Query 020280
Match_columns 328
No_of_seqs 370 out of 1598
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:29:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3002 Zn finger protein [Gen 100.0 1.1E-39 2.3E-44 304.4 11.7 240 78-317 41-293 (299)
2 PF03145 Sina: Seven in absent 100.0 2.8E-29 6E-34 223.8 5.8 183 130-312 1-198 (198)
3 KOG0297 TNF receptor-associate 99.4 3.8E-14 8.2E-19 138.5 2.4 123 83-209 19-149 (391)
4 cd03829 Sina Seven in absentia 99.4 3.1E-13 6.8E-18 108.7 3.9 95 220-314 22-126 (127)
5 KOG0823 Predicted E3 ubiquitin 98.7 5.6E-09 1.2E-13 93.2 3.2 46 82-128 44-95 (230)
6 PF15227 zf-C3HC4_4: zinc fing 98.7 4.4E-09 9.6E-14 70.3 1.4 35 88-123 1-42 (42)
7 KOG0320 Predicted E3 ubiquitin 98.7 1.5E-08 3.2E-13 86.9 3.6 46 83-128 129-178 (187)
8 PLN03208 E3 ubiquitin-protein 98.7 9.7E-09 2.1E-13 90.0 2.3 45 84-129 17-80 (193)
9 PF13923 zf-C3HC4_2: Zinc fing 98.6 2.6E-08 5.7E-13 65.3 1.6 36 88-123 1-39 (39)
10 PF14835 zf-RING_6: zf-RING of 98.5 1.3E-08 2.9E-13 73.1 -0.2 45 84-128 6-51 (65)
11 smart00504 Ubox Modified RING 98.5 3.9E-08 8.5E-13 71.0 0.4 42 86-128 2-46 (63)
12 PF13639 zf-RING_2: Ring finge 98.3 2.2E-07 4.9E-12 62.5 1.0 38 87-124 2-44 (44)
13 TIGR00599 rad18 DNA repair pro 98.3 1.2E-07 2.7E-12 92.2 -0.8 45 83-128 24-71 (397)
14 KOG0287 Postreplication repair 98.3 3.7E-08 8.1E-13 92.0 -4.2 45 83-128 21-68 (442)
15 KOG0317 Predicted E3 ubiquitin 98.2 3.2E-07 6.9E-12 84.4 1.3 46 83-129 237-285 (293)
16 PF13920 zf-C3HC4_3: Zinc fing 98.2 4.2E-07 9.1E-12 62.9 1.4 43 85-128 2-48 (50)
17 PF00097 zf-C3HC4: Zinc finger 98.2 7E-07 1.5E-11 59.0 1.9 36 88-123 1-41 (41)
18 PF14634 zf-RING_5: zinc-RING 98.1 8.7E-07 1.9E-11 59.7 0.9 39 87-125 1-44 (44)
19 PHA02929 N1R/p28-like protein; 98.1 1.6E-06 3.4E-11 79.2 1.7 47 83-129 172-228 (238)
20 PF02176 zf-TRAF: TRAF-type zi 98.0 1.3E-06 2.8E-11 62.6 0.8 51 141-193 7-60 (60)
21 PF04564 U-box: U-box domain; 98.0 6.5E-07 1.4E-11 67.1 -0.9 57 83-140 2-65 (73)
22 cd00162 RING RING-finger (Real 98.0 2.8E-06 6.1E-11 56.1 1.3 40 87-126 1-44 (45)
23 KOG0311 Predicted E3 ubiquitin 97.9 7.1E-07 1.5E-11 84.1 -4.2 83 40-131 7-93 (381)
24 COG5432 RAD18 RING-finger-cont 97.8 3E-06 6.5E-11 77.9 -0.4 110 85-197 25-182 (391)
25 PF02176 zf-TRAF: TRAF-type zi 97.7 1.3E-05 2.8E-10 57.3 1.6 43 165-207 1-43 (60)
26 KOG2164 Predicted E3 ubiquitin 97.7 1.2E-05 2.5E-10 79.5 1.1 44 85-129 186-237 (513)
27 COG5574 PEX10 RING-finger-cont 97.7 1.1E-05 2.4E-10 73.5 0.7 45 83-128 213-262 (271)
28 PF13445 zf-RING_UBOX: RING-ty 97.7 1.1E-05 2.5E-10 54.0 0.6 27 88-116 1-31 (43)
29 PHA02926 zinc finger-like prot 97.6 1.6E-05 3.4E-10 71.0 0.3 46 83-129 168-231 (242)
30 smart00184 RING Ring finger. E 97.5 3.1E-05 6.6E-10 49.2 0.8 35 88-123 1-39 (39)
31 TIGR00570 cdk7 CDK-activating 97.4 6.5E-05 1.4E-09 70.7 2.0 45 84-128 2-54 (309)
32 KOG0978 E3 ubiquitin ligase in 97.3 4.6E-05 1E-09 78.6 0.1 46 83-129 641-690 (698)
33 KOG2177 Predicted E3 ubiquitin 97.3 5.5E-05 1.2E-09 69.6 0.2 42 83-125 11-55 (386)
34 PF12678 zf-rbx1: RING-H2 zinc 97.1 0.00033 7.2E-09 52.4 2.3 38 87-124 21-73 (73)
35 KOG4159 Predicted E3 ubiquitin 96.7 0.00043 9.4E-09 67.8 0.1 45 83-128 82-129 (398)
36 KOG1813 Predicted E3 ubiquitin 96.6 0.00076 1.7E-08 62.6 1.2 42 86-128 242-286 (313)
37 COG5152 Uncharacterized conser 96.6 0.00048 1E-08 60.4 -0.2 42 85-127 196-240 (259)
38 PLN03086 PRLI-interacting fact 96.6 0.00064 1.4E-08 69.2 0.4 50 142-195 406-455 (567)
39 PF11789 zf-Nse: Zinc-finger o 96.5 0.00089 1.9E-08 47.6 0.5 32 85-116 11-42 (57)
40 PF07800 DUF1644: Protein of u 96.3 0.0023 5E-08 54.4 2.4 29 172-200 106-134 (162)
41 PLN03086 PRLI-interacting fact 96.3 0.0014 3.1E-08 66.7 1.4 52 153-208 459-510 (567)
42 PF14570 zf-RING_4: RING/Ubox 96.1 0.0023 4.9E-08 43.7 1.1 40 88-127 1-47 (48)
43 KOG2879 Predicted E3 ubiquitin 96.1 0.0033 7.2E-08 57.9 2.3 45 84-128 238-287 (298)
44 PF12861 zf-Apc11: Anaphase-pr 96.1 0.0023 5E-08 49.0 0.9 41 88-128 35-82 (85)
45 COG5222 Uncharacterized conser 95.9 0.0026 5.6E-08 59.1 0.5 40 86-125 275-318 (427)
46 KOG2660 Locus-specific chromos 95.8 0.0017 3.8E-08 61.2 -1.0 46 83-128 13-61 (331)
47 KOG4739 Uncharacterized protei 95.7 0.0053 1.1E-07 55.7 1.7 44 85-128 3-48 (233)
48 COG5540 RING-finger-containing 95.5 0.0056 1.2E-07 57.1 1.3 43 86-128 324-372 (374)
49 COG5175 MOT2 Transcriptional r 95.3 0.0046 1E-07 58.4 0.1 47 81-128 11-64 (480)
50 PF11793 FANCL_C: FANCL C-term 95.2 0.0056 1.2E-07 45.4 0.1 45 85-129 2-67 (70)
51 KOG1002 Nucleotide excision re 94.9 0.0076 1.7E-07 60.1 0.1 47 81-128 532-586 (791)
52 PF05290 Baculo_IE-1: Baculovi 94.8 0.014 3E-07 48.2 1.5 52 77-129 73-133 (140)
53 KOG0802 E3 ubiquitin ligase [P 94.5 0.011 2.4E-07 60.7 0.1 42 85-127 291-340 (543)
54 KOG0824 Predicted E3 ubiquitin 94.2 0.02 4.3E-07 53.5 1.2 42 86-128 8-53 (324)
55 KOG0825 PHD Zn-finger protein 93.9 0.017 3.6E-07 60.1 0.1 45 84-128 122-171 (1134)
56 KOG3039 Uncharacterized conser 92.7 0.071 1.5E-06 48.6 2.1 45 84-129 220-271 (303)
57 KOG4628 Predicted E3 ubiquitin 92.5 0.059 1.3E-06 51.9 1.5 43 86-128 230-278 (348)
58 COG5219 Uncharacterized conser 92.4 0.031 6.8E-07 59.3 -0.6 44 85-128 1469-1523(1525)
59 COG5243 HRD1 HRD ubiquitin lig 92.3 0.067 1.4E-06 51.4 1.6 46 83-128 285-345 (491)
60 KOG4172 Predicted E3 ubiquitin 92.1 0.021 4.6E-07 39.8 -1.5 42 86-128 8-54 (62)
61 KOG4265 Predicted E3 ubiquitin 92.1 0.051 1.1E-06 52.0 0.5 43 85-128 290-336 (349)
62 PF14447 Prok-RING_4: Prokaryo 92.0 0.13 2.8E-06 36.1 2.3 42 86-128 8-50 (55)
63 KOG1785 Tyrosine kinase negati 91.8 0.044 9.5E-07 53.1 -0.3 41 87-128 371-416 (563)
64 KOG4275 Predicted E3 ubiquitin 91.3 0.051 1.1E-06 50.6 -0.5 41 85-127 300-341 (350)
65 KOG1039 Predicted E3 ubiquitin 91.3 0.09 1.9E-06 50.7 1.2 48 82-129 158-222 (344)
66 PF07975 C1_4: TFIIH C1-like d 90.4 0.18 3.9E-06 35.0 1.7 37 88-124 2-50 (51)
67 KOG4692 Predicted E3 ubiquitin 90.3 0.084 1.8E-06 50.4 0.1 49 78-127 415-466 (489)
68 COG5236 Uncharacterized conser 90.3 0.055 1.2E-06 51.5 -1.2 112 82-201 58-180 (493)
69 KOG1734 Predicted RING-contain 89.5 0.077 1.7E-06 49.0 -0.8 46 84-129 223-282 (328)
70 KOG0804 Cytoplasmic Zn-finger 89.5 0.15 3.2E-06 50.2 1.0 43 84-126 174-220 (493)
71 PF04641 Rtf2: Rtf2 RING-finge 88.3 0.35 7.5E-06 45.0 2.6 46 83-128 111-161 (260)
72 KOG4367 Predicted Zn-finger pr 87.8 0.14 2.9E-06 50.3 -0.5 32 84-116 3-34 (699)
73 KOG2932 E3 ubiquitin ligase in 86.6 0.12 2.7E-06 48.5 -1.4 78 83-166 88-167 (389)
74 KOG2817 Predicted E3 ubiquitin 85.3 0.39 8.4E-06 46.7 1.2 43 83-126 332-383 (394)
75 KOG1645 RING-finger-containing 85.1 0.32 6.9E-06 47.5 0.5 41 86-126 5-54 (463)
76 PF07191 zinc-ribbons_6: zinc- 85.1 0.36 7.7E-06 35.7 0.6 38 86-128 2-41 (70)
77 PF10571 UPF0547: Uncharacteri 83.8 0.49 1.1E-05 28.1 0.7 22 87-108 2-24 (26)
78 COG5194 APC11 Component of SCF 83.4 0.41 8.8E-06 36.2 0.3 44 86-129 21-82 (88)
79 KOG1952 Transcription factor N 82.8 1 2.2E-05 47.9 3.0 43 83-125 189-244 (950)
80 KOG3161 Predicted E3 ubiquitin 81.0 0.3 6.5E-06 50.2 -1.5 37 84-121 10-51 (861)
81 KOG1001 Helicase-like transcri 79.9 0.54 1.2E-05 49.5 -0.1 41 86-128 455-500 (674)
82 KOG3608 Zn finger proteins [Ge 79.3 0.48 1E-05 45.5 -0.7 113 83-199 205-346 (467)
83 KOG0828 Predicted E3 ubiquitin 78.6 0.57 1.2E-05 46.8 -0.4 44 85-128 571-634 (636)
84 KOG3800 Predicted E3 ubiquitin 78.1 0.83 1.8E-05 42.7 0.5 41 87-127 2-50 (300)
85 KOG1571 Predicted E3 ubiquitin 77.9 0.9 2E-05 43.7 0.7 44 83-128 303-347 (355)
86 PF14446 Prok-RING_1: Prokaryo 77.6 1.4 3.1E-05 30.8 1.5 42 85-127 5-51 (54)
87 PF02891 zf-MIZ: MIZ/SP-RING z 76.9 1 2.2E-05 31.0 0.6 42 85-126 2-50 (50)
88 KOG1814 Predicted E3 ubiquitin 76.8 0.72 1.6E-05 45.1 -0.3 88 83-173 182-303 (445)
89 PF05605 zf-Di19: Drought indu 76.4 0.77 1.7E-05 31.9 -0.1 24 173-199 31-54 (54)
90 KOG3039 Uncharacterized conser 76.0 1.2 2.7E-05 40.7 1.0 30 86-116 44-73 (303)
91 KOG0826 Predicted E3 ubiquitin 76.0 1.8 3.9E-05 41.2 2.1 46 82-127 297-345 (357)
92 KOG4185 Predicted E3 ubiquitin 75.5 1.6 3.4E-05 41.1 1.6 42 85-127 3-54 (296)
93 KOG2930 SCF ubiquitin ligase, 75.3 0.58 1.3E-05 37.1 -1.1 46 82-127 43-107 (114)
94 KOG1812 Predicted E3 ubiquitin 75.1 0.72 1.6E-05 45.4 -0.8 33 84-116 145-180 (384)
95 PHA00616 hypothetical protein 74.9 3.3 7.2E-05 27.8 2.6 33 173-207 1-34 (44)
96 PF04606 Ogr_Delta: Ogr/Delta- 74.1 3.4 7.4E-05 27.9 2.6 40 119-160 1-40 (47)
97 PF13909 zf-H2C2_5: C2H2-type 72.7 2.2 4.8E-05 24.2 1.2 23 175-199 2-24 (24)
98 PF04216 FdhE: Protein involve 72.5 3.7 8.1E-05 38.7 3.4 72 86-161 173-252 (290)
99 TIGR00622 ssl1 transcription f 72.1 2.8 6.1E-05 33.9 2.1 38 87-124 57-110 (112)
100 PF01485 IBR: IBR domain; Int 69.7 2.9 6.4E-05 29.3 1.6 34 83-116 16-58 (64)
101 PF02459 Adeno_terminal: Adeno 69.1 3.3 7.2E-05 42.0 2.3 9 307-315 510-518 (548)
102 smart00647 IBR In Between Ring 69.0 3.8 8.3E-05 28.7 2.0 33 84-116 17-58 (64)
103 PF14851 FAM176: FAM176 family 68.8 6.9 0.00015 33.5 3.8 7 25-31 58-64 (153)
104 PRK04023 DNA polymerase II lar 68.8 4 8.7E-05 44.5 2.9 42 85-128 626-674 (1121)
105 KOG3579 Predicted E3 ubiquitin 68.3 14 0.0003 34.8 5.9 34 83-116 266-302 (352)
106 PF14569 zf-UDP: Zinc-binding 67.0 3.1 6.6E-05 31.4 1.2 45 84-128 8-62 (80)
107 KOG2807 RNA polymerase II tran 66.6 3.1 6.7E-05 39.7 1.4 37 88-124 333-374 (378)
108 PF10367 Vps39_2: Vacuolar sor 65.7 3.7 8E-05 32.1 1.5 29 87-115 80-109 (109)
109 PF01363 FYVE: FYVE zinc finge 65.0 2.9 6.3E-05 30.3 0.8 34 83-116 7-43 (69)
110 KOG2462 C2H2-type Zn-finger pr 64.3 9.4 0.0002 35.6 4.1 14 83-96 128-141 (279)
111 KOG4362 Transcriptional regula 64.1 1.7 3.8E-05 45.4 -0.8 43 84-127 20-68 (684)
112 PRK11088 rrmA 23S rRNA methylt 63.8 3 6.5E-05 38.7 0.8 24 85-108 2-27 (272)
113 smart00154 ZnF_AN1 AN1-like Zi 63.0 4.1 8.9E-05 26.5 1.1 25 88-113 1-27 (39)
114 PF05605 zf-Di19: Drought indu 62.1 6.2 0.00013 27.3 2.0 28 174-203 3-30 (54)
115 PF01428 zf-AN1: AN1-like Zinc 61.9 6.8 0.00015 25.9 2.0 33 88-121 1-36 (43)
116 smart00301 DM Doublesex DNA-bi 61.2 4.8 0.0001 28.3 1.2 39 153-193 8-46 (54)
117 COG5109 Uncharacterized conser 61.1 4.9 0.00011 38.2 1.7 42 83-125 334-384 (396)
118 PF06906 DUF1272: Protein of u 60.8 3.5 7.7E-05 29.0 0.5 42 87-128 7-52 (57)
119 KOG0957 PHD finger protein [Ge 59.6 17 0.00037 36.8 5.1 22 107-128 171-193 (707)
120 KOG1493 Anaphase-promoting com 59.4 1.5 3.3E-05 32.9 -1.6 26 103-128 50-81 (84)
121 PF15616 TerY-C: TerY-C metal 59.1 5.2 0.00011 33.3 1.3 39 86-128 78-116 (131)
122 TIGR01562 FdhE formate dehydro 58.7 7 0.00015 37.3 2.3 40 86-125 185-232 (305)
123 COG3813 Uncharacterized protei 58.0 4.1 8.9E-05 30.2 0.5 29 101-129 24-53 (84)
124 smart00064 FYVE Protein presen 57.4 5.7 0.00012 28.6 1.2 33 84-116 9-44 (68)
125 PF03854 zf-P11: P-11 zinc fin 56.5 4.5 9.7E-05 27.6 0.4 41 86-128 3-46 (50)
126 PRK14714 DNA polymerase II lar 55.8 12 0.00026 42.0 3.7 42 85-128 667-720 (1337)
127 KOG2114 Vacuolar assembly/sort 55.7 4.9 0.00011 42.9 0.7 41 86-126 841-881 (933)
128 PF05502 Dynactin_p62: Dynacti 54.3 14 0.00031 37.5 3.8 67 84-157 4-96 (483)
129 KOG1812 Predicted E3 ubiquitin 53.1 6.1 0.00013 38.9 1.0 31 85-116 306-341 (384)
130 COG2888 Predicted Zn-ribbon RN 53.1 14 0.00031 26.4 2.5 34 142-186 26-61 (61)
131 KOG2231 Predicted E3 ubiquitin 52.9 10 0.00022 39.8 2.6 41 87-128 2-52 (669)
132 COG5242 TFB4 RNA polymerase II 51.8 7.2 0.00016 35.4 1.1 15 85-99 260-274 (296)
133 PRK09678 DNA-binding transcrip 51.5 13 0.00027 27.7 2.2 45 119-165 3-47 (72)
134 PF08746 zf-RING-like: RING-li 51.5 9.1 0.0002 25.4 1.3 35 88-123 1-43 (43)
135 PLN02189 cellulose synthase 50.7 8.6 0.00019 42.3 1.6 43 86-128 35-87 (1040)
136 PF10083 DUF2321: Uncharacteri 50.3 4.2 9.2E-05 34.7 -0.6 22 107-128 29-50 (158)
137 PF14812 PBP1_TM: Transmembran 49.9 5.4 0.00012 30.4 0.0 10 52-61 49-58 (81)
138 PLN02436 cellulose synthase A 49.5 9.3 0.0002 42.1 1.7 43 86-128 37-89 (1094)
139 smart00744 RINGv The RING-vari 49.5 6.6 0.00014 26.8 0.4 37 87-124 1-49 (49)
140 PF13240 zinc_ribbon_2: zinc-r 49.4 7.3 0.00016 22.3 0.5 7 119-125 15-21 (23)
141 KOG1819 FYVE finger-containing 49.2 12 0.00026 37.8 2.2 35 80-114 896-933 (990)
142 KOG1815 Predicted E3 ubiquitin 49.1 7.8 0.00017 38.9 1.0 20 96-116 177-196 (444)
143 KOG0827 Predicted E3 ubiquitin 49.1 5.8 0.00012 38.8 0.0 39 86-125 5-53 (465)
144 PRK03564 formate dehydrogenase 48.2 13 0.00029 35.5 2.3 41 85-125 187-234 (309)
145 cd00065 FYVE FYVE domain; Zinc 47.6 9 0.0002 26.4 0.9 30 87-116 4-36 (57)
146 PLN02638 cellulose synthase A 46.7 11 0.00024 41.7 1.7 43 86-128 18-70 (1079)
147 PF00412 LIM: LIM domain; Int 46.5 11 0.00023 25.9 1.1 33 83-115 24-56 (58)
148 PF10426 zf-RAG1: Recombinatio 46.2 11 0.00024 23.1 1.0 23 174-196 3-25 (30)
149 KOG3268 Predicted E3 ubiquitin 46.0 8.2 0.00018 33.8 0.5 44 86-129 166-229 (234)
150 PF13913 zf-C2HC_2: zinc-finge 45.8 4.2 9.2E-05 23.7 -0.9 14 181-194 8-21 (25)
151 PF12660 zf-TFIIIC: Putative z 45.1 7.2 0.00016 30.8 0.0 41 86-127 15-65 (99)
152 PF10272 Tmpp129: Putative tra 44.8 10 0.00022 36.9 1.1 31 98-128 305-351 (358)
153 KOG0298 DEAD box-containing he 44.8 3.9 8.4E-05 45.6 -2.0 45 83-127 1151-1198(1394)
154 KOG0297 TNF receptor-associate 44.6 6 0.00013 39.1 -0.6 34 142-178 113-147 (391)
155 COG4306 Uncharacterized protei 44.4 6.8 0.00015 32.3 -0.2 22 107-128 29-50 (160)
156 KOG1100 Predicted E3 ubiquitin 44.4 20 0.00042 32.3 2.7 39 88-128 161-200 (207)
157 PF03145 Sina: Seven in absent 44.2 6.5 0.00014 34.7 -0.4 46 123-168 24-69 (198)
158 COG4647 AcxC Acetone carboxyla 43.9 8.5 0.00018 31.9 0.3 21 90-111 62-82 (165)
159 PLN02195 cellulose synthase A 43.3 14 0.00031 40.4 1.9 43 86-128 7-59 (977)
160 PLN02400 cellulose synthase 43.1 14 0.00031 40.8 1.9 43 86-128 37-89 (1085)
161 KOG3576 Ovo and related transc 42.8 25 0.00055 31.6 3.1 44 81-128 113-156 (267)
162 cd00350 rubredoxin_like Rubred 42.0 21 0.00045 22.1 1.8 9 118-126 18-26 (33)
163 PF02318 FYVE_2: FYVE-type zin 40.7 18 0.00038 29.4 1.7 39 86-125 55-102 (118)
164 PF05253 zf-U11-48K: U11-48K-l 40.6 5.1 0.00011 23.8 -1.1 13 183-195 11-23 (27)
165 COG5220 TFB3 Cdk activating ki 39.4 6.8 0.00015 35.9 -1.0 42 85-126 10-62 (314)
166 COG1645 Uncharacterized Zn-fin 39.2 16 0.00035 30.4 1.2 24 85-113 28-51 (131)
167 KOG2068 MOT2 transcription fac 39.1 21 0.00045 34.3 2.1 43 86-128 250-298 (327)
168 PRK14890 putative Zn-ribbon RN 39.0 24 0.00051 25.2 1.9 16 109-124 39-55 (59)
169 PF03833 PolC_DP2: DNA polymer 39.0 10 0.00022 40.8 0.0 43 84-128 654-703 (900)
170 PF08882 Acetone_carb_G: Aceto 38.6 14 0.0003 29.8 0.7 25 82-111 12-36 (112)
171 PF03604 DNA_RNApol_7kD: DNA d 38.0 24 0.00051 22.0 1.5 8 87-94 2-9 (32)
172 PRK00398 rpoP DNA-directed RNA 37.7 18 0.00039 24.1 1.1 31 85-129 3-33 (46)
173 PHA03096 p28-like protein; Pro 37.4 10 0.00022 35.8 -0.2 31 86-116 179-216 (284)
174 PF05883 Baculo_RING: Baculovi 37.3 7.2 0.00016 32.6 -1.1 32 85-116 26-65 (134)
175 PF13717 zinc_ribbon_4: zinc-r 37.3 25 0.00055 22.3 1.7 12 86-97 3-14 (36)
176 PF13901 DUF4206: Domain of un 37.1 21 0.00046 31.8 1.8 39 85-125 152-197 (202)
177 PF13894 zf-C2H2_4: C2H2-type 36.9 23 0.0005 19.0 1.3 22 175-198 2-24 (24)
178 KOG1941 Acetylcholine receptor 36.7 6.7 0.00015 38.4 -1.6 41 85-125 365-413 (518)
179 PF13834 DUF4193: Domain of un 36.4 36 0.00077 26.9 2.7 38 75-112 58-98 (99)
180 PF09788 Tmemb_55A: Transmembr 36.0 63 0.0014 29.9 4.6 21 140-162 120-140 (256)
181 smart00734 ZnF_Rad18 Rad18-lik 35.1 28 0.00061 20.4 1.5 20 174-195 2-21 (26)
182 PLN02915 cellulose synthase A 35.0 20 0.00043 39.6 1.4 43 86-128 16-68 (1044)
183 PF01286 XPA_N: XPA protein N- 35.0 24 0.00052 22.3 1.2 30 85-114 3-32 (34)
184 PF13248 zf-ribbon_3: zinc-rib 34.7 17 0.00036 21.3 0.5 6 119-124 18-23 (26)
185 PTZ00415 transmission-blocking 34.5 31 0.00067 40.2 2.8 11 139-149 286-296 (2849)
186 KOG1356 Putative transcription 34.4 12 0.00026 40.0 -0.2 31 86-116 230-261 (889)
187 PF10529 Hist_rich_Ca-bd: Hist 34.3 20 0.00043 18.4 0.6 6 33-38 6-11 (15)
188 KOG2487 RNA polymerase II tran 33.3 11 0.00025 35.1 -0.6 21 108-128 275-298 (314)
189 KOG0943 Predicted ubiquitin-pr 33.2 36 0.00078 38.4 2.9 15 11-25 1692-1707(3015)
190 PRK00420 hypothetical protein; 32.7 25 0.00055 28.5 1.4 25 86-114 24-48 (112)
191 PRK14559 putative protein seri 31.9 28 0.0006 36.8 1.9 41 87-128 3-52 (645)
192 KOG2462 C2H2-type Zn-finger pr 31.7 34 0.00073 32.1 2.2 73 118-196 162-237 (279)
193 PF14445 Prok-RING_2: Prokaryo 31.6 4.1 8.8E-05 28.1 -2.8 42 85-126 7-50 (57)
194 PF00096 zf-C2H2: Zinc finger, 31.1 24 0.00052 19.3 0.7 20 175-196 2-22 (23)
195 PF09297 zf-NADH-PPase: NADH p 29.1 14 0.0003 22.7 -0.6 19 106-124 3-28 (32)
196 PF12756 zf-C2H2_2: C2H2 type 29.1 41 0.00088 25.3 2.0 36 163-200 40-77 (100)
197 COG1198 PriA Primosomal protei 29.0 48 0.001 35.5 3.1 11 119-129 446-456 (730)
198 PF10497 zf-4CXXC_R1: Zinc-fin 28.9 31 0.00067 27.5 1.3 40 87-126 9-70 (105)
199 TIGR00927 2A1904 K+-dependent 28.3 39 0.00084 37.2 2.2 8 119-126 921-928 (1096)
200 smart00659 RPOLCX RNA polymera 28.2 44 0.00096 22.3 1.7 9 119-127 21-29 (44)
201 KOG2857 Predicted MYND Zn-fing 27.6 39 0.00085 28.5 1.7 28 102-130 2-30 (157)
202 PF00130 C1_1: Phorbol esters/ 27.1 48 0.001 22.3 1.9 37 85-121 11-51 (53)
203 KOG3113 Uncharacterized conser 26.4 41 0.0009 31.1 1.8 46 83-128 109-158 (293)
204 PF10587 EF-1_beta_acid: Eukar 26.0 29 0.00062 20.9 0.4 7 34-40 3-9 (28)
205 PHA02862 5L protein; Provision 25.9 27 0.00059 29.6 0.5 42 87-128 4-53 (156)
206 PF06677 Auto_anti-p27: Sjogre 25.9 44 0.00095 22.0 1.4 23 86-112 18-40 (41)
207 KOG3815 Transcription factor D 25.8 32 0.0007 33.0 1.0 37 152-190 41-77 (322)
208 KOG1819 FYVE finger-containing 25.6 41 0.00089 34.1 1.7 30 33-62 423-452 (990)
209 KOG3183 Predicted Zn-finger pr 25.1 35 0.00077 31.3 1.1 50 87-137 10-75 (250)
210 KOG3970 Predicted E3 ubiquitin 24.9 33 0.00072 31.2 0.9 45 85-129 50-106 (299)
211 KOG2272 Focal adhesion protein 24.8 45 0.00097 30.9 1.7 45 83-128 161-206 (332)
212 COG4357 Zinc finger domain con 24.7 46 0.001 26.2 1.5 23 107-129 63-92 (105)
213 PRK14559 putative protein seri 24.7 43 0.00094 35.3 1.8 28 87-116 17-51 (645)
214 PRK11595 DNA utilization prote 24.7 44 0.00095 30.2 1.6 34 87-126 7-43 (227)
215 PF00751 DM: DM DNA binding do 24.6 12 0.00027 25.4 -1.5 29 157-187 12-40 (47)
216 PF09723 Zn-ribbon_8: Zinc rib 24.6 50 0.0011 21.5 1.5 8 118-125 27-34 (42)
217 PF14205 Cys_rich_KTR: Cystein 24.3 52 0.0011 23.1 1.5 10 138-147 23-32 (55)
218 COG1592 Rubrerythrin [Energy p 24.3 46 0.001 28.9 1.6 12 85-96 134-145 (166)
219 KOG1842 FYVE finger-containing 24.0 21 0.00045 35.6 -0.6 37 80-116 175-214 (505)
220 COG5151 SSL1 RNA polymerase II 24.0 34 0.00074 32.6 0.8 9 87-95 364-372 (421)
221 PF07649 C1_3: C1-like domain; 23.9 32 0.0007 20.6 0.4 23 87-109 2-26 (30)
222 TIGR00416 sms DNA repair prote 23.8 34 0.00074 34.5 0.8 13 114-126 18-30 (454)
223 PRK11823 DNA repair protein Ra 23.8 38 0.00082 34.0 1.1 23 99-126 7-30 (446)
224 PRK14892 putative transcriptio 23.4 61 0.0013 25.7 2.0 30 83-113 19-49 (99)
225 KOG4445 Uncharacterized conser 23.2 14 0.0003 35.0 -1.9 47 83-129 113-187 (368)
226 cd00729 rubredoxin_SM Rubredox 23.2 62 0.0013 20.2 1.6 9 118-126 19-27 (34)
227 KOG1815 Predicted E3 ubiquitin 23.0 29 0.00063 34.8 0.2 34 83-116 68-101 (444)
228 PF10005 DUF2248: Uncharacteri 22.7 1.1E+02 0.0025 29.6 4.1 30 142-171 52-82 (343)
229 PF14319 Zn_Tnp_IS91: Transpos 22.3 45 0.00099 26.8 1.1 15 108-125 54-68 (111)
230 PHA02825 LAP/PHD finger-like p 22.1 37 0.0008 29.3 0.6 44 85-128 8-59 (162)
231 COG2816 NPY1 NTP pyrophosphohy 22.0 53 0.0012 30.9 1.7 29 104-132 109-144 (279)
232 PHA00626 hypothetical protein 22.0 48 0.001 23.4 1.0 22 107-128 12-34 (59)
233 PF03107 C1_2: C1 domain; Int 21.9 60 0.0013 19.5 1.3 23 87-109 2-26 (30)
234 PF06827 zf-FPG_IleRS: Zinc fi 21.8 39 0.00084 20.2 0.5 26 87-113 3-28 (30)
235 PF08271 TF_Zn_Ribbon: TFIIB z 21.3 62 0.0013 21.1 1.4 7 87-93 2-8 (43)
236 COG1198 PriA Primosomal protei 20.5 66 0.0014 34.5 2.2 40 85-126 435-484 (730)
237 PF14471 DUF4428: Domain of un 20.5 39 0.00084 23.3 0.3 28 87-116 1-30 (51)
238 KOG1829 Uncharacterized conser 20.5 31 0.00067 35.8 -0.3 43 83-125 509-558 (580)
239 TIGR02098 MJ0042_CXXC MJ0042 f 20.4 69 0.0015 20.0 1.5 13 86-98 3-15 (38)
240 TIGR00627 tfb4 transcription f 20.4 54 0.0012 30.9 1.4 20 107-126 256-278 (279)
241 PF04438 zf-HIT: HIT zinc fing 20.2 69 0.0015 19.5 1.4 21 87-110 4-25 (30)
242 smart00132 LIM Zinc-binding do 20.1 78 0.0017 19.1 1.7 35 88-127 2-37 (39)
243 KOG3896 Dynactin, subunit p62 20.1 78 0.0017 30.6 2.3 79 83-165 22-123 (449)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=100.00 E-value=1.1e-39 Score=304.42 Aligned_cols=240 Identities=40% Similarity=0.784 Sum_probs=203.4
Q ss_pred eeeCCCCeeeecccccccccccccccCCeeecccchhccCCCCCCCCcCCccccccccceeeeeeeeecccCCCCCceEE
Q 020280 78 VTVTDPEVFDCPICYESLTAPVFQCENGHIACSTCCSKIMNKCPSCCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKVTM 157 (328)
Q Consensus 78 ~~~~d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~~~CP~Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~~~ 157 (328)
+.+.+.+.|.||||++.+.+|++||..||+.|++|..+..+.||.|+.+++.+|++++|++++++.|+|+|..+||++.+
T Consensus 41 ~~~~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~ 120 (299)
T KOG3002|consen 41 VTLLDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSF 120 (299)
T ss_pred ccccchhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHHHHhceecccccccCCceee
Confidence 45566889999999999999999999999999999988889999999999999999999999999999999999999999
Q ss_pred eecccccccCCCCCCCccCCCC--CCCcccccchHhhHhhhhcCCCce-----eEEeceEEEEEEecC---CcEEEEEec
Q 020280 158 SYGKKHDHEKICPHVPCSCPIP--DCNFVGSANHLYKHFSAKHKNSAL-----HFLYNEVVEVTLNVK---NRFIVLQEE 227 (328)
Q Consensus 158 ~~~~~~~He~~C~~~~~~Cp~~--gC~~~g~~~~L~~Hl~~~H~~~~~-----~~~y~~~~~~~l~~~---~~~~vl~~~ 227 (328)
+|.+...||+.|.|+++.||.+ .|+|.|..++|..|+...|+..+. .+.|.......+.+. .++.++.+.
T Consensus 121 ~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (299)
T KOG3002|consen 121 PYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFVATDENLLGAATWTLKTSVCFGR 200 (299)
T ss_pred ccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChhhhhhccccceecccCCccccccchhheeeeecCcE
Confidence 9999999999999999999998 899999999999999999999877 444443333333333 244445566
Q ss_pred cCceEEEEeecccccccEEEEEeecC--CCCCCceEEEEEecCCCeEEEeeeeeeeccccC-CCCCcCeEEEcCcccCCC
Q 020280 228 GDGVLFILSSRSETLGHVISVSCIAP--SCKGCLFYSIFAGPAGSTVRFQSFTKNIQNRVD-NPPSTGFLLVPIESFGSS 304 (328)
Q Consensus 228 ~d~~lFll~~~~~~~g~~vsV~cIgp--~~a~~f~Yel~~~~~~~~l~~~s~~~~i~~~~~-~~~~~~fL~VP~~ll~~~ 304 (328)
.++.+|.++...++.|.+++|++|.| .++++|+|+|.+.+.+++|+|++.++++...+. ..+..+||+||..++...
T Consensus 201 ~~~~~~~~q~~~~~~~~y~tv~~i~~~~~e~~~fsy~L~~~~~~~klt~~s~~~s~~~kvs~~~p~~dfm~ip~~~~~~~ 280 (299)
T KOG3002|consen 201 EFGLLFEVQCFREPHGVYVTVNRIAPSAPEAGEFSYSLALGGSGRKLTWQSPPRSIIQKVSKVRPEDDFMLIPRSLLCLF 280 (299)
T ss_pred EEeeeeeehhhcCCCceEEEeehhccCCCcccccceeeecCCCCceEeecCCcceeecccceeccCCCceeccHHHhhcc
Confidence 78889999999999999999999987 457899999999999999999999999865444 556778999999877553
Q ss_pred CceEEEEEEEecc
Q 020280 305 GDLKLELCIRRLD 317 (328)
Q Consensus 305 ~~l~l~V~I~~~~ 317 (328)
..++++|+|....
T Consensus 281 ~~~~~~l~i~~~~ 293 (299)
T KOG3002|consen 281 SLLKMELKIRVTG 293 (299)
T ss_pred cccCCceeeccch
Confidence 3444455555444
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=2.8e-29 Score=223.84 Aligned_cols=183 Identities=30% Similarity=0.556 Sum_probs=116.5
Q ss_pred ccccccceeeeeeeeecccCCCCCceEEeecccccccCCCCCCCccCCC--CCCCcccccchHhhHhhhhcCCCceeEEe
Q 020280 130 NRCRAIEKVLESVKVTCRNSNYGCKVTMSYGKKHDHEKICPHVPCSCPI--PDCNFVGSANHLYKHFSAKHKNSALHFLY 207 (328)
Q Consensus 130 ~r~~~le~~l~~l~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~--~gC~~~g~~~~L~~Hl~~~H~~~~~~~~y 207 (328)
+||++||+++++++++|+|+.+||++.++|.++.+||+.|+|+|+.||. .+|+|.|+.++|..|+...|.+.+....+
T Consensus 1 iR~~alE~v~~~~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~~~~~~ 80 (198)
T PF03145_consen 1 IRNRALEKVAESIKFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNVTDNGT 80 (198)
T ss_dssp --------------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSEEEESS
T ss_pred CCcHHHHHHHhhceecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCccccCcc
Confidence 4899999999999999999999999999999999999999999999999 78999999999999999999998765433
Q ss_pred -ceEEEEEEec--CC-cEEEEEeccCceEEEEeecc-ccccc--EEE-EEeecC-CCCCCceEEEEEecCCCeEEEeeee
Q 020280 208 -NEVVEVTLNV--KN-RFIVLQEEGDGVLFILSSRS-ETLGH--VIS-VSCIAP-SCKGCLFYSIFAGPAGSTVRFQSFT 278 (328)
Q Consensus 208 -~~~~~~~l~~--~~-~~~vl~~~~d~~lFll~~~~-~~~g~--~vs-V~cIgp-~~a~~f~Yel~~~~~~~~l~~~s~~ 278 (328)
...+...... .. .|.+++.+++|.+|+|++.. +..|. +++ |++||+ .+|++|+|+|++.+++++|+|++++
T Consensus 81 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~~~~rkl~~~~~p 160 (198)
T PF03145_consen 81 FSISFLHSDINSVESPDWVLVQFSCFGKLFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVRSNGRKLTWQSFP 160 (198)
T ss_dssp -EEEEEECTTT-SSSEEEEEEE-EETTEEEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEEETTEEEEEEE--
T ss_pred ceEEEeeecccccCCceEEEeecccCCccEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEecCCcEEEEEEcC
Confidence 1122111111 11 34433336899999999643 32344 443 556787 4689999999999999999999999
Q ss_pred eeeccccCCC-CCcCeEEEcC---cccCCCCceEEEEE
Q 020280 279 KNIQNRVDNP-PSTGFLLVPI---ESFGSSGDLKLELC 312 (328)
Q Consensus 279 ~~i~~~~~~~-~~~~fL~VP~---~ll~~~~~l~l~V~ 312 (328)
++++...+.. .+.+||++.. .+|.++|.|.++|+
T Consensus 161 ~si~~~~~~~~~~~d~li~~~~~~~~f~~~~~L~~~v~ 198 (198)
T PF03145_consen 161 RSIREDIDDAIESRDCLIINENAAQFFSEDGNLRYRVT 198 (198)
T ss_dssp EETTT-SHHHHHCT-SEEEEHHHHHHHECTTEEEEEEE
T ss_pred cchhhhHHhhccCCcEEEEchHHHHhcCCCCeEEEEeC
Confidence 9998766643 3446776654 58888889998885
No 3
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=99.43 E-value=3.8e-14 Score=138.52 Aligned_cols=123 Identities=27% Similarity=0.543 Sum_probs=108.8
Q ss_pred CCeeeeccccccccccccc-ccCCeeecccchhcc---CCCCCCCCcCCccc----cccccceeeeeeeeecccCCCCCc
Q 020280 83 PEVFDCPICYESLTAPVFQ-CENGHIACSTCCSKI---MNKCPSCCTPIGYN----RCRAIEKVLESVKVTCRNSNYGCK 154 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~-c~CGH~fC~~C~~~~---~~~CP~Cr~~~~~~----r~~~le~~l~~l~v~C~n~~~GC~ 154 (328)
.+++.|++|..++.+|+ + ..|||.||..|+.++ ...||.|+..+... ....+.+++.++.+.|.+...||.
T Consensus 19 ~~~l~C~~C~~vl~~p~-~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~GC~ 97 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPV-QTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASRGCR 97 (391)
T ss_pred cccccCccccccccCCC-CCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCCCcc
Confidence 45689999999999999 6 589999999999998 36899998887643 245677888999999999999999
Q ss_pred eEEeecccccccCCCCCCCccCCCCCCCcccccchHhhHhhhhcCCCceeEEece
Q 020280 155 VTMSYGKKHDHEKICPHVPCSCPIPDCNFVGSANHLYKHFSAKHKNSALHFLYNE 209 (328)
Q Consensus 155 ~~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~~~L~~Hl~~~H~~~~~~~~y~~ 209 (328)
|.+.+..++.|+..| .+++||+. |+..+.+.++.+|++..|..+...+.+.+
T Consensus 98 ~~~~l~~~~~Hl~~c--~~~~C~~~-C~~~~~~~d~~~hl~~~C~~~~~~c~~~~ 149 (391)
T KOG0297|consen 98 ADLELEALQGHLSTC--DPLKCPHR-CGVQVPRDDLEDHLEAECPRRSLKCSLCQ 149 (391)
T ss_pred ccccHHHHHhHhccC--CcccCccc-cccccchHHHHHHHhcccccccccchhhc
Confidence 999999999999999 89999975 99999999999999999999888877653
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=99.37 E-value=3.1e-13 Score=108.69 Aligned_cols=95 Identities=15% Similarity=0.194 Sum_probs=79.9
Q ss_pred cEEEEEeccCceEEEEeeccccccc-----EEEEEeecC-CCCCCceEEEEEecCCCeEEEeeeeeeeccccCC-CCCcC
Q 020280 220 RFIVLQEEGDGVLFILSSRSETLGH-----VISVSCIAP-SCKGCLFYSIFAGPAGSTVRFQSFTKNIQNRVDN-PPSTG 292 (328)
Q Consensus 220 ~~~vl~~~~d~~lFll~~~~~~~g~-----~vsV~cIgp-~~a~~f~Yel~~~~~~~~l~~~s~~~~i~~~~~~-~~~~~ 292 (328)
.|++.+..+.|+.|+|+..+..++. ++.|++||+ ++|.+|+|.|++.+++|+|+||+.|+||+++... ..+.|
T Consensus 22 ~~w~mv~sCfG~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~~n~RkL~we~~PRSIrds~~~~~~~~D 101 (127)
T cd03829 22 TDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELNGNRRRLTWEATPRSIREGHASVIDNSD 101 (127)
T ss_pred eeeeehhhhcCceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEcCCCcEEEeecCCccHHHhhHHHhhcCc
Confidence 4556666899999999998776522 367889996 6799999999999999999999999999988775 34568
Q ss_pred eEEEcC---cccCCCCceEEEEEEE
Q 020280 293 FLLVPI---ESFGSSGDLKLELCIR 314 (328)
Q Consensus 293 fL~VP~---~ll~~~~~l~l~V~I~ 314 (328)
||+|-. .||.++|.+.|+|+|+
T Consensus 102 ~Lii~~~~A~~Fs~~g~l~l~v~It 126 (127)
T cd03829 102 CLVFDTSIAQLFSENGNLGINVTIS 126 (127)
T ss_pred ceEEechHhhhccCCCccEEEEEec
Confidence 999974 6888899999999996
No 5
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.74 E-value=5.6e-09 Score=93.22 Aligned_cols=46 Identities=33% Similarity=0.754 Sum_probs=40.6
Q ss_pred CCCeeeecccccccccccccccCCeeecccchhcc------CCCCCCCCcCCc
Q 020280 82 DPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI------MNKCPSCCTPIG 128 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~------~~~CP~Cr~~~~ 128 (328)
+-..|.|.||++..++|| .+.|||+||..|+.+| .+.||+|+..++
T Consensus 44 ~~~~FdCNICLd~akdPV-vTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPV-VTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccccCCCE-EeecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 445799999999999999 5789999999999999 367999998765
No 6
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.71 E-value=4.4e-09 Score=70.27 Aligned_cols=35 Identities=37% Similarity=1.029 Sum_probs=27.4
Q ss_pred ecccccccccccccccCCeeecccchhccC-------CCCCCC
Q 020280 88 CPICYESLTAPVFQCENGHIACSTCCSKIM-------NKCPSC 123 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~-------~~CP~C 123 (328)
||||+++|++|| +..|||+||..|+.++. ..||.|
T Consensus 1 CpiC~~~~~~Pv-~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPV-SLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEE-E-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCcc-ccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999999999 78999999999999871 358876
No 7
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=1.5e-08 Score=86.93 Aligned_cols=46 Identities=37% Similarity=0.906 Sum_probs=38.2
Q ss_pred CCeeeeccccccccccc-ccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPV-FQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv-~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
...+.||||+..+..-+ +.+.|||+||+.|+... ..+||+|++.++
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 44689999999987544 36899999999999987 579999998665
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.66 E-value=9.7e-09 Score=90.05 Aligned_cols=45 Identities=36% Similarity=0.783 Sum_probs=38.8
Q ss_pred CeeeecccccccccccccccCCeeecccchhccC-------------------CCCCCCCcCCcc
Q 020280 84 EVFDCPICYESLTAPVFQCENGHIACSTCCSKIM-------------------NKCPSCCTPIGY 129 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~-------------------~~CP~Cr~~~~~ 129 (328)
+.+.|+||++.+++|+ .+.|||+||..|+.+|. ..||.|+..+..
T Consensus 17 ~~~~CpICld~~~dPV-vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVRDPV-VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCCCcE-EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 4678999999999999 58999999999998871 379999998753
No 9
>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=98.56 E-value=2.6e-08 Score=65.35 Aligned_cols=36 Identities=44% Similarity=1.023 Sum_probs=30.4
Q ss_pred ecccccccccccccccCCeeecccchhcc---CCCCCCC
Q 020280 88 CPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSC 123 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~C 123 (328)
|+||++.+.+|+...+|||+||..|+.++ ..+||.|
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 89999999999657899999999999988 4688887
No 10
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.54 E-value=1.3e-08 Score=73.11 Aligned_cols=45 Identities=38% Similarity=0.833 Sum_probs=25.3
Q ss_pred CeeeecccccccccccccccCCeeecccchhcc-CCCCCCCCcCCc
Q 020280 84 EVFDCPICYESLTAPVFQCENGHIACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
+.|.|++|.++|+.||....|.|+||+.|+... ...||+|+.+..
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw 51 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAW 51 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHH
Confidence 357899999999999855679999999999875 467999998853
No 11
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.45 E-value=3.9e-08 Score=71.05 Aligned_cols=42 Identities=26% Similarity=0.409 Sum_probs=37.9
Q ss_pred eeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
|.||||++++.+|+ ..+|||+||..|+.++ ...||.|+.++.
T Consensus 2 ~~Cpi~~~~~~~Pv-~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDPV-ILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCCE-ECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 68999999999999 5799999999999988 468999999875
No 12
>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=98.29 E-value=2.2e-07 Score=62.47 Aligned_cols=38 Identities=34% Similarity=0.842 Sum_probs=31.7
Q ss_pred eecccccccc--cccccccCCeeecccchhcc---CCCCCCCC
Q 020280 87 DCPICYESLT--APVFQCENGHIACSTCCSKI---MNKCPSCC 124 (328)
Q Consensus 87 ~CpiC~~~l~--~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr 124 (328)
.|+||++.+. ..++..+|||.||..|+.+| ...||+||
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 5999999985 45557889999999999999 57999996
No 13
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.27 E-value=1.2e-07 Score=92.24 Aligned_cols=45 Identities=29% Similarity=0.620 Sum_probs=39.5
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.+.+.|+||.+++..|+ ...|||.||..|+..+ ...||.|+..+.
T Consensus 24 e~~l~C~IC~d~~~~Pv-itpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPV-LTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred ccccCCCcCchhhhCcc-CCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 45689999999999999 6899999999999877 357999999875
No 14
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.27 E-value=3.7e-08 Score=91.97 Aligned_cols=45 Identities=31% Similarity=0.882 Sum_probs=40.1
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.+.|.|.||+++|+.|+ .++|+|.||+-||.+. .+.||.|..++.
T Consensus 21 D~lLRC~IC~eyf~ip~-itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPM-ITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT 68 (442)
T ss_pred HHHHHHhHHHHHhcCce-eccccchHHHHHHHHHhccCCCCCceecccc
Confidence 45789999999999999 5789999999999987 478999998875
No 15
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=3.2e-07 Score=84.44 Aligned_cols=46 Identities=26% Similarity=0.608 Sum_probs=40.2
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCcc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIGY 129 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~~ 129 (328)
.....|.+|++...+|- .++|||+||.+||..| ...||.||..+..
T Consensus 237 ~a~~kC~LCLe~~~~pS-aTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNPS-ATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCCceEEEecCCCCCC-cCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 44679999999999997 6789999999999999 4689999998764
No 16
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.23 E-value=4.2e-07 Score=62.89 Aligned_cols=43 Identities=37% Similarity=0.898 Sum_probs=36.2
Q ss_pred eeeecccccccccccccccCCee-ecccchhcc---CCCCCCCCcCCc
Q 020280 85 VFDCPICYESLTAPVFQCENGHI-ACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~-fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
+..|+||++...+++ ..+|||. ||..|+.++ ...||.||+++.
T Consensus 2 ~~~C~iC~~~~~~~~-~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVV-LLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEE-EETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceE-EeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 468999999999888 4699999 999999998 479999999865
No 17
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.20 E-value=7e-07 Score=58.95 Aligned_cols=36 Identities=44% Similarity=0.980 Sum_probs=31.7
Q ss_pred ecccccccccccccccCCeeecccchhcc-----CCCCCCC
Q 020280 88 CPICYESLTAPVFQCENGHIACSTCCSKI-----MNKCPSC 123 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-----~~~CP~C 123 (328)
|+||.+++..|++..+|||.||..|+.++ ...||.|
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 89999999999866789999999999987 2578877
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.11 E-value=8.7e-07 Score=59.69 Aligned_cols=39 Identities=36% Similarity=0.799 Sum_probs=31.9
Q ss_pred eeccccccc--ccccccccCCeeecccchhccC---CCCCCCCc
Q 020280 87 DCPICYESL--TAPVFQCENGHIACSTCCSKIM---NKCPSCCT 125 (328)
Q Consensus 87 ~CpiC~~~l--~~Pv~~c~CGH~fC~~C~~~~~---~~CP~Cr~ 125 (328)
.|++|++.+ ..+.+.++|||+||..|+.++. ..||+|++
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 499999998 2333468999999999999884 58999974
No 19
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.05 E-value=1.6e-06 Score=79.19 Aligned_cols=47 Identities=28% Similarity=0.624 Sum_probs=37.4
Q ss_pred CCeeeecccccccccc-c------ccccCCeeecccchhcc---CCCCCCCCcCCcc
Q 020280 83 PEVFDCPICYESLTAP-V------FQCENGHIACSTCCSKI---MNKCPSCCTPIGY 129 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~P-v------~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~~ 129 (328)
.+...|+||++.+..+ + ....|||.||..|+.+| ...||.||.++..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 3457899999987653 1 24689999999999999 4689999998764
No 20
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.05 E-value=1.3e-06 Score=62.59 Aligned_cols=51 Identities=27% Similarity=0.526 Sum_probs=35.8
Q ss_pred eeeeecccCCCCCceEEeecccccccC-CCCCCCccCCC--CCCCcccccchHhhH
Q 020280 141 SVKVTCRNSNYGCKVTMSYGKKHDHEK-ICPHVPCSCPI--PDCNFVGSANHLYKH 193 (328)
Q Consensus 141 ~l~v~C~n~~~GC~~~~~~~~~~~He~-~C~~~~~~Cp~--~gC~~~g~~~~L~~H 193 (328)
...|.|+|. +|...+...++.+|++ .|+++++.|++ .||++.+.+.+|..|
T Consensus 7 ~~~v~C~~~--cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 7 FRPVPCPNG--CCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp TSEEE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCEeeCCCC--CcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 456889874 6778899999999977 89999999998 589999999888877
No 21
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.04 E-value=6.5e-07 Score=67.07 Aligned_cols=57 Identities=26% Similarity=0.427 Sum_probs=40.8
Q ss_pred CCeeeecccccccccccccccCCeeecccchhccC----CCCCCCCcCCcc---ccccccceeee
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKIM----NKCPSCCTPIGY---NRCRAIEKVLE 140 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~----~~CP~Cr~~~~~---~r~~~le~~l~ 140 (328)
++.|.|||+++++.+|| ..++||+|+..++.+|. ..||.++.++.. ..|..|.+.+.
T Consensus 2 P~~f~CpIt~~lM~dPV-i~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~ 65 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPV-ILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIE 65 (73)
T ss_dssp SGGGB-TTTSSB-SSEE-EETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHH
T ss_pred CcccCCcCcCcHhhCce-eCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHH
Confidence 46799999999999999 67899999999999982 569999988764 35555555443
No 22
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.97 E-value=2.8e-06 Score=56.13 Aligned_cols=40 Identities=45% Similarity=1.049 Sum_probs=33.1
Q ss_pred eecccccccccccccccCCeeecccchhcc----CCCCCCCCcC
Q 020280 87 DCPICYESLTAPVFQCENGHIACSTCCSKI----MNKCPSCCTP 126 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~ 126 (328)
.|+||.+.+..++....|||.||..|+.++ ...||.|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 499999999778755559999999999877 3579999875
No 23
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.86 E-value=7.1e-07 Score=84.10 Aligned_cols=83 Identities=23% Similarity=0.295 Sum_probs=58.1
Q ss_pred hhhhccccccccccccCCCCCCcCccccCCCCCCCCceeeeCCCCeeeecccccccccccccccCCeeecccchhcc---
Q 020280 40 EEEETHHQEEDDESVDNGGNGEKADLDLAGPSRNGPFSVTVTDPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI--- 116 (328)
Q Consensus 40 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~--- 116 (328)
+++|+++ .+..+.+.+|.+-.+++.+ ..+++.. -...+.||||+.+|+..+..-.|+|.||..||-+.
T Consensus 7 a~~e~~E-l~l~~~er~p~~~~~d~~E-------i~~~l~~-~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~ 77 (381)
T KOG0311|consen 7 AREEGRE-LELDSKERSPSSYNGDPSE-------IMVDLAM-FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRS 77 (381)
T ss_pred ccchhhh-cchhhhhcChhhhcCCchh-------heecHHH-hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHh
Confidence 3334443 6667777888876666553 2222211 13368999999999998844459999999999886
Q ss_pred -CCCCCCCCcCCcccc
Q 020280 117 -MNKCPSCCTPIGYNR 131 (328)
Q Consensus 117 -~~~CP~Cr~~~~~~r 131 (328)
.+.||.||+.+...|
T Consensus 78 gn~ecptcRk~l~Skr 93 (381)
T KOG0311|consen 78 GNNECPTCRKKLVSKR 93 (381)
T ss_pred cCCCCchHHhhccccc
Confidence 479999999887543
No 24
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.85 E-value=3e-06 Score=77.91 Aligned_cols=110 Identities=21% Similarity=0.470 Sum_probs=71.0
Q ss_pred eeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCcccc---cccc-----------ceeeeeeeeecc
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIGYNR---CRAI-----------EKVLESVKVTCR 147 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~~~r---~~~l-----------e~~l~~l~v~C~ 147 (328)
.+.|-||...++.|+ .++|||.||+-||... .+.||+|+.+....+ +..+ ..+..-|++.|+
T Consensus 25 ~lrC~IC~~~i~ip~-~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~~~ei~es~~~~r~~l~~~L~~~~~ 103 (391)
T COG5432 25 MLRCRICDCRISIPC-ETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSGSREINESHARNRDLLRKVLESLCR 103 (391)
T ss_pred HHHhhhhhheeecce-ecccccchhHHHHHHHhcCCCCCccccccHHhhhcccchhHHHHHHhhhhccHHHHHHHhcccC
Confidence 578999999999999 6899999999999887 478999998864221 1011 112233456663
Q ss_pred cC-----CCCCceEEeecccccc--cC--------CCC----------------CCCccCCCCCCCcccccchHhhHhhh
Q 020280 148 NS-----NYGCKVTMSYGKKHDH--EK--------ICP----------------HVPCSCPIPDCNFVGSANHLYKHFSA 196 (328)
Q Consensus 148 n~-----~~GC~~~~~~~~~~~H--e~--------~C~----------------~~~~~Cp~~gC~~~g~~~~L~~Hl~~ 196 (328)
-. ..-|.|......-.+- ++ +=+ -..+.|| -|....+.+.|..||..
T Consensus 104 ~p~p~~ee~p~~~E~v~~~dS~S~~~~~eD~~~~~sS~~~iAKkt~~D~~KrK~E~l~~CP--~C~~~~P~~~i~~HLD~ 181 (391)
T COG5432 104 LPRPIKEERPCRWETVIAQDSASGDEEWEDDLASNSSPASIAKKTSRDSKKRKREDLVHCP--ACSNLVPHNQINQHLDS 181 (391)
T ss_pred CCCchhhcCCCchhheeccccccccchhhhhhhhccChHHHHhhhhhHHHHhHHHhhhcCc--hhhccCchHHHHHHHHH
Confidence 32 3356664333221100 00 000 2347898 59988999999999975
Q ss_pred h
Q 020280 197 K 197 (328)
Q Consensus 197 ~ 197 (328)
.
T Consensus 182 C 182 (391)
T COG5432 182 C 182 (391)
T ss_pred H
Confidence 3
No 25
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.74 E-value=1.3e-05 Score=57.31 Aligned_cols=43 Identities=28% Similarity=0.538 Sum_probs=35.6
Q ss_pred ccCCCCCCCccCCCCCCCcccccchHhhHhhhhcCCCceeEEe
Q 020280 165 HEKICPHVPCSCPIPDCNFVGSANHLYKHFSAKHKNSALHFLY 207 (328)
Q Consensus 165 He~~C~~~~~~Cp~~gC~~~g~~~~L~~Hl~~~H~~~~~~~~y 207 (328)
|++.|+++++.||+.+|.....+.+|..|+...|+++.+.+.|
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 7888999999999877877799999999999999999999988
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.70 E-value=1.2e-05 Score=79.50 Aligned_cols=44 Identities=36% Similarity=0.840 Sum_probs=37.2
Q ss_pred eeeecccccccccccccccCCeeecccchhcc--------CCCCCCCCcCCcc
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKI--------MNKCPSCCTPIGY 129 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~--------~~~CP~Cr~~~~~ 129 (328)
...||||++...-|+ .+.|||+||..|+-.. ...||.|+..+..
T Consensus 186 ~~~CPICL~~~~~p~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCccc-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 678999999988888 5789999999998764 2689999987764
No 27
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.69 E-value=1.1e-05 Score=73.55 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=38.7
Q ss_pred CCeeeecccccccccccccccCCeeecccchhc-cC----CCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSK-IM----NKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~-~~----~~CP~Cr~~~~ 128 (328)
..++.|+||.+....|. .+.|||+||..|+.. |. ..||.||....
T Consensus 213 ~~d~kC~lC~e~~~~ps-~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPS-CTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCcc-cccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 56889999999999998 678999999999988 62 46999998654
No 28
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.68 E-value=1.1e-05 Score=53.97 Aligned_cols=27 Identities=41% Similarity=1.052 Sum_probs=18.1
Q ss_pred eccccccccc----ccccccCCeeecccchhcc
Q 020280 88 CPICYESLTA----PVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 88 CpiC~~~l~~----Pv~~c~CGH~fC~~C~~~~ 116 (328)
||||++ +.. |+ ...|||+||..|+.++
T Consensus 1 CpIc~e-~~~~~n~P~-~L~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPM-VLPCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EE-E-SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCE-EEeCccHHHHHHHHHH
Confidence 899999 776 88 4679999999999988
No 29
>PHA02926 zinc finger-like protein; Provisional
Probab=97.60 E-value=1.6e-05 Score=71.02 Aligned_cols=46 Identities=30% Similarity=0.623 Sum_probs=35.7
Q ss_pred CCeeeeccccccccc---------ccccccCCeeecccchhccC---------CCCCCCCcCCcc
Q 020280 83 PEVFDCPICYESLTA---------PVFQCENGHIACSTCCSKIM---------NKCPSCCTPIGY 129 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~---------Pv~~c~CGH~fC~~C~~~~~---------~~CP~Cr~~~~~ 129 (328)
..+..|+||++.... ++ .-+|+|.||..|+.+|. ..||.||..+..
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGI-L~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGL-LDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred cCCCCCccCccccccccccccccccc-cCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 345789999997643 23 34799999999999993 239999998764
No 30
>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=97.51 E-value=3.1e-05 Score=49.20 Aligned_cols=35 Identities=49% Similarity=1.070 Sum_probs=29.5
Q ss_pred ecccccccccccccccCCeeecccchhcc----CCCCCCC
Q 020280 88 CPICYESLTAPVFQCENGHIACSTCCSKI----MNKCPSC 123 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~----~~~CP~C 123 (328)
|+||++....++ ...|||.||..|+..| ...||.|
T Consensus 1 C~iC~~~~~~~~-~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPV-VLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcE-EecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789999988777 5789999999999877 2568876
No 31
>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=97.42 E-value=6.5e-05 Score=70.75 Aligned_cols=45 Identities=27% Similarity=0.682 Sum_probs=33.9
Q ss_pred Ceeeeccccc--cccccc--ccccCCeeecccchhcc----CCCCCCCCcCCc
Q 020280 84 EVFDCPICYE--SLTAPV--FQCENGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~--~l~~Pv--~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
+...||+|.. ++.+-+ +.-.|||.||.+|+..+ ...||.|+.++.
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 3468999999 444432 22379999999999985 358999998765
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=4.6e-05 Score=78.57 Aligned_cols=46 Identities=28% Similarity=0.754 Sum_probs=40.2
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc----CCCCCCCCcCCcc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI----MNKCPSCCTPIGY 129 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~~ 129 (328)
...|.||+|..-+++-| ...|||.||..|+.+. ..+||.|..+|+.
T Consensus 641 K~~LkCs~Cn~R~Kd~v-I~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 641 KELLKCSVCNTRWKDAV-ITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred HhceeCCCccCchhhHH-HHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 45789999998888888 5789999999999876 4799999999874
No 33
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=5.5e-05 Score=69.64 Aligned_cols=42 Identities=36% Similarity=0.814 Sum_probs=37.1
Q ss_pred CCeeeecccccccccccccccCCeeecccchhccC---CCCCCCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKIM---NKCPSCCT 125 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~---~~CP~Cr~ 125 (328)
.+.+.|+||++.|..|. .-+|||.||..|+..+. ..||.|+.
T Consensus 11 ~~~~~C~iC~~~~~~p~-~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYFREPV-LLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHhhcCc-cccccchHhHHHHHHhcCCCcCCcccCC
Confidence 46789999999999995 67899999999999874 68999993
No 34
>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=97.08 E-value=0.00033 Score=52.40 Aligned_cols=38 Identities=39% Similarity=0.783 Sum_probs=29.7
Q ss_pred eecccccccccc------------cccccCCeeecccchhcc---CCCCCCCC
Q 020280 87 DCPICYESLTAP------------VFQCENGHIACSTCCSKI---MNKCPSCC 124 (328)
Q Consensus 87 ~CpiC~~~l~~P------------v~~c~CGH~fC~~C~~~~---~~~CP~Cr 124 (328)
.|.||++.|.+| +..-.|||.|...|+.+| ...||.||
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 499999999433 223369999999999998 46899996
No 35
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.69 E-value=0.00043 Score=67.76 Aligned_cols=45 Identities=29% Similarity=0.689 Sum_probs=39.8
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.+.|.|.||...|.+|| .++|||.||..|+.+. ...||.|+.++.
T Consensus 82 ~sef~c~vc~~~l~~pv-~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPV-VTPCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCCc-cccccccccHHHHHHHhccCCCCcccccccc
Confidence 56899999999999999 6799999999998776 368999998875
No 36
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.00076 Score=62.60 Aligned_cols=42 Identities=33% Similarity=0.677 Sum_probs=36.7
Q ss_pred eeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
+.|-||...+..|| .+.|||.||..|..+- ...|++|.+.+.
T Consensus 242 f~c~icr~~f~~pV-vt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYRPV-VTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred ccccccccccccch-hhcCCceeehhhhccccccCCcceecccccc
Confidence 57999999999999 7899999999997765 368999998764
No 37
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.60 E-value=0.00048 Score=60.37 Aligned_cols=42 Identities=33% Similarity=0.697 Sum_probs=35.9
Q ss_pred eeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCC
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
-|.|.||..-+..|| .+.|||.||+.|..+- ...|-+|.+..
T Consensus 196 PF~C~iCKkdy~spv-vt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYESPV-VTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccchh-hhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 478999999999999 6899999999997654 46899998764
No 38
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.57 E-value=0.00064 Score=69.22 Aligned_cols=50 Identities=28% Similarity=0.497 Sum_probs=45.0
Q ss_pred eeeecccCCCCCceEEeecccccccCCCCCCCccCCCCCCCcccccchHhhHhh
Q 020280 142 VKVTCRNSNYGCKVTMSYGKKHDHEKICPHVPCSCPIPDCNFVGSANHLYKHFS 195 (328)
Q Consensus 142 l~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~~~L~~Hl~ 195 (328)
-.+.|+| |.|.++..++..|+..|.|..+.||+.+|+....+.++..|+.
T Consensus 406 ~~V~C~N----C~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~ 455 (567)
T PLN03086 406 DTVECRN----CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVH 455 (567)
T ss_pred CeEECCC----CCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCcc
Confidence 4678998 9999999999999999999999999777888888888888863
No 39
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.46 E-value=0.00089 Score=47.65 Aligned_cols=32 Identities=22% Similarity=0.388 Sum_probs=24.3
Q ss_pred eeeecccccccccccccccCCeeecccchhcc
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~ 116 (328)
.+.|||.+.+|.+||....|||+|.+..+..+
T Consensus 11 ~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~ 42 (57)
T PF11789_consen 11 SLKCPITLQPFEDPVKSKKCGHTFEKEAILQY 42 (57)
T ss_dssp -SB-TTTSSB-SSEEEESSS--EEEHHHHHHH
T ss_pred ccCCCCcCChhhCCcCcCCCCCeecHHHHHHH
Confidence 57999999999999965679999999998877
No 40
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=96.35 E-value=0.0023 Score=54.42 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=24.9
Q ss_pred CCccCCCCCCCcccccchHhhHhhhhcCC
Q 020280 172 VPCSCPIPDCNFVGSANHLYKHFSAKHKN 200 (328)
Q Consensus 172 ~~~~Cp~~gC~~~g~~~~L~~Hl~~~H~~ 200 (328)
.+-.|+..+|.|.|.+.+|..|.+.+|+.
T Consensus 106 K~RsC~~e~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 106 KKRSCSQESCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred CCccCcccccccccCHHHHHHHHHhhCCC
Confidence 34567777999999999999999999985
No 41
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.35 E-value=0.0014 Score=66.71 Aligned_cols=52 Identities=21% Similarity=0.476 Sum_probs=24.7
Q ss_pred CceEEeecccccccCCCCCCCccCCCCCCCcccccchHhhHhhhhcCCCceeEEec
Q 020280 153 CKVTMSYGKKHDHEKICPHVPCSCPIPDCNFVGSANHLYKHFSAKHKNSALHFLYN 208 (328)
Q Consensus 153 C~~~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~~~L~~Hl~~~H~~~~~~~~y~ 208 (328)
|...+...+++.|...| +.++.|| |+....+.+|..|+...|+.+...|.|+
T Consensus 459 Cgk~f~~s~LekH~~~~-Hkpv~Cp---Cg~~~~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 459 CGQAFQQGEMEKHMKVF-HEPLQCP---CGVVLEKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred CCCccchHHHHHHHHhc-CCCccCC---CCCCcchhHHHhhhhccCCCCceeCCCC
Confidence 43333344444444444 3445554 4444445555555555555555555544
No 42
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.14 E-value=0.0023 Score=43.74 Aligned_cols=40 Identities=38% Similarity=0.994 Sum_probs=20.6
Q ss_pred eccccccccc---ccccccCCeeecccchhcc----CCCCCCCCcCC
Q 020280 88 CPICYESLTA---PVFQCENGHIACSTCCSKI----MNKCPSCCTPI 127 (328)
Q Consensus 88 CpiC~~~l~~---Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~ 127 (328)
||+|.+.+.. -++-|+||..+|..|+.++ ...||.||+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7888887732 3456999999999998877 36899999875
No 43
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0033 Score=57.86 Aligned_cols=45 Identities=31% Similarity=0.648 Sum_probs=37.0
Q ss_pred CeeeecccccccccccccccCCeeecccchhcc-----CCCCCCCCcCCc
Q 020280 84 EVFDCPICYESLTAPVFQCENGHIACSTCCSKI-----MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-----~~~CP~Cr~~~~ 128 (328)
+.-.||+|.+.-..|...-+|||++|-.|+.+. ...||.|..+..
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 356899999999999844459999999999875 258999987653
No 44
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.06 E-value=0.0023 Score=49.02 Aligned_cols=41 Identities=27% Similarity=0.496 Sum_probs=31.0
Q ss_pred eccccccccc-ccccccCCeeecccchhcc------CCCCCCCCcCCc
Q 020280 88 CPICYESLTA-PVFQCENGHIACSTCCSKI------MNKCPSCCTPIG 128 (328)
Q Consensus 88 CpiC~~~l~~-Pv~~c~CGH~fC~~C~~~~------~~~CP~Cr~~~~ 128 (328)
||.|..+-.+ |+....|+|.|-..||.+| +..||.||+++.
T Consensus 35 Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 35 CPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 5555555433 5545689999999999998 268999998764
No 45
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.87 E-value=0.0026 Score=59.13 Aligned_cols=40 Identities=33% Similarity=0.752 Sum_probs=34.6
Q ss_pred eeecccccccccccccccCCeeecccchhcc----CCCCCCCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI----MNKCPSCCT 125 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~ 125 (328)
|.||.|..++++|+.+-.|||.||..|+... ...||.|..
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 8999999999999944359999999999975 378999965
No 46
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.79 E-value=0.0017 Score=61.17 Aligned_cols=46 Identities=26% Similarity=0.483 Sum_probs=39.5
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.....|.+|..+|.++-....|-|.||++||.+. .+.||.|...+.
T Consensus 13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 4467899999999999866789999999999876 589999987764
No 47
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.68 E-value=0.0053 Score=55.72 Aligned_cols=44 Identities=25% Similarity=0.625 Sum_probs=35.5
Q ss_pred eeeecccccc-cccccccccCCeeecccchhccCC-CCCCCCcCCc
Q 020280 85 VFDCPICYES-LTAPVFQCENGHIACSTCCSKIMN-KCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~-l~~Pv~~c~CGH~fC~~C~~~~~~-~CP~Cr~~~~ 128 (328)
-..|..|+.- -..|.|.+.|+|+||..|.....+ .||.|++++.
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 3578888773 356778899999999999887755 9999999854
No 48
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.53 E-value=0.0056 Score=57.13 Aligned_cols=43 Identities=30% Similarity=0.575 Sum_probs=35.6
Q ss_pred eeecccccccc--cccccccCCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT--APVFQCENGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~--~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
.+|.||++-+. +-+...+|.|.|=..|+.+| ..+||+|+.++.
T Consensus 324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred ceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 68999999764 33446789999999999999 479999998764
No 49
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.35 E-value=0.0046 Score=58.43 Aligned_cols=47 Identities=32% Similarity=0.858 Sum_probs=37.6
Q ss_pred CCCCeeeecccccccc---cccccccCCeeecccchhcc----CCCCCCCCcCCc
Q 020280 81 TDPEVFDCPICYESLT---APVFQCENGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 81 ~d~~~l~CpiC~~~l~---~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
+|.+++ ||+|.+++. .-.|-|+||-.+|..|+..+ ...||.||..+.
T Consensus 11 edeed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 11 EDEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred cccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 355566 999999875 24567999999999999877 479999997653
No 50
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.17 E-value=0.0056 Score=45.39 Aligned_cols=45 Identities=31% Similarity=0.759 Sum_probs=20.8
Q ss_pred eeeecccccccc----cccccc---cCCeeecccchhcc--------------CCCCCCCCcCCcc
Q 020280 85 VFDCPICYESLT----APVFQC---ENGHIACSTCCSKI--------------MNKCPSCCTPIGY 129 (328)
Q Consensus 85 ~l~CpiC~~~l~----~Pv~~c---~CGH~fC~~C~~~~--------------~~~CP~Cr~~~~~ 129 (328)
.+.|+||+..+. .|...| .|+..|=..|+.+| ...||.|+.++..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 468999999754 366677 49999999999998 1369999887653
No 51
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.89 E-value=0.0076 Score=60.07 Aligned_cols=47 Identities=17% Similarity=0.508 Sum_probs=40.4
Q ss_pred CCCCeeeecccccccccccccccCCeeecccchhcc--------CCCCCCCCcCCc
Q 020280 81 TDPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI--------MNKCPSCCTPIG 128 (328)
Q Consensus 81 ~d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~--------~~~CP~Cr~~~~ 128 (328)
.+.....|.+|.++..+++ ...|.|.||+-|+... ...||+|...+.
T Consensus 532 enk~~~~C~lc~d~aed~i-~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYI-ESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred cccCceeecccCChhhhhH-hhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 3466789999999999999 7899999999999665 358999988765
No 52
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=94.83 E-value=0.014 Score=48.23 Aligned_cols=52 Identities=27% Similarity=0.645 Sum_probs=40.1
Q ss_pred eeeeCCCCeeeecccccccccccccc---cCCeeecccchhcc------CCCCCCCCcCCcc
Q 020280 77 SVTVTDPEVFDCPICYESLTAPVFQC---ENGHIACSTCCSKI------MNKCPSCCTPIGY 129 (328)
Q Consensus 77 ~~~~~d~~~l~CpiC~~~l~~Pv~~c---~CGH~fC~~C~~~~------~~~CP~Cr~~~~~ 129 (328)
+++++ +..++|.||.+...+..|-- .||-..|..|...+ -+.||+|+..+..
T Consensus 73 nvF~d-~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 73 NVFLD-PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eeecC-CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 44454 48999999999887665432 39999999997765 3799999988764
No 53
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.46 E-value=0.011 Score=60.71 Aligned_cols=42 Identities=33% Similarity=0.652 Sum_probs=35.7
Q ss_pred eeeeccccccccc-----ccccccCCeeecccchhcc---CCCCCCCCcCC
Q 020280 85 VFDCPICYESLTA-----PVFQCENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 85 ~l~CpiC~~~l~~-----Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
...|+||.+.+.. |- .-+|||+|+..|+.+| ...||.||..+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~-rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPK-RLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred CCeeeeechhhccccccccc-eeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 5689999999887 44 4689999999999999 57999999843
No 54
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.21 E-value=0.02 Score=53.52 Aligned_cols=42 Identities=31% Similarity=0.625 Sum_probs=36.1
Q ss_pred eeecccccccccccccccCCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-+|+||+.-..-|+ .-.|+|.||.-|++.. ...|++||.++.
T Consensus 8 ~eC~IC~nt~n~Pv-~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 8 KECLICYNTGNCPV-NLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred CcceeeeccCCcCc-cccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 47999999888887 6789999999999876 256999999975
No 55
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.90 E-value=0.017 Score=60.12 Aligned_cols=45 Identities=22% Similarity=0.507 Sum_probs=35.7
Q ss_pred Ceeeecccccccccccccc--cCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 84 EVFDCPICYESLTAPVFQC--ENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c--~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
..-.||+|..-+.+-.... .|+|.||..|+..| ...||+|+..|.
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 3457999998877654333 59999999999999 378999998875
No 56
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.68 E-value=0.071 Score=48.58 Aligned_cols=45 Identities=24% Similarity=0.597 Sum_probs=37.9
Q ss_pred Ceeeecccccccccccccc----cCCeeecccchhccC---CCCCCCCcCCcc
Q 020280 84 EVFDCPICYESLTAPVFQC----ENGHIACSTCCSKIM---NKCPSCCTPIGY 129 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c----~CGH~fC~~C~~~~~---~~CP~Cr~~~~~ 129 (328)
..|.||+|.+.|.+.+ .| +|||+||..|.+++. ..||+|..++..
T Consensus 220 ~ryiCpvtrd~LtNt~-~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTT-PCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred cceecccchhhhcCcc-ceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence 4689999999999865 44 699999999999983 579999888753
No 57
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.53 E-value=0.059 Score=51.89 Aligned_cols=43 Identities=23% Similarity=0.403 Sum_probs=35.0
Q ss_pred eeeccccccccc--ccccccCCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTA--PVFQCENGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~--Pv~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
..|.||++-+.. -+..-+|.|.|=..|+..| ...||+|+..+.
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 489999998863 4445689999999999999 245999998754
No 58
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.36 E-value=0.031 Score=59.32 Aligned_cols=44 Identities=30% Similarity=0.635 Sum_probs=36.4
Q ss_pred eeeecccccccc-----ccccccc-CCeeecccchhcc-----CCCCCCCCcCCc
Q 020280 85 VFDCPICYESLT-----APVFQCE-NGHIACSTCCSKI-----MNKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~-----~~~CP~Cr~~~~ 128 (328)
.-+|+||+.++. -|-..|. |.|-|-.+|+.+| ...||.||..++
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 357999999986 3655676 9999999999999 378999997764
No 59
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=92.35 E-value=0.067 Score=51.43 Aligned_cols=46 Identities=24% Similarity=0.507 Sum_probs=35.9
Q ss_pred CCeeeecccccc-ccccc-----------ccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYES-LTAPV-----------FQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~-l~~Pv-----------~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.++-.|.||++- +.+|- ..-+|||++=-.|+..| +..||.||.++.
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 345679999996 44441 13589999999999999 589999999953
No 60
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.15 E-value=0.021 Score=39.82 Aligned_cols=42 Identities=36% Similarity=0.863 Sum_probs=32.6
Q ss_pred eeecccccccccccccccCCee-ecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHI-ACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~-fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-+|.||.+-..+-|+ =.|||. .|..|-.++ ...||.||.++.
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 479999997766663 369996 899996654 468999998864
No 61
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.15 E-value=0.051 Score=52.02 Aligned_cols=43 Identities=33% Similarity=0.720 Sum_probs=36.9
Q ss_pred eeeecccccccccccccccCCee-ecccchhcc---CCCCCCCCcCCc
Q 020280 85 VFDCPICYESLTAPVFQCENGHI-ACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~-fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
--+|-||+.-.++-+ .-+|-|. .|+.|.+.+ .++||.||+++.
T Consensus 290 gkeCVIClse~rdt~-vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 290 GKECVICLSESRDTV-VLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCeeEEEecCCcceE-EecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 458999999988877 5799997 999998887 478999999875
No 62
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=91.99 E-value=0.13 Score=36.10 Aligned_cols=42 Identities=31% Similarity=0.574 Sum_probs=31.7
Q ss_pred eeecccccccccccccccCCeeecccchhccC-CCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKIM-NKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~-~~CP~Cr~~~~ 128 (328)
..|-.|...-...+ .-+|||++|..|+.-.. +-||.|..++.
T Consensus 8 ~~~~~~~~~~~~~~-~~pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 8 QPCVFCGFVGTKGT-VLPCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred eeEEEccccccccc-cccccceeeccccChhhccCCCCCCCccc
Confidence 45666777655555 46899999999987653 68999998875
No 63
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=91.83 E-value=0.044 Score=53.08 Aligned_cols=41 Identities=32% Similarity=0.637 Sum_probs=33.7
Q ss_pred eecccccccccccccccCCeeecccchhccC-----CCCCCCCcCCc
Q 020280 87 DCPICYESLTAPVFQCENGHIACSTCCSKIM-----NKCPSCCTPIG 128 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~-----~~CP~Cr~~~~ 128 (328)
.|.||-+-=++ |..-+|||+.|..|+..|+ ..||.||..+.
T Consensus 371 LCKICaendKd-vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 371 LCKICAENDKD-VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHhhccCCC-cccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 59999997665 4345799999999999993 68999998765
No 64
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.27 E-value=0.051 Score=50.64 Aligned_cols=41 Identities=37% Similarity=0.834 Sum_probs=34.6
Q ss_pred eeeecccccccccccccccCCee-ecccchhccCCCCCCCCcCC
Q 020280 85 VFDCPICYESLTAPVFQCENGHI-ACSTCCSKIMNKCPSCCTPI 127 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~-fC~~C~~~~~~~CP~Cr~~~ 127 (328)
...|.||++...+-+| -+|||. -|..|-.++ +.||+||+.+
T Consensus 300 ~~LC~ICmDaP~DCvf-LeCGHmVtCt~CGkrm-~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVF-LECGHMVTCTKCGKRM-NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEE-eecCcEEeehhhcccc-ccCchHHHHH
Confidence 4679999999888875 689995 799999888 5999999864
No 65
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.27 E-value=0.09 Score=50.74 Aligned_cols=48 Identities=27% Similarity=0.650 Sum_probs=37.8
Q ss_pred CCCeeeeccccccccccc-----cc--ccCCeeecccchhccC----------CCCCCCCcCCcc
Q 020280 82 DPEVFDCPICYESLTAPV-----FQ--CENGHIACSTCCSKIM----------NKCPSCCTPIGY 129 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv-----~~--c~CGH~fC~~C~~~~~----------~~CP~Cr~~~~~ 129 (328)
......|.||++....+. +. -.|-|.||..|+.+|. +.||.||.....
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 345678999999887665 32 2599999999999993 689999987653
No 66
>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=90.41 E-value=0.18 Score=34.96 Aligned_cols=37 Identities=24% Similarity=0.673 Sum_probs=20.5
Q ss_pred ecccccccccc--------ccccc-CCeeecccchhcc---CCCCCCCC
Q 020280 88 CPICYESLTAP--------VFQCE-NGHIACSTCCSKI---MNKCPSCC 124 (328)
Q Consensus 88 CpiC~~~l~~P--------v~~c~-CGH~fC~~C~~~~---~~~CP~Cr 124 (328)
|--|...|..+ +|+|+ |++.||..|=.=+ ...||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 56677777653 57887 9999999993322 37899884
No 67
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.34 E-value=0.084 Score=50.42 Aligned_cols=49 Identities=31% Similarity=0.640 Sum_probs=38.4
Q ss_pred eeeCCCCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCC
Q 020280 78 VTVTDPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 78 ~~~~d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
..+.|.++-.||||+---...|| .+|+|.-|+.||.+. .+.|-.|+..+
T Consensus 415 ~~lp~sEd~lCpICyA~pi~Avf-~PC~H~SC~~CI~qHlmN~k~CFfCktTv 466 (489)
T KOG4692|consen 415 KDLPDSEDNLCPICYAGPINAVF-APCSHRSCYGCITQHLMNCKRCFFCKTTV 466 (489)
T ss_pred CCCCCcccccCcceecccchhhc-cCCCCchHHHHHHHHHhcCCeeeEeccee
Confidence 34556677789999987777785 699999999999987 36777787654
No 68
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.28 E-value=0.055 Score=51.53 Aligned_cols=112 Identities=23% Similarity=0.444 Sum_probs=62.5
Q ss_pred CCCeeeecccccccccccccccCCeeecccchhcc-----CCCCCCCCcCCcccc-ccccceeeeeeeeec-ccCCCCCc
Q 020280 82 DPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI-----MNKCPSCCTPIGYNR-CRAIEKVLESVKVTC-RNSNYGCK 154 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-----~~~CP~Cr~~~~~~r-~~~le~~l~~l~v~C-~n~~~GC~ 154 (328)
|.+...|.||-.-+.--- ..+|+|..|..|.-++ .+.||.|+....... -...+.-|......| .+.++|
T Consensus 58 DEen~~C~ICA~~~TYs~-~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~~~~~DI~D~~~~k~~~EK~G-- 134 (493)
T COG5236 58 DEENMNCQICAGSTTYSA-RYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDRRQWKGREEKVG-- 134 (493)
T ss_pred ccccceeEEecCCceEEE-eccCCchHHHHHHHHHHHHHhccCCCccccccceEEEecCCCCcchhHhhhccccccee--
Confidence 466778999999766432 3589999999998776 478999998743210 000011111111111 222222
Q ss_pred eEEeecccccccCCCCCCCccCCCCC----CCcccccchHhhHhhhhcCCC
Q 020280 155 VTMSYGKKHDHEKICPHVPCSCPIPD----CNFVGSANHLYKHFSAKHKNS 201 (328)
Q Consensus 155 ~~~~~~~~~~He~~C~~~~~~Cp~~g----C~~~g~~~~L~~Hl~~~H~~~ 201 (328)
+.|..-..-+++=..-...||... |++ .++|..|++..|..-
T Consensus 135 --I~y~~E~v~~E~~~LL~F~CP~skc~~~C~~---~k~lk~H~K~~H~~~ 180 (493)
T COG5236 135 --IFYEGEDVRDEMEDLLSFKCPKSKCHRRCGS---LKELKKHYKAQHGFV 180 (493)
T ss_pred --eeecchHHHHHHHHHHHhcCCchhhhhhhhh---HHHHHHHHHhhcCcE
Confidence 333332222222223335666543 543 579999999998753
No 69
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.52 E-value=0.077 Score=48.95 Aligned_cols=46 Identities=15% Similarity=0.439 Sum_probs=36.1
Q ss_pred Ceeeeccccccccc---------ccccccCCeeecccchhcc-----CCCCCCCCcCCcc
Q 020280 84 EVFDCPICYESLTA---------PVFQCENGHIACSTCCSKI-----MNKCPSCCTPIGY 129 (328)
Q Consensus 84 ~~l~CpiC~~~l~~---------Pv~~c~CGH~fC~~C~~~~-----~~~CP~Cr~~~~~ 129 (328)
++-.|.+|..-+.. ..++-+|+|+|=..||.-| .+.||.|++.+..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence 34569999986643 3467789999999999988 4789999987653
No 70
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=89.48 E-value=0.15 Score=50.22 Aligned_cols=43 Identities=26% Similarity=0.576 Sum_probs=35.3
Q ss_pred Ceeeeccccccccccc---ccccCCeeecccchhccC-CCCCCCCcC
Q 020280 84 EVFDCPICYESLTAPV---FQCENGHIACSTCCSKIM-NKCPSCCTP 126 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv---~~c~CGH~fC~~C~~~~~-~~CP~Cr~~ 126 (328)
+.-.||+|++-+-+-+ ....|.|.|=..|+.+|. ..||+||--
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~ 220 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYC 220 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhh
Confidence 3558999999887654 566799999999999994 689999754
No 71
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.35 E-value=0.35 Score=44.97 Aligned_cols=46 Identities=22% Similarity=0.494 Sum_probs=37.7
Q ss_pred CCeeeeccccccccc---ccccccCCeeecccchhccC--CCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTA---PVFQCENGHIACSTCCSKIM--NKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~---Pv~~c~CGH~fC~~C~~~~~--~~CP~Cr~~~~ 128 (328)
...|.|||....|.. =|+.-+|||+|+..++..+. ..||.|..++.
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 567999999999853 23445799999999999984 47999999886
No 72
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=87.83 E-value=0.14 Score=50.30 Aligned_cols=32 Identities=28% Similarity=0.702 Sum_probs=28.4
Q ss_pred CeeeecccccccccccccccCCeeecccchhcc
Q 020280 84 EVFDCPICYESLTAPVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~ 116 (328)
+.|.||||...+++|| .-+|+|..|..|...+
T Consensus 3 eelkc~vc~~f~~epi-il~c~h~lc~~ca~~~ 34 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPI-ILPCSHNLCQACARNI 34 (699)
T ss_pred ccccCceehhhccCce-EeecccHHHHHHHHhh
Confidence 5789999999999999 5799999999997654
No 73
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=86.59 E-value=0.12 Score=48.48 Aligned_cols=78 Identities=22% Similarity=0.373 Sum_probs=48.9
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc-CCCCCCCCcCCccccccccceeeeeeeeecccCCCCCce-EEeec
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI-MNKCPSCCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKV-TMSYG 160 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-~~~CP~Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~-~~~~~ 160 (328)
+..-.|--|..++..==..-+|.|+||..|...- .+.||.|..++. .+|.....-.+-|. ...||.- .+.-.
T Consensus 88 p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vq-----rIeq~~~g~iFmC~-~~~GC~RTyLsqr 161 (389)
T KOG2932|consen 88 PRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQ-----RIEQIMMGGIFMCA-APHGCLRTYLSQR 161 (389)
T ss_pred cceEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHH-----HHHHhcccceEEee-cchhHHHHHhhHH
Confidence 3355688898876643224589999999996543 368999977653 23444444456676 3467754 33444
Q ss_pred cccccc
Q 020280 161 KKHDHE 166 (328)
Q Consensus 161 ~~~~He 166 (328)
+++.|.
T Consensus 162 DlqAHI 167 (389)
T KOG2932|consen 162 DLQAHI 167 (389)
T ss_pred HHHHHh
Confidence 555554
No 74
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.32 E-value=0.39 Score=46.73 Aligned_cols=43 Identities=28% Similarity=0.583 Sum_probs=34.0
Q ss_pred CCeeeecccccccc---cccccccCCeeecccchhccC------CCCCCCCcC
Q 020280 83 PEVFDCPICYESLT---APVFQCENGHIACSTCCSKIM------NKCPSCCTP 126 (328)
Q Consensus 83 ~~~l~CpiC~~~l~---~Pv~~c~CGH~fC~~C~~~~~------~~CP~Cr~~ 126 (328)
...|.|||=.+--. ||+ +-.|||++|+.=+.++. .+||+|-..
T Consensus 332 HSvF~CPVlKeqtsdeNPPm-~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPM-MLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred cceeecccchhhccCCCCCe-eeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 55799999777543 566 78999999999999882 579999654
No 75
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.13 E-value=0.32 Score=47.48 Aligned_cols=41 Identities=34% Similarity=0.683 Sum_probs=33.2
Q ss_pred eeeccccccccccccc----ccCCeeecccchhcc-----CCCCCCCCcC
Q 020280 86 FDCPICYESLTAPVFQ----CENGHIACSTCCSKI-----MNKCPSCCTP 126 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~----c~CGH~fC~~C~~~~-----~~~CP~Cr~~ 126 (328)
-.||||++-+.-|.-. -.|||.|-+.|+++| ...||.|...
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 4799999988766522 369999999999999 3689999865
No 76
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=85.12 E-value=0.36 Score=35.68 Aligned_cols=38 Identities=32% Similarity=0.792 Sum_probs=23.2
Q ss_pred eeecccccccccccccccCCeeecccchhcc--CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI--MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~--~~~CP~Cr~~~~ 128 (328)
+.||.|...|.. . -|+..|..|.... ...||.|..++.
T Consensus 2 ~~CP~C~~~L~~-~----~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEW-Q----GGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEE-E----TTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEE-e----CCEEECccccccceecccCCCcccHHH
Confidence 579999998553 2 3899999998876 368999988764
No 77
>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=83.75 E-value=0.49 Score=28.07 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=12.8
Q ss_pred eeccccccccccccccc-CCeee
Q 020280 87 DCPICYESLTAPVFQCE-NGHIA 108 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~-CGH~f 108 (328)
.||.|...+..-...|+ |||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 47777776544333565 66655
No 78
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=83.42 E-value=0.41 Score=36.17 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=32.4
Q ss_pred eeecccccccccccccc---------------cCCeeecccchhcc---CCCCCCCCcCCcc
Q 020280 86 FDCPICYESLTAPVFQC---------------ENGHIACSTCCSKI---MNKCPSCCTPIGY 129 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c---------------~CGH~fC~~C~~~~---~~~CP~Cr~~~~~ 129 (328)
-.|.||+..+..+-.+| .|.|.|=..||.+| .+.||.+++.+..
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 35777777666543333 37789999999999 4789999987654
No 79
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=82.78 E-value=1 Score=47.86 Aligned_cols=43 Identities=33% Similarity=0.782 Sum_probs=36.7
Q ss_pred CCeeeecccccccc--ccccccc-CCeeecccchhcc----------CCCCCCCCc
Q 020280 83 PEVFDCPICYESLT--APVFQCE-NGHIACSTCCSKI----------MNKCPSCCT 125 (328)
Q Consensus 83 ~~~l~CpiC~~~l~--~Pv~~c~-CGH~fC~~C~~~~----------~~~CP~Cr~ 125 (328)
.+.+.|-||.+-+. .||+.|. |-|+|=..||.+| ...||.|+.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 56799999999875 6888886 9999999999999 258999984
No 80
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.02 E-value=0.3 Score=50.17 Aligned_cols=37 Identities=30% Similarity=0.771 Sum_probs=29.7
Q ss_pred Ceeeecccccccc----cccccccCCeeecccchhcc-CCCCC
Q 020280 84 EVFDCPICYESLT----APVFQCENGHIACSTCCSKI-MNKCP 121 (328)
Q Consensus 84 ~~l~CpiC~~~l~----~Pv~~c~CGH~fC~~C~~~~-~~~CP 121 (328)
+.|.|+||+..|. .|| .-.|||+.|+.|.+++ ...||
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pv-sl~cghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPV-SLQCGHTICGHCVQLLYNASCP 51 (861)
T ss_pred HHhhchHHHHHHHHHhcCcc-cccccchHHHHHHHhHhhccCC
Confidence 4678999977653 577 4579999999999988 56788
No 81
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=79.92 E-value=0.54 Score=49.51 Aligned_cols=41 Identities=29% Similarity=0.589 Sum_probs=33.8
Q ss_pred eeecccccccccccccccCCeeecccchhcc-----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI-----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-----~~~CP~Cr~~~~ 128 (328)
+.|++|.+ ...++ .+.|||.||..|+.+. ...||.|+..+.
T Consensus 455 ~~c~ic~~-~~~~~-it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-LDSFF-ITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-cccce-eecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 89999999 66666 6899999999999886 247999987543
No 82
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=79.34 E-value=0.48 Score=45.52 Aligned_cols=113 Identities=19% Similarity=0.462 Sum_probs=74.5
Q ss_pred CCeeeeccccccccccc-------ccc--cCCeeecccchhcc---------------CCCCCCCCcCCccc---ccccc
Q 020280 83 PEVFDCPICYESLTAPV-------FQC--ENGHIACSTCCSKI---------------MNKCPSCCTPIGYN---RCRAI 135 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv-------~~c--~CGH~fC~~C~~~~---------------~~~CP~Cr~~~~~~---r~~~l 135 (328)
...+-||.|.++|..-- -|+ .-.+..|+.|..+. ..+||.|....+.. ++...
T Consensus 205 eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r 284 (467)
T KOG3608|consen 205 EKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIR 284 (467)
T ss_pred CeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHH
Confidence 45688999999986421 122 23478899998775 25899998765431 22222
Q ss_pred ceeeeeeeeecccCCCCCce-EEeecccccccCCCCCCCccCCCCCCCccc-ccchHhhHhhhhcC
Q 020280 136 EKVLESVKVTCRNSNYGCKV-TMSYGKKHDHEKICPHVPCSCPIPDCNFVG-SANHLYKHFSAKHK 199 (328)
Q Consensus 136 e~~l~~l~v~C~n~~~GC~~-~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g-~~~~L~~Hl~~~H~ 199 (328)
-+-..+-.+.|. -|.. -++..+|..|...=.-..+.|..+.|.+.. .+.+|..|+...|.
T Consensus 285 ~rHs~dkpfKCd----~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 285 YRHSKDKPFKCD----ECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred hhhccCCCcccc----chhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 233345566665 4554 356678888876444555788888898776 57889999998884
No 83
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.62 E-value=0.57 Score=46.78 Aligned_cols=44 Identities=27% Similarity=0.540 Sum_probs=32.3
Q ss_pred eeeeccccccccc-----c-----------cccccCCeeecccchhccC----CCCCCCCcCCc
Q 020280 85 VFDCPICYESLTA-----P-----------VFQCENGHIACSTCCSKIM----NKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~-----P-----------v~~c~CGH~fC~~C~~~~~----~~CP~Cr~~~~ 128 (328)
.-.|+||.....- | ...++|.|+|=..|+.+|. -.||+||.++.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 3469999875421 1 1125899999999999993 37999998864
No 84
>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=78.12 E-value=0.83 Score=42.74 Aligned_cols=41 Identities=32% Similarity=0.838 Sum_probs=30.4
Q ss_pred eeccccc-ccccc-c--ccccCCeeecccchhcc----CCCCCCCCcCC
Q 020280 87 DCPICYE-SLTAP-V--FQCENGHIACSTCCSKI----MNKCPSCCTPI 127 (328)
Q Consensus 87 ~CpiC~~-~l~~P-v--~~c~CGH~fC~~C~~~~----~~~CP~Cr~~~ 127 (328)
.||+|.. .+..| + +.-+|||..|.+|...+ ...||.|...+
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 4888876 33444 3 12369999999999988 47899998765
No 85
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.94 E-value=0.9 Score=43.72 Aligned_cols=44 Identities=30% Similarity=0.797 Sum_probs=32.8
Q ss_pred CCeeeecccccccccccccccCCeeecc-cchhccCCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACS-TCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~-~C~~~~~~~CP~Cr~~~~ 128 (328)
+....|-||.+-.++.+| -+|||+-|. .|...+ .+||+||+.+.
T Consensus 303 ~~p~lcVVcl~e~~~~~f-vpcGh~ccct~cs~~l-~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPKSAVF-VPCGHVCCCTLCSKHL-PQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCccceee-ecCCcEEEchHHHhhC-CCCchhHHHHH
Confidence 445679999999888885 699998762 244444 67999998764
No 86
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.56 E-value=1.4 Score=30.82 Aligned_cols=42 Identities=24% Similarity=0.566 Sum_probs=31.9
Q ss_pred eeeeccccccc--cccccccc-CCeeecccchhccCCCCCC--CCcCC
Q 020280 85 VFDCPICYESL--TAPVFQCE-NGHIACSTCCSKIMNKCPS--CCTPI 127 (328)
Q Consensus 85 ~l~CpiC~~~l--~~Pv~~c~-CGH~fC~~C~~~~~~~CP~--Cr~~~ 127 (328)
.-.|++|.+.| .+.+.+|+ ||-.+=+.|+.+. ..|-. |..++
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~-g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA-GGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC-CceEeccCCCCc
Confidence 35799999999 56777887 9988888998876 46655 55443
No 87
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=76.88 E-value=1 Score=30.99 Aligned_cols=42 Identities=29% Similarity=0.639 Sum_probs=21.9
Q ss_pred eeeecccccccccccccccCCeeecccchhcc-------CCCCCCCCcC
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKI-------MNKCPSCCTP 126 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~-------~~~CP~Cr~~ 126 (328)
.|.||+-...+..|+.--.|.|.-|-+=..-+ ...||.|.++
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 36899999999999966679999875521111 2479999764
No 88
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.80 E-value=0.72 Score=45.14 Aligned_cols=88 Identities=23% Similarity=0.396 Sum_probs=52.6
Q ss_pred CCeeeeccccccccc--ccccccCCeeecccchhcc-----------CCCCCCCCcC--Ccc------------cc--cc
Q 020280 83 PEVFDCPICYESLTA--PVFQCENGHIACSTCCSKI-----------MNKCPSCCTP--IGY------------NR--CR 133 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~--Pv~~c~CGH~fC~~C~~~~-----------~~~CP~Cr~~--~~~------------~r--~~ 133 (328)
...+.|.||++-..- -++..+|+|+||..|.... .-+||.++-. ... .| ..
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 347899999998764 3344689999999998765 1478865433 111 01 12
Q ss_pred ccceeeeeee--eecccCCCCCceEEeecccccccC---CCCCCC
Q 020280 134 AIEKVLESVK--VTCRNSNYGCKVTMSYGKKHDHEK---ICPHVP 173 (328)
Q Consensus 134 ~le~~l~~l~--v~C~n~~~GC~~~~~~~~~~~He~---~C~~~~ 173 (328)
.+++.+..+. ++||++ -|.... ..+...-.. .|.|+.
T Consensus 262 ~lqk~l~~msdv~yCPr~--~Cq~p~-~~d~~~~l~~CskCnFaF 303 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRA--CCQLPV-KQDPGRALAICSKCNFAF 303 (445)
T ss_pred HHHHHHHhhcccccCChh--hccCcc-ccCchhhhhhhccCccHH
Confidence 3344444444 899986 566554 444444433 455543
No 89
>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=76.41 E-value=0.77 Score=31.91 Aligned_cols=24 Identities=29% Similarity=0.773 Sum_probs=16.2
Q ss_pred CccCCCCCCCcccccchHhhHhhhhcC
Q 020280 173 PCSCPIPDCNFVGSANHLYKHFSAKHK 199 (328)
Q Consensus 173 ~~~Cp~~gC~~~g~~~~L~~Hl~~~H~ 199 (328)
.+.||. |.... ..+|..|+...|.
T Consensus 31 ~v~CPi--C~~~~-~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPI--CSSRV-TDNLIRHLNSQHR 54 (54)
T ss_pred CccCCC--chhhh-hhHHHHHHHHhcC
Confidence 477874 76543 3588888887763
No 90
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.02 E-value=1.2 Score=40.73 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=26.7
Q ss_pred eeecccccccccccccccCCeeecccchhcc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~ 116 (328)
-.|+.|+.++.+|| .|.-||+||..||.+.
T Consensus 44 dcCsLtLqPc~dPv-it~~GylfdrEaILe~ 73 (303)
T KOG3039|consen 44 DCCSLTLQPCRDPV-ITPDGYLFDREAILEY 73 (303)
T ss_pred ceeeeecccccCCc-cCCCCeeeeHHHHHHH
Confidence 36889999999999 6899999999998764
No 91
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=75.98 E-value=1.8 Score=41.25 Aligned_cols=46 Identities=24% Similarity=0.570 Sum_probs=35.1
Q ss_pred CCCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCC
Q 020280 82 DPEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
.++.-.||+|..--.+|-....-|-+||..|+.+. -+.||+=..+.
T Consensus 297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred CCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 35566899999988888633347999999999876 37899855543
No 92
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.47 E-value=1.6 Score=41.13 Aligned_cols=42 Identities=33% Similarity=0.788 Sum_probs=32.7
Q ss_pred eeeeccccccccc------ccccccCCeeecccchhccC----CCCCCCCcCC
Q 020280 85 VFDCPICYESLTA------PVFQCENGHIACSTCCSKIM----NKCPSCCTPI 127 (328)
Q Consensus 85 ~l~CpiC~~~l~~------Pv~~c~CGH~fC~~C~~~~~----~~CP~Cr~~~ 127 (328)
.+.|-||.+.+.. |- .-.|||.+|..|+.++. ..||.||.+.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~-~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPR-VLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCc-ccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 4679999887753 33 23599999999999982 4789999984
No 93
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=75.26 E-value=0.58 Score=37.06 Aligned_cols=46 Identities=26% Similarity=0.437 Sum_probs=34.2
Q ss_pred CCCeeeecccccccccccccc----------------cCCeeecccchhcc---CCCCCCCCcCC
Q 020280 82 DPEVFDCPICYESLTAPVFQC----------------ENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv~~c----------------~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
|...-.|.||+.-+.++-+.| .|.|.|=..|+.+| .+.||+|.+..
T Consensus 43 Di~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 43 DIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred eeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 444557999998766554343 37788888999998 47899998764
No 94
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.07 E-value=0.72 Score=45.40 Aligned_cols=33 Identities=30% Similarity=0.666 Sum_probs=23.1
Q ss_pred Ceeeecccc-ccccc-ccc-cccCCeeecccchhcc
Q 020280 84 EVFDCPICY-ESLTA-PVF-QCENGHIACSTCCSKI 116 (328)
Q Consensus 84 ~~l~CpiC~-~~l~~-Pv~-~c~CGH~fC~~C~~~~ 116 (328)
....|.||. +.... -.| ...|+|.||..|+.+.
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 43332 122 3469999999998865
No 95
>PHA00616 hypothetical protein
Probab=74.91 E-value=3.3 Score=27.78 Aligned_cols=33 Identities=21% Similarity=0.409 Sum_probs=26.3
Q ss_pred CccCCCCCCCccc-ccchHhhHhhhhcCCCceeEEe
Q 020280 173 PCSCPIPDCNFVG-SANHLYKHFSAKHKNSALHFLY 207 (328)
Q Consensus 173 ~~~Cp~~gC~~~g-~~~~L~~Hl~~~H~~~~~~~~y 207 (328)
|+.|| .|+... .+++|..|+...|.....++.|
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 46787 588666 5789999999999987777765
No 96
>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=74.08 E-value=3.4 Score=27.90 Aligned_cols=40 Identities=20% Similarity=0.516 Sum_probs=30.2
Q ss_pred CCCCCCcCCccccccccceeeeeeeeecccCCCCCceEEeec
Q 020280 119 KCPSCCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKVTMSYG 160 (328)
Q Consensus 119 ~CP~Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~~~~~~ 160 (328)
.||.|...........+...+..+-..|.|. -|.+.+...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~--~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNP--ECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCC--cCCCEEEEE
Confidence 5999988766556677778888999999997 566655543
No 97
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=72.73 E-value=2.2 Score=24.15 Aligned_cols=23 Identities=30% Similarity=0.826 Sum_probs=17.4
Q ss_pred cCCCCCCCcccccchHhhHhhhhcC
Q 020280 175 SCPIPDCNFVGSANHLYKHFSAKHK 199 (328)
Q Consensus 175 ~Cp~~gC~~~g~~~~L~~Hl~~~H~ 199 (328)
.|+ -|+|......|..|++..|+
T Consensus 2 ~C~--~C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCP--HCSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp E-S--SSS-EESHHHHHHHHHHHHS
T ss_pred CCC--CCCCcCCHHHHHHHHHhhCc
Confidence 576 48888888899999998774
No 98
>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=72.48 E-value=3.7 Score=38.66 Aligned_cols=72 Identities=21% Similarity=0.368 Sum_probs=31.2
Q ss_pred eeecccccccccccccccC--C--eeecccchhcc---CCCCCCCCcCCccccccccceeeeeeee-ecccCCCCCceEE
Q 020280 86 FDCPICYESLTAPVFQCEN--G--HIACSTCCSKI---MNKCPSCCTPIGYNRCRAIEKVLESVKV-TCRNSNYGCKVTM 157 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~C--G--H~fC~~C~~~~---~~~CP~Cr~~~~~~r~~~le~~l~~l~v-~C~n~~~GC~~~~ 157 (328)
-.||+|+..-.--++.-.- | +.+|+-|-..| ...||.|...-...........-...++ .|. .|...+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~----~C~~Yl 248 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCE----SCGSYL 248 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEET----TTTEEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECC----cccchH
Confidence 4799999965443322222 4 68999999999 3689999764221111111112223344 575 587776
Q ss_pred eecc
Q 020280 158 SYGK 161 (328)
Q Consensus 158 ~~~~ 161 (328)
+.-+
T Consensus 249 K~vd 252 (290)
T PF04216_consen 249 KTVD 252 (290)
T ss_dssp EEEE
T ss_pred HHHh
Confidence 6655
No 99
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.09 E-value=2.8 Score=33.90 Aligned_cols=38 Identities=24% Similarity=0.687 Sum_probs=27.2
Q ss_pred eecccccccccc------------ccccc-CCeeecccchhcc---CCCCCCCC
Q 020280 87 DCPICYESLTAP------------VFQCE-NGHIACSTCCSKI---MNKCPSCC 124 (328)
Q Consensus 87 ~CpiC~~~l~~P------------v~~c~-CGH~fC~~C~~~~---~~~CP~Cr 124 (328)
.|-.|...|..+ .|+|+ |.+.||.+|-.-+ ...||-|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 488888877543 36786 8999999994433 36788885
No 100
>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=69.68 E-value=2.9 Score=29.29 Aligned_cols=34 Identities=24% Similarity=0.553 Sum_probs=20.3
Q ss_pred CCeeeecc--ccccccc-----c-ccccc-CCeeecccchhcc
Q 020280 83 PEVFDCPI--CYESLTA-----P-VFQCE-NGHIACSTCCSKI 116 (328)
Q Consensus 83 ~~~l~Cpi--C~~~l~~-----P-v~~c~-CGH~fC~~C~~~~ 116 (328)
.+...||- |..++.. . .++|+ |++.||..|...|
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 34457988 9987752 1 14798 9999999998877
No 101
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=69.07 E-value=3.3 Score=41.98 Aligned_cols=9 Identities=11% Similarity=0.316 Sum_probs=4.1
Q ss_pred eEEEEEEEe
Q 020280 307 LKLELCIRR 315 (328)
Q Consensus 307 l~l~V~I~~ 315 (328)
+.|.++|+-
T Consensus 510 VelSFR~k~ 518 (548)
T PF02459_consen 510 VELSFRFKL 518 (548)
T ss_pred eEEEEEEee
Confidence 444444443
No 102
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=68.99 E-value=3.8 Score=28.75 Aligned_cols=33 Identities=21% Similarity=0.496 Sum_probs=23.1
Q ss_pred Ceeeec--ccccccc------cccccc-cCCeeecccchhcc
Q 020280 84 EVFDCP--ICYESLT------APVFQC-ENGHIACSTCCSKI 116 (328)
Q Consensus 84 ~~l~Cp--iC~~~l~------~Pv~~c-~CGH~fC~~C~~~~ 116 (328)
+..-|| -|..++. .+.++| .||+.||..|...|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 334577 7766543 234578 69999999998877
No 103
>PF14851 FAM176: FAM176 family
Probab=68.84 E-value=6.9 Score=33.50 Aligned_cols=7 Identities=14% Similarity=0.515 Sum_probs=2.6
Q ss_pred CCCCCCC
Q 020280 25 APHRHPQ 31 (328)
Q Consensus 25 ~~~~~~~ 31 (328)
.|..+.+
T Consensus 58 ~~~~~~~ 64 (153)
T PF14851_consen 58 SPKKKQL 64 (153)
T ss_pred Ccccccc
Confidence 3333333
No 104
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.79 E-value=4 Score=44.48 Aligned_cols=42 Identities=21% Similarity=0.549 Sum_probs=33.2
Q ss_pred eeeeccccccccccccccc-CCe-----eecccchhcc-CCCCCCCCcCCc
Q 020280 85 VFDCPICYESLTAPVFQCE-NGH-----IACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~-CGH-----~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
...|+-|.... +.+.|+ ||. .||..|.... ...||.|.....
T Consensus 626 ~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 626 RRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred CccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCC
Confidence 56799999985 456797 984 6999997766 367999988765
No 105
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.31 E-value=14 Score=34.75 Aligned_cols=34 Identities=26% Similarity=0.595 Sum_probs=27.0
Q ss_pred CCeeeeccccccccccc-cccc--CCeeecccchhcc
Q 020280 83 PEVFDCPICYESLTAPV-FQCE--NGHIACSTCCSKI 116 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv-~~c~--CGH~fC~~C~~~~ 116 (328)
..-|.|.+|.+-|.+-. .||+ -.|-||..|-...
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRes 302 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRES 302 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHH
Confidence 44599999999998764 3786 7899999996543
No 106
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=67.04 E-value=3.1 Score=31.35 Aligned_cols=45 Identities=22% Similarity=0.493 Sum_probs=18.0
Q ss_pred Ceeeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 84 EVFDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
..-.|.||.+-.- ++..-|. |+--+|+.|.+-- ...||.|+.++.
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 3457999998643 3433454 8999999997643 478999997764
No 107
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=66.56 E-value=3.1 Score=39.67 Aligned_cols=37 Identities=32% Similarity=0.810 Sum_probs=21.6
Q ss_pred eccc-cccccccccccc-CCeeecccchhcc---CCCCCCCC
Q 020280 88 CPIC-YESLTAPVFQCE-NGHIACSTCCSKI---MNKCPSCC 124 (328)
Q Consensus 88 CpiC-~~~l~~Pv~~c~-CGH~fC~~C~~~~---~~~CP~Cr 124 (328)
|-.| .+.+..+.|+|. |.+.||.+|-.-+ ...||.|.
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 6666 333445666775 7777777773222 24677764
No 108
>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=65.66 E-value=3.7 Score=32.05 Aligned_cols=29 Identities=24% Similarity=0.619 Sum_probs=23.2
Q ss_pred eeccccccccccc-ccccCCeeecccchhc
Q 020280 87 DCPICYESLTAPV-FQCENGHIACSTCCSK 115 (328)
Q Consensus 87 ~CpiC~~~l~~Pv-~~c~CGH~fC~~C~~~ 115 (328)
.|++|...+.... ...+|||+|...|+.+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 5999999987654 3458999999999753
No 109
>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=65.00 E-value=2.9 Score=30.26 Aligned_cols=34 Identities=29% Similarity=0.730 Sum_probs=16.6
Q ss_pred CCeeeeccccccccc--cccccc-CCeeecccchhcc
Q 020280 83 PEVFDCPICYESLTA--PVFQCE-NGHIACSTCCSKI 116 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~--Pv~~c~-CGH~fC~~C~~~~ 116 (328)
.+.-.|.+|...|.- .-..|. ||++||..|....
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 344579999998742 123565 9999999997654
No 110
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=64.28 E-value=9.4 Score=35.64 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=10.2
Q ss_pred CCeeeecccccccc
Q 020280 83 PEVFDCPICYESLT 96 (328)
Q Consensus 83 ~~~l~CpiC~~~l~ 96 (328)
...+.|+-|...+.
T Consensus 128 ~~r~~c~eCgk~ys 141 (279)
T KOG2462|consen 128 HPRYKCPECGKSYS 141 (279)
T ss_pred CCceeccccccccc
Confidence 55688888887664
No 111
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=64.08 E-value=1.7 Score=45.36 Aligned_cols=43 Identities=30% Similarity=0.744 Sum_probs=35.7
Q ss_pred CeeeecccccccccccccccCCeeecccchhcc------CCCCCCCCcCC
Q 020280 84 EVFDCPICYESLTAPVFQCENGHIACSTCCSKI------MNKCPSCCTPI 127 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~------~~~CP~Cr~~~ 127 (328)
..+.||||......|+ ...|-|.||..|+... ...||+|+..+
T Consensus 20 k~lEc~ic~~~~~~p~-~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 20 KILECPICLEHVKEPS-LLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hhccCCceeEEeeccc-hhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 3679999999999997 5789999999998875 25799998544
No 112
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=63.77 E-value=3 Score=38.67 Aligned_cols=24 Identities=29% Similarity=0.812 Sum_probs=19.1
Q ss_pred eeeecccccccc--cccccccCCeee
Q 020280 85 VFDCPICYESLT--APVFQCENGHIA 108 (328)
Q Consensus 85 ~l~CpiC~~~l~--~Pv~~c~CGH~f 108 (328)
.|.||+|..+|. +.-+.|.+||.|
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 378999999986 344579999987
No 113
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=63.01 E-value=4.1 Score=26.47 Aligned_cols=25 Identities=20% Similarity=0.648 Sum_probs=17.8
Q ss_pred eccccccccc-cccccc-CCeeecccch
Q 020280 88 CPICYESLTA-PVFQCE-NGHIACSTCC 113 (328)
Q Consensus 88 CpiC~~~l~~-Pv~~c~-CGH~fC~~C~ 113 (328)
|.+|.....- |+ .|. |+..||..=.
T Consensus 1 C~~C~~~~~l~~f-~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLTGF-KCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCcccccCe-ECCccCCccccccC
Confidence 5667765444 76 788 9999987543
No 114
>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=62.05 E-value=6.2 Score=27.28 Aligned_cols=28 Identities=25% Similarity=0.492 Sum_probs=23.1
Q ss_pred ccCCCCCCCcccccchHhhHhhhhcCCCce
Q 020280 174 CSCPIPDCNFVGSANHLYKHFSAKHKNSAL 203 (328)
Q Consensus 174 ~~Cp~~gC~~~g~~~~L~~Hl~~~H~~~~~ 203 (328)
+.||+ |+.......|..|+...|.....
T Consensus 3 f~CP~--C~~~~~~~~L~~H~~~~H~~~~~ 30 (54)
T PF05605_consen 3 FTCPY--CGKGFSESSLVEHCEDEHRSESK 30 (54)
T ss_pred cCCCC--CCCccCHHHHHHHHHhHCcCCCC
Confidence 57885 88867889999999999987644
No 115
>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=61.95 E-value=6.8 Score=25.86 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=18.6
Q ss_pred ecc--ccccccccccccc-CCeeecccchhccCCCCC
Q 020280 88 CPI--CYESLTAPVFQCE-NGHIACSTCCSKIMNKCP 121 (328)
Q Consensus 88 Cpi--C~~~l~~Pv~~c~-CGH~fC~~C~~~~~~~CP 121 (328)
|.+ |......|+ .|. |+..||..-...-...|+
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 888777787 798 999999877665444554
No 116
>smart00301 DM Doublesex DNA-binding motif.
Probab=61.23 E-value=4.8 Score=28.25 Aligned_cols=39 Identities=23% Similarity=0.503 Sum_probs=30.6
Q ss_pred CceEEeecccccccCCCCCCCccCCCCCCCcccccchHhhH
Q 020280 153 CKVTMSYGKKHDHEKICPHVPCSCPIPDCNFVGSANHLYKH 193 (328)
Q Consensus 153 C~~~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~~~L~~H 193 (328)
|.-.+....++.|-..|+|+.+.|+ .|..+..+..+...
T Consensus 8 CrnHg~~~~lKGHKr~C~~r~C~C~--kC~Li~~Rq~vma~ 46 (54)
T smart00301 8 CENHGVKVPLKGHKPECPFRDCECE--KCTLVEKRRALMAL 46 (54)
T ss_pred HhcCCCeeccCCcCCCCCCCCCcCC--CCcChHHHHHHHHH
Confidence 4455667788999999999999998 69887776666554
No 117
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.09 E-value=4.9 Score=38.18 Aligned_cols=42 Identities=36% Similarity=0.614 Sum_probs=31.4
Q ss_pred CCeeeecccccccc---cccccccCCeeecccchhcc------CCCCCCCCc
Q 020280 83 PEVFDCPICYESLT---APVFQCENGHIACSTCCSKI------MNKCPSCCT 125 (328)
Q Consensus 83 ~~~l~CpiC~~~l~---~Pv~~c~CGH~fC~~C~~~~------~~~CP~Cr~ 125 (328)
...|.||+=.+.-. +|+ .-.|||++=..-+..+ ..+||+|-.
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~-ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 334 HSLFICPVLKELCTDENPPV-MLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred cceeeccccHhhhcccCCCe-eeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 56799999777653 566 7899999977776665 257999854
No 118
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=60.77 E-value=3.5 Score=29.02 Aligned_cols=42 Identities=21% Similarity=0.672 Sum_probs=30.5
Q ss_pred eeccccccccc---ccccccCCeeecccchhcc-CCCCCCCCcCCc
Q 020280 87 DCPICYESLTA---PVFQCENGHIACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 87 ~CpiC~~~l~~---Pv~~c~CGH~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
.|-.|..-|-+ .-+.|+-..+||..|.+.. ...||.|...+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 36666665532 1246777788999999987 789999988764
No 119
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=59.64 E-value=17 Score=36.79 Aligned_cols=22 Identities=23% Similarity=0.623 Sum_probs=12.5
Q ss_pred eecccchhccC-CCCCCCCcCCc
Q 020280 107 IACSTCCSKIM-NKCPSCCTPIG 128 (328)
Q Consensus 107 ~fC~~C~~~~~-~~CP~Cr~~~~ 128 (328)
+||..|+..+. +.|-.|-..++
T Consensus 171 WfCeaC~~Gvs~P~CElCPn~~G 193 (707)
T KOG0957|consen 171 WFCEACLYGVSLPHCELCPNRFG 193 (707)
T ss_pred hhhhhHhcCCCCCccccCCCcCC
Confidence 56666665553 55666655444
No 120
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=59.38 E-value=1.5 Score=32.86 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=21.4
Q ss_pred cCCeeecccchhcc------CCCCCCCCcCCc
Q 020280 103 ENGHIACSTCCSKI------MNKCPSCCTPIG 128 (328)
Q Consensus 103 ~CGH~fC~~C~~~~------~~~CP~Cr~~~~ 128 (328)
.|.|.|=..|+.+| +..||.||+.+.
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 48899999999998 368999998754
No 121
>PF15616 TerY-C: TerY-C metal binding domain
Probab=59.09 E-value=5.2 Score=33.32 Aligned_cols=39 Identities=23% Similarity=0.494 Sum_probs=28.5
Q ss_pred eeecccccccccccccccCCeeecccchhccCCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~~~CP~Cr~~~~ 128 (328)
--||-|...+--. .|.||+++|.+=-. ...||.|.....
T Consensus 78 PgCP~CGn~~~fa--~C~CGkl~Ci~g~~--~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQYAFA--VCGCGKLFCIDGEG--EVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcChhcEE--EecCCCEEEeCCCC--CEECCCCCCeee
Confidence 4699999976543 59999999854322 258999987654
No 122
>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=58.67 E-value=7 Score=37.28 Aligned_cols=40 Identities=30% Similarity=0.659 Sum_probs=28.3
Q ss_pred eeecccccccccccccc---cCC--eeecccchhccC---CCCCCCCc
Q 020280 86 FDCPICYESLTAPVFQC---ENG--HIACSTCCSKIM---NKCPSCCT 125 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c---~CG--H~fC~~C~~~~~---~~CP~Cr~ 125 (328)
-.||+|...-.--++.- .-| +..|+-|-..|. .+||.|..
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 37999998643332221 244 689999999993 68999975
No 123
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.04 E-value=4.1 Score=30.20 Aligned_cols=29 Identities=21% Similarity=0.620 Sum_probs=24.0
Q ss_pred cccCCeeecccchh-ccCCCCCCCCcCCcc
Q 020280 101 QCENGHIACSTCCS-KIMNKCPSCCTPIGY 129 (328)
Q Consensus 101 ~c~CGH~fC~~C~~-~~~~~CP~Cr~~~~~ 129 (328)
.|.-.+.||..|.+ ++...||.|...+..
T Consensus 24 ICtfEcTFCadCae~~l~g~CPnCGGelv~ 53 (84)
T COG3813 24 ICTFECTFCADCAENRLHGLCPNCGGELVA 53 (84)
T ss_pred EEEEeeehhHhHHHHhhcCcCCCCCchhhc
Confidence 57888999999998 456899999987653
No 124
>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 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=56.53 E-value=4.5 Score=27.57 Aligned_cols=41 Identities=24% Similarity=0.867 Sum_probs=23.2
Q ss_pred eeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
+.|.-|.-.-+.=| .| -.|..|..|+..+ +..||.|..++.
T Consensus 3 ~nCKsCWf~~k~Li-~C-~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCWFANKGLI-KC-SDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ----SS-S--SSEE-E--SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred ccChhhhhcCCCee-ee-cchhHHHHHHHHHhccccCCCcccCcCc
Confidence 45666766555544 33 4699999999877 478999998764
No 126
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.75 E-value=12 Score=41.96 Aligned_cols=42 Identities=24% Similarity=0.641 Sum_probs=31.6
Q ss_pred eeeeccccccccccccccc-CCee-----ecccchhccC------CCCCCCCcCCc
Q 020280 85 VFDCPICYESLTAPVFQCE-NGHI-----ACSTCCSKIM------NKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~-CGH~-----fC~~C~~~~~------~~CP~Cr~~~~ 128 (328)
.+.||-|...... . .|+ ||.. .|..|-.++. ..||.|..++.
T Consensus 667 ~rkCPkCG~~t~~-~-fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYE-N-RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCcccc-c-cCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 6899999996543 2 576 9954 5999988762 37999998764
No 127
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.68 E-value=4.9 Score=42.94 Aligned_cols=41 Identities=27% Similarity=0.592 Sum_probs=35.4
Q ss_pred eeecccccccccccccccCCeeecccchhccCCCCCCCCcC
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCSKIMNKCPSCCTP 126 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~~~CP~Cr~~ 126 (328)
-.|..|.-.|.-|+.-=.|||.|=..|.+.-...||.|+..
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhccCcccCCccchh
Confidence 48999999999997555799999999999655799999874
No 128
>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=54.27 E-value=14 Score=37.53 Aligned_cols=67 Identities=19% Similarity=0.531 Sum_probs=37.9
Q ss_pred Ceeeeccccccccccccccc---CCeeecccchhcc------------C---CCCCCCCcCCcccccc--------ccce
Q 020280 84 EVFDCPICYESLTAPVFQCE---NGHIACSTCCSKI------------M---NKCPSCCTPIGYNRCR--------AIEK 137 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~---CGH~fC~~C~~~~------------~---~~CP~Cr~~~~~~r~~--------~le~ 137 (328)
++|.|..|..+-. |. |. =--.||..|+... . ..||.|...+...... .-..
T Consensus 4 ~L~fC~~C~~irc-~~--c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~ 80 (483)
T PF05502_consen 4 ELYFCEHCHKIRC-PR--CVSEEIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASDTPPSPPDPSSDS 80 (483)
T ss_pred cceecccccccCC-hh--hcccccceeECccccccCChhhheeccceeccccccCCCCCCcceeEecccccccccccccC
Confidence 3567777777543 22 22 2246777777554 1 4699998877532111 1112
Q ss_pred eeeeeeeecccCCCCCceEE
Q 020280 138 VLESVKVTCRNSNYGCKVTM 157 (328)
Q Consensus 138 ~l~~l~v~C~n~~~GC~~~~ 157 (328)
.-..+.+.|.| |.|.-
T Consensus 81 ~~~~~~l~C~~----C~Wss 96 (483)
T PF05502_consen 81 GGKPYYLSCSY----CRWSS 96 (483)
T ss_pred CCCCEEEECCC----ceeec
Confidence 22346678985 88853
No 129
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.14 E-value=6.1 Score=38.91 Aligned_cols=31 Identities=26% Similarity=0.594 Sum_probs=24.6
Q ss_pred eeeecccccccc-----cccccccCCeeecccchhcc
Q 020280 85 VFDCPICYESLT-----APVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 85 ~l~CpiC~~~l~-----~Pv~~c~CGH~fC~~C~~~~ 116 (328)
-..||.|.-.+. ..+ +|.|||-||..|...|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm-~CrC~~~fcy~C~~~~ 341 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHM-TCRCGHQFCYMCGGDW 341 (384)
T ss_pred cCcCcccceeeeecCCcceE-EeeccccchhhcCcch
Confidence 357999998753 345 8899999999999776
No 130
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=53.07 E-value=14 Score=26.37 Aligned_cols=34 Identities=35% Similarity=0.741 Sum_probs=20.1
Q ss_pred eeeecccCCCCCceEEeecccc--cccCCCCCCCccCCCCCCCcccc
Q 020280 142 VKVTCRNSNYGCKVTMSYGKKH--DHEKICPHVPCSCPIPDCNFVGS 186 (328)
Q Consensus 142 l~v~C~n~~~GC~~~~~~~~~~--~He~~C~~~~~~Cp~~gC~~~g~ 186 (328)
..++||| |...+.+.-.+ .| -.++.|| .|+|.|+
T Consensus 26 v~F~CPn----CGe~~I~Rc~~CRk~-----g~~Y~Cp--~CGF~GP 61 (61)
T COG2888 26 VKFPCPN----CGEVEIYRCAKCRKL-----GNPYRCP--KCGFEGP 61 (61)
T ss_pred eEeeCCC----CCceeeehhhhHHHc-----CCceECC--CcCccCC
Confidence 4677875 66444443221 11 3567888 5998874
No 131
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.88 E-value=10 Score=39.79 Aligned_cols=41 Identities=32% Similarity=0.698 Sum_probs=30.5
Q ss_pred eecccccccccccccccCCe-eecccchhcc---------CCCCCCCCcCCc
Q 020280 87 DCPICYESLTAPVFQCENGH-IACSTCCSKI---------MNKCPSCCTPIG 128 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CGH-~fC~~C~~~~---------~~~CP~Cr~~~~ 128 (328)
.|+||-.-..-+. .=.||| .+|..|..++ ...||.|+..+.
T Consensus 2 ~c~ic~~s~~~~~-~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDFVG-RGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCccccc-cccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 4888887666665 347999 8999998776 145799988654
No 132
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=51.85 E-value=7.2 Score=35.41 Aligned_cols=15 Identities=33% Similarity=0.853 Sum_probs=11.7
Q ss_pred eeeeccccccccccc
Q 020280 85 VFDCPICYESLTAPV 99 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv 99 (328)
-|.|++|+.+|.+|+
T Consensus 260 GfvCsVCLsvfc~p~ 274 (296)
T COG5242 260 GFVCSVCLSVFCRPV 274 (296)
T ss_pred eeehhhhheeecCCc
Confidence 367888888887776
No 133
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=51.54 E-value=13 Score=27.75 Aligned_cols=45 Identities=20% Similarity=0.361 Sum_probs=31.8
Q ss_pred CCCCCCcCCccccccccceeeeeeeeecccCCCCCceEEeecccccc
Q 020280 119 KCPSCCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKVTMSYGKKHDH 165 (328)
Q Consensus 119 ~CP~Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~~~~~~~~~~H 165 (328)
.||.|+........+.+...+..+.-.|.|- .|...++..+--.|
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 6999988764445566666677888889986 57776666655555
No 134
>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=51.52 E-value=9.1 Score=25.36 Aligned_cols=35 Identities=31% Similarity=0.693 Sum_probs=18.6
Q ss_pred eccccccccccccccc---CCeeecccchhcc-----CCCCCCC
Q 020280 88 CPICYESLTAPVFQCE---NGHIACSTCCSKI-----MNKCPSC 123 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~---CGH~fC~~C~~~~-----~~~CP~C 123 (328)
|.+|.++...-+ .|+ |+-.+=..|+.+. ...||.|
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 678999888777 576 7766666777665 1358887
No 135
>PLN02189 cellulose synthase
Probab=50.73 E-value=8.6 Score=42.29 Aligned_cols=43 Identities=26% Similarity=0.621 Sum_probs=33.3
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-+- +|..-|. |+--+|..|.+-- +..||.|+..+.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 47999999754 3444676 9999999998644 478999998765
No 136
>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=50.29 E-value=4.2 Score=34.70 Aligned_cols=22 Identities=45% Similarity=1.065 Sum_probs=18.8
Q ss_pred eecccchhccCCCCCCCCcCCc
Q 020280 107 IACSTCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 107 ~fC~~C~~~~~~~CP~Cr~~~~ 128 (328)
-||..|-.+....||.|..++.
T Consensus 29 ~fC~kCG~~tI~~Cp~C~~~Ir 50 (158)
T PF10083_consen 29 KFCSKCGAKTITSCPNCSTPIR 50 (158)
T ss_pred HHHHHhhHHHHHHCcCCCCCCC
Confidence 5999999888789999988764
No 137
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=49.88 E-value=5.4 Score=30.36 Aligned_cols=10 Identities=20% Similarity=0.169 Sum_probs=0.0
Q ss_pred ccccCCCCCC
Q 020280 52 ESVDNGGNGE 61 (328)
Q Consensus 52 ~~~~~~~~~~ 61 (328)
|+..-+.++.
T Consensus 49 eee~m~rK~k 58 (81)
T PF14812_consen 49 EEEPMPRKGK 58 (81)
T ss_dssp ----------
T ss_pred hccccccccc
Confidence 3333344433
No 138
>PLN02436 cellulose synthase A
Probab=49.53 E-value=9.3 Score=42.14 Aligned_cols=43 Identities=26% Similarity=0.664 Sum_probs=33.1
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-+- +|..-|. |+--+|..|.+-- +..||.|+..+.
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 37999999652 3544676 9999999998644 478999998765
No 139
>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=49.52 E-value=6.6 Score=26.77 Aligned_cols=37 Identities=19% Similarity=0.451 Sum_probs=24.0
Q ss_pred eecccccc--cccccccccCC-----eeecccchhcc-----CCCCCCCC
Q 020280 87 DCPICYES--LTAPVFQCENG-----HIACSTCCSKI-----MNKCPSCC 124 (328)
Q Consensus 87 ~CpiC~~~--l~~Pv~~c~CG-----H~fC~~C~~~~-----~~~CP~Cr 124 (328)
.|-||++. -..|+ ..+|. |.+=..|+.+| ...||+|+
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 37888862 22343 33432 77888999998 24799984
No 140
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.44 E-value=7.3 Score=22.25 Aligned_cols=7 Identities=57% Similarity=1.364 Sum_probs=3.2
Q ss_pred CCCCCCc
Q 020280 119 KCPSCCT 125 (328)
Q Consensus 119 ~CP~Cr~ 125 (328)
.||.|..
T Consensus 15 fC~~CG~ 21 (23)
T PF13240_consen 15 FCPNCGT 21 (23)
T ss_pred chhhhCC
Confidence 4555443
No 141
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=49.24 E-value=12 Score=37.85 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=24.4
Q ss_pred eCCCCeeeecccccccccc--ccccc-CCeeecccchh
Q 020280 80 VTDPEVFDCPICYESLTAP--VFQCE-NGHIACSTCCS 114 (328)
Q Consensus 80 ~~d~~~l~CpiC~~~l~~P--v~~c~-CGH~fC~~C~~ 114 (328)
+.|.+.-.|-.|..+|..= ..-|. ||-+||..|-.
T Consensus 896 ipd~~a~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 896 IPDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred CCCCcchhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 4566667888998887531 12364 99999998854
No 142
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.07 E-value=7.8 Score=38.86 Aligned_cols=20 Identities=30% Similarity=0.672 Sum_probs=16.9
Q ss_pred ccccccccCCeeecccchhcc
Q 020280 96 TAPVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 96 ~~Pv~~c~CGH~fC~~C~~~~ 116 (328)
..+| .|.|||.||..|...+
T Consensus 177 ~~~v-~C~~g~~FC~~C~~~~ 196 (444)
T KOG1815|consen 177 SVEV-DCGCGHEFCFACGEES 196 (444)
T ss_pred ccce-eCCCCchhHhhccccc
Confidence 3456 8999999999998887
No 143
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.05 E-value=5.8 Score=38.76 Aligned_cols=39 Identities=28% Similarity=0.537 Sum_probs=27.8
Q ss_pred eeeccccccccccc---cc-ccCCeeecccchhcc-----C-CCCCCCCc
Q 020280 86 FDCPICYESLTAPV---FQ-CENGHIACSTCCSKI-----M-NKCPSCCT 125 (328)
Q Consensus 86 l~CpiC~~~l~~Pv---~~-c~CGH~fC~~C~~~~-----~-~~CP~Cr~ 125 (328)
-.|.||-+ +++-. -- -.|||+|=-.|+..| . ..||.|+-
T Consensus 5 A~C~Ic~d-~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 5 AECHICID-GRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred ceeeEecc-CCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence 47999954 44321 11 249999999999999 2 47999983
No 144
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=48.25 E-value=13 Score=35.47 Aligned_cols=41 Identities=29% Similarity=0.598 Sum_probs=28.6
Q ss_pred eeeeccccccccccccc--ccCC--eeecccchhccC---CCCCCCCc
Q 020280 85 VFDCPICYESLTAPVFQ--CENG--HIACSTCCSKIM---NKCPSCCT 125 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~--c~CG--H~fC~~C~~~~~---~~CP~Cr~ 125 (328)
.-.||+|...-.--+.. -.-| +..|+-|-..|. ..||.|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 45799999864322211 2345 679999999993 68999975
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=47.62 E-value=9 Score=26.37 Aligned_cols=30 Identities=33% Similarity=0.675 Sum_probs=21.0
Q ss_pred eeccccccccc--cccccc-CCeeecccchhcc
Q 020280 87 DCPICYESLTA--PVFQCE-NGHIACSTCCSKI 116 (328)
Q Consensus 87 ~CpiC~~~l~~--Pv~~c~-CGH~fC~~C~~~~ 116 (328)
.|++|...|.. .-..|. ||++||..|....
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 58888775542 123565 9999999998754
No 146
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=46.71 E-value=11 Score=41.67 Aligned_cols=43 Identities=26% Similarity=0.651 Sum_probs=32.5
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-.- +|..-|. ||--+|+.|.+-- +..||.|+..+.
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 37999999643 3444675 9999999998533 478999998765
No 147
>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=46.52 E-value=11 Score=25.88 Aligned_cols=33 Identities=33% Similarity=0.721 Sum_probs=24.5
Q ss_pred CCeeeecccccccccccccccCCeeecccchhc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSK 115 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~ 115 (328)
.+=|.|..|...|.+.-+.-..|..+|..|..+
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred ccccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 455788889888876644556788888888754
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=46.16 E-value=11 Score=23.08 Aligned_cols=23 Identities=30% Similarity=0.619 Sum_probs=13.0
Q ss_pred ccCCCCCCCcccccchHhhHhhh
Q 020280 174 CSCPIPDCNFVGSANHLYKHFSA 196 (328)
Q Consensus 174 ~~Cp~~gC~~~g~~~~L~~Hl~~ 196 (328)
++||..+|...........|+++
T Consensus 3 vrCPvkdC~EEv~lgKY~~H~ss 25 (30)
T PF10426_consen 3 VRCPVKDCDEEVSLGKYSHHLSS 25 (30)
T ss_dssp EE--STT---EEEHHHHHHHHHT
T ss_pred cccccccCcchhhhhhhcccccc
Confidence 57887788877777777777764
No 149
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.95 E-value=8.2 Score=33.76 Aligned_cols=44 Identities=30% Similarity=0.686 Sum_probs=29.5
Q ss_pred eeecccccccc---cccccc---cCCeeecccchhcc--------------CCCCCCCCcCCcc
Q 020280 86 FDCPICYESLT---APVFQC---ENGHIACSTCCSKI--------------MNKCPSCCTPIGY 129 (328)
Q Consensus 86 l~CpiC~~~l~---~Pv~~c---~CGH~fC~~C~~~~--------------~~~CP~Cr~~~~~ 129 (328)
-.|.||+-+-. .|=++| +||..|=.-|+..| -..||+|..++..
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 34566655432 244455 48888888899888 1589999988753
No 150
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=45.83 E-value=4.2 Score=23.66 Aligned_cols=14 Identities=29% Similarity=0.297 Sum_probs=7.3
Q ss_pred CCcccccchHhhHh
Q 020280 181 CNFVGSANHLYKHF 194 (328)
Q Consensus 181 C~~~g~~~~L~~Hl 194 (328)
|+-......|..|+
T Consensus 8 CgR~F~~~~l~~H~ 21 (25)
T PF13913_consen 8 CGRKFNPDRLEKHE 21 (25)
T ss_pred CCCEECHHHHHHHH
Confidence 55445555555554
No 151
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=45.10 E-value=7.2 Score=30.76 Aligned_cols=41 Identities=34% Similarity=0.768 Sum_probs=14.1
Q ss_pred eeecccccccc--cc-cccccCCeeecccchhcc-------CCCCCCCCcCC
Q 020280 86 FDCPICYESLT--AP-VFQCENGHIACSTCCSKI-------MNKCPSCCTPI 127 (328)
Q Consensus 86 l~CpiC~~~l~--~P-v~~c~CGH~fC~~C~~~~-------~~~CP~Cr~~~ 127 (328)
-.|++|...+. ++ +.+|..||.| ..|.... ...|+.|...+
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~~GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCENGHVW-PRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-TTS-EE-EB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECCCCCEE-eeeeeeeeeeccCCeeEcCCCCCEE
Confidence 37999999653 43 3579999998 4554433 15799997653
No 152
>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=44.81 E-value=10 Score=36.92 Aligned_cols=31 Identities=29% Similarity=0.627 Sum_probs=23.4
Q ss_pred ccccccCCeeecccchhcc----------------CCCCCCCCcCCc
Q 020280 98 PVFQCENGHIACSTCCSKI----------------MNKCPSCCTPIG 128 (328)
Q Consensus 98 Pv~~c~CGH~fC~~C~~~~----------------~~~CP~Cr~~~~ 128 (328)
+-.+|-|-=.-|.+|+.+| ...||+||+.+.
T Consensus 305 ~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 305 PCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred CCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 3345667778899999998 147999998764
No 153
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=44.77 E-value=3.9 Score=45.56 Aligned_cols=45 Identities=27% Similarity=0.527 Sum_probs=35.8
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc---CCCCCCCCcCC
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI---MNKCPSCCTPI 127 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~ 127 (328)
.....|+||.++++.--....|||.+|..|...| ...||.|+...
T Consensus 1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred hcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhhh
Confidence 4456899999999854335679999999999888 46899997543
No 154
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=44.61 E-value=6 Score=39.06 Aligned_cols=34 Identities=24% Similarity=0.572 Sum_probs=26.4
Q ss_pred eeeecccCCCCCceEEeeccccccc-CCCCCCCccCCC
Q 020280 142 VKVTCRNSNYGCKVTMSYGKKHDHE-KICPHVPCSCPI 178 (328)
Q Consensus 142 l~v~C~n~~~GC~~~~~~~~~~~He-~~C~~~~~~Cp~ 178 (328)
-.+.|+| +|...+...++.+|. ..|+++...|..
T Consensus 113 ~~~~C~~---~C~~~~~~~d~~~hl~~~C~~~~~~c~~ 147 (391)
T KOG0297|consen 113 DPLKCPH---RCGVQVPRDDLEDHLEAECPRRSLKCSL 147 (391)
T ss_pred CcccCcc---ccccccchHHHHHHHhcccccccccchh
Confidence 4677886 488888888888884 788888887775
No 155
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.40 E-value=6.8 Score=32.26 Aligned_cols=22 Identities=32% Similarity=0.860 Sum_probs=17.5
Q ss_pred eecccchhccCCCCCCCCcCCc
Q 020280 107 IACSTCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 107 ~fC~~C~~~~~~~CP~Cr~~~~ 128 (328)
.||+.|-+.....||.|..++.
T Consensus 29 afcskcgeati~qcp~csasir 50 (160)
T COG4306 29 AFCSKCGEATITQCPICSASIR 50 (160)
T ss_pred HHHhhhchHHHhcCCccCCccc
Confidence 4899998776678999987753
No 156
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.38 E-value=20 Score=32.29 Aligned_cols=39 Identities=28% Similarity=0.632 Sum_probs=28.4
Q ss_pred ecccccccccccccccCCe-eecccchhccCCCCCCCCcCCc
Q 020280 88 CPICYESLTAPVFQCENGH-IACSTCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 88 CpiC~~~l~~Pv~~c~CGH-~fC~~C~~~~~~~CP~Cr~~~~ 128 (328)
|-.|.+--.. |..-+|-| .+|..|-... ..||+|+.+..
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 8888874433 44567886 5999998763 68999987643
No 157
>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=44.21 E-value=6.5 Score=34.75 Aligned_cols=46 Identities=24% Similarity=0.349 Sum_probs=28.2
Q ss_pred CCcCCccccccccceeeeeeeeecccCCCCCceEEeecccccccCC
Q 020280 123 CCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKVTMSYGKKHDHEKI 168 (328)
Q Consensus 123 Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~~~~~~~~~~He~~ 168 (328)
|...+.+..-...|+...--+..||....||.|.+.+.++..|...
T Consensus 24 C~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~ 69 (198)
T PF03145_consen 24 CTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRD 69 (198)
T ss_dssp ---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHH
T ss_pred CcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHH
Confidence 5555555444556667777789999866799999999999999765
No 158
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=43.88 E-value=8.5 Score=31.86 Aligned_cols=21 Identities=33% Similarity=0.593 Sum_probs=14.7
Q ss_pred ccccccccccccccCCeeeccc
Q 020280 90 ICYESLTAPVFQCENGHIACST 111 (328)
Q Consensus 90 iC~~~l~~Pv~~c~CGH~fC~~ 111 (328)
||...-+. |..|+|||.||..
T Consensus 62 i~qs~~~r-v~rcecghsf~d~ 82 (165)
T COG4647 62 ICQSAQKR-VIRCECGHSFGDY 82 (165)
T ss_pred EEeccccc-EEEEeccccccCh
Confidence 34455444 6689999999863
No 159
>PLN02195 cellulose synthase A
Probab=43.28 E-value=14 Score=40.38 Aligned_cols=43 Identities=21% Similarity=0.464 Sum_probs=32.7
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-+- +|..-|. |+--+|+.|.+-- +..||.|+.++.
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 36999998543 4544675 9999999998533 478999999876
No 160
>PLN02400 cellulose synthase
Probab=43.14 E-value=14 Score=40.80 Aligned_cols=43 Identities=23% Similarity=0.541 Sum_probs=32.4
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-.- +|..-|. |+--+|+.|.+-- +..||.|+..+.
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 47999998643 3444575 9999999998643 478999998765
No 161
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=42.81 E-value=25 Score=31.57 Aligned_cols=44 Identities=20% Similarity=0.545 Sum_probs=30.3
Q ss_pred CCCCeeeecccccccccccccccCCeeecccchhccCCCCCCCCcCCc
Q 020280 81 TDPEVFDCPICYESLTAPVFQCENGHIACSTCCSKIMNKCPSCCTPIG 128 (328)
Q Consensus 81 ~d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~~~CP~Cr~~~~ 128 (328)
.|.+.|.|-+|..-|.-.. .-+.|+-|.+=+.+ ..|..|.+.+.
T Consensus 113 sd~d~ftCrvCgK~F~lQR--mlnrh~kch~~vkr--~lct~cgkgfn 156 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQR--MLNRHLKCHSDVKR--HLCTFCGKGFN 156 (267)
T ss_pred CCCCeeeeehhhhhhhHHH--HHHHHhhhccHHHH--HHHhhccCccc
Confidence 4678999999999887433 23667776654444 36888877665
No 162
>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=41.98 E-value=21 Score=22.08 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=6.5
Q ss_pred CCCCCCCcC
Q 020280 118 NKCPSCCTP 126 (328)
Q Consensus 118 ~~CP~Cr~~ 126 (328)
..||.|..+
T Consensus 18 ~~CP~Cg~~ 26 (33)
T cd00350 18 WVCPVCGAP 26 (33)
T ss_pred CcCcCCCCc
Confidence 478888654
No 163
>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=40.66 E-value=18 Score=29.36 Aligned_cols=39 Identities=21% Similarity=0.425 Sum_probs=24.8
Q ss_pred eeecccccccc----ccccccc-CCeeecccchhccC----CCCCCCCc
Q 020280 86 FDCPICYESLT----APVFQCE-NGHIACSTCCSKIM----NKCPSCCT 125 (328)
Q Consensus 86 l~CpiC~~~l~----~Pv~~c~-CGH~fC~~C~~~~~----~~CP~Cr~ 125 (328)
-.|.+|..+|. ... .|. |+|.+|+.|..... ..|.+|.+
T Consensus 55 ~~C~~C~~~fg~l~~~~~-~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGR-VCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp SB-TTTS-BCSCTSTTCE-EETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred cchhhhCCcccccCCCCC-cCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 37999988653 234 565 99999999976541 24666654
No 164
>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=40.62 E-value=5.1 Score=23.77 Aligned_cols=13 Identities=31% Similarity=0.291 Sum_probs=6.3
Q ss_pred cccccchHhhHhh
Q 020280 183 FVGSANHLYKHFS 195 (328)
Q Consensus 183 ~~g~~~~L~~Hl~ 195 (328)
-.....+|..|+.
T Consensus 11 H~v~~~~l~~Hi~ 23 (27)
T PF05253_consen 11 HRVPASELQKHIK 23 (27)
T ss_dssp -EEEGGGHHHHHH
T ss_pred cCcCHHHHHHHHH
Confidence 3445555555554
No 165
>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=39.39 E-value=6.8 Score=35.85 Aligned_cols=42 Identities=26% Similarity=0.657 Sum_probs=29.1
Q ss_pred eeeeccccc--cccccc--cccc-CCeeecccchhcc----CCCCC--CCCcC
Q 020280 85 VFDCPICYE--SLTAPV--FQCE-NGHIACSTCCSKI----MNKCP--SCCTP 126 (328)
Q Consensus 85 ~l~CpiC~~--~l~~Pv--~~c~-CGH~fC~~C~~~~----~~~CP--~Cr~~ 126 (328)
+-.||+|.. +|.+-| +.-+ |-|..|.+|..++ +..|| -|.+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 447999986 333333 2233 9999999999987 36788 47554
No 166
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.22 E-value=16 Score=30.42 Aligned_cols=24 Identities=33% Similarity=0.931 Sum_probs=18.0
Q ss_pred eeeecccccccccccccccCCeeecccch
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCC 113 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~ 113 (328)
..+||.|..+| |. .-|-+||..|-
T Consensus 28 ~~hCp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcc----ee-eCCeEECCCCC
Confidence 45899999855 44 67888877665
No 167
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=39.13 E-value=21 Score=34.28 Aligned_cols=43 Identities=37% Similarity=0.915 Sum_probs=34.2
Q ss_pred eeecccccccc---cccccccCCeeecccchhcc---CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT---APVFQCENGHIACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~---~Pv~~c~CGH~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
-.||+|.+++. .+.+-|+||+..|..|+..+ ...||.|+++..
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 46999999772 34456899999999999887 378999997754
No 168
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.05 E-value=24 Score=25.21 Aligned_cols=16 Identities=31% Similarity=0.955 Sum_probs=8.5
Q ss_pred cccchhcc-CCCCCCCC
Q 020280 109 CSTCCSKI-MNKCPSCC 124 (328)
Q Consensus 109 C~~C~~~~-~~~CP~Cr 124 (328)
|..|.... ...||.|.
T Consensus 39 C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 39 CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred chhHHhcCCceECCCCC
Confidence 55555543 24566664
No 169
>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=38.96 E-value=10 Score=40.79 Aligned_cols=43 Identities=23% Similarity=0.629 Sum_probs=0.0
Q ss_pred Ceeeeccccccccccccccc-CCe-----eecccchhcc-CCCCCCCCcCCc
Q 020280 84 EVFDCPICYESLTAPVFQCE-NGH-----IACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 84 ~~l~CpiC~~~l~~Pv~~c~-CGH-----~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
....||-|...-... .|+ ||- .+|..|.... ...||.|.....
T Consensus 654 ~~r~Cp~Cg~~t~~~--~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~ 703 (900)
T PF03833_consen 654 GRRRCPKCGKETFYN--RCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETT 703 (900)
T ss_dssp ----------------------------------------------------
T ss_pred ecccCcccCCcchhh--cCcccCCccccceeccccccccCccccccccccCc
Confidence 367899999975443 585 884 5999998887 368999987754
No 170
>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=38.64 E-value=14 Score=29.80 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=16.5
Q ss_pred CCCeeeecccccccccccccccCCeeeccc
Q 020280 82 DPEVFDCPICYESLTAPVFQCENGHIACST 111 (328)
Q Consensus 82 d~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~ 111 (328)
++..+.|.. .-+ +.+|.|||.||..
T Consensus 12 ~~~l~i~~~---~~k--~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 12 GPHLWIVQK---KDK--VVKCDCGHEFCDA 36 (112)
T ss_pred CCcEEEEEe---cCc--eeeccCCCeecCh
Confidence 355665543 222 6689999999863
No 171
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=37.96 E-value=24 Score=21.97 Aligned_cols=8 Identities=25% Similarity=0.463 Sum_probs=3.9
Q ss_pred eecccccc
Q 020280 87 DCPICYES 94 (328)
Q Consensus 87 ~CpiC~~~ 94 (328)
.|.-|...
T Consensus 2 ~C~~Cg~~ 9 (32)
T PF03604_consen 2 ICGECGAE 9 (32)
T ss_dssp BESSSSSS
T ss_pred CCCcCCCe
Confidence 35555544
No 172
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.66 E-value=18 Score=24.06 Aligned_cols=31 Identities=19% Similarity=0.524 Sum_probs=17.4
Q ss_pred eeeecccccccccccccccCCeeecccchhccCCCCCCCCcCCcc
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCSKIMNKCPSCCTPIGY 129 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~~~CP~Cr~~~~~ 129 (328)
.+.|+-|...+...-.. . ...||.|..++..
T Consensus 3 ~y~C~~CG~~~~~~~~~-~-------------~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDEYG-T-------------GVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECCCC-C-------------ceECCCCCCeEEE
Confidence 46677777765432211 0 1468888776654
No 173
>PHA03096 p28-like protein; Provisional
Probab=37.37 E-value=10 Score=35.77 Aligned_cols=31 Identities=26% Similarity=0.358 Sum_probs=23.1
Q ss_pred eeeccccccccc-cc----c--cccCCeeecccchhcc
Q 020280 86 FDCPICYESLTA-PV----F--QCENGHIACSTCCSKI 116 (328)
Q Consensus 86 l~CpiC~~~l~~-Pv----~--~c~CGH~fC~~C~~~~ 116 (328)
-.|.||++.... +. | .-.|-|.||..|+..|
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~w 216 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIW 216 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHH
Confidence 479999996542 22 1 1369999999999988
No 174
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=37.29 E-value=7.2 Score=32.57 Aligned_cols=32 Identities=22% Similarity=0.743 Sum_probs=23.5
Q ss_pred eeeeccccccccc--ccccccCC------eeecccchhcc
Q 020280 85 VFDCPICYESLTA--PVFQCENG------HIACSTCCSKI 116 (328)
Q Consensus 85 ~l~CpiC~~~l~~--Pv~~c~CG------H~fC~~C~~~~ 116 (328)
..+|.||++-+.. =|.--+|| |.||..|+.+|
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 5789999998766 33222333 57999999999
No 175
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.29 E-value=25 Score=22.26 Aligned_cols=12 Identities=25% Similarity=0.730 Sum_probs=7.1
Q ss_pred eeeccccccccc
Q 020280 86 FDCPICYESLTA 97 (328)
Q Consensus 86 l~CpiC~~~l~~ 97 (328)
+.||-|...+..
T Consensus 3 i~Cp~C~~~y~i 14 (36)
T PF13717_consen 3 ITCPNCQAKYEI 14 (36)
T ss_pred EECCCCCCEEeC
Confidence 456666665553
No 176
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=37.05 E-value=21 Score=31.81 Aligned_cols=39 Identities=26% Similarity=0.718 Sum_probs=27.5
Q ss_pred eeeecccccc--c---cc-cccccc-CCeeecccchhccCCCCCCCCc
Q 020280 85 VFDCPICYES--L---TA-PVFQCE-NGHIACSTCCSKIMNKCPSCCT 125 (328)
Q Consensus 85 ~l~CpiC~~~--l---~~-Pv~~c~-CGH~fC~~C~~~~~~~CP~Cr~ 125 (328)
-+.|.+|... + .. -+++|+ |+.+|=..|+.+ ..||.|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~--~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK--KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC--CCCCCcHh
Confidence 4789999852 2 22 334575 888888889886 68999954
No 177
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=36.90 E-value=23 Score=19.03 Aligned_cols=22 Identities=32% Similarity=0.596 Sum_probs=15.0
Q ss_pred cCCCCCCCccc-ccchHhhHhhhhc
Q 020280 175 SCPIPDCNFVG-SANHLYKHFSAKH 198 (328)
Q Consensus 175 ~Cp~~gC~~~g-~~~~L~~Hl~~~H 198 (328)
.|+ -|+... .+.+|..|+...|
T Consensus 2 ~C~--~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCP--ICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-S--STS-EESSHHHHHHHHHHHS
T ss_pred CCc--CCCCcCCcHHHHHHHHHhhC
Confidence 466 377665 6789999998766
No 178
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=36.67 E-value=6.7 Score=38.37 Aligned_cols=41 Identities=29% Similarity=0.597 Sum_probs=31.7
Q ss_pred eeeeccccccc--cccccc-ccCCeeecccchhcc-----CCCCCCCCc
Q 020280 85 VFDCPICYESL--TAPVFQ-CENGHIACSTCCSKI-----MNKCPSCCT 125 (328)
Q Consensus 85 ~l~CpiC~~~l--~~Pv~~-c~CGH~fC~~C~~~~-----~~~CP~Cr~ 125 (328)
.|.|..|.+.+ ++--+| -+|.|+|=..|...+ ...||.|++
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 47899999975 444334 479999999999865 368999984
No 179
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=36.43 E-value=36 Score=26.92 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=26.5
Q ss_pred CceeeeC--CCCeeeecccccccccc-cccccCCeeecccc
Q 020280 75 PFSVTVT--DPEVFDCPICYESLTAP-VFQCENGHIACSTC 112 (328)
Q Consensus 75 ~~~~~~~--d~~~l~CpiC~~~l~~P-v~~c~CGH~fC~~C 112 (328)
.++|.+. ..+.|.|..|+.+-..- +-.-.-|+.+|..|
T Consensus 58 EL~V~ViP~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 58 ELSVRVIPKQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eEEEEEecCCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 3455543 47899999999986532 22234789999998
No 180
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=35.96 E-value=63 Score=29.94 Aligned_cols=21 Identities=24% Similarity=0.589 Sum_probs=13.3
Q ss_pred eeeeeecccCCCCCceEEeeccc
Q 020280 140 ESVKVTCRNSNYGCKVTMSYGKK 162 (328)
Q Consensus 140 ~~l~v~C~n~~~GC~~~~~~~~~ 162 (328)
.+.++.||- .+|+-.+.+...
T Consensus 120 sS~rIaCPR--p~CkRiI~L~~~ 140 (256)
T PF09788_consen 120 SSQRIACPR--PNCKRIINLGPS 140 (256)
T ss_pred ccccccCCC--CCCcceEEeCCc
Confidence 455667764 367777776665
No 181
>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=35.11 E-value=28 Score=20.42 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=16.8
Q ss_pred ccCCCCCCCcccccchHhhHhh
Q 020280 174 CSCPIPDCNFVGSANHLYKHFS 195 (328)
Q Consensus 174 ~~Cp~~gC~~~g~~~~L~~Hl~ 195 (328)
+.|| -|++......+..|+.
T Consensus 2 v~CP--iC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCP--VCFREVPENLINSHLD 21 (26)
T ss_pred CcCC--CCcCcccHHHHHHHHH
Confidence 5788 4988888889999987
No 182
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=35.05 E-value=20 Score=39.60 Aligned_cols=43 Identities=26% Similarity=0.664 Sum_probs=32.3
Q ss_pred eeecccccccc-----ccccccc-CCeeecccchhcc----CCCCCCCCcCCc
Q 020280 86 FDCPICYESLT-----APVFQCE-NGHIACSTCCSKI----MNKCPSCCTPIG 128 (328)
Q Consensus 86 l~CpiC~~~l~-----~Pv~~c~-CGH~fC~~C~~~~----~~~CP~Cr~~~~ 128 (328)
-.|.||.+-.- +|..-|. |+--+|+.|.+-- +..||.|+.++.
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 36999998643 3544675 9999999998533 478999998865
No 183
>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=35.01 E-value=24 Score=22.32 Aligned_cols=30 Identities=13% Similarity=0.304 Sum_probs=16.1
Q ss_pred eeeecccccccccccccccCCeeecccchh
Q 020280 85 VFDCPICYESLTAPVFQCENGHIACSTCCS 114 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~ 114 (328)
...|--|...|.+..+.-.-++.+|..|..
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 457888999888887666678888888764
No 184
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=34.66 E-value=17 Score=21.25 Aligned_cols=6 Identities=50% Similarity=1.453 Sum_probs=2.7
Q ss_pred CCCCCC
Q 020280 119 KCPSCC 124 (328)
Q Consensus 119 ~CP~Cr 124 (328)
.||.|.
T Consensus 18 fC~~CG 23 (26)
T PF13248_consen 18 FCPNCG 23 (26)
T ss_pred cChhhC
Confidence 344443
No 185
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=34.54 E-value=31 Score=40.18 Aligned_cols=11 Identities=36% Similarity=0.552 Sum_probs=5.5
Q ss_pred eeeeeeecccC
Q 020280 139 LESVKVTCRNS 149 (328)
Q Consensus 139 l~~l~v~C~n~ 149 (328)
+..+++-||-+
T Consensus 286 ~~~v~iicp~k 296 (2849)
T PTZ00415 286 LIKVKIICPLK 296 (2849)
T ss_pred cceeEEEccCC
Confidence 34455556543
No 186
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=34.39 E-value=12 Score=40.01 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=26.0
Q ss_pred eeeccccccccccccccc-CCeeecccchhcc
Q 020280 86 FDCPICYESLTAPVFQCE-NGHIACSTCCSKI 116 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~-CGH~fC~~C~~~~ 116 (328)
-.|..|..-+.+-...|+ ||+.+|-.|+..|
T Consensus 230 ~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 230 EMCDRCETTLFNIHWRCPRCGFGVCLDCYRKW 261 (889)
T ss_pred hhhhhhcccccceeEEccccCCeeeecchhhc
Confidence 469999988776555787 9999999999888
No 187
>PF10529 Hist_rich_Ca-bd: Histidine-rich Calcium-binding repeat region; InterPro: IPR019552 This entry represents a histidine-rich calcium-binding repeat which appears in proteins called histidine-rich-calcium binding proteins (HRC). HRC is a high capacity, low affinity Ca2+-binding protein, residing in the lumen of the sarcoplasmic reticulum. HRC binds directly to triadin. This binding interaction occurs between the histidine-rich region of HRC and multiple clusters of charged amino acids, named KEKE motifs, in the lumenal domain of triadin. This repeat is found in the acidic region of the protein, which can be long and variable. There is also a cysteine-rich region further towards the C terminus []. HRC may regulate sarcoplasmic reticular calcium transport, play a critical role in maintaining calcium homeostasis, and function in the heart. HRC is a candidate regulator of sarcoplasmic reticular calcium uptake.
Probab=34.26 E-value=20 Score=18.45 Aligned_cols=6 Identities=0% Similarity=0.224 Sum_probs=2.3
Q ss_pred CCCCCc
Q 020280 33 NLRDGE 38 (328)
Q Consensus 33 ~~~~~~ 38 (328)
+++|++
T Consensus 6 H~~eeD 11 (15)
T PF10529_consen 6 HREEED 11 (15)
T ss_pred cccccc
Confidence 334433
No 188
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=33.26 E-value=11 Score=35.08 Aligned_cols=21 Identities=29% Similarity=0.751 Sum_probs=12.4
Q ss_pred ecccchhcc---CCCCCCCCcCCc
Q 020280 108 ACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 108 fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
+|+-|+.-+ .+.|+.|...+.
T Consensus 275 VCSVCLSVfC~~~PiC~~C~s~F~ 298 (314)
T KOG2487|consen 275 VCSVCLSVFCRFVPICKTCKSKFS 298 (314)
T ss_pred ehHHHHHHhhCCCCccchhhhhcc
Confidence 455554433 357888877764
No 189
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=33.16 E-value=36 Score=38.37 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=7.7
Q ss_pred CCCCCCC-CcccccCC
Q 020280 11 EGEGPSG-NSKRQRRA 25 (328)
Q Consensus 11 ~~~~~~~-~~~~~~~~ 25 (328)
+.+..++ +..||||.
T Consensus 1692 ddeaqd~iptprrrrl 1707 (3015)
T KOG0943|consen 1692 DDEAQDDIPTPRRRRL 1707 (3015)
T ss_pred CccccccCCCchhhhh
Confidence 3444444 66665554
No 190
>PRK00420 hypothetical protein; Validated
Probab=32.70 E-value=25 Score=28.46 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=16.7
Q ss_pred eeecccccccccccccccCCeeecccchh
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTCCS 114 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~ 114 (328)
-.||+|..+|. .-.-|..||..|-.
T Consensus 24 ~~CP~Cg~pLf----~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLF----ELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcce----ecCCCceECCCCCC
Confidence 57999997554 33567777666644
No 191
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.95 E-value=28 Score=36.78 Aligned_cols=41 Identities=29% Similarity=0.792 Sum_probs=20.5
Q ss_pred eeccccccccc-cccccc-CCe----eecccchhcc---CCCCCCCCcCCc
Q 020280 87 DCPICYESLTA-PVFQCE-NGH----IACSTCCSKI---MNKCPSCCTPIG 128 (328)
Q Consensus 87 ~CpiC~~~l~~-Pv~~c~-CGH----~fC~~C~~~~---~~~CP~Cr~~~~ 128 (328)
.||-|.....+ ..| |. ||. .+|..|-... .+.||.|..++.
T Consensus 3 ~Cp~Cg~~n~~~akF-C~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRF-CQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCcc-ccccCCCCCCCcCCCCCCCCCcccccccccCCccc
Confidence 46666654322 222 32 443 2466665554 246777766654
No 192
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=31.71 E-value=34 Score=32.06 Aligned_cols=73 Identities=18% Similarity=0.286 Sum_probs=37.9
Q ss_pred CCCCCCCcCCccccccccceeeeeeeeecccCCCCCceEEeec-ccccccCC-CCCCCccCCCCCCCccc-ccchHhhHh
Q 020280 118 NKCPSCCTPIGYNRCRAIEKVLESVKVTCRNSNYGCKVTMSYG-KKHDHEKI-CPHVPCSCPIPDCNFVG-SANHLYKHF 194 (328)
Q Consensus 118 ~~CP~Cr~~~~~~r~~~le~~l~~l~v~C~n~~~GC~~~~~~~-~~~~He~~-C~~~~~~Cp~~gC~~~g-~~~~L~~Hl 194 (328)
..|+.|.+.+.....+.|....-.+...|. =|...+... -|+.|.++ =--.|+.|| -|+-.+ .|.+|..|+
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l~c~C~----iCGKaFSRPWLLQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTLPCECG----ICGKAFSRPWLLQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAHM 235 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCCCcccc----cccccccchHHhhcccccccCCCCccCC--cccchhcchHHHHHHH
Confidence 567777766544333333333344455554 355544422 23334321 123456677 476544 577888887
Q ss_pred hh
Q 020280 195 SA 196 (328)
Q Consensus 195 ~~ 196 (328)
++
T Consensus 236 QT 237 (279)
T KOG2462|consen 236 QT 237 (279)
T ss_pred Hh
Confidence 75
No 193
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=31.64 E-value=4.1 Score=28.08 Aligned_cols=42 Identities=29% Similarity=0.678 Sum_probs=30.0
Q ss_pred eeeecccccccc-ccccccc-CCeeecccchhccCCCCCCCCcC
Q 020280 85 VFDCPICYESLT-APVFQCE-NGHIACSTCCSKIMNKCPSCCTP 126 (328)
Q Consensus 85 ~l~CpiC~~~l~-~Pv~~c~-CGH~fC~~C~~~~~~~CP~Cr~~ 126 (328)
.+.|..|...+. .-..||. ||...|.+|+..--..|-.|...
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~Gi 50 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNGI 50 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhch
Confidence 577999988543 2234786 99999999998643567777543
No 194
>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=31.12 E-value=24 Score=19.28 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=14.6
Q ss_pred cCCCCCCCccc-ccchHhhHhhh
Q 020280 175 SCPIPDCNFVG-SANHLYKHFSA 196 (328)
Q Consensus 175 ~Cp~~gC~~~g-~~~~L~~Hl~~ 196 (328)
.|+ .|+... .+..|..|++.
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 566 587666 56788889876
No 195
>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=29.11 E-value=14 Score=22.67 Aligned_cols=19 Identities=37% Similarity=0.973 Sum_probs=8.2
Q ss_pred eeecccchhcc-------CCCCCCCC
Q 020280 106 HIACSTCCSKI-------MNKCPSCC 124 (328)
Q Consensus 106 H~fC~~C~~~~-------~~~CP~Cr 124 (328)
|.||..|-... ...||.|.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 45666664443 23566664
No 196
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=29.07 E-value=41 Score=25.25 Aligned_cols=36 Identities=28% Similarity=0.366 Sum_probs=19.8
Q ss_pred ccccCCCCCCCccCCCCCCCccc-ccchHhhHhhhh-cCC
Q 020280 163 HDHEKICPHVPCSCPIPDCNFVG-SANHLYKHFSAK-HKN 200 (328)
Q Consensus 163 ~~He~~C~~~~~~Cp~~gC~~~g-~~~~L~~Hl~~~-H~~ 200 (328)
..+...-......|+ -|+... ....|..|++.. |..
T Consensus 40 ~~~~~~~~~~~~~C~--~C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 40 LNYLRKKVKESFRCP--YCNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp ---------SSEEBS--SSS-EESSHHHHHHHHHHTTTTC
T ss_pred ccccccccCCCCCCC--ccCCCCcCHHHHHHHHcCccCCC
Confidence 344444444468888 487665 789999999975 544
No 197
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.00 E-value=48 Score=35.52 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=6.8
Q ss_pred CCCCCCcCCcc
Q 020280 119 KCPSCCTPIGY 129 (328)
Q Consensus 119 ~CP~Cr~~~~~ 129 (328)
.||.|...+++
T Consensus 446 ~Cp~Cd~~lt~ 456 (730)
T COG1198 446 ECPNCDSPLTL 456 (730)
T ss_pred cCCCCCcceEE
Confidence 57777665543
No 198
>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=28.89 E-value=31 Score=27.52 Aligned_cols=40 Identities=23% Similarity=0.433 Sum_probs=24.7
Q ss_pred eecccccccccccccc-------cC---Ceeecccchhcc------------CCCCCCCCcC
Q 020280 87 DCPICYESLTAPVFQC-------EN---GHIACSTCCSKI------------MNKCPSCCTP 126 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c-------~C---GH~fC~~C~~~~------------~~~CP~Cr~~ 126 (328)
.|..|..--.+....| .| .-.||..|+... ...||.|+..
T Consensus 9 ~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 9 TCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred CchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 5777776444333344 24 567999996554 1469998764
No 199
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=28.26 E-value=39 Score=37.20 Aligned_cols=8 Identities=13% Similarity=0.235 Sum_probs=4.6
Q ss_pred CCCCCCcC
Q 020280 119 KCPSCCTP 126 (328)
Q Consensus 119 ~CP~Cr~~ 126 (328)
.+|-|+++
T Consensus 921 TIPDcrk~ 928 (1096)
T TIGR00927 921 TVPDVRRQ 928 (1096)
T ss_pred ecCCCCcc
Confidence 56666653
No 200
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.18 E-value=44 Score=22.27 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=5.0
Q ss_pred CCCCCCcCC
Q 020280 119 KCPSCCTPI 127 (328)
Q Consensus 119 ~CP~Cr~~~ 127 (328)
.||.|...+
T Consensus 21 rC~~CG~rI 29 (44)
T smart00659 21 RCRECGYRI 29 (44)
T ss_pred ECCCCCceE
Confidence 566665543
No 201
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=27.57 E-value=39 Score=28.47 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=19.5
Q ss_pred ccCCeeecccchhcc-CCCCCCCCcCCccc
Q 020280 102 CENGHIACSTCCSKI-MNKCPSCCTPIGYN 130 (328)
Q Consensus 102 c~CGH~fC~~C~~~~-~~~CP~Cr~~~~~~ 130 (328)
|.| -+.|.-|.+.. ..+||.|+.++...
T Consensus 2 ~kc-t~tC~ic~e~~~KYKCpkC~vPYCSl 30 (157)
T KOG2857|consen 2 CKC-TTTCVICLESEIKYKCPKCSVPYCSL 30 (157)
T ss_pred Ccc-eeeehhhhcchhhccCCCCCCccccc
Confidence 556 67788887754 46888888776543
No 202
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=27.05 E-value=48 Score=22.28 Aligned_cols=37 Identities=22% Similarity=0.538 Sum_probs=24.0
Q ss_pred eeeeccccccc---cccccccc-CCeeecccchhccCCCCC
Q 020280 85 VFDCPICYESL---TAPVFQCE-NGHIACSTCCSKIMNKCP 121 (328)
Q Consensus 85 ~l~CpiC~~~l---~~Pv~~c~-CGH~fC~~C~~~~~~~CP 121 (328)
.-.|.+|.+.+ ...-+.|. |+-.+=..|...+...|+
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C~ 51 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSCG 51 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBSS
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCCC
Confidence 34799999988 33345676 777777778877765554
No 203
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.42 E-value=41 Score=31.14 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=35.2
Q ss_pred CCeeeecccccccccccc---cccCCeeecccchhcc-CCCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVF---QCENGHIACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~---~c~CGH~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
...|+|||=...+..-.. .-.|||+|=..-+.++ ...|++|...+.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCccc
Confidence 457999999888875431 2369999988877777 468999998875
No 204
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=25.97 E-value=29 Score=20.94 Aligned_cols=7 Identities=57% Similarity=0.525 Sum_probs=3.0
Q ss_pred CCCCchh
Q 020280 34 LRDGEEE 40 (328)
Q Consensus 34 ~~~~~~~ 40 (328)
||||+||
T Consensus 3 GSddEee 9 (28)
T PF10587_consen 3 GSDDEEE 9 (28)
T ss_pred CCccccc
Confidence 3454433
No 205
>PHA02862 5L protein; Provisional
Probab=25.93 E-value=27 Score=29.57 Aligned_cols=42 Identities=19% Similarity=0.355 Sum_probs=29.5
Q ss_pred eecccccccccccccccCC---eeecccchhcc-----CCCCCCCCcCCc
Q 020280 87 DCPICYESLTAPVFQCENG---HIACSTCCSKI-----MNKCPSCCTPIG 128 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CG---H~fC~~C~~~~-----~~~CP~Cr~~~~ 128 (328)
.|=||++--.+.+.-|.|. ...=..|+.+| ...|+.|+.++.
T Consensus 4 iCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 4 ICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred EEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 5888888765555556652 45667898888 367999987654
No 206
>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=25.90 E-value=44 Score=22.01 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=15.8
Q ss_pred eeecccccccccccccccCCeeecccc
Q 020280 86 FDCPICYESLTAPVFQCENGHIACSTC 112 (328)
Q Consensus 86 l~CpiC~~~l~~Pv~~c~CGH~fC~~C 112 (328)
-.||.|..+|. +-..|.+||..|
T Consensus 18 ~~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred CccCCCCCeeE----EecCCCEECCCC
Confidence 36999965443 435778888776
No 207
>KOG3815 consensus Transcription factor Doublesex [Transcription]
Probab=25.78 E-value=32 Score=32.97 Aligned_cols=37 Identities=22% Similarity=0.639 Sum_probs=30.5
Q ss_pred CCceEEeecccccccCCCCCCCccCCCCCCCcccccchH
Q 020280 152 GCKVTMSYGKKHDHEKICPHVPCSCPIPDCNFVGSANHL 190 (328)
Q Consensus 152 GC~~~~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~~~L 190 (328)
-|.-.+.+..++.|-+.|+|+.|.|. .|.....+..+
T Consensus 41 RCrnHG~~~~LKGHk~~C~~~~C~C~--kC~li~eRqrv 77 (322)
T KOG3815|consen 41 RCENHGVLSRLKGHKRSCPYRDCPCE--KCGLVEERRRV 77 (322)
T ss_pred hhhccCcceeccCCCCCCCCCCCCch--HhcchHHHHHH
Confidence 67778899999999999999999997 68766654444
No 208
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=25.65 E-value=41 Score=34.12 Aligned_cols=30 Identities=23% Similarity=0.599 Sum_probs=19.6
Q ss_pred CCCCCchhhhhccccccccccccCCCCCCc
Q 020280 33 NLRDGEEEEEETHHQEEDDESVDNGGNGEK 62 (328)
Q Consensus 33 ~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~ 62 (328)
.-+|+|||.+++++.+.++++.++-.++..
T Consensus 423 d~~dgdde~eddddidvdeediessddgtd 452 (990)
T KOG1819|consen 423 DNEDGDDEAEDDDDIDVDEEDIESSDDGTD 452 (990)
T ss_pred ccccCcccccCcccccccccccccccccch
Confidence 346666666666777777777776655443
No 209
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=25.14 E-value=35 Score=31.26 Aligned_cols=50 Identities=26% Similarity=0.531 Sum_probs=33.6
Q ss_pred eec--cccccccccccccc-CCeeecccchhcc-------------CCCCCCCCcCCccccccccce
Q 020280 87 DCP--ICYESLTAPVFQCE-NGHIACSTCCSKI-------------MNKCPSCCTPIGYNRCRAIEK 137 (328)
Q Consensus 87 ~Cp--iC~~~l~~Pv~~c~-CGH~fC~~C~~~~-------------~~~CP~Cr~~~~~~r~~~le~ 137 (328)
+|. .|..+=.-|+ .|. |+++||..=...- -+.||.|..++.......+.+
T Consensus 10 HCs~~~CkqlDFLPf-~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~~ 75 (250)
T KOG3183|consen 10 HCSVPYCKQLDFLPF-KCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPDK 75 (250)
T ss_pred ccCcchhhhccccce-eeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchhh
Confidence 577 7888766677 787 9999998643332 157888888776554444433
No 210
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.91 E-value=33 Score=31.18 Aligned_cols=45 Identities=20% Similarity=0.339 Sum_probs=34.1
Q ss_pred eeeeccccccccccc-ccccCCeeecccchhcc-----------CCCCCCCCcCCcc
Q 020280 85 VFDCPICYESLTAPV-FQCENGHIACSTCCSKI-----------MNKCPSCCTPIGY 129 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv-~~c~CGH~fC~~C~~~~-----------~~~CP~Cr~~~~~ 129 (328)
.-.|..|.-.|..-- ..-.|-|+|=..|+..+ ...||.|..++..
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 456999999886432 13459999999999887 2589999988753
No 211
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=24.84 E-value=45 Score=30.92 Aligned_cols=45 Identities=31% Similarity=0.684 Sum_probs=33.1
Q ss_pred CCeeeecccccccccccccccCCeeecccchhccC-CCCCCCCcCCc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKIM-NKCPSCCTPIG 128 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~-~~CP~Cr~~~~ 128 (328)
+..|.|..|...|..-- ..--|-+||..|..+.. +.|-.|+.++.
T Consensus 161 ~yHFkCt~C~keL~sda-Revk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 161 PYHFKCTTCGKELTSDA-REVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred ccceecccccccccchh-hhhccceeccccccccCCcccccccCchH
Confidence 56789999999887655 34588999999999873 34555666554
No 212
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=24.73 E-value=46 Score=26.18 Aligned_cols=23 Identities=30% Similarity=0.847 Sum_probs=17.6
Q ss_pred eecccchhcc-------CCCCCCCCcCCcc
Q 020280 107 IACSTCCSKI-------MNKCPSCCTPIGY 129 (328)
Q Consensus 107 ~fC~~C~~~~-------~~~CP~Cr~~~~~ 129 (328)
+.|..|...+ ...||.|+.+++.
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp 92 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNP 92 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCc
Confidence 7888887766 2679999988763
No 213
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.72 E-value=43 Score=35.34 Aligned_cols=28 Identities=32% Similarity=0.653 Sum_probs=13.3
Q ss_pred eeccccccccccccccc-CCee------ecccchhcc
Q 020280 87 DCPICYESLTAPVFQCE-NGHI------ACSTCCSKI 116 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~-CGH~------fC~~C~~~~ 116 (328)
.|+-|...+... .|+ ||+. ||..|-.+.
T Consensus 17 FC~~CG~~l~~~--~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 17 FCQKCGTSLTHK--PCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred cccccCCCCCCC--cCCCCCCCCCcccccccccCCcc
Confidence 355555555322 232 5543 555554443
No 214
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.66 E-value=44 Score=30.19 Aligned_cols=34 Identities=29% Similarity=0.670 Sum_probs=23.3
Q ss_pred eecccccccccccccccCCeeecccchhccC---CCCCCCCcC
Q 020280 87 DCPICYESLTAPVFQCENGHIACSTCCSKIM---NKCPSCCTP 126 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~---~~CP~Cr~~ 126 (328)
.|.+|..++..+ ...+|..|...+. ..||.|..+
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 588888765322 1347999988763 469999765
No 215
>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=24.63 E-value=12 Score=25.40 Aligned_cols=29 Identities=21% Similarity=0.626 Sum_probs=16.3
Q ss_pred EeecccccccCCCCCCCccCCCCCCCccccc
Q 020280 157 MSYGKKHDHEKICPHVPCSCPIPDCNFVGSA 187 (328)
Q Consensus 157 ~~~~~~~~He~~C~~~~~~Cp~~gC~~~g~~ 187 (328)
+....++.|...|+|+.+.|. .|.....+
T Consensus 12 G~~~~lKgHk~~C~~~~C~C~--kC~li~eR 40 (47)
T PF00751_consen 12 GVIVPLKGHKRYCPFRDCQCD--KCALIAER 40 (47)
T ss_dssp T---TTTT-GGG-TTTT--SH--HHHHHHHH
T ss_pred CcccchhhhccccCcCCCcCC--CCcCcHHH
Confidence 345678899999999999997 57655433
No 216
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.56 E-value=50 Score=21.53 Aligned_cols=8 Identities=38% Similarity=1.144 Sum_probs=6.1
Q ss_pred CCCCCCCc
Q 020280 118 NKCPSCCT 125 (328)
Q Consensus 118 ~~CP~Cr~ 125 (328)
..||.|+.
T Consensus 27 ~~CP~Cg~ 34 (42)
T PF09723_consen 27 VPCPECGS 34 (42)
T ss_pred CcCCCCCC
Confidence 57888876
No 217
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=24.32 E-value=52 Score=23.11 Aligned_cols=10 Identities=30% Similarity=0.650 Sum_probs=5.3
Q ss_pred eeeeeeeecc
Q 020280 138 VLESVKVTCR 147 (328)
Q Consensus 138 ~l~~l~v~C~ 147 (328)
.+.++.++||
T Consensus 23 ~LkNfPlyCp 32 (55)
T PF14205_consen 23 VLKNFPLYCP 32 (55)
T ss_pred eeccccccCC
Confidence 4455555555
No 218
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.28 E-value=46 Score=28.86 Aligned_cols=12 Identities=33% Similarity=0.850 Sum_probs=8.3
Q ss_pred eeeecccccccc
Q 020280 85 VFDCPICYESLT 96 (328)
Q Consensus 85 ~l~CpiC~~~l~ 96 (328)
.+.|++|..+..
T Consensus 134 ~~vC~vCGy~~~ 145 (166)
T COG1592 134 VWVCPVCGYTHE 145 (166)
T ss_pred EEEcCCCCCccc
Confidence 677888866554
No 219
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=24.03 E-value=21 Score=35.63 Aligned_cols=37 Identities=30% Similarity=0.671 Sum_probs=28.3
Q ss_pred eCCCCeeeeccccccccccc--cccc-CCeeecccchhcc
Q 020280 80 VTDPEVFDCPICYESLTAPV--FQCE-NGHIACSTCCSKI 116 (328)
Q Consensus 80 ~~d~~~l~CpiC~~~l~~Pv--~~c~-CGH~fC~~C~~~~ 116 (328)
+.|.+...||+|.+.|.--. --|. ||-+.|.+|..-+
T Consensus 175 ~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~i 214 (505)
T KOG1842|consen 175 LDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFI 214 (505)
T ss_pred cCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHhc
Confidence 56778899999999886432 2365 9999999997654
No 220
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=23.98 E-value=34 Score=32.61 Aligned_cols=9 Identities=22% Similarity=0.836 Sum_probs=4.6
Q ss_pred eeccccccc
Q 020280 87 DCPICYESL 95 (328)
Q Consensus 87 ~CpiC~~~l 95 (328)
.|-+|..+|
T Consensus 364 ~Cf~CQ~~f 372 (421)
T COG5151 364 HCFVCQGPF 372 (421)
T ss_pred cceeccCCC
Confidence 455555544
No 221
>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=23.89 E-value=32 Score=20.59 Aligned_cols=23 Identities=13% Similarity=0.398 Sum_probs=6.0
Q ss_pred eeccccccccc-cccccc-CCeeec
Q 020280 87 DCPICYESLTA-PVFQCE-NGHIAC 109 (328)
Q Consensus 87 ~CpiC~~~l~~-Pv~~c~-CGH~fC 109 (328)
.|.+|...... .+|.|. |.-.+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH 26 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLH 26 (30)
T ss_dssp --TTTS----S--EEE-TTT-----
T ss_pred cCCcCCCcCCCCceEECccCCCccC
Confidence 46777776665 555554 443333
No 222
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.81 E-value=34 Score=34.47 Aligned_cols=13 Identities=38% Similarity=0.779 Sum_probs=9.3
Q ss_pred hccCCCCCCCCcC
Q 020280 114 SKIMNKCPSCCTP 126 (328)
Q Consensus 114 ~~~~~~CP~Cr~~ 126 (328)
.+|..+||.|+.-
T Consensus 18 ~~~~g~Cp~C~~w 30 (454)
T TIGR00416 18 PKWQGKCPACHAW 30 (454)
T ss_pred ccccEECcCCCCc
Confidence 4556789999764
No 223
>PRK11823 DNA repair protein RadA; Provisional
Probab=23.79 E-value=38 Score=34.04 Aligned_cols=23 Identities=26% Similarity=0.745 Sum_probs=13.8
Q ss_pred ccccc-CCeeecccchhccCCCCCCCCcC
Q 020280 99 VFQCE-NGHIACSTCCSKIMNKCPSCCTP 126 (328)
Q Consensus 99 v~~c~-CGH~fC~~C~~~~~~~CP~Cr~~ 126 (328)
.|.|. ||+.. .+|..+||.|+.-
T Consensus 7 ~y~C~~Cg~~~-----~~~~g~Cp~C~~w 30 (446)
T PRK11823 7 AYVCQECGAES-----PKWLGRCPECGAW 30 (446)
T ss_pred eEECCcCCCCC-----cccCeeCcCCCCc
Confidence 44554 55433 4556789999654
No 224
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.42 E-value=61 Score=25.66 Aligned_cols=30 Identities=27% Similarity=0.744 Sum_probs=16.9
Q ss_pred CCeeeecccccccc-cccccccCCeeecccch
Q 020280 83 PEVFDCPICYESLT-APVFQCENGHIACSTCC 113 (328)
Q Consensus 83 ~~~l~CpiC~~~l~-~Pv~~c~CGH~fC~~C~ 113 (328)
+..+.||.|.+... -++-. .-+|+.|..|-
T Consensus 19 pt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG 49 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKK-NIAIITCGNCG 49 (99)
T ss_pred CcEeECCCCCCeEeeeecCC-CcceEECCCCC
Confidence 56899999996322 22211 23466655553
No 225
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=23.23 E-value=14 Score=35.04 Aligned_cols=47 Identities=21% Similarity=0.420 Sum_probs=35.3
Q ss_pred CCeeeecccccccc-cc-cccccCCeeecccchhcc--------------------------CCCCCCCCcCCcc
Q 020280 83 PEVFDCPICYESLT-AP-VFQCENGHIACSTCCSKI--------------------------MNKCPSCCTPIGY 129 (328)
Q Consensus 83 ~~~l~CpiC~~~l~-~P-v~~c~CGH~fC~~C~~~~--------------------------~~~CP~Cr~~~~~ 129 (328)
...-.|.||+.-|. .| +..+.|-|.+=..|+.+. ...||+|+..+.+
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 44678999998774 45 556789999988998765 1359999888764
No 226
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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), 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=23.23 E-value=62 Score=20.19 Aligned_cols=9 Identities=56% Similarity=1.446 Sum_probs=6.4
Q ss_pred CCCCCCCcC
Q 020280 118 NKCPSCCTP 126 (328)
Q Consensus 118 ~~CP~Cr~~ 126 (328)
..||.|..+
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 578888764
No 227
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.99 E-value=29 Score=34.77 Aligned_cols=34 Identities=26% Similarity=0.547 Sum_probs=26.7
Q ss_pred CCeeeecccccccccccccccCCeeecccchhcc
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~ 116 (328)
.....|.||...+...+..-.|||.||..|+...
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~y 101 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGY 101 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcHHHHHHHHHH
Confidence 4467899999987653334579999999999875
No 228
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=22.69 E-value=1.1e+02 Score=29.59 Aligned_cols=30 Identities=13% Similarity=0.215 Sum_probs=19.5
Q ss_pred eeeecccC-CCCCceEEeecccccccCCCCC
Q 020280 142 VKVTCRNS-NYGCKVTMSYGKKHDHEKICPH 171 (328)
Q Consensus 142 l~v~C~n~-~~GC~~~~~~~~~~~He~~C~~ 171 (328)
.-..|.|. ..+|+|.++-.+-..-=..|.+
T Consensus 52 ~~~~C~N~~~~~CNWlvp~~~~~~~C~aCrl 82 (343)
T PF10005_consen 52 RYRRCANAEHAVCNWLVPADDPDALCRACRL 82 (343)
T ss_pred eeeeCCCCCccccceeecCCCCCCcchhhhc
Confidence 45689987 4569999987665433334444
No 229
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=22.31 E-value=45 Score=26.76 Aligned_cols=15 Identities=33% Similarity=1.019 Sum_probs=7.4
Q ss_pred ecccchhccCCCCCCCCc
Q 020280 108 ACSTCCSKIMNKCPSCCT 125 (328)
Q Consensus 108 fC~~C~~~~~~~CP~Cr~ 125 (328)
+..+|..+ .||.|..
T Consensus 54 ~~~SCk~R---~CP~C~~ 68 (111)
T PF14319_consen 54 VYNSCKNR---HCPSCQA 68 (111)
T ss_pred ecCcccCc---CCCCCCC
Confidence 44444442 4666654
No 230
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=22.15 E-value=37 Score=29.25 Aligned_cols=44 Identities=20% Similarity=0.408 Sum_probs=29.3
Q ss_pred eeeecccccccccccccccCCe---eecccchhcc-----CCCCCCCCcCCc
Q 020280 85 VFDCPICYESLTAPVFQCENGH---IACSTCCSKI-----MNKCPSCCTPIG 128 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c~CGH---~fC~~C~~~~-----~~~CP~Cr~~~~ 128 (328)
.-.|-||++--.+-..-|.|.. ..=.+|+.+| ...|+.|+.++.
T Consensus 8 ~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 8 DKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCeeEecCCCCCCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3479999886543233466543 4567799988 367999987654
No 231
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.00 E-value=53 Score=30.91 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=21.5
Q ss_pred CCeeecccchhcc-------CCCCCCCCcCCccccc
Q 020280 104 NGHIACSTCCSKI-------MNKCPSCCTPIGYNRC 132 (328)
Q Consensus 104 CGH~fC~~C~~~~-------~~~CP~Cr~~~~~~r~ 132 (328)
-.|.||..|-.+. ...||.|+.......+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR~d 144 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHFPRID 144 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccCCCCC
Confidence 5689999998876 2579999887554333
No 232
>PHA00626 hypothetical protein
Probab=21.98 E-value=48 Score=23.43 Aligned_cols=22 Identities=14% Similarity=-0.050 Sum_probs=11.0
Q ss_pred eecccchhcc-CCCCCCCCcCCc
Q 020280 107 IACSTCCSKI-MNKCPSCCTPIG 128 (328)
Q Consensus 107 ~fC~~C~~~~-~~~CP~Cr~~~~ 128 (328)
+-|..|.... ...||.|.-.++
T Consensus 12 vrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 12 AKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred eeeceecccCcceEcCCCCCeec
Confidence 3444554422 246777765443
No 233
>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=21.87 E-value=60 Score=19.49 Aligned_cols=23 Identities=13% Similarity=0.429 Sum_probs=13.9
Q ss_pred eecccccccccc-ccccc-CCeeec
Q 020280 87 DCPICYESLTAP-VFQCE-NGHIAC 109 (328)
Q Consensus 87 ~CpiC~~~l~~P-v~~c~-CGH~fC 109 (328)
.|.+|.+.+... .|.|. |+-.+-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh 26 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLH 26 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEc
Confidence 577777776666 66664 443333
No 234
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.78 E-value=39 Score=20.18 Aligned_cols=26 Identities=19% Similarity=0.553 Sum_probs=11.6
Q ss_pred eecccccccccccccccCCeeecccch
Q 020280 87 DCPICYESLTAPVFQCENGHIACSTCC 113 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~CGH~fC~~C~ 113 (328)
.|+.|..++..-. +-.-...||..|.
T Consensus 3 ~C~rC~~~~~~~~-~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIG-INGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEE-ETTEEEEE-TTTC
T ss_pred cCccCCCcceEeE-ecCCCCeECcCCc
Confidence 4778887765433 2233345666664
No 235
>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=21.30 E-value=62 Score=21.06 Aligned_cols=7 Identities=43% Similarity=1.165 Sum_probs=3.8
Q ss_pred eeccccc
Q 020280 87 DCPICYE 93 (328)
Q Consensus 87 ~CpiC~~ 93 (328)
.||.|..
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555555
No 236
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.51 E-value=66 Score=34.50 Aligned_cols=40 Identities=25% Similarity=0.669 Sum_probs=27.5
Q ss_pred eeeecccccccccccccc--------cCCeeecccchhcc--CCCCCCCCcC
Q 020280 85 VFDCPICYESLTAPVFQC--------ENGHIACSTCCSKI--MNKCPSCCTP 126 (328)
Q Consensus 85 ~l~CpiC~~~l~~Pv~~c--------~CGH~fC~~C~~~~--~~~CP~Cr~~ 126 (328)
.+.|..|..+++=|- | .-+...|..|-..- ...||.|...
T Consensus 435 ~l~C~~Cg~v~~Cp~--Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPN--CDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCC--CCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 456777777665442 2 23568999997653 4789999876
No 237
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=20.48 E-value=39 Score=23.28 Aligned_cols=28 Identities=25% Similarity=0.740 Sum_probs=19.8
Q ss_pred eecccccccc--cccccccCCeeecccchhcc
Q 020280 87 DCPICYESLT--APVFQCENGHIACSTCCSKI 116 (328)
Q Consensus 87 ~CpiC~~~l~--~Pv~~c~CGH~fC~~C~~~~ 116 (328)
.|+||..-+. ..+ ...-| .+|.+|..++
T Consensus 1 ~C~iCg~kigl~~~~-k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF-KIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce-eccCc-cchHHHHHHh
Confidence 4889988432 222 45677 7999999886
No 238
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=20.46 E-value=31 Score=35.81 Aligned_cols=43 Identities=21% Similarity=0.486 Sum_probs=29.2
Q ss_pred CCeeeecccccc-----c-cccccccc-CCeeecccchhccCCCCCCCCc
Q 020280 83 PEVFDCPICYES-----L-TAPVFQCE-NGHIACSTCCSKIMNKCPSCCT 125 (328)
Q Consensus 83 ~~~l~CpiC~~~-----l-~~Pv~~c~-CGH~fC~~C~~~~~~~CP~Cr~ 125 (328)
..-+.|.+|..- | ..-+..|. ||++|=..|+.+....||.|-.
T Consensus 509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~s~~CPrC~R 558 (580)
T KOG1829|consen 509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRKSPCCPRCER 558 (580)
T ss_pred cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhccCCCCCchHH
Confidence 335778888441 1 11223564 9999999999988767999943
No 239
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=20.39 E-value=69 Score=20.04 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=8.5
Q ss_pred eeecccccccccc
Q 020280 86 FDCPICYESLTAP 98 (328)
Q Consensus 86 l~CpiC~~~l~~P 98 (328)
+.||-|...+..+
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 5677777766544
No 240
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.37 E-value=54 Score=30.87 Aligned_cols=20 Identities=35% Similarity=0.806 Sum_probs=12.3
Q ss_pred eecccchhcc---CCCCCCCCcC
Q 020280 107 IACSTCCSKI---MNKCPSCCTP 126 (328)
Q Consensus 107 ~fC~~C~~~~---~~~CP~Cr~~ 126 (328)
.+|+.|+... ...||.|+..
T Consensus 256 yvCs~Clsi~C~~p~~C~~Cgt~ 278 (279)
T TIGR00627 256 FVCSVCLSVLCQYTPICKTCKTA 278 (279)
T ss_pred EECCCccCCcCCCCCCCCCCCCC
Confidence 4555555443 3689999764
No 241
>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=20.17 E-value=69 Score=19.47 Aligned_cols=21 Identities=29% Similarity=0.778 Sum_probs=10.0
Q ss_pred eeccccccccccccccc-CCeeecc
Q 020280 87 DCPICYESLTAPVFQCE-NGHIACS 110 (328)
Q Consensus 87 ~CpiC~~~l~~Pv~~c~-CGH~fC~ 110 (328)
.|.||.. ..-|.|+ |+-.+|+
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 4667766 2234565 6666665
No 242
>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=20.11 E-value=78 Score=19.09 Aligned_cols=35 Identities=23% Similarity=0.594 Sum_probs=16.3
Q ss_pred ecccccccccc-cccccCCeeecccchhccCCCCCCCCcCC
Q 020280 88 CPICYESLTAP-VFQCENGHIACSTCCSKIMNKCPSCCTPI 127 (328)
Q Consensus 88 CpiC~~~l~~P-v~~c~CGH~fC~~C~~~~~~~CP~Cr~~~ 127 (328)
|..|...+.+. ...-.-+..|-..| ..|..|+.++
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~C-----f~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPEC-----FKCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccC-----CCCcccCCcC
Confidence 66677766542 11222344444444 2455555443
No 243
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=20.07 E-value=78 Score=30.64 Aligned_cols=79 Identities=18% Similarity=0.392 Sum_probs=43.3
Q ss_pred CCeeeecccccccccccccccCCeeecccchhccC--------------CCCCCCCcCCccc---------cccccceee
Q 020280 83 PEVFDCPICYESLTAPVFQCENGHIACSTCCSKIM--------------NKCPSCCTPIGYN---------RCRAIEKVL 139 (328)
Q Consensus 83 ~~~l~CpiC~~~l~~Pv~~c~CGH~fC~~C~~~~~--------------~~CP~Cr~~~~~~---------r~~~le~~l 139 (328)
++.+-|-.|.++=..--..=.-...||.+|++... .-||.|...+... .+.+-..+-
T Consensus 22 ~~L~FCRyC~klrc~~Cv~hEvdshfCp~CLEn~ps~EArlKKn~CAnCfDCP~C~htLSaRa~~~stq~p~dpaktt~k 101 (449)
T KOG3896|consen 22 PDLVFCRYCFKLRCDDCVLHEVDSHFCPRCLENSPSPEARLKKNKCANCFDCPKCAHTLSARAENDSTQLPDDPAKTTMK 101 (449)
T ss_pred cceeeeecccccccccccccccccccchhhccCCCchHHHhhhccccccccCcchhhhhhhhcccccccCCCChhhhhhh
Confidence 55677887877533211011233579999998871 3578886555421 112222233
Q ss_pred eeeeeecccCCCCCceEEeecccccc
Q 020280 140 ESVKVTCRNSNYGCKVTMSYGKKHDH 165 (328)
Q Consensus 140 ~~l~v~C~n~~~GC~~~~~~~~~~~H 165 (328)
...-+.|.| |.|+..--.+.+.
T Consensus 102 k~yYL~C~~----CRWtsRdvg~~Dq 123 (449)
T KOG3896|consen 102 KNYYLVCQY----CRWTSRDVGQEDQ 123 (449)
T ss_pred heeEEeeee----eeccccccCCccc
Confidence 345677875 8887665554443
Done!