC
Q 038068 50 TDQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-----KRNCPTCSSPT 96 (269)
Q Consensus 50 ~~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~ 96 (269)
.|.+.-.|.||-+-+.--. ..+|+|..|-.|--++ +..|+.|+...
T Consensus 57 tDEen~~C~ICA~~~TYs~-~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 57 TDEENMNCQICAGSTTYSA-RYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccccceeEEecCCceEEE-eccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 3457789999999777544 3599999999998776 67899999764
No 55
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.05 E-value=0.0072 Score=54.09 Aligned_cols=46 Identities=33% Similarity=0.920 Sum_probs=36.4
Q ss_pred CCCeeeccCCCCCCcCc---eeeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 51 DQDIFDCPICFEPLTVP---VFQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 51 ~~~~l~C~iC~~~l~~P---v~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
|.+++ ||.|.+++... .+-|+||..+|.-|+..+ ..+||.||....
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 33555 99999987543 566999999999999877 578999997543
No 56
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=94.63 E-value=0.02 Score=44.64 Aligned_cols=53 Identities=23% Similarity=0.519 Sum_probs=41.6
Q ss_pred ceeecCCCCeeeccCCCCCCcCceeecc---CCceechhchhhc------CCCCCCCCCCCcc
Q 038068 45 EALTITDQDIFDCPICFEPLTVPVFQCV---NGHLACSDCCAKI------KRNCPTCSSPTVI 98 (269)
Q Consensus 45 ~~~~~~~~~~l~C~iC~~~l~~Pv~~c~---cgH~fC~~C~~~~------~~~Cp~C~~~~~~ 98 (269)
+.+|.+. ..++|.||.+...+..+.-+ ||-..|..|...+ -+.||.|+..+..
T Consensus 72 mnvF~d~-~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 72 MNVFLDP-KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred heeecCC-CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 3455555 88999999998877766543 8999999998875 3689999987753
No 57
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.0095 Score=52.32 Aligned_cols=41 Identities=29% Similarity=0.737 Sum_probs=35.8
Q ss_pred eeeccCCCCCCcCceeeccCCce-echhchhhcCCCCCCCCCCC
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHL-ACSDCCAKIKRNCPTCSSPT 96 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~-fC~~C~~~~~~~Cp~C~~~~ 96 (269)
...|.||++...+-+++ +|||. .|..|-.++. .||+||+-+
T Consensus 300 ~~LC~ICmDaP~DCvfL-eCGHmVtCt~CGkrm~-eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFL-ECGHMVTCTKCGKRMN-ECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEe-ecCcEEeehhhccccc-cCchHHHHH
Confidence 67899999999999986 99996 7999998884 899998754
No 58
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.029 Score=50.91 Aligned_cols=44 Identities=23% Similarity=0.621 Sum_probs=35.9
Q ss_pred CeeeccCCCCC-CcCc------------eeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEP-LTVP------------VFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~-l~~P------------v~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
++-.|.||++- +.+| - ..+|||.+=-.|+..| +..||+||.++.
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pK-rLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPK-RLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcc-cccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 56789999987 4444 3 2489999999999999 789999999853
No 59
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.60 E-value=0.052 Score=35.78 Aligned_cols=43 Identities=28% Similarity=0.502 Sum_probs=32.2
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc-CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
...|-.|...-...+. .+|||++|..|+... -+-||.|..++.
T Consensus 7 ~~~~~~~~~~~~~~~~-~pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 7 EQPCVFCGFVGTKGTV-LPCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred ceeEEEcccccccccc-ccccceeeccccChhhccCCCCCCCccc
Confidence 3456677776555553 499999999998866 257999998875
No 60
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.47 E-value=0.029 Score=50.62 Aligned_cols=47 Identities=26% Similarity=0.596 Sum_probs=38.7
Q ss_pred CCCCeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 50 TDQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 50 ~~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
.+.++-.||||.--....|++ +|+|.-|..||.+. .+.|-.|+..+.
T Consensus 418 p~sEd~lCpICyA~pi~Avf~-PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 418 PDSEDNLCPICYAGPINAVFA-PCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred CCcccccCcceecccchhhcc-CCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 345788999999988888875 99999999999986 467888877654
No 61
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.40 E-value=0.025 Score=53.55 Aligned_cols=45 Identities=20% Similarity=0.541 Sum_probs=38.3
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc--------CCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI--------KRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~--------~~~Cp~C~~~~~ 97 (269)
.....|.+|.++..+++ ...|.|.||.-|+... .-.||.|...++
T Consensus 534 k~~~~C~lc~d~aed~i-~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 534 KGEVECGLCHDPAEDYI-ESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred cCceeecccCChhhhhH-hhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 46789999999999998 5699999999999664 457999987664
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.22 E-value=0.037 Score=50.50 Aligned_cols=45 Identities=29% Similarity=0.693 Sum_probs=37.2
Q ss_pred CeeeccCCCCCCcCce-----e--eccCCceechhchhhcC----------CCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPV-----F--QCVNGHLACSDCCAKIK----------RNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv-----~--~c~cgH~fC~~C~~~~~----------~~Cp~C~~~~~ 97 (269)
.+-.|-||++....+. + .-+|-|.||..|+..|. ..||.||....
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 6788999999988776 3 23699999999999992 67999998765
No 63
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.87 E-value=0.063 Score=48.89 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=35.6
Q ss_pred eeccCCCCCCc--CceeeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLT--VPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~--~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
..|.||++-+. +-+...+|+|.|=..|+..| ...||+|++.+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence 48999999876 34556799999999999999 345999998764
No 64
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=91.94 E-value=0.06 Score=37.58 Aligned_cols=44 Identities=30% Similarity=0.628 Sum_probs=18.8
Q ss_pred eeeccCCCCCCc----Cceeec---cCCceechhchhhc--------------CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLT----VPVFQC---VNGHLACSDCCAKI--------------KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~----~Pv~~c---~cgH~fC~~C~~~~--------------~~~Cp~C~~~~~ 97 (269)
.+.|+||...+. .|...| .|+..|=..|+.+| ...||.|+.++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 468999998754 355566 47777667788888 124888887765
No 65
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=91.80 E-value=0.053 Score=50.26 Aligned_cols=32 Identities=25% Similarity=0.642 Sum_probs=29.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~ 85 (269)
++|.|+||...+.+||.. +|||..|..|...+
T Consensus 3 eelkc~vc~~f~~epiil-~c~h~lc~~ca~~~ 34 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPIIL-PCSHNLCQACARNI 34 (699)
T ss_pred ccccCceehhhccCceEe-ecccHHHHHHHHhh
Confidence 679999999999999965 99999999998765
No 66
>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=91.34 E-value=0.14 Score=33.64 Aligned_cols=49 Identities=24% Similarity=0.527 Sum_probs=31.6
Q ss_pred ecccCCCCCccccccccchhhhhcc--CC-CeeeeCCCCCCCCccChhHHhhhhhhhCC
Q 038068 113 VNCKNAEYGCQQKMSFSKKRGHEKT--CQ-HSPLPCPLSDCSFLGCSSQFVRHFMAKHN 168 (269)
Q Consensus 113 v~C~~~~~GC~~~~~~~~~~~He~~--C~-~~p~~Cp~~~C~~~g~~~~l~~Hl~~~H~ 168 (269)
+.||| |...+....|..|..+ .. -..+.||. |... ...+|..|+...|.
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 6666666677777543 11 12578885 8754 33588889888773
No 67
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.31 E-value=0.15 Score=43.92 Aligned_cols=45 Identities=22% Similarity=0.449 Sum_probs=37.6
Q ss_pred CeeeccCCCCCCcCce---eeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPV---FQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv---~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
..+.||+|.+.|...+ ++-+|||+||..|.+++ ...||+|..++.
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plk 270 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLK 270 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCc
Confidence 6799999999998764 23379999999999998 467999988775
No 68
>PF04641 Rtf2: Rtf2 RING-finger
Probab=90.94 E-value=0.27 Score=43.32 Aligned_cols=46 Identities=22% Similarity=0.491 Sum_probs=37.8
Q ss_pred CCeeeccCCCCCCcC---ceeeccCCceechhchhhcC--CCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTV---PVFQCVNGHLACSDCCAKIK--RNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~---Pv~~c~cgH~fC~~C~~~~~--~~Cp~C~~~~~ 97 (269)
...+.|||....|.. =|+.-+|||+|+..++..+. ..||.|..++.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccc
Confidence 367999999999854 24555899999999999984 47999999876
No 69
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.86 E-value=0.11 Score=47.04 Aligned_cols=44 Identities=25% Similarity=0.651 Sum_probs=33.8
Q ss_pred CCeeeccCCCCCCcCceeeccCCceec-hhchhhcCCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLAC-SDCCAKIKRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC-~~C~~~~~~~Cp~C~~~~~ 97 (269)
+....|.||.+-.++.++. +|||+-| ..|...+ ..||.||+.+.
T Consensus 303 ~~p~lcVVcl~e~~~~~fv-pcGh~ccct~cs~~l-~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPKSAVFV-PCGHVCCCTLCSKHL-PQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCccceeee-cCCcEEEchHHHhhC-CCCchhHHHHH
Confidence 4556899999999998875 9999966 2344444 46999998764
No 70
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.93 E-value=0.094 Score=51.98 Aligned_cols=45 Identities=18% Similarity=0.433 Sum_probs=34.0
Q ss_pred CeeeccCCCCCCcCceeec--cCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQC--VNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c--~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
..-.||+|+.-+.+-.... .|+|.||..|+..| ...||+||..+.
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 4456888887665543222 59999999999999 478999998764
No 71
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=89.68 E-value=0.14 Score=47.74 Aligned_cols=44 Identities=23% Similarity=0.620 Sum_probs=36.2
Q ss_pred CeeeccCCCCCCcCce---eeccCCceechhchhhc-CCCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTVPV---FQCVNGHLACSDCCAKI-KRNCPTCSSPT 96 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv---~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~ 96 (269)
+.-.||||++-+-+-+ ....|.|.|=.+|+.+| ...||+||--.
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q 221 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQ 221 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhc
Confidence 6779999999887664 44579999999999999 46899998643
No 72
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=89.32 E-value=0.24 Score=44.07 Aligned_cols=77 Identities=22% Similarity=0.412 Sum_probs=49.4
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc-CCCCCCCCCCCccccchhHHHHhhcceecccCCCCCcccc-ccccc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-KRNCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQK-MSFSK 130 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~-~~~~~ 130 (269)
..-.|.-|..++..==..-+|.|+||..|-..- .+.||.|...+ ..++.....-.+-|. ...||.-+ +.-.+
T Consensus 89 ~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V-----qrIeq~~~g~iFmC~-~~~GC~RTyLsqrD 162 (389)
T KOG2932|consen 89 RVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV-----QRIEQIMMGGIFMCA-APHGCLRTYLSQRD 162 (389)
T ss_pred ceEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH-----HHHHHhcccceEEee-cchhHHHHHhhHHH
Confidence 356688999887754444589999999996543 45899996543 335555555566675 34566543 23345
Q ss_pred hhhhh
Q 038068 131 KRGHE 135 (269)
Q Consensus 131 ~~~He 135 (269)
|+.|.
T Consensus 163 lqAHI 167 (389)
T KOG2932|consen 163 LQAHI 167 (389)
T ss_pred HHHHh
Confidence 55554
No 73
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=89.01 E-value=0.18 Score=28.01 Aligned_cols=22 Identities=23% Similarity=0.347 Sum_probs=14.0
Q ss_pred eccCCCCCCcCceeecc-CCcee
Q 038068 56 DCPICFEPLTVPVFQCV-NGHLA 77 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~-cgH~f 77 (269)
.||.|...+..-...|+ |||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 47777776655555566 77765
No 74
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.00 E-value=0.083 Score=53.41 Aligned_cols=45 Identities=29% Similarity=0.661 Sum_probs=36.0
Q ss_pred CeeeccCCCCCCc-----Cceeecc-CCceechhchhhc-----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLT-----VPVFQCV-NGHLACSDCCAKI-----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~-----~Pv~~c~-cgH~fC~~C~~~~-----~~~Cp~C~~~~~ 97 (269)
..-+|+||..++. -|-..|+ |.|-|=.+|+.+| ...||.||..++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3457999999885 4544565 9999999999999 578999997764
No 75
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.73 E-value=0.32 Score=44.97 Aligned_cols=100 Identities=26% Similarity=0.472 Sum_probs=60.5
Q ss_pred CeeeccCCCCCCcCc--eeeccCCceechhchhhc-----------CCCCCCCCCCCcc--------------c--cchh
Q 038068 53 DIFDCPICFEPLTVP--VFQCVNGHLACSDCCAKI-----------KRNCPTCSSPTVI--------------V--RNWA 103 (269)
Q Consensus 53 ~~l~C~iC~~~l~~P--v~~c~cgH~fC~~C~~~~-----------~~~Cp~C~~~~~~--------------~--~~~~ 103 (269)
..+.|.||.+-.... ++..+|+|+||.+|.... .-+||.+..+-.. . ....
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~ 262 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKLM 262 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHHH
Confidence 578999999977653 444599999999998764 3468775543210 0 1223
Q ss_pred HHHHhhcce--ecccCCCCCccccccccchhhhhc---cCCCeee-eCCC-----CCCCCccC
Q 038068 104 IEKVIELVQ--VNCKNAEYGCQQKMSFSKKRGHEK---TCQHSPL-PCPL-----SDCSFLGC 155 (269)
Q Consensus 104 l~~~i~~l~--v~C~~~~~GC~~~~~~~~~~~He~---~C~~~p~-~Cp~-----~~C~~~g~ 155 (269)
+++.+..+. +.||++ -|+.-. ..+...-.. .|.|+-| .|.. ..|++.+.
T Consensus 263 lqk~l~~msdv~yCPr~--~Cq~p~-~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~ 322 (445)
T KOG1814|consen 263 LQKTLELMSDVVYCPRA--CCQLPV-KQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAE 322 (445)
T ss_pred HHHHHHhhcccccCChh--hccCcc-ccCchhhhhhhccCccHHHHHHHHhhcCCCcccCchH
Confidence 455555555 899997 566554 444444443 4555532 2221 36887754
No 76
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.03 E-value=0.23 Score=45.82 Aligned_cols=42 Identities=38% Similarity=0.719 Sum_probs=33.9
Q ss_pred eeccCCCCCCcCcee----eccCCceechhchhhc-----CCCCCCCCCCC
Q 038068 55 FDCPICFEPLTVPVF----QCVNGHLACSDCCAKI-----KRNCPTCSSPT 96 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~----~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~ 96 (269)
..||||++-..-|.- .-.|||.|-++|+++| ...||.|....
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 579999998776642 2379999999999999 46899997643
No 77
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=87.38 E-value=0.75 Score=41.36 Aligned_cols=45 Identities=27% Similarity=0.574 Sum_probs=35.4
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
+.-.||+|..-...|-.....|-+||..|+-.. -+.||+-..+..
T Consensus 299 ~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 556899999998888655567999999999775 468998665543
No 78
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.91 E-value=0.17 Score=44.24 Aligned_cols=45 Identities=20% Similarity=0.449 Sum_probs=35.2
Q ss_pred CeeeccCCCCCCcCc---------eeeccCCceechhchhhc-----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVP---------VFQCVNGHLACSDCCAKI-----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~P---------v~~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~~ 97 (269)
++-.|.+|..-+... .++.+|+|+|=..|+..| ++.||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 445788888766543 356789999999999998 578999988664
No 79
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=86.45 E-value=0.46 Score=25.42 Aligned_cols=24 Identities=33% Similarity=0.722 Sum_probs=17.7
Q ss_pred eeCCCCCCCCccChhHHhhhhhhhCC
Q 038068 143 LPCPLSDCSFLGCSSQFVRHFMAKHN 168 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~~l~~Hl~~~H~ 168 (269)
+.|+. |+|......|..|+...|.
T Consensus 1 y~C~~--C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPH--CSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SS--SS-EESHHHHHHHHHHHHS
T ss_pred CCCCC--CCCcCCHHHHHHHHHhhCc
Confidence 36774 9998888899999988773
No 80
>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=86.11 E-value=0.2 Score=34.79 Aligned_cols=38 Identities=32% Similarity=0.781 Sum_probs=22.8
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhc--CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKI--KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~--~~~Cp~C~~~~~ 97 (269)
+.||.|..+|.. .-|+..|..|-... ...||.|..++.
T Consensus 2 ~~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH
Confidence 689999997542 23899999998876 467999988764
No 81
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.72 E-value=0.6 Score=43.00 Aligned_cols=42 Identities=26% Similarity=0.652 Sum_probs=31.8
Q ss_pred CeeeccCCCCC---CcCceeeccCCceechhchhhc------CCCCCCCCCC
Q 038068 53 DIFDCPICFEP---LTVPVFQCVNGHLACSDCCAKI------KRNCPTCSSP 95 (269)
Q Consensus 53 ~~l~C~iC~~~---l~~Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~~~ 95 (269)
..|.|||=.+- =.||+. -.|||+.|..-+.++ +.+||.|=..
T Consensus 333 SvF~CPVlKeqtsdeNPPm~-L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMM-LICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ceeecccchhhccCCCCCee-eeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 67899995443 358885 599999999998887 2568888543
No 82
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=85.14 E-value=0.59 Score=42.50 Aligned_cols=114 Identities=19% Similarity=0.438 Sum_probs=79.5
Q ss_pred CCCeeeccCCCCCCcCcee-------ec--cCCceechhchhhc---------------CCCCCCCCCCCcc---ccchh
Q 038068 51 DQDIFDCPICFEPLTVPVF-------QC--VNGHLACSDCCAKI---------------KRNCPTCSSPTVI---VRNWA 103 (269)
Q Consensus 51 ~~~~l~C~iC~~~l~~Pv~-------~c--~cgH~fC~~C~~~~---------------~~~Cp~C~~~~~~---~~~~~ 103 (269)
....+-||-|.++|..--. |+ .-.+--|+.|..+. ..+||+|....+. .++..
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHH
Confidence 3467899999998865411 11 23477899998765 3579999876652 24455
Q ss_pred HHHHhhcceecccCCCCCcccc-ccccchhhhhccCCCeeeeCCCCCCCCccC-hhHHhhhhhhhCC
Q 038068 104 IEKVIELVQVNCKNAEYGCQQK-MSFSKKRGHEKTCQHSPLPCPLSDCSFLGC-SSQFVRHFMAKHN 168 (269)
Q Consensus 104 l~~~i~~l~v~C~~~~~GC~~~-~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~-~~~l~~Hl~~~H~ 168 (269)
+-+-.++-.+.|. -|... +...+|..|...=..-.+.|..++|.+... +..|..|+...|.
T Consensus 284 r~rHs~dkpfKCd----~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 284 RYRHSKDKPFKCD----ECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred HhhhccCCCcccc----chhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 5566667778876 46554 456788999874444567888888988765 5689999998884
No 83
>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=84.63 E-value=0.88 Score=29.63 Aligned_cols=37 Identities=32% Similarity=0.742 Sum_probs=20.6
Q ss_pred ccCCCCCCcCc--------eeecc-CCceechhchhhc---CCCCCCCC
Q 038068 57 CPICFEPLTVP--------VFQCV-NGHLACSDCCAKI---KRNCPTCS 93 (269)
Q Consensus 57 C~iC~~~l~~P--------v~~c~-cgH~fC~~C~~~~---~~~Cp~C~ 93 (269)
|--|..+|..+ +++|+ |++.||..|=.-+ -..||-|.
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 56677777664 67886 9999999994433 35799884
No 84
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=84.62 E-value=0.41 Score=33.98 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=22.5
Q ss_pred cCCceechhchhhc---CCCCCCCCCCCcc
Q 038068 72 VNGHLACSDCCAKI---KRNCPTCSSPTVI 98 (269)
Q Consensus 72 ~cgH~fC~~C~~~~---~~~Cp~C~~~~~~ 98 (269)
.|.|.|=..|+.+| +..||+++++...
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 47788888999999 6789999987654
No 85
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.22 E-value=0.35 Score=45.71 Aligned_cols=45 Identities=27% Similarity=0.591 Sum_probs=33.9
Q ss_pred CeeeccCCCCCCcCc----------------eeeccCCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVP----------------VFQCVNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~P----------------v~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
....|+||+.++..- .+.++|.|+|=..|+.+| +-.||.||.++.
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 346799998865321 123589999999999999 457999999864
No 86
>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=84.11 E-value=0.64 Score=30.09 Aligned_cols=42 Identities=33% Similarity=0.751 Sum_probs=22.0
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchhhc-------CCCCCCCCCC
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-------KRNCPTCSSP 95 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-------~~~Cp~C~~~ 95 (269)
.|.||+-...+..|+.--.|.|.-|-+=..-+ ...||.|.++
T Consensus 2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp ESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 37899999999999987789999764321111 3469999753
No 87
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.89 E-value=0.22 Score=48.48 Aligned_cols=37 Identities=30% Similarity=0.728 Sum_probs=30.1
Q ss_pred CeeeccCCCCCC----cCceeeccCCceechhchhhc-CCCCC
Q 038068 53 DIFDCPICFEPL----TVPVFQCVNGHLACSDCCAKI-KRNCP 90 (269)
Q Consensus 53 ~~l~C~iC~~~l----~~Pv~~c~cgH~fC~~C~~~~-~~~Cp 90 (269)
+.|.|+||+..| ..|+.. .|||+.|+.|.+.+ ...||
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl-~cghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSL-QCGHTICGHCVQLLYNASCP 51 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccc-cccchHHHHHHHhHhhccCC
Confidence 678999997665 467754 89999999999987 56788
No 88
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=82.02 E-value=0.53 Score=46.97 Aligned_cols=40 Identities=30% Similarity=0.603 Sum_probs=33.0
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhc-----CCCCCCCCCCC
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKI-----KRNCPTCSSPT 96 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-----~~~Cp~C~~~~ 96 (269)
+.|++|.+ ...++ ...|||.+|..|+... ...||.|+..+
T Consensus 455 ~~c~ic~~-~~~~~-it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-LDSFF-ITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-cccce-eecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 89999999 66776 5799999999999876 34699997644
No 89
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.78 E-value=1.3 Score=39.55 Aligned_cols=57 Identities=32% Similarity=0.687 Sum_probs=39.2
Q ss_pred eeeccCCCCCCc------CceeeccCCceechhchhhc----CCCCCCCCCCCc--c------ccchhHHHHhhcc
Q 038068 54 IFDCPICFEPLT------VPVFQCVNGHLACSDCCAKI----KRNCPTCSSPTV--I------VRNWAIEKVIELV 111 (269)
Q Consensus 54 ~l~C~iC~~~l~------~Pv~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~~--~------~~~~~l~~~i~~l 111 (269)
.+.|-||.+.+. .|... .|||.+|..|..++ ...||.||.+.. . ..|+++-..+..+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~~~~~~l~kNf~ll~~~~~~ 77 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVL-KCGHTICQNCASKLLGNSRILCPFCRETTEIPDGDVKSLQKNFALLQAIEHM 77 (296)
T ss_pred CCceeecCccccccCcccCCccc-ccCceehHhHHHHHhcCceeeccCCCCcccCCchhHhhhhhhHHHHHHHHHH
Confidence 356777777653 34322 69999999999987 356999999842 1 3566666665554
No 90
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.80 E-value=1.8 Score=29.00 Aligned_cols=37 Identities=27% Similarity=0.652 Sum_probs=20.6
Q ss_pred cceecccCCCCCccccccccchhhhhccCCCeeeeCCCCCCCCccC
Q 038068 110 LVQVNCKNAEYGCQQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGC 155 (269)
Q Consensus 110 ~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~ 155 (269)
...++||| |.+.+-+.-..--+ .-.++.|| .|+|.|+
T Consensus 25 ~v~F~CPn----CGe~~I~Rc~~CRk---~g~~Y~Cp--~CGF~GP 61 (61)
T COG2888 25 AVKFPCPN----CGEVEIYRCAKCRK---LGNPYRCP--KCGFEGP 61 (61)
T ss_pred eeEeeCCC----CCceeeehhhhHHH---cCCceECC--CcCccCC
Confidence 45677876 66443332221111 12478898 5999874
No 91
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=80.51 E-value=0.75 Score=25.21 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=9.6
Q ss_pred ccccccccchhhhhccC
Q 038068 122 CQQKMSFSKKRGHEKTC 138 (269)
Q Consensus 122 C~~~~~~~~~~~He~~C 138 (269)
|.-++....+..|+..|
T Consensus 8 CgR~F~~~~l~~H~~~C 24 (25)
T PF13913_consen 8 CGRKFNPDRLEKHEKIC 24 (25)
T ss_pred CCCEECHHHHHHHHHhc
Confidence 55555555555555555
No 92
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=79.97 E-value=1.9 Score=28.20 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=22.6
Q ss_pred eeCCCCCCCCccChhHHhhhhhhhCCCCc
Q 038068 143 LPCPLSDCSFLGCSSQFVRHFMAKHNISA 171 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~~l~~Hl~~~H~~~~ 171 (269)
+.||+ |+.......|..|+...|....
T Consensus 3 f~CP~--C~~~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 3 FTCPY--CGKGFSESSLVEHCEDEHRSES 29 (54)
T ss_pred cCCCC--CCCccCHHHHHHHHHhHCcCCC
Confidence 57886 9986677899999999998754
No 93
>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=79.75 E-value=0.97 Score=39.98 Aligned_cols=41 Identities=29% Similarity=0.673 Sum_probs=29.7
Q ss_pred eccCCCC--CCcCce--eeccCCceechhchhhc----CCCCCCCCCCC
Q 038068 56 DCPICFE--PLTVPV--FQCVNGHLACSDCCAKI----KRNCPTCSSPT 96 (269)
Q Consensus 56 ~C~iC~~--~l~~Pv--~~c~cgH~fC~~C~~~~----~~~Cp~C~~~~ 96 (269)
.||+|.. ++.+-+ +.-+|||..|.+|...+ +..||.|...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 4788865 233332 22379999999999998 67899997654
No 94
>PHA00616 hypothetical protein
Probab=79.49 E-value=1.9 Score=27.17 Aligned_cols=34 Identities=15% Similarity=0.381 Sum_probs=26.3
Q ss_pred eeeCCCCCCCCcc-ChhHHhhhhhhhCCCCccceeec
Q 038068 142 PLPCPLSDCSFLG-CSSQFVRHFMAKHNISAVPFKYN 177 (269)
Q Consensus 142 p~~Cp~~~C~~~g-~~~~l~~Hl~~~H~~~~~~~~~~ 177 (269)
|+.|| .||..- .+++|..|+...|.....++.|-
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 46788 598764 46799999999999877766653
No 95
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.22 E-value=0.69 Score=43.09 Aligned_cols=33 Identities=30% Similarity=0.562 Sum_probs=22.9
Q ss_pred CeeeccCCC-CCCcCc-e-eeccCCceechhchhhc
Q 038068 53 DIFDCPICF-EPLTVP-V-FQCVNGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~iC~-~~l~~P-v-~~c~cgH~fC~~C~~~~ 85 (269)
....|.||. +..... . ....|+|.||..|..+.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ 180 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQH 180 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHH
Confidence 467899999 443321 1 12469999999999864
No 96
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.60 E-value=1.2 Score=38.45 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=26.4
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~ 85 (269)
-.|+.|+.+..+|| .|+-||+||..||...
T Consensus 44 dcCsLtLqPc~dPv-it~~GylfdrEaILe~ 73 (303)
T KOG3039|consen 44 DCCSLTLQPCRDPV-ITPDGYLFDREAILEY 73 (303)
T ss_pred ceeeeecccccCCc-cCCCCeeeeHHHHHHH
Confidence 45899999999999 5899999999998764
No 97
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=75.87 E-value=2 Score=28.56 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=21.7
Q ss_pred eecc--CCCCCCc------Cceeec-cCCceechhchhhc
Q 038068 55 FDCP--ICFEPLT------VPVFQC-VNGHLACSDCCAKI 85 (269)
Q Consensus 55 l~C~--iC~~~l~------~Pv~~c-~cgH~fC~~C~~~~ 85 (269)
.-|| -|..++. .+...| .||+.||..|...|
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 3466 5654432 335578 69999999998877
No 98
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.51 E-value=2.1 Score=42.38 Aligned_cols=41 Identities=24% Similarity=0.613 Sum_probs=31.4
Q ss_pred eccCCCCCCcCceeeccCCc-eechhchhhc---------CCCCCCCCCCCc
Q 038068 56 DCPICFEPLTVPVFQCVNGH-LACSDCCAKI---------KRNCPTCSSPTV 97 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH-~fC~~C~~~~---------~~~Cp~C~~~~~ 97 (269)
.|+||-.-..-+.+ =.||| .+|..|..++ ...||.|+..+.
T Consensus 2 ~c~ic~~s~~~~~~-~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDFVGR-GSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCcccccc-ccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 48888887777765 38999 8999999887 234699988654
No 99
>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=73.46 E-value=1.6 Score=39.00 Aligned_cols=43 Identities=30% Similarity=0.676 Sum_probs=22.1
Q ss_pred CeeeccCCCCCCcCceeeccC--C--ceechhchhhc---CCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTVPVFQCVN--G--HLACSDCCAKI---KRNCPTCSSP 95 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~c--g--H~fC~~C~~~~---~~~Cp~C~~~ 95 (269)
..-.||+|.....--+..-.- | +.+|+-|-..| ...||.|...
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 456899999976665544233 4 67999999999 5689999764
No 100
>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=71.83 E-value=1.3 Score=24.68 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=14.3
Q ss_pred ecccCCCCCccccccccchhhhhccCC
Q 038068 113 VNCKNAEYGCQQKMSFSKKRGHEKTCQ 139 (269)
Q Consensus 113 v~C~~~~~GC~~~~~~~~~~~He~~C~ 139 (269)
+.|||. -.-.++..+|+.|+..|+
T Consensus 3 v~CPyn---~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 3 VRCPYN---PSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EE-TTT---SS-EEEGGGHHHHHHHHH
T ss_pred eeCCCC---CCcCcCHHHHHHHHHHcC
Confidence 567764 456677777777776664
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=69.13 E-value=4.5 Score=41.90 Aligned_cols=44 Identities=20% Similarity=0.545 Sum_probs=34.7
Q ss_pred CCeeeccCCCCCCcCceeecc-CCc-----eechhchhhc-CCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCV-NGH-----LACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~-cgH-----~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
.....|+-|.... +.+.|+ ||. .||..|.... ...||.|.....
T Consensus 624 Vg~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCC
Confidence 3667899999985 445787 994 5999998776 467999998765
No 102
>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=68.95 E-value=3.7 Score=34.40 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=31.8
Q ss_pred CCCCCccccchhHHHHhhcceecccCCCCCccccccccchhhhhccCC
Q 038068 92 CSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMSFSKKRGHEKTCQ 139 (269)
Q Consensus 92 C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~ 139 (269)
|...+.+..-...++...-.+..||....||.|.+.+.++..|...--
T Consensus 24 C~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H 71 (198)
T PF03145_consen 24 CTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKH 71 (198)
T ss_dssp ---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHT
T ss_pred CcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHC
Confidence 555555555677899999999999996679999999999999987643
No 103
>smart00301 DM Doublesex DNA-binding motif.
Probab=68.12 E-value=2.9 Score=27.51 Aligned_cols=39 Identities=15% Similarity=0.448 Sum_probs=29.9
Q ss_pred ccccccccchhhhhccCCCeeeeCCCCCCCCccChhHHhhh
Q 038068 122 CQQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGCSSQFVRH 162 (269)
Q Consensus 122 C~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~~~~l~~H 162 (269)
|........++.|-..|+|+.|.|+ .|.....+..+...
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 4444556678899999999999999 69987776666543
No 104
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=67.78 E-value=3 Score=36.68 Aligned_cols=24 Identities=33% Similarity=0.890 Sum_probs=19.3
Q ss_pred eeeccCCCCCCc--CceeeccCCcee
Q 038068 54 IFDCPICFEPLT--VPVFQCVNGHLA 77 (269)
Q Consensus 54 ~l~C~iC~~~l~--~Pv~~c~cgH~f 77 (269)
.|.||+|..+|. ..-..|++||.|
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 378999999996 444578999987
No 105
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.48 E-value=4.5 Score=28.18 Aligned_cols=29 Identities=28% Similarity=0.724 Sum_probs=24.1
Q ss_pred eccCCceechhchhh-cCCCCCCCCCCCcc
Q 038068 70 QCVNGHLACSDCCAK-IKRNCPTCSSPTVI 98 (269)
Q Consensus 70 ~c~cgH~fC~~C~~~-~~~~Cp~C~~~~~~ 98 (269)
.|.--++||..|.+. +...||.|...+..
T Consensus 24 ICtfEcTFCadCae~~l~g~CPnCGGelv~ 53 (84)
T COG3813 24 ICTFECTFCADCAENRLHGLCPNCGGELVA 53 (84)
T ss_pred EEEEeeehhHhHHHHhhcCcCCCCCchhhc
Confidence 577788999999984 47899999987764
No 106
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=67.44 E-value=4 Score=24.91 Aligned_cols=23 Identities=26% Similarity=0.791 Sum_probs=17.0
Q ss_pred ccCCCCCCcC-ceeecc-CCceechh
Q 038068 57 CPICFEPLTV-PVFQCV-NGHLACSD 80 (269)
Q Consensus 57 C~iC~~~l~~-Pv~~c~-cgH~fC~~ 80 (269)
|.+|.....- |+ .|. |+..||..
T Consensus 1 C~~C~~~~~l~~f-~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGF-KCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCe-ECCccCCccccc
Confidence 5677776555 76 688 99999864
No 107
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=65.92 E-value=6.7 Score=24.31 Aligned_cols=33 Identities=24% Similarity=0.566 Sum_probs=18.5
Q ss_pred ccC--CCCCCcCceeecc-CCceechhchhhcCCCCC
Q 038068 57 CPI--CFEPLTVPVFQCV-NGHLACSDCCAKIKRNCP 90 (269)
Q Consensus 57 C~i--C~~~l~~Pv~~c~-cgH~fC~~C~~~~~~~Cp 90 (269)
|.+ |......|+ .|. |+..||..=+..-...|+
T Consensus 1 C~~~~C~~~~~~~~-~C~~C~~~FC~~Hr~~e~H~C~ 36 (43)
T PF01428_consen 1 CSFPGCKKKDFLPF-KCKHCGKSFCLKHRLPEDHNCS 36 (43)
T ss_dssp -SSTTT--BCTSHE-E-TTTS-EE-TTTHSTTTCT-S
T ss_pred CccCcCcCccCCCe-ECCCCCcccCccccCccccCCc
Confidence 455 888777887 688 999999877655444454
No 108
>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=64.91 E-value=4.2 Score=36.70 Aligned_cols=41 Identities=27% Similarity=0.631 Sum_probs=29.5
Q ss_pred eeeccCCCCCCcCceeec---cCC--ceechhchhhc---CCCCCCCCC
Q 038068 54 IFDCPICFEPLTVPVFQC---VNG--HLACSDCCAKI---KRNCPTCSS 94 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c---~cg--H~fC~~C~~~~---~~~Cp~C~~ 94 (269)
.-.||+|.....--+..- .-| +..|+-|-..| ...||.|..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 448999999765443221 244 67999999999 467999975
No 109
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.81 E-value=7.4 Score=25.62 Aligned_cols=38 Identities=24% Similarity=0.528 Sum_probs=27.9
Q ss_pred CeeeccCCCCCC--cCceeecc-CCceechhchhhcCCCCCC
Q 038068 53 DIFDCPICFEPL--TVPVFQCV-NGHLACSDCCAKIKRNCPT 91 (269)
Q Consensus 53 ~~l~C~iC~~~l--~~Pv~~c~-cgH~fC~~C~~~~~~~Cp~ 91 (269)
..-.|++|.+.| .+.+.+|+ ||-.+=+.|..+. ..|-.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~-g~C~~ 44 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA-GGCIN 44 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC-CceEe
Confidence 345799999999 67777886 8876667777765 35544
No 110
>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=64.53 E-value=4 Score=27.85 Aligned_cols=33 Identities=24% Similarity=0.683 Sum_probs=16.6
Q ss_pred CeeeccCCCCCCcC--ceeecc-CCceechhchhhc
Q 038068 53 DIFDCPICFEPLTV--PVFQCV-NGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~iC~~~l~~--Pv~~c~-cgH~fC~~C~~~~ 85 (269)
+.-.|.+|...|.- .-..|. ||++||+.|....
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 45689999998742 233564 9999999998654
No 111
>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=64.16 E-value=5.1 Score=29.59 Aligned_cols=30 Identities=23% Similarity=0.487 Sum_probs=23.5
Q ss_pred eeeccCCCCCCcCc-eeeccCCceechhchh
Q 038068 54 IFDCPICFEPLTVP-VFQCVNGHLACSDCCA 83 (269)
Q Consensus 54 ~l~C~iC~~~l~~P-v~~c~cgH~fC~~C~~ 83 (269)
.-.|++|...+... +..-+|||+|-..|..
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 34699999998855 4445899999988875
No 112
>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=62.64 E-value=3.8 Score=27.09 Aligned_cols=33 Identities=24% Similarity=0.459 Sum_probs=19.4
Q ss_pred CeeeccC--CCCCCcCc------eeecc-CCceechhchhhc
Q 038068 53 DIFDCPI--CFEPLTVP------VFQCV-NGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~i--C~~~l~~P------v~~c~-cgH~fC~~C~~~~ 85 (269)
+...||- |..++... .++|+ |++.||..|...|
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 4457877 88776432 14688 9999999998876
No 113
>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=61.19 E-value=8.4 Score=25.50 Aligned_cols=41 Identities=27% Similarity=0.709 Sum_probs=29.2
Q ss_pred ccCCCCCCcC---ceeeccCCceechhchhhc-CCCCCCCCCCCc
Q 038068 57 CPICFEPLTV---PVFQCVNGHLACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 57 C~iC~~~l~~---Pv~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
|-.|..-|.+ ..+.|+--.+||..|.+.+ ...||.|...+.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 4455544422 2346776779999999988 789999988765
No 114
>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=61.07 E-value=3 Score=26.51 Aligned_cols=38 Identities=21% Similarity=0.539 Sum_probs=28.5
Q ss_pred CCCCCCCCCccccchhHHHHhhcceecccCCCCCcccccc
Q 038068 88 NCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMS 127 (269)
Q Consensus 88 ~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~ 127 (269)
.||.|+..........+...+.++...|.|. -|.+.+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~--~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNP--ECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCC--cCCCEEE
Confidence 4999988776556667788888899999987 3655544
No 115
>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=61.03 E-value=9.1 Score=19.48 Aligned_cols=22 Identities=27% Similarity=0.632 Sum_probs=15.1
Q ss_pred eCCCCCCCCcc-ChhHHhhhhhhhC
Q 038068 144 PCPLSDCSFLG-CSSQFVRHFMAKH 167 (269)
Q Consensus 144 ~Cp~~~C~~~g-~~~~l~~Hl~~~H 167 (269)
.|+. |+... ...+|..|+...|
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 5774 88775 4678999998776
No 116
>PF15616 TerY-C: TerY-C metal binding domain
Probab=60.09 E-value=6.6 Score=30.86 Aligned_cols=41 Identities=27% Similarity=0.567 Sum_probs=29.4
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhcCCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~~~ 97 (269)
..--||-|....--. .|.||+++|..=-. ...||.|.....
T Consensus 76 g~PgCP~CGn~~~fa--~C~CGkl~Ci~g~~--~~~CPwCg~~g~ 116 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFA--VCGCGKLFCIDGEG--EVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCCcChhcEE--EecCCCEEEeCCCC--CEECCCCCCeee
Confidence 457899999965543 58999999743222 357999988654
No 117
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=58.81 E-value=8.2 Score=34.86 Aligned_cols=42 Identities=26% Similarity=0.572 Sum_probs=30.1
Q ss_pred CeeeccCCCCCCcCceee--ccCC--ceechhchhhc---CCCCCCCCC
Q 038068 53 DIFDCPICFEPLTVPVFQ--CVNG--HLACSDCCAKI---KRNCPTCSS 94 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~--c~cg--H~fC~~C~~~~---~~~Cp~C~~ 94 (269)
..-.||+|.....--+.. -.-| +..|+-|-..| ...||.|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 457899999976544321 1345 67899999999 467999975
No 118
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.91 E-value=7.6 Score=34.95 Aligned_cols=40 Identities=28% Similarity=0.619 Sum_probs=29.4
Q ss_pred CeeeccCCCCCC---cCceeeccCCceechhchhhc------CCCCCCCC
Q 038068 53 DIFDCPICFEPL---TVPVFQCVNGHLACSDCCAKI------KRNCPTCS 93 (269)
Q Consensus 53 ~~l~C~iC~~~l---~~Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~ 93 (269)
..+.||+=.+.- .+|++. .|||+.-..-+.++ +.+||.|-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml-~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 335 SLFICPVLKELCTDENPPVML-ECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred ceeeccccHhhhcccCCCeee-eccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 689999855543 578754 99999987777666 35688884
No 119
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=57.85 E-value=2.4 Score=42.10 Aligned_cols=44 Identities=30% Similarity=0.671 Sum_probs=36.5
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc------CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI------KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~~~~~ 97 (269)
..++|+||......|+ ...|-|.||..|+... ...||+|+..+.
T Consensus 20 k~lEc~ic~~~~~~p~-~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 20 KILECPICLEHVKEPS-LLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhccCCceeEEeeccc-hhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 6789999999999997 4589999999998765 357999986553
No 120
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=57.81 E-value=4.7 Score=31.40 Aligned_cols=51 Identities=18% Similarity=0.259 Sum_probs=28.6
Q ss_pred CCCCCCcCceeeccCCceechhchhhcCCCCCCCCCCCccccc--hhHHHHhhcceecccC
Q 038068 59 ICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSPTVIVRN--WAIEKVIELVQVNCKN 117 (269)
Q Consensus 59 iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~~~~~~~--~~l~~~i~~l~v~C~~ 117 (269)
||.+.-+. |..|+|||.||.. ...|+.. . ..+.|+ ..|+++..+..++=|+
T Consensus 62 i~qs~~~r-v~rcecghsf~d~-r~nwkl~-----a-~i~vrdtee~lreiyp~s~ipdp~ 114 (165)
T COG4647 62 ICQSAQKR-VIRCECGHSFGDY-RENWKLH-----A-NIYVRDTEEKLREIYPKSDIPDPQ 114 (165)
T ss_pred EEeccccc-EEEEeccccccCh-hhCceee-----e-EEEEcchHHHHHHhCcccCCCCch
Confidence 45565555 6689999999863 3344210 0 112343 3456666666666554
No 121
>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=57.30 E-value=4.9 Score=23.66 Aligned_cols=15 Identities=27% Similarity=0.459 Sum_probs=7.1
Q ss_pred CCCccChhHHhhhhh
Q 038068 150 CSFLGCSSQFVRHFM 164 (269)
Q Consensus 150 C~~~g~~~~l~~Hl~ 164 (269)
|+-......+..||+
T Consensus 10 C~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 10 CGRPVAASRFAPHLE 24 (33)
T ss_dssp TSSEEEGGGHHHHHH
T ss_pred CcCCcchhhhHHHHH
Confidence 444444444444443
No 122
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.95 E-value=29 Score=30.88 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=26.7
Q ss_pred CCeeeccCCCCCCcCc-eeecc--CCceechhchhh
Q 038068 52 QDIFDCPICFEPLTVP-VFQCV--NGHLACSDCCAK 84 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~P-v~~c~--cgH~fC~~C~~~ 84 (269)
..-|.|.+|.+-|.+. .+||+ -.|-||-.|-..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 3669999999999987 34676 579999999654
No 123
>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=56.71 E-value=9.2 Score=21.07 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=16.6
Q ss_pred eeCCCCCCCCccChhHHhhhhhh
Q 038068 143 LPCPLSDCSFLGCSSQFVRHFMA 165 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~~l~~Hl~~ 165 (269)
+.||. |+.......+.+|+..
T Consensus 2 v~CPi--C~~~v~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLDS 22 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHHH
Confidence 56885 9888888888899873
No 124
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.77 E-value=10 Score=40.32 Aligned_cols=43 Identities=28% Similarity=0.654 Sum_probs=32.5
Q ss_pred CeeeccCCCCCCcCceeecc-CCce-----echhchhhc-C-----CCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCV-NGHL-----ACSDCCAKI-K-----RNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~-cgH~-----fC~~C~~~~-~-----~~Cp~C~~~~~ 97 (269)
..+.||-|....... .|+ ||.. .|..|-..+ . ..||.|..++.
T Consensus 666 ~~rkCPkCG~~t~~~--fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 666 GRRRCPSCGTETYEN--RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EEEECCCCCCccccc--cCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 468999999965443 466 9965 599998876 2 27999998765
No 125
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=55.48 E-value=2.1 Score=30.14 Aligned_cols=42 Identities=26% Similarity=0.460 Sum_probs=27.1
Q ss_pred eccCCCCCCc-CceeeccCCceechhchhhc------CCCCCCCCCCCc
Q 038068 56 DCPICFEPLT-VPVFQCVNGHLACSDCCAKI------KRNCPTCSSPTV 97 (269)
Q Consensus 56 ~C~iC~~~l~-~Pv~~c~cgH~fC~~C~~~~------~~~Cp~C~~~~~ 97 (269)
.||-|..+=. -|+..-.|.|.|=..|+.+| +..||.||+...
T Consensus 33 ~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 33 CCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred cCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 3444444332 23323347888888899988 468999998754
No 126
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.44 E-value=11 Score=28.74 Aligned_cols=39 Identities=28% Similarity=0.667 Sum_probs=27.6
Q ss_pred eeccCCCCCCcCc------------eeecc-CCceechhchhhc---CCCCCCCC
Q 038068 55 FDCPICFEPLTVP------------VFQCV-NGHLACSDCCAKI---KRNCPTCS 93 (269)
Q Consensus 55 l~C~iC~~~l~~P------------v~~c~-cgH~fC~~C~~~~---~~~Cp~C~ 93 (269)
-.|-.|+..|..+ .++|+ |.+.||.+|=.-+ -..||-|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3599999987644 35675 8899998884433 35688885
No 127
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.44 E-value=5 Score=37.05 Aligned_cols=38 Identities=26% Similarity=0.641 Sum_probs=27.7
Q ss_pred eeccCCCCCCcCcee----eccCCceechhchhhc-----C-CCCCCCC
Q 038068 55 FDCPICFEPLTVPVF----QCVNGHLACSDCCAKI-----K-RNCPTCS 93 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~----~c~cgH~fC~~C~~~~-----~-~~Cp~C~ 93 (269)
-.|.||.+ +++-.. .-.|||+|=..|+..| + ..||.|+
T Consensus 5 A~C~Ic~d-~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 5 AECHICID-GRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred ceeeEecc-CCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 47999966 433211 1259999999999999 3 4799998
No 128
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=53.98 E-value=10 Score=35.51 Aligned_cols=34 Identities=21% Similarity=0.528 Sum_probs=27.5
Q ss_pred ceecccCCCCCccccccccchhhhh-ccCCCeeeeCCC
Q 038068 111 VQVNCKNAEYGCQQKMSFSKKRGHE-KTCQHSPLPCPL 147 (269)
Q Consensus 111 l~v~C~~~~~GC~~~~~~~~~~~He-~~C~~~p~~Cp~ 147 (269)
-.++|++. |...+...++.+|. .+|+++...|..
T Consensus 113 ~~~~C~~~---C~~~~~~~d~~~hl~~~C~~~~~~c~~ 147 (391)
T KOG0297|consen 113 DPLKCPHR---CGVQVPRDDLEDHLEAECPRRSLKCSL 147 (391)
T ss_pred CcccCccc---cccccchHHHHHHHhcccccccccchh
Confidence 57888874 99999888999995 678888877765
No 129
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=53.64 E-value=19 Score=24.10 Aligned_cols=17 Identities=29% Similarity=0.925 Sum_probs=9.8
Q ss_pred chhchhhc-CCCCCCCCC
Q 038068 78 CSDCCAKI-KRNCPTCSS 94 (269)
Q Consensus 78 C~~C~~~~-~~~Cp~C~~ 94 (269)
|.+|.... ...||.|..
T Consensus 39 C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 39 CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred chhHHhcCCceECCCCCC
Confidence 56666554 355777653
No 130
>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=53.53 E-value=10 Score=24.48 Aligned_cols=32 Identities=34% Similarity=0.697 Sum_probs=25.1
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhh
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAK 84 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~ 84 (269)
+=+.|..|...|.+.-+.-.-|..+|..|..+
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 66889999999887744446889999998764
No 131
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=51.23 E-value=15 Score=21.93 Aligned_cols=13 Identities=38% Similarity=0.974 Sum_probs=9.1
Q ss_pred eeccCCCCCCcCc
Q 038068 55 FDCPICFEPLTVP 67 (269)
Q Consensus 55 l~C~iC~~~l~~P 67 (269)
..||-|...+..|
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 4677777777655
No 132
>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=50.51 E-value=5.1 Score=25.59 Aligned_cols=40 Identities=25% Similarity=0.782 Sum_probs=22.5
Q ss_pred eccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 56 DCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
.|--|--..+.-| .| -.|-.|..|+..+ +..||+|..++.
T Consensus 4 nCKsCWf~~k~Li-~C-~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 4 NCKSCWFANKGLI-KC-SDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ---SS-S--SSEE-E--SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cChhhhhcCCCee-ee-cchhHHHHHHHHHhccccCCCcccCcCc
Confidence 4555555444444 22 4699999999987 678999987754
No 133
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=50.03 E-value=8.9 Score=35.38 Aligned_cols=28 Identities=36% Similarity=0.765 Sum_probs=20.6
Q ss_pred eccCCceechhchhhc----------------CCCCCCCCCCCc
Q 038068 70 QCVNGHLACSDCCAKI----------------KRNCPTCSSPTV 97 (269)
Q Consensus 70 ~c~cgH~fC~~C~~~~----------------~~~Cp~C~~~~~ 97 (269)
+|-|.=+-|..|+.+| +..||+||..+.
T Consensus 308 ~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 308 QCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred cccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 4455666788899998 246999998764
No 134
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.00 E-value=8.6 Score=39.04 Aligned_cols=43 Identities=23% Similarity=0.620 Sum_probs=36.8
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhcCCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSP 95 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~ 95 (269)
..-.|..|...|..|++.=.|||.|=..|.+.-...||.|+..
T Consensus 839 q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e 881 (933)
T KOG2114|consen 839 QVSKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPE 881 (933)
T ss_pred eeeeecccCCccccceeeeecccHHHHHhhccCcccCCccchh
Confidence 4468999999999998766899999999998665789999874
No 135
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=49.38 E-value=9.4 Score=28.97 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=12.6
Q ss_pred eeeccCCceechhchhhc
Q 038068 68 VFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 68 v~~c~cgH~fC~~C~~~~ 85 (269)
+.+|.|||.||.. ...|
T Consensus 24 ~vkc~CGh~f~d~-r~Nw 40 (112)
T PF08882_consen 24 VVKCDCGHEFCDA-RENW 40 (112)
T ss_pred eeeccCCCeecCh-hcCh
Confidence 6789999999863 3444
No 136
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.77 E-value=15 Score=31.28 Aligned_cols=39 Identities=36% Similarity=0.707 Sum_probs=29.4
Q ss_pred ccCCCCCCcCceeeccCCce-echhchhhcCCCCCCCCCCCc
Q 038068 57 CPICFEPLTVPVFQCVNGHL-ACSDCCAKIKRNCPTCSSPTV 97 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~cgH~-fC~~C~~~~~~~Cp~C~~~~~ 97 (269)
|-.|.+--.. |..-+|.|. .|..|-..+ ..||+|+.+..
T Consensus 161 Cr~C~~~~~~-VlllPCrHl~lC~~C~~~~-~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGEREAT-VLLLPCRHLCLCGICDESL-RICPICRSPKT 200 (207)
T ss_pred ceecCcCCce-EEeecccceEecccccccC-ccCCCCcChhh
Confidence 9999885555 555699975 899998754 57999987643
No 137
>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=48.73 E-value=5.2 Score=31.48 Aligned_cols=32 Identities=28% Similarity=0.777 Sum_probs=24.8
Q ss_pred eeeccCCCCCCcC--ceeeccCC------ceechhchhhc
Q 038068 54 IFDCPICFEPLTV--PVFQCVNG------HLACSDCCAKI 85 (269)
Q Consensus 54 ~l~C~iC~~~l~~--Pv~~c~cg------H~fC~~C~~~~ 85 (269)
..+|.||++-+.. -|.--++| |.||..|+.+|
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 7899999998876 33333444 57999999999
No 138
>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=48.39 E-value=6 Score=34.18 Aligned_cols=42 Identities=26% Similarity=0.604 Sum_probs=30.3
Q ss_pred CeeeccCCCC--CCcCcee--ecc-CCceechhchhhc----CCCCC--CCCC
Q 038068 53 DIFDCPICFE--PLTVPVF--QCV-NGHLACSDCCAKI----KRNCP--TCSS 94 (269)
Q Consensus 53 ~~l~C~iC~~--~l~~Pv~--~c~-cgH~fC~~C~~~~----~~~Cp--~C~~ 94 (269)
.+-.||+|.. +|.+-+. .-+ |=|..|.+|..++ ...|| -|..
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 5568999986 3444432 223 9999999999998 57899 4654
No 139
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.35 E-value=10 Score=35.45 Aligned_cols=32 Identities=25% Similarity=0.532 Sum_probs=24.0
Q ss_pred eeeccCCCCCCcCc----eeeccCCceechhchhhc
Q 038068 54 IFDCPICFEPLTVP----VFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 54 ~l~C~iC~~~l~~P----v~~c~cgH~fC~~C~~~~ 85 (269)
-..||.|...+.-- .++|.|||-||..|...|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~ 341 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDW 341 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcch
Confidence 46799998875432 346889999999998777
No 140
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.79 E-value=18 Score=21.49 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=5.6
Q ss_pred eeccCCCCCCc
Q 038068 55 FDCPICFEPLT 65 (269)
Q Consensus 55 l~C~iC~~~l~ 65 (269)
..||-|...+.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 34555555444
No 141
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=47.76 E-value=14 Score=26.22 Aligned_cols=45 Identities=20% Similarity=0.464 Sum_probs=18.0
Q ss_pred CeeeccCCCCCCc-----Cceeec-cCCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLT-----VPVFQC-VNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~-----~Pv~~c-~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
..-.|.||.+-+- .+...| .|+-.+|..|.+-- ...||.|+.+..
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 4457999987653 333344 48899999998753 468999987654
No 142
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=47.22 E-value=13 Score=33.72 Aligned_cols=38 Identities=34% Similarity=0.703 Sum_probs=23.6
Q ss_pred eccCC-CCCCcCceeecc-CCceechhchhhc---CCCCCCCC
Q 038068 56 DCPIC-FEPLTVPVFQCV-NGHLACSDCCAKI---KRNCPTCS 93 (269)
Q Consensus 56 ~C~iC-~~~l~~Pv~~c~-cgH~fC~~C~~~~---~~~Cp~C~ 93 (269)
.|-.| .+.+..+.|+|. |.+.||.+|=.-+ -..||.|.
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 37777 444556667775 7778877774332 24577774
No 143
>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=47.16 E-value=6.2 Score=31.78 Aligned_cols=22 Identities=45% Similarity=0.949 Sum_probs=18.3
Q ss_pred eechhchhhcCCCCCCCCCCCc
Q 038068 76 LACSDCCAKIKRNCPTCSSPTV 97 (269)
Q Consensus 76 ~fC~~C~~~~~~~Cp~C~~~~~ 97 (269)
.||.+|-.+.-..||.|..+|.
T Consensus 29 ~fC~kCG~~tI~~Cp~C~~~Ir 50 (158)
T PF10083_consen 29 KFCSKCGAKTITSCPNCSTPIR 50 (158)
T ss_pred HHHHHhhHHHHHHCcCCCCCCC
Confidence 5999998887568999988875
No 144
>PHA03096 p28-like protein; Provisional
Probab=46.33 E-value=7.3 Score=34.77 Aligned_cols=40 Identities=20% Similarity=0.231 Sum_probs=28.2
Q ss_pred eeccCCCCCCcCc--e-----eeccCCceechhchhhc------CCCCCCCCC
Q 038068 55 FDCPICFEPLTVP--V-----FQCVNGHLACSDCCAKI------KRNCPTCSS 94 (269)
Q Consensus 55 l~C~iC~~~l~~P--v-----~~c~cgH~fC~~C~~~~------~~~Cp~C~~ 94 (269)
-.|.||++....- . ....|-|.||..|+..| ...||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 5799999976432 1 12369999999999988 345666654
No 145
>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=45.85 E-value=11 Score=24.47 Aligned_cols=30 Identities=30% Similarity=0.735 Sum_probs=20.2
Q ss_pred eccCCCCCCcCc--eeec-cCCceechhchhhc
Q 038068 56 DCPICFEPLTVP--VFQC-VNGHLACSDCCAKI 85 (269)
Q Consensus 56 ~C~iC~~~l~~P--v~~c-~cgH~fC~~C~~~~ 85 (269)
.|++|...|..- -..| .||++||..|....
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 577887655422 2245 49999999998654
No 146
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=45.48 E-value=25 Score=35.92 Aligned_cols=42 Identities=33% Similarity=0.787 Sum_probs=34.4
Q ss_pred CeeeccCCCCCCc--Cceeecc-CCceechhchhhc----------CCCCCCCCC
Q 038068 53 DIFDCPICFEPLT--VPVFQCV-NGHLACSDCCAKI----------KRNCPTCSS 94 (269)
Q Consensus 53 ~~l~C~iC~~~l~--~Pv~~c~-cgH~fC~~C~~~~----------~~~Cp~C~~ 94 (269)
..+.|.||.+.+. .|+..|. |=|+|=..||.+| ...||.|..
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 6899999999875 6676664 7799988999999 257999983
No 147
>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=44.05 E-value=10 Score=22.44 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=16.1
Q ss_pred eeeccCCCCCCcCceeeccCCceechhchh
Q 038068 54 IFDCPICFEPLTVPVFQCVNGHLACSDCCA 83 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~ 83 (269)
...|-.|..+|.+....-.-++.+|..|..
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD 32 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCRD 32 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-S
T ss_pred CchHhHhCCHHHHHHHHHhCCccccccccC
Confidence 467888999888887655678888888864
No 148
>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=43.77 E-value=12 Score=21.53 Aligned_cols=22 Identities=23% Similarity=0.603 Sum_probs=10.0
Q ss_pred eeCCCCCCCCccChhHHhhhhh
Q 038068 143 LPCPLSDCSFLGCSSQFVRHFM 164 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~~l~~Hl~ 164 (269)
+.||..+|...........|+.
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 4566666666665555555554
No 149
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=43.51 E-value=25 Score=29.82 Aligned_cols=114 Identities=19% Similarity=0.346 Sum_probs=69.8
Q ss_pred CCCeeeccCCCCCCcCceeeccCCceechhchhhcCCCCCCCCCCCccccchhHHHHhhcceecccCCCCCcccccc-cc
Q 038068 51 DQDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMS-FS 129 (269)
Q Consensus 51 ~~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~-~~ 129 (269)
+.+.+.|.+|..-|.-..+ -..|+-|-+=+.+ ..|..|...+... +.+.+-+..-.--=||+-.-|...++ .-
T Consensus 114 d~d~ftCrvCgK~F~lQRm--lnrh~kch~~vkr--~lct~cgkgfndt--fdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRM--LNRHLKCHSDVKR--HLCTFCGKGFNDT--FDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred CCCeeeeehhhhhhhHHHH--HHHHhhhccHHHH--HHHhhccCcccch--hhhhhhhccccCccccchhhhhHHHHhhc
Confidence 4588999999998876543 3677765433333 4788898877532 22233333322233333334665544 45
Q ss_pred chhhhhcc-----CCC-------eeeeCCCCCCCCccCh-hHHhhhhhhhCCCCcc
Q 038068 130 KKRGHEKT-----CQH-------SPLPCPLSDCSFLGCS-SQFVRHFMAKHNISAV 172 (269)
Q Consensus 130 ~~~~He~~-----C~~-------~p~~Cp~~~C~~~g~~-~~l~~Hl~~~H~~~~~ 172 (269)
.++.|.+. =.| ..+.|. .|++...+ ..+..|+...|.....
T Consensus 188 sleshl~kvhgv~~~yaykerr~kl~vce--dcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 188 SLESHLKKVHGVQHQYAYKERRAKLYVCE--DCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred cHHHHHHHHcCchHHHHHHHhhhheeeec--ccCCCCCChhHHHHHHHhcCCCCHH
Confidence 67777642 111 257787 69998865 5688999999988653
No 150
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=42.88 E-value=12 Score=26.27 Aligned_cols=45 Identities=16% Similarity=0.329 Sum_probs=29.6
Q ss_pred CCCCCCCCCccccchhHHHHhhcceecccCCCCCccccccccchhhh
Q 038068 88 NCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMSFSKKRGH 134 (269)
Q Consensus 88 ~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~~~~~~~H 134 (269)
.||.|+........+.+...+..+.-.|.|- .|...+...+--.|
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~--eCg~tF~t~es~s~ 47 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNV--NCSATFITYESVQR 47 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCC--CCCCEEEEEEEEEE
Confidence 6999988764444555666678888888887 46665555444444
No 151
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=42.86 E-value=12 Score=33.67 Aligned_cols=74 Identities=20% Similarity=0.342 Sum_probs=49.8
Q ss_pred CCCCCCCCCCcc--ccc----hhHHHHhhcceecccCCCCCccccccccchhhhhccCCCeeeeCCCC--CCCCccChhH
Q 038068 87 RNCPTCSSPTVI--VRN----WAIEKVIELVQVNCKNAEYGCQQKMSFSKKRGHEKTCQHSPLPCPLS--DCSFLGCSSQ 158 (269)
Q Consensus 87 ~~Cp~C~~~~~~--~~~----~~l~~~i~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~p~~Cp~~--~C~~~g~~~~ 158 (269)
..||.|...+.. ..+ .+-..-...+...||. |..-++...-..=|+.+.-..++||+. ||.+...+..
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~----Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPT----CRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhcccCCc----cccccccHHHHHHHHHHHhceecccccccCCceeecccc
Confidence 368888776652 111 2223333377788995 888777444445577799999999985 9999888776
Q ss_pred Hhhhhh
Q 038068 159 FVRHFM 164 (269)
Q Consensus 159 l~~Hl~ 164 (269)
-..|.+
T Consensus 125 ~~~HE~ 130 (299)
T KOG3002|consen 125 KSKHEK 130 (299)
T ss_pred cccccc
Confidence 677754
No 152
>PLN02189 cellulose synthase
Probab=42.58 E-value=19 Score=37.78 Aligned_cols=45 Identities=27% Similarity=0.566 Sum_probs=34.1
Q ss_pred CeeeccCCCCCCc-----Cceeecc-CCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLT-----VPVFQCV-NGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~-----~Pv~~c~-cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
..-.|.||.+-+- .|..-|. ||--+|..|.+-- +..||.|+....
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3348999999754 3455565 9999999999754 578999998764
No 153
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=41.70 E-value=13 Score=32.83 Aligned_cols=76 Identities=20% Similarity=0.353 Sum_probs=49.0
Q ss_pred CCCCCCCCCCCccccchhH----HHHhhcceecccCCCCCcccccc-ccchhhhhcc-CCCeeeeCCCCCCCCccCh-hH
Q 038068 86 KRNCPTCSSPTVIVRNWAI----EKVIELVQVNCKNAEYGCQQKMS-FSKKRGHEKT-CQHSPLPCPLSDCSFLGCS-SQ 158 (269)
Q Consensus 86 ~~~Cp~C~~~~~~~~~~~l----~~~i~~l~v~C~~~~~GC~~~~~-~~~~~~He~~-C~~~p~~Cp~~~C~~~g~~-~~ 158 (269)
...|++|.+.+. |...| +.-..+-++.|+. |..-+. ..+|+.|..+ =...++.|+ .|+-...+ ..
T Consensus 187 ~c~C~iCGKaFS--RPWLLQGHiRTHTGEKPF~C~h----C~kAFADRSNLRAHmQTHS~~K~~qC~--~C~KsFsl~Sy 258 (279)
T KOG2462|consen 187 PCECGICGKAFS--RPWLLQGHIRTHTGEKPFSCPH----CGKAFADRSNLRAHMQTHSDVKKHQCP--RCGKSFALKSY 258 (279)
T ss_pred Cccccccccccc--chHHhhcccccccCCCCccCCc----ccchhcchHHHHHHHHhhcCCccccCc--chhhHHHHHHH
Confidence 346888887664 33333 3334566778874 776655 5788888765 444577888 69866554 46
Q ss_pred HhhhhhhhCCC
Q 038068 159 FVRHFMAKHNI 169 (269)
Q Consensus 159 l~~Hl~~~H~~ 169 (269)
|..|++..+..
T Consensus 259 LnKH~ES~C~~ 269 (279)
T KOG2462|consen 259 LNKHSESACLK 269 (279)
T ss_pred HHHhhhhcccc
Confidence 77887776543
No 154
>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=40.21 E-value=9.9 Score=24.29 Aligned_cols=31 Identities=16% Similarity=0.514 Sum_probs=16.9
Q ss_pred cccccccchhhhhccCCCeeeeCCCCCCCCccC
Q 038068 123 QQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGC 155 (269)
Q Consensus 123 ~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~ 155 (269)
...+....++.|...|+|+.+.|. .|.....
T Consensus 9 rnHG~~~~lKgHk~~C~~~~C~C~--kC~li~e 39 (47)
T PF00751_consen 9 RNHGVIVPLKGHKRYCPFRDCQCD--KCALIAE 39 (47)
T ss_dssp HTTT---TTTT-GGG-TTTT--SH--HHHHHHH
T ss_pred hcCCcccchhhhccccCcCCCcCC--CCcCcHH
Confidence 334456678899999999999997 4764433
No 155
>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=40.15 E-value=6.9 Score=22.53 Aligned_cols=19 Identities=42% Similarity=1.067 Sum_probs=8.6
Q ss_pred ceechhchhhc-------CCCCCCCC
Q 038068 75 HLACSDCCAKI-------KRNCPTCS 93 (269)
Q Consensus 75 H~fC~~C~~~~-------~~~Cp~C~ 93 (269)
|.||+.|-... ...||.|+
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 56666665544 23466664
No 156
>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=39.34 E-value=21 Score=34.38 Aligned_cols=35 Identities=20% Similarity=0.462 Sum_probs=20.3
Q ss_pred CCCCCCCCCcccc-ch-------hHHHHhhcceecccCCCCCccccc
Q 038068 88 NCPTCSSPTVIVR-NW-------AIEKVIELVQVNCKNAEYGCQQKM 126 (269)
Q Consensus 88 ~Cp~C~~~~~~~~-~~-------~l~~~i~~l~v~C~~~~~GC~~~~ 126 (269)
.||.|..++.... +. .-...-..+.+.|.| |.|..
T Consensus 54 ~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~----C~Wss 96 (483)
T PF05502_consen 54 DCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSY----CRWSS 96 (483)
T ss_pred cCCCCCCcceeEecccccccccccccCCCCCEEEECCC----ceeec
Confidence 6999988776321 11 111223456778886 88854
No 157
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.66 E-value=28 Score=30.47 Aligned_cols=45 Identities=16% Similarity=0.219 Sum_probs=35.3
Q ss_pred CeeeccCCCCCCcCcee---eccCCceechhchhhc-CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVF---QCVNGHLACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~---~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
..|+|||=...+..-.. .=.|||+|-.+-+.++ ...|+.|...+.
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~ 158 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQ 158 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCccc
Confidence 67999998887766532 2269999998888887 568999998775
No 158
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=38.56 E-value=16 Score=28.70 Aligned_cols=25 Identities=32% Similarity=0.646 Sum_probs=18.6
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhch
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCC 82 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~ 82 (269)
-..+||.|..||.. .-|-+||.-|-
T Consensus 27 L~~hCp~Cg~PLF~-----KdG~v~CPvC~ 51 (131)
T COG1645 27 LAKHCPKCGTPLFR-----KDGEVFCPVCG 51 (131)
T ss_pred HHhhCcccCCccee-----eCCeEECCCCC
Confidence 34689999987654 45888877665
No 159
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=38.35 E-value=12 Score=20.43 Aligned_cols=6 Identities=50% Similarity=1.254 Sum_probs=2.5
Q ss_pred ccCCCC
Q 038068 57 CPICFE 62 (269)
Q Consensus 57 C~iC~~ 62 (269)
||-|..
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444443
No 160
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=37.85 E-value=5 Score=42.47 Aligned_cols=44 Identities=30% Similarity=0.552 Sum_probs=34.8
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPT 96 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~ 96 (269)
....|++|.+++..--....|||.+|..|...| +..||.|....
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred cccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhhh
Confidence 566999999999833223579999999999988 56899997543
No 161
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=37.55 E-value=24 Score=22.48 Aligned_cols=37 Identities=19% Similarity=0.541 Sum_probs=22.7
Q ss_pred eccCCCC--CCcCceeeccCC-----ceechhchhhc-----CCCCCCCC
Q 038068 56 DCPICFE--PLTVPVFQCVNG-----HLACSDCCAKI-----KRNCPTCS 93 (269)
Q Consensus 56 ~C~iC~~--~l~~Pv~~c~cg-----H~fC~~C~~~~-----~~~Cp~C~ 93 (269)
.|.||++ --..|+ ..+|. |.+=..|+.+| ...||+|+
T Consensus 1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3778886 223444 23543 45556789988 34788884
No 162
>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 PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=37.43 E-value=22 Score=18.16 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=14.1
Q ss_pred eCCCCCCCCccC-hhHHhhhhhh
Q 038068 144 PCPLSDCSFLGC-SSQFVRHFMA 165 (269)
Q Consensus 144 ~Cp~~~C~~~g~-~~~l~~Hl~~ 165 (269)
.|| .|+.... ...|..|++.
T Consensus 2 ~C~--~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCP--ICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EET--TTTEEESSHHHHHHHHHH
T ss_pred CCC--CCCCccCCHHHHHHHHhH
Confidence 577 5887644 5688888775
No 164
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=37.16 E-value=31 Score=20.84 Aligned_cols=15 Identities=27% Similarity=0.262 Sum_probs=8.9
Q ss_pred EEecCCeEEEEeeee
Q 038068 239 ARCVTGTTLKIQSST 253 (269)
Q Consensus 239 ~~~~~~~~l~~~s~~ 253 (269)
+...+|||++||+-|
T Consensus 20 l~D~~gRTiWFqGdP 34 (39)
T PF09292_consen 20 LRDRNGRTIWFQGDP 34 (39)
T ss_dssp EE-TTS-EEEESS--
T ss_pred ccccCCCEEEeeCCC
Confidence 344789999999865
No 165
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=37.04 E-value=30 Score=26.05 Aligned_cols=40 Identities=20% Similarity=0.435 Sum_probs=23.7
Q ss_pred eeccCCCCCCcCceeec-------cC---Cceechhchhhc------------CCCCCCCCC
Q 038068 55 FDCPICFEPLTVPVFQC-------VN---GHLACSDCCAKI------------KRNCPTCSS 94 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c-------~c---gH~fC~~C~~~~------------~~~Cp~C~~ 94 (269)
..|..|..--.+..+.| .| .-.||..|+... ...||.|+.
T Consensus 8 ~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 8 KTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 35666666444444344 24 556888886543 235888765
No 166
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.40 E-value=18 Score=34.40 Aligned_cols=27 Identities=33% Similarity=0.700 Sum_probs=19.8
Q ss_pred cCceeeccCCceechhchhhc--CCCCCCC
Q 038068 65 TVPVFQCVNGHLACSDCCAKI--KRNCPTC 92 (269)
Q Consensus 65 ~~Pv~~c~cgH~fC~~C~~~~--~~~Cp~C 92 (269)
..+| .|.|||.||..|...+ ...|+..
T Consensus 177 ~~~v-~C~~g~~FC~~C~~~~H~p~~C~~~ 205 (444)
T KOG1815|consen 177 SVEV-DCGCGHEFCFACGEESHSPVSCPGA 205 (444)
T ss_pred ccce-eCCCCchhHhhccccccCCCcccch
Confidence 3445 7999999999999888 2345443
No 167
>PLN02436 cellulose synthase A
Probab=35.39 E-value=28 Score=36.59 Aligned_cols=45 Identities=22% Similarity=0.577 Sum_probs=34.0
Q ss_pred CeeeccCCCCCCc-----Cceeecc-CCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLT-----VPVFQCV-NGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~-----~Pv~~c~-cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
..-.|.||.+-+- +|..-|. ||--+|..|.+-- +..||.|+....
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3448999998652 3555565 9999999999754 578999988764
No 168
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=35.22 E-value=27 Score=28.59 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=6.9
Q ss_pred CCCCCCCCCC
Q 038068 86 KRNCPTCSSP 95 (269)
Q Consensus 86 ~~~Cp~C~~~ 95 (269)
...||+|..+
T Consensus 149 P~~CPiCga~ 158 (166)
T COG1592 149 PEVCPICGAP 158 (166)
T ss_pred CCcCCCCCCh
Confidence 4578888764
No 169
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=34.35 E-value=14 Score=37.49 Aligned_cols=32 Identities=28% Similarity=0.447 Sum_probs=26.5
Q ss_pred eeeccCCCCCCcCceeecc-CCceechhchhhc
Q 038068 54 IFDCPICFEPLTVPVFQCV-NGHLACSDCCAKI 85 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~~c~-cgH~fC~~C~~~~ 85 (269)
.-.|..|..-+..-...|+ ||+.+|-.|+..|
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKW 261 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhc
Confidence 4579999998876555676 9999999999887
No 170
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.07 E-value=25 Score=35.13 Aligned_cols=42 Identities=26% Similarity=0.583 Sum_probs=18.7
Q ss_pred eccCCCCCCcC-ceeeccCCce----echhchhhc---CCCCCCCCCCCc
Q 038068 56 DCPICFEPLTV-PVFQCVNGHL----ACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 56 ~C~iC~~~l~~-Pv~~c~cgH~----fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
.||.|.....+ ..|+-.||.. .|..|-... ...||.|+..+.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCCCcccccccccCCccc
Confidence 56666664322 1221124422 355554443 245666655543
No 171
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=33.90 E-value=26 Score=27.85 Aligned_cols=33 Identities=30% Similarity=0.661 Sum_probs=21.9
Q ss_pred ccCCceechhchhhc-CCCCCCCCCCCccccchhH
Q 038068 71 CVNGHLACSDCCAKI-KRNCPTCSSPTVIVRNWAI 104 (269)
Q Consensus 71 c~cgH~fC~~C~~~~-~~~Cp~C~~~~~~~~~~~l 104 (269)
|.| ...|.-|.... +.+||.|+.+.....++.+
T Consensus 2 ~kc-t~tC~ic~e~~~KYKCpkC~vPYCSl~CfKi 35 (157)
T KOG2857|consen 2 CKC-TTTCVICLESEIKYKCPKCSVPYCSLPCFKI 35 (157)
T ss_pred Ccc-eeeehhhhcchhhccCCCCCCccccchhhhh
Confidence 456 67788887755 6678888877654444433
No 172
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.68 E-value=38 Score=21.38 Aligned_cols=12 Identities=33% Similarity=0.509 Sum_probs=8.1
Q ss_pred eccCCCCCCcCc
Q 038068 56 DCPICFEPLTVP 67 (269)
Q Consensus 56 ~C~iC~~~l~~P 67 (269)
-||-|..++..+
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 377787776554
No 173
>PLN02195 cellulose synthase A
Probab=33.04 E-value=37 Score=35.45 Aligned_cols=43 Identities=21% Similarity=0.454 Sum_probs=32.4
Q ss_pred eeccCCCCCCc-----Cceeec-cCCceechhchhhc----CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLT-----VPVFQC-VNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~-----~Pv~~c-~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
-.|.||.+-+- .|..-| .||--+|..|.+-- +..||.|+....
T Consensus 7 ~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 7 PICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred ccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 47999998442 455456 49999999998643 568999998765
No 174
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=32.92 E-value=18 Score=31.18 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=12.4
Q ss_pred eeeccCCCCCCcCcee
Q 038068 54 IFDCPICFEPLTVPVF 69 (269)
Q Consensus 54 ~l~C~iC~~~l~~Pv~ 69 (269)
-+.|++|+.+|.+|+.
T Consensus 260 GfvCsVCLsvfc~p~~ 275 (296)
T COG5242 260 GFVCSVCLSVFCRPVP 275 (296)
T ss_pred eeehhhhheeecCCcC
Confidence 4779999988877763
No 175
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=32.87 E-value=34 Score=22.29 Aligned_cols=27 Identities=30% Similarity=0.610 Sum_probs=17.5
Q ss_pred eeeeCCCCCCCCccC-hhHHhhhhhhhCCC
Q 038068 141 SPLPCPLSDCSFLGC-SSQFVRHFMAKHNI 169 (269)
Q Consensus 141 ~p~~Cp~~~C~~~g~-~~~l~~Hl~~~H~~ 169 (269)
.|-.||. |+-..+ ..+|..|++..|..
T Consensus 23 ~PatCP~--C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPI--CGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TT--T--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCc--chhhccchhhHHHHHHHHhcc
Confidence 3568985 998766 46899999998864
No 176
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=32.21 E-value=48 Score=20.51 Aligned_cols=35 Identities=31% Similarity=0.693 Sum_probs=15.8
Q ss_pred ccCCCCCCcCceeecc---CCceechhchhhc-----CCCCCCC
Q 038068 57 CPICFEPLTVPVFQCV---NGHLACSDCCAKI-----KRNCPTC 92 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c~---cgH~fC~~C~~~~-----~~~Cp~C 92 (269)
|.+|.++...-+ .|+ |+-.+=..|+... ...||.|
T Consensus 1 C~~C~~iv~~G~-~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQ-RCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSE-E-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeec-cCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 678888888777 465 5533333455543 2258876
No 177
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=32.05 E-value=36 Score=24.16 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=19.6
Q ss_pred hhhccCCCeeeeCCCCCCCCcc-ChhHHhhhhhhh-CCC
Q 038068 133 GHEKTCQHSPLPCPLSDCSFLG-CSSQFVRHFMAK-HNI 169 (269)
Q Consensus 133 ~He~~C~~~p~~Cp~~~C~~~g-~~~~l~~Hl~~~-H~~ 169 (269)
.+...-......|+. |+... ....|..|++.. |..
T Consensus 41 ~~~~~~~~~~~~C~~--C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 41 NYLRKKVKESFRCPY--CNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp --------SSEEBSS--SS-EESSHHHHHHHHHHTTTTC
T ss_pred cccccccCCCCCCCc--cCCCCcCHHHHHHHHcCccCCC
Confidence 344443444688885 88764 678999999975 554
No 178
>PRK00420 hypothetical protein; Validated
Probab=31.69 E-value=32 Score=26.27 Aligned_cols=26 Identities=27% Similarity=0.537 Sum_probs=17.7
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhh
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAK 84 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~ 84 (269)
-.||+|..+|.. -.-|..||..|-..
T Consensus 24 ~~CP~Cg~pLf~----lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFE----LKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCccee----cCCCceECCCCCCe
Confidence 589999976653 24578877666543
No 179
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.50 E-value=10 Score=23.75 Aligned_cols=11 Identities=27% Similarity=0.872 Sum_probs=7.1
Q ss_pred CCCCCCCCCcc
Q 038068 88 NCPTCSSPTVI 98 (269)
Q Consensus 88 ~Cp~C~~~~~~ 98 (269)
.||.|+.++..
T Consensus 23 ~Cp~CG~~~~~ 33 (46)
T PRK00398 23 RCPYCGYRILF 33 (46)
T ss_pred ECCCCCCeEEE
Confidence 67777766553
No 180
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.43 E-value=37 Score=35.83 Aligned_cols=44 Identities=25% Similarity=0.600 Sum_probs=32.6
Q ss_pred eeeccCCCCCCc-----Cceeec-cCCceechhchhhc----CCCCCCCCCCCc
Q 038068 54 IFDCPICFEPLT-----VPVFQC-VNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 54 ~l~C~iC~~~l~-----~Pv~~c-~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
.-.|.||.+-+- +|..-| .||--+|..|.+-- +..||.|+....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 348999998643 344456 49999999998643 568999988664
No 181
>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=31.19 E-value=44 Score=20.64 Aligned_cols=23 Identities=35% Similarity=0.873 Sum_probs=15.5
Q ss_pred eeccCCCCCCcCceeeccCCceechhc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDC 81 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C 81 (269)
-.||.|..|+ +.-.-|..||..|
T Consensus 18 ~~Cp~C~~PL----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPL----MRDKDGKIYCVSC 40 (41)
T ss_pred CccCCCCCee----EEecCCCEECCCC
Confidence 4799996544 3435678888766
No 182
>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=31.15 E-value=42 Score=19.39 Aligned_cols=9 Identities=44% Similarity=1.328 Sum_probs=6.6
Q ss_pred CCCCCCCCC
Q 038068 87 RNCPTCSSP 95 (269)
Q Consensus 87 ~~Cp~C~~~ 95 (269)
..||.|..+
T Consensus 18 ~~CP~Cg~~ 26 (33)
T cd00350 18 WVCPVCGAP 26 (33)
T ss_pred CcCcCCCCc
Confidence 478888764
No 183
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=30.67 E-value=62 Score=28.69 Aligned_cols=75 Identities=20% Similarity=0.406 Sum_probs=46.2
Q ss_pred CCCCCCCCCCCccccchhHHHHhhcceecccCCCCCcccccccc-chhhhhcc-CCCeeeeCCCCCCCCc-cChhHHhhh
Q 038068 86 KRNCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMSFS-KKRGHEKT-CQHSPLPCPLSDCSFL-GCSSQFVRH 162 (269)
Q Consensus 86 ~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~~~-~~~~He~~-C~~~p~~Cp~~~C~~~-g~~~~l~~H 162 (269)
...|+.|...........|.-..-.+...|+. |...+..- -|+.|.++ =.-.|+.|| -|+-. ..+..|..|
T Consensus 161 a~~C~~C~K~YvSmpALkMHirTH~l~c~C~i----CGKaFSRPWLLQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIRTHTLPCECGI----CGKAFSRPWLLQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAH 234 (279)
T ss_pred cccCCCCCceeeehHHHhhHhhccCCCccccc----ccccccchHHhhcccccccCCCCccCC--cccchhcchHHHHHH
Confidence 35799997765544444444444455566653 66655532 44566553 344677898 58854 457899999
Q ss_pred hhhh
Q 038068 163 FMAK 166 (269)
Q Consensus 163 l~~~ 166 (269)
+++.
T Consensus 235 mQTH 238 (279)
T KOG2462|consen 235 MQTH 238 (279)
T ss_pred HHhh
Confidence 8763
No 184
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=30.51 E-value=61 Score=29.40 Aligned_cols=99 Identities=24% Similarity=0.560 Sum_probs=55.8
Q ss_pred CCCCeeeccCCCCCCcCce--eeccCCceechhchhhc------------------CCCCCC-CCCCCc----cc-----
Q 038068 50 TDQDIFDCPICFEPLTVPV--FQCVNGHLACSDCCAKI------------------KRNCPT-CSSPTV----IV----- 99 (269)
Q Consensus 50 ~~~~~l~C~iC~~~l~~Pv--~~c~cgH~fC~~C~~~~------------------~~~Cp~-C~~~~~----~~----- 99 (269)
.++....|-.|-++ .+|| ++|...|+.|..|+.-. +..||. |-..+. .+
T Consensus 217 ~N~~ni~C~~Ctdv-~~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~agc~~s~i~e~HHF~ilg~ 295 (446)
T KOG0006|consen 217 TNSRNITCITCTDV-RSPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGE 295 (446)
T ss_pred cccccceeEEecCC-ccceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccCCCchHHHHhhhhheecch
Confidence 34567889999995 4454 55666699999998632 123443 322211 00
Q ss_pred ------cchhHHHHh-hcceecccCCCCCccccccccchhhhhccCCCeeeeCCCCCCCCccChhHHh
Q 038068 100 ------RNWAIEKVI-ELVQVNCKNAEYGCQQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGCSSQFV 160 (269)
Q Consensus 100 ------~~~~l~~~i-~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~~~~l~ 160 (269)
.-.+.++.+ ..=-|.||+- ||...+-.+- ..+.+.|+. ||+|..-++-++
T Consensus 296 e~Y~rYQr~atEe~vlq~gGVlCP~p--gCG~gll~EP--------D~rkvtC~~-gCgf~FCR~C~e 352 (446)
T KOG0006|consen 296 EQYNRYQRYATEECVLQMGGVLCPRP--GCGAGLLPEP--------DQRKVTCEG-GCGFAFCRECKE 352 (446)
T ss_pred hHHHHHHHhhhhhheeecCCEecCCC--CCCcccccCC--------CCCcccCCC-CchhHhHHHHHh
Confidence 012233332 2225788875 8887655432 234567775 788876655444
No 185
>KOG4471 consensus Phosphatidylinositol 3-phosphate 3-phosphatase myotubularin MTM1 [Lipid transport and metabolism; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.22 E-value=67 Score=31.69 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=35.1
Q ss_pred eEEEEEcCccCccceEEEEEeecCC-CCCeEEEEEEecCCeEEEEeeee
Q 038068 206 VLFILNNNTGSLGNLVSVCCIASVR-KDLYYDIVARCVTGTTLKIQSST 253 (269)
Q Consensus 206 ~lF~l~~~~~~~g~~v~v~ci~~~~-~~f~Y~l~~~~~~~~~l~~~s~~ 253 (269)
..|++.+ ++|..-.|..+|+.. ++-+|.|++.+.|.|.|++.-.+
T Consensus 75 ~~~~~~V---PLg~Ie~vek~~~~~~g~ns~~L~i~CKDmr~lR~~fk~ 120 (717)
T KOG4471|consen 75 PPFVLDV---PLGVIERVEKRGGATSGENSFGLEITCKDMRNLRCAFKQ 120 (717)
T ss_pred CceeEee---chhhhhhhhhcCccccCCcceeEEEEeccccceeeecCc
Confidence 3555554 677777888899877 88899999998899988887544
No 186
>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=29.64 E-value=46 Score=25.38 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=21.0
Q ss_pred CeeeccCCCCCCc----Cceeec-cCCceechhchhhc
Q 038068 53 DIFDCPICFEPLT----VPVFQC-VNGHLACSDCCAKI 85 (269)
Q Consensus 53 ~~l~C~iC~~~l~----~Pv~~c-~cgH~fC~~C~~~~ 85 (269)
..-.|.+|..+|. ... .| .|+|.+|..|....
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~-~C~~C~~~VC~~C~~~~ 89 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGR-VCVDCKHRVCKKCGVYS 89 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCE-EETTTTEEEETTSEEET
T ss_pred CCcchhhhCCcccccCCCCC-cCCcCCccccCccCCcC
Confidence 3458999987642 344 45 49999999997653
No 187
>PRK11595 DNA utilization protein GntX; Provisional
Probab=29.38 E-value=43 Score=28.63 Aligned_cols=34 Identities=35% Similarity=0.789 Sum_probs=18.3
Q ss_pred eccCCCCCCcCceeeccCCceechhchhhc---CCCCCCCCCC
Q 038068 56 DCPICFEPLTVPVFQCVNGHLACSDCCAKI---KRNCPTCSSP 95 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~ 95 (269)
.|.+|..++..+ ....|..|...+ ...|+.|..+
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCc
Confidence 477777655321 123566666654 2346666554
No 188
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=29.30 E-value=43 Score=34.12 Aligned_cols=31 Identities=26% Similarity=0.511 Sum_probs=23.3
Q ss_pred eeccCCCCCCcC-------ceeecc-CCceechhchhhc
Q 038068 55 FDCPICFEPLTV-------PVFQCV-NGHLACSDCCAKI 85 (269)
Q Consensus 55 l~C~iC~~~l~~-------Pv~~c~-cgH~fC~~C~~~~ 85 (269)
-.|..|...|.. -...|. ||.+||..|..+.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnR 499 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKR 499 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCc
Confidence 469999999853 122474 9999999998653
No 189
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.19 E-value=51 Score=33.48 Aligned_cols=48 Identities=33% Similarity=0.897 Sum_probs=0.0
Q ss_pred ceeecc-CCceechhchhhcCCCCCCCCCCCccccchhHHHHhhcceecccCCCCCccccccccchhhhhccCCCeeeeC
Q 038068 67 PVFQCV-NGHLACSDCCAKIKRNCPTCSSPTVIVRNWAIEKVIELVQVNCKNAEYGCQQKMSFSKKRGHEKTCQHSPLPC 145 (269)
Q Consensus 67 Pv~~c~-cgH~fC~~C~~~~~~~Cp~C~~~~~~~~~~~l~~~i~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~p~~C 145 (269)
|..+|. |||++ .||.|...++.-+.. =...|.| |... .-.|..|
T Consensus 434 ~~l~C~~Cg~v~----------~Cp~Cd~~lt~H~~~--------~~L~CH~----Cg~~-------------~~~p~~C 478 (730)
T COG1198 434 PLLLCRDCGYIA----------ECPNCDSPLTLHKAT--------GQLRCHY----CGYQ-------------EPIPQSC 478 (730)
T ss_pred ceeecccCCCcc----------cCCCCCcceEEecCC--------CeeEeCC----CCCC-------------CCCCCCC
Q ss_pred CCCCCC
Q 038068 146 PLSDCS 151 (269)
Q Consensus 146 p~~~C~ 151 (269)
| .|+
T Consensus 479 p--~Cg 482 (730)
T COG1198 479 P--ECG 482 (730)
T ss_pred C--CCC
No 190
>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=28.86 E-value=36 Score=27.54 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCccccc
Q 038068 86 KRNCPTCSSPTVIVRN 101 (269)
Q Consensus 86 ~~~Cp~C~~~~~~~~~ 101 (269)
...||.|+.++....|
T Consensus 128 ~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 128 NFTCPRCGAMLDYLDN 143 (158)
T ss_pred CCcCCCCCCEeeeccC
Confidence 4689999998875444
No 191
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=28.33 E-value=5 Score=25.91 Aligned_cols=42 Identities=26% Similarity=0.740 Sum_probs=29.1
Q ss_pred CeeeccCCCCCCcC-ceeecc-CCceechhchhhcCCCCCCCCC
Q 038068 53 DIFDCPICFEPLTV-PVFQCV-NGHLACSDCCAKIKRNCPTCSS 94 (269)
Q Consensus 53 ~~l~C~iC~~~l~~-Pv~~c~-cgH~fC~~C~~~~~~~Cp~C~~ 94 (269)
..+.|..|...... -..||. ||...|.+|+..--..|..|..
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~G 49 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNG 49 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhc
Confidence 45789999886532 245775 9999999998764345666644
No 192
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=27.60 E-value=49 Score=20.57 Aligned_cols=30 Identities=30% Similarity=0.804 Sum_probs=21.2
Q ss_pred eeccCCCCCCcCceeecc-CC-ceechhchhh
Q 038068 55 FDCPICFEPLTVPVFQCV-NG-HLACSDCCAK 84 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~-cg-H~fC~~C~~~ 84 (269)
+.|..|..++....+.|. |. -..|..|...
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCc
Confidence 368899998877777764 54 5677777654
No 193
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=27.45 E-value=65 Score=18.29 Aligned_cols=35 Identities=23% Similarity=0.613 Sum_probs=17.3
Q ss_pred ccCCCCCCcCc-eeeccCCceechhchhhcCCCCCCCCCCC
Q 038068 57 CPICFEPLTVP-VFQCVNGHLACSDCCAKIKRNCPTCSSPT 96 (269)
Q Consensus 57 C~iC~~~l~~P-v~~c~cgH~fC~~C~~~~~~~Cp~C~~~~ 96 (269)
|..|.+++.+. ...-.-+..|-..|+ .|..|+.++
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~Cf-----~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPECF-----KCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccCC-----CCcccCCcC
Confidence 67777776653 222233444433442 455555443
No 194
>PLN02400 cellulose synthase
Probab=27.26 E-value=48 Score=35.01 Aligned_cols=45 Identities=20% Similarity=0.452 Sum_probs=33.2
Q ss_pred CeeeccCCCCCCc-----Cceeec-cCCceechhchhhc----CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLT-----VPVFQC-VNGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~-----~Pv~~c-~cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
..-.|.||.+-+- +|..-| .|+--+|..|.+-- +..||.|+....
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 3348999998643 344456 49999999998643 568999998764
No 195
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=27.10 E-value=21 Score=36.53 Aligned_cols=44 Identities=27% Similarity=0.690 Sum_probs=0.0
Q ss_pred CCeeeccCCCCCCcCceeecc-CCc-----eechhchhhc-CCCCCCCCCCCc
Q 038068 52 QDIFDCPICFEPLTVPVFQCV-NGH-----LACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~-cgH-----~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
.....||-|...-... .|+ ||- .+|..|-... ...||.|.....
T Consensus 653 i~~r~Cp~Cg~~t~~~--~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~ 703 (900)
T PF03833_consen 653 IGRRRCPKCGKETFYN--RCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETT 703 (900)
T ss_dssp -----------------------------------------------------
T ss_pred eecccCcccCCcchhh--cCcccCCccccceeccccccccCccccccccccCc
Confidence 3678899999965444 475 884 4899999887 568999987654
No 196
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.99 E-value=47 Score=27.43 Aligned_cols=14 Identities=21% Similarity=0.425 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCccc
Q 038068 86 KRNCPTCSSPTVIV 99 (269)
Q Consensus 86 ~~~Cp~C~~~~~~~ 99 (269)
...||.|...+...
T Consensus 136 ~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 136 GFRCPQCGEMLEEY 149 (178)
T ss_pred CCcCCCCCCCCeec
Confidence 56899999988754
No 197
>KOG3815 consensus Transcription factor Doublesex [Transcription]
Probab=26.99 E-value=24 Score=32.09 Aligned_cols=36 Identities=22% Similarity=0.689 Sum_probs=29.9
Q ss_pred ccccccccchhhhhccCCCeeeeCCCCCCCCccChhHH
Q 038068 122 CQQKMSFSKKRGHEKTCQHSPLPCPLSDCSFLGCSSQF 159 (269)
Q Consensus 122 C~~~~~~~~~~~He~~C~~~p~~Cp~~~C~~~g~~~~l 159 (269)
|.-.+.+..++-|-+.|+|+.|.|. .|.-...+..+
T Consensus 42 CrnHG~~~~LKGHk~~C~~~~C~C~--kC~li~eRqrv 77 (322)
T KOG3815|consen 42 CENHGVLSRLKGHKRSCPYRDCPCE--KCGLVEERRRV 77 (322)
T ss_pred hhccCcceeccCCCCCCCCCCCCch--HhcchHHHHHH
Confidence 7778889999999999999999998 69866555443
No 198
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=26.98 E-value=45 Score=18.65 Aligned_cols=22 Identities=18% Similarity=0.448 Sum_probs=6.3
Q ss_pred eccCCCCCCcC-ceeecc-CCcee
Q 038068 56 DCPICFEPLTV-PVFQCV-NGHLA 77 (269)
Q Consensus 56 ~C~iC~~~l~~-Pv~~c~-cgH~f 77 (269)
.|.+|...... .+|.|. |.-.+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 57777777766 666553 44433
No 199
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.85 E-value=32 Score=30.06 Aligned_cols=44 Identities=32% Similarity=0.590 Sum_probs=33.7
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhchhhc-CCCCCCCCCCCc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI-KRNCPTCSSPTV 97 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~-~~~Cp~C~~~~~ 97 (269)
..+.|..|...|..... .--|-+||.+|..++ -+.|-.|+.+|.
T Consensus 162 yHFkCt~C~keL~sdaR-evk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 162 YHFKCTTCGKELTSDAR-EVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred cceecccccccccchhh-hhccceeccccccccCCcccccccCchH
Confidence 78899999999887654 367899999999987 245555666654
No 200
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.67 E-value=24 Score=27.43 Aligned_cols=22 Identities=32% Similarity=0.738 Sum_probs=17.6
Q ss_pred eechhchhhcCCCCCCCCCCCc
Q 038068 76 LACSDCCAKIKRNCPTCSSPTV 97 (269)
Q Consensus 76 ~fC~~C~~~~~~~Cp~C~~~~~ 97 (269)
.||+.|-+..-..||.|..++.
T Consensus 29 afcskcgeati~qcp~csasir 50 (160)
T COG4306 29 AFCSKCGEATITQCPICSASIR 50 (160)
T ss_pred HHHhhhchHHHhcCCccCCccc
Confidence 4899998776568999988764
No 201
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.58 E-value=26 Score=31.32 Aligned_cols=27 Identities=37% Similarity=0.875 Sum_probs=20.2
Q ss_pred ccCCceechhchhhc----------------CCCCCCCCCCCc
Q 038068 71 CVNGHLACSDCCAKI----------------KRNCPTCSSPTV 97 (269)
Q Consensus 71 c~cgH~fC~~C~~~~----------------~~~Cp~C~~~~~ 97 (269)
|-|.-.-|.+|+.+| +..||.||+.+.
T Consensus 323 c~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 323 CICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred cccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 345667788898887 357999998764
No 202
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=24.54 E-value=60 Score=29.53 Aligned_cols=43 Identities=35% Similarity=0.822 Sum_probs=32.8
Q ss_pred eeccCCCCCC---cCceeeccCCceechhchhhc---CCCCCCCCCCCc
Q 038068 55 FDCPICFEPL---TVPVFQCVNGHLACSDCCAKI---KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l---~~Pv~~c~cgH~fC~~C~~~~---~~~Cp~C~~~~~ 97 (269)
-.||+|.+++ ..+..=|+||+..|..|+..+ ...||.|+.+..
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 4799999976 233444789999999998876 468999997654
No 203
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=24.01 E-value=59 Score=21.70 Aligned_cols=23 Identities=22% Similarity=0.754 Sum_probs=13.3
Q ss_pred ccCCCCCCcCceeec-cCCceechh
Q 038068 57 CPICFEPLTVPVFQC-VNGHLACSD 80 (269)
Q Consensus 57 C~iC~~~l~~Pv~~c-~cgH~fC~~ 80 (269)
|..|... ...+..| .||+++|.+
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5677765 3334455 599999873
No 204
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.57 E-value=46 Score=28.60 Aligned_cols=45 Identities=27% Similarity=0.413 Sum_probs=35.1
Q ss_pred CeeeccCCCCCCc--CceeeccCCceechhchhhc-----------CCCCCCCCCCCcc
Q 038068 53 DIFDCPICFEPLT--VPVFQCVNGHLACSDCCAKI-----------KRNCPTCSSPTVI 98 (269)
Q Consensus 53 ~~l~C~iC~~~l~--~Pv~~c~cgH~fC~~C~~~~-----------~~~Cp~C~~~~~~ 98 (269)
..-.|..|.-+|. +.+. ..|=|+|=.+|+..+ ..+||.|..++-.
T Consensus 49 Y~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 49 YNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 4567999999886 3453 379999999999887 3679999988753
No 205
>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=23.40 E-value=51 Score=24.11 Aligned_cols=37 Identities=24% Similarity=0.537 Sum_probs=27.6
Q ss_pred eeccCCCCCCcCceeeccCCceechhchhhcCCCCCCCCCCCcc
Q 038068 55 FDCPICFEPLTVPVFQCVNGHLACSDCCAKIKRNCPTCSSPTVI 98 (269)
Q Consensus 55 l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~~~~Cp~C~~~~~~ 98 (269)
-.|-+|..-+. +-||.||..|--+- ..|.+|...+..
T Consensus 45 ~~C~~CK~~v~------q~g~~YCq~CAYkk-GiCamCGKki~d 81 (90)
T PF10235_consen 45 SKCKICKTKVH------QPGAKYCQTCAYKK-GICAMCGKKILD 81 (90)
T ss_pred ccccccccccc------cCCCccChhhhccc-CcccccCCeecc
Confidence 36888887332 34899999997664 689999987753
No 206
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=23.07 E-value=60 Score=24.02 Aligned_cols=23 Identities=30% Similarity=0.716 Sum_probs=16.4
Q ss_pred eechhchhhc-------CCCCCCCCCCCcc
Q 038068 76 LACSDCCAKI-------KRNCPTCSSPTVI 98 (269)
Q Consensus 76 ~fC~~C~~~~-------~~~Cp~C~~~~~~ 98 (269)
+.|+-|...+ ...||.|+.++++
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp 92 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNP 92 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCc
Confidence 6777777665 3568888888763
No 207
>PF12907 zf-met2: Zinc-binding
Probab=22.78 E-value=43 Score=20.61 Aligned_cols=17 Identities=24% Similarity=0.190 Sum_probs=14.0
Q ss_pred cChhHHhhhhhhhCCCC
Q 038068 154 GCSSQFVRHFMAKHNIS 170 (269)
Q Consensus 154 g~~~~l~~Hl~~~H~~~ 170 (269)
.....|.+|..++|.-.
T Consensus 15 ~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 15 TNEPQLKEHAENKHPKN 31 (40)
T ss_pred CCHHHHHHHHHccCCCC
Confidence 45679999999999863
No 208
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.68 E-value=93 Score=17.44 Aligned_cols=21 Identities=14% Similarity=0.385 Sum_probs=13.6
Q ss_pred eccCCCCCCcCc-eeecc-CCce
Q 038068 56 DCPICFEPLTVP-VFQCV-NGHL 76 (269)
Q Consensus 56 ~C~iC~~~l~~P-v~~c~-cgH~ 76 (269)
.|.+|.+.+... .|.|. |+..
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~ 24 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFT 24 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCe
Confidence 577887777776 66664 4433
No 209
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=22.55 E-value=70 Score=19.76 Aligned_cols=29 Identities=28% Similarity=0.587 Sum_probs=20.1
Q ss_pred eccCCCCCCcCceeecc-C-Cceechhchhh
Q 038068 56 DCPICFEPLTVPVFQCV-N-GHLACSDCCAK 84 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~-c-gH~fC~~C~~~ 84 (269)
.|..|..++....+.|. | .-.+|..|...
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 58888888777777775 4 35667777643
No 210
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=21.98 E-value=62 Score=31.18 Aligned_cols=34 Identities=26% Similarity=0.645 Sum_probs=22.7
Q ss_pred CCCCeeeccCCCCCCcCc--eeec-cCCceechhchh
Q 038068 50 TDQDIFDCPICFEPLTVP--VFQC-VNGHLACSDCCA 83 (269)
Q Consensus 50 ~~~~~l~C~iC~~~l~~P--v~~c-~cgH~fC~~C~~ 83 (269)
.+.+.-.|-.|..+|..= ...| .||-+||..|..
T Consensus 897 pd~~a~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 897 PDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred CCCcchhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 334566788888877421 1235 599999998854
No 211
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.74 E-value=68 Score=33.83 Aligned_cols=43 Identities=23% Similarity=0.650 Sum_probs=32.1
Q ss_pred eeccCCCCCCc-----Cceeecc-CCceechhchhhc----CCCCCCCCCCCc
Q 038068 55 FDCPICFEPLT-----VPVFQCV-NGHLACSDCCAKI----KRNCPTCSSPTV 97 (269)
Q Consensus 55 l~C~iC~~~l~-----~Pv~~c~-cgH~fC~~C~~~~----~~~Cp~C~~~~~ 97 (269)
-.|.||.+-+- +|..-|. |+--+|..|.+-- +..||.|+....
T Consensus 16 ~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 16 KTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred chhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 47999988643 3444564 9999999998643 568999998765
No 212
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.11 E-value=82 Score=19.22 Aligned_cols=25 Identities=36% Similarity=0.781 Sum_probs=12.0
Q ss_pred eccCCCCCCcCceeeccCCceechhch
Q 038068 56 DCPICFEPLTVPVFQCVNGHLACSDCC 82 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~cgH~fC~~C~ 82 (269)
.||.|.... -++--.-|-.+|..|-
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCC
Confidence 567776632 1211124566666663
No 213
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=21.02 E-value=55 Score=17.91 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=8.2
Q ss_pred eeCCCCCCCCccChh
Q 038068 143 LPCPLSDCSFLGCSS 157 (269)
Q Consensus 143 ~~Cp~~~C~~~g~~~ 157 (269)
..| .++|+|.|+..
T Consensus 2 ~~C-~~gCgf~Gs~~ 15 (25)
T PF01754_consen 2 SLC-ANGCGFYGSPA 15 (25)
T ss_dssp SB--TTTSSSB-BGG
T ss_pred Ccc-cCCCCCccccc
Confidence 456 45899888754
No 214
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=20.92 E-value=70 Score=18.19 Aligned_cols=21 Identities=29% Similarity=0.708 Sum_probs=10.3
Q ss_pred eccCCCCCCcCceeecc-CCceech
Q 038068 56 DCPICFEPLTVPVFQCV-NGHLACS 79 (269)
Q Consensus 56 ~C~iC~~~l~~Pv~~c~-cgH~fC~ 79 (269)
.|.||.. ...+.|+ |+-.+|+
T Consensus 4 ~C~vC~~---~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN---PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS---EESEE-TTT--EESS
T ss_pred CCccCcC---CCEEECCCcCCceeC
Confidence 5677776 2234554 6666665
No 215
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.88 E-value=35 Score=26.71 Aligned_cols=35 Identities=40% Similarity=0.759 Sum_probs=27.0
Q ss_pred CceeecCCCCeeeccCCCCCCcCceeeccCC-ceech
Q 038068 44 SEALTITDQDIFDCPICFEPLTVPVFQCVNG-HLACS 79 (269)
Q Consensus 44 ~~~~~~~~~~~l~C~iC~~~l~~Pv~~c~cg-H~fC~ 79 (269)
.....+.+.+.|.|..|.++++.-.+ .+.| |-||.
T Consensus 71 hiAIaLVdq~~Lhcdlceeplk~ccf-spnghhcfcr 106 (167)
T KOG4621|consen 71 HIAIALVDQDKLHCDLCEEPLKSCCF-SPNGHHCFCR 106 (167)
T ss_pred eEEEEEecCCceehHHHHhHHHHhcc-CCCCcccccc
Confidence 45566778899999999999998775 4777 45654
No 216
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.68 E-value=42 Score=31.87 Aligned_cols=34 Identities=24% Similarity=0.486 Sum_probs=26.6
Q ss_pred CCeeeccCCCCCCcCceeeccCCceechhchhhc
Q 038068 52 QDIFDCPICFEPLTVPVFQCVNGHLACSDCCAKI 85 (269)
Q Consensus 52 ~~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C~~~~ 85 (269)
.....|.||.+.....+..-.|||.||..|+...
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~y 101 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGY 101 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcHHHHHHHHHH
Confidence 3668999999988753323479999999999874
No 217
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.54 E-value=83 Score=20.74 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=6.9
Q ss_pred HHhhcceecccC
Q 038068 106 KVIELVQVNCKN 117 (269)
Q Consensus 106 ~~i~~l~v~C~~ 117 (269)
.++.++++.||.
T Consensus 22 T~LkNfPlyCpK 33 (55)
T PF14205_consen 22 TVLKNFPLYCPK 33 (55)
T ss_pred ceeccccccCCC
Confidence 345566666663
No 218
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.51 E-value=40 Score=30.01 Aligned_cols=25 Identities=32% Similarity=0.784 Sum_probs=18.1
Q ss_pred CCceechhchhhc-------CCCCCCCCCCCc
Q 038068 73 NGHLACSDCCAKI-------KRNCPTCSSPTV 97 (269)
Q Consensus 73 cgH~fC~~C~~~~-------~~~Cp~C~~~~~ 97 (269)
-.|.||+.|-.+. ...||.|+...-
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence 4688888888776 356888876544
No 219
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=20.38 E-value=47 Score=25.15 Aligned_cols=26 Identities=19% Similarity=0.383 Sum_probs=12.0
Q ss_pred CeeeccCCCCCCcCceeeccCCceechhc
Q 038068 53 DIFDCPICFEPLTVPVFQCVNGHLACSDC 81 (269)
Q Consensus 53 ~~l~C~iC~~~l~~Pv~~c~cgH~fC~~C 81 (269)
..+.|+-|...-..+. +|++.+|..|
T Consensus 41 ~~~~C~~Cg~~~~~~~---SCk~R~CP~C 66 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYN---SCKNRHCPSC 66 (111)
T ss_pred ceeecCCCCceEEecC---cccCcCCCCC
Confidence 3456666555443221 4555444333
No 220
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.22 E-value=71 Score=23.79 Aligned_cols=32 Identities=25% Similarity=0.541 Sum_probs=18.1
Q ss_pred CCCeeeccCCCCCCcCceeec-cCCceechhchh
Q 038068 51 DQDIFDCPICFEPLTVPVFQC-VNGHLACSDCCA 83 (269)
Q Consensus 51 ~~~~l~C~iC~~~l~~Pv~~c-~cgH~fC~~C~~ 83 (269)
.+..+.||.|.+. ..++..- .-+|+.|..|-.
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~ 50 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIKKNIAIITCGNCGL 50 (99)
T ss_pred CCcEeECCCCCCe-EeeeecCCCcceEECCCCCC
Confidence 3478999999963 3332111 234666655543
No 221
>PHA00626 hypothetical protein
Probab=20.09 E-value=71 Score=21.21 Aligned_cols=10 Identities=20% Similarity=0.451 Sum_probs=5.5
Q ss_pred CCCCCCCCCC
Q 038068 87 RNCPTCSSPT 96 (269)
Q Consensus 87 ~~Cp~C~~~~ 96 (269)
..||.|.-.+
T Consensus 24 YkCkdCGY~f 33 (59)
T PHA00626 24 YVCCDCGYND 33 (59)
T ss_pred eEcCCCCCee
Confidence 4566665443
Done!