Query 042263
Match_columns 159
No_of_seqs 149 out of 720
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 04:33:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042263hhsearch_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 2E-30 4.3E-35 216.3 7.0 148 11-158 41-213 (299)
2 PF03145 Sina: Seven in absent 99.6 3.9E-16 8.4E-21 123.2 5.4 95 62-156 1-115 (198)
3 KOG0297 TNF receptor-associate 98.8 1.8E-09 3.9E-14 93.6 3.7 103 16-121 19-143 (391)
4 PF14835 zf-RING_6: zf-RING of 98.8 2.3E-09 5.1E-14 70.4 2.7 55 17-71 6-65 (65)
5 PF15227 zf-C3HC4_4: zinc fing 98.8 1.3E-09 2.9E-14 66.1 0.3 35 21-56 1-42 (42)
6 PF13923 zf-C3HC4_2: Zinc fing 98.6 7.9E-09 1.7E-13 61.3 0.7 36 21-56 1-39 (39)
7 KOG0287 Postreplication repair 98.6 4E-09 8.7E-14 89.2 -1.4 65 7-72 12-83 (442)
8 PLN03208 E3 ubiquitin-protein 98.6 1.7E-08 3.6E-13 79.7 1.9 54 6-60 6-78 (193)
9 smart00504 Ubox Modified RING 98.6 3.5E-08 7.6E-13 63.6 2.4 53 18-71 1-60 (63)
10 PF13920 zf-C3HC4_3: Zinc fing 98.5 2.1E-08 4.6E-13 62.5 0.6 42 18-60 2-47 (50)
11 TIGR00599 rad18 DNA repair pro 98.5 3.3E-08 7.1E-13 85.8 1.6 56 16-72 24-86 (397)
12 PF13639 zf-RING_2: Ring finge 98.3 1E-07 2.2E-12 57.8 0.1 38 20-57 2-44 (44)
13 COG5432 RAD18 RING-finger-cont 98.3 1.5E-07 3.3E-12 78.4 1.0 45 15-60 22-69 (391)
14 KOG0823 Predicted E3 ubiquitin 98.3 3.4E-07 7.5E-12 73.8 1.5 46 14-60 43-94 (230)
15 KOG0320 Predicted E3 ubiquitin 98.3 1.6E-07 3.5E-12 73.1 -0.4 44 17-60 130-177 (187)
16 PF14634 zf-RING_5: zinc-RING 98.2 3.8E-07 8.3E-12 55.5 1.0 39 20-58 1-44 (44)
17 PF00097 zf-C3HC4: Zinc finger 98.2 3.8E-07 8.3E-12 54.2 1.0 36 21-56 1-41 (41)
18 PF04564 U-box: U-box domain; 98.2 8.6E-07 1.9E-11 59.6 1.8 56 16-72 2-65 (73)
19 PHA02929 N1R/p28-like protein; 98.2 6E-07 1.3E-11 73.2 1.0 45 16-60 172-226 (238)
20 cd00162 RING RING-finger (Real 98.1 6.4E-07 1.4E-11 52.8 0.6 41 20-60 1-45 (45)
21 KOG2177 Predicted E3 ubiquitin 97.9 4.3E-06 9.4E-11 66.3 0.9 58 14-72 9-71 (386)
22 KOG0317 Predicted E3 ubiquitin 97.8 4.1E-06 8.9E-11 69.6 -0.1 46 14-60 235-283 (293)
23 PF07800 DUF1644: Protein of u 97.8 5.5E-05 1.2E-09 58.0 5.5 28 91-118 107-134 (162)
24 TIGR00570 cdk7 CDK-activating 97.7 1.6E-05 3.6E-10 67.0 2.3 44 17-60 2-53 (309)
25 PHA02926 zinc finger-like prot 97.7 6.4E-06 1.4E-10 66.5 -0.5 44 16-60 168-229 (242)
26 KOG2164 Predicted E3 ubiquitin 97.7 1.1E-05 2.4E-10 71.5 0.2 42 18-60 186-235 (513)
27 smart00184 RING Ring finger. E 97.7 1.3E-05 2.9E-10 45.4 0.4 35 21-56 1-39 (39)
28 PF02176 zf-TRAF: TRAF-type zi 97.6 1.9E-05 4.1E-10 50.5 0.9 37 75-111 21-60 (60)
29 PF13445 zf-RING_UBOX: RING-ty 97.6 1.6E-05 3.4E-10 48.4 0.1 28 21-50 1-32 (43)
30 COG5574 PEX10 RING-finger-cont 97.5 2.3E-05 5.1E-10 64.5 0.0 44 16-60 213-261 (271)
31 PF02176 zf-TRAF: TRAF-type zi 97.5 7E-05 1.5E-09 47.8 2.0 43 83-125 1-43 (60)
32 KOG0311 Predicted E3 ubiquitin 97.3 1E-05 2.2E-10 69.0 -4.0 43 18-60 43-89 (381)
33 KOG0978 E3 ubiquitin ligase in 97.1 7.4E-05 1.6E-09 68.9 -1.4 44 16-60 641-688 (698)
34 PF12678 zf-rbx1: RING-H2 zinc 97.0 0.00051 1.1E-08 46.1 2.4 44 14-57 15-73 (73)
35 PF14570 zf-RING_4: RING/Ubox 97.0 0.00025 5.4E-09 44.2 0.5 39 21-59 1-46 (48)
36 KOG4159 Predicted E3 ubiquitin 96.8 0.00029 6.3E-09 61.5 -0.0 44 16-60 82-128 (398)
37 COG5152 Uncharacterized conser 96.6 0.00067 1.4E-08 54.2 0.4 56 16-72 194-255 (259)
38 KOG1813 Predicted E3 ubiquitin 96.5 0.0016 3.5E-08 54.5 2.4 48 18-66 241-292 (313)
39 PLN03086 PRLI-interacting fact 96.0 0.0098 2.1E-07 54.1 5.0 17 13-29 402-418 (567)
40 KOG4739 Uncharacterized protei 96.0 0.0047 1E-07 50.3 2.3 44 17-60 2-47 (233)
41 KOG4172 Predicted E3 ubiquitin 95.7 0.00064 1.4E-08 43.5 -2.8 41 19-60 8-53 (62)
42 KOG0802 E3 ubiquitin ligase [P 95.7 0.002 4.4E-08 58.2 -0.7 42 18-60 291-340 (543)
43 KOG4275 Predicted E3 ubiquitin 95.6 0.002 4.4E-08 54.0 -1.0 41 18-60 300-341 (350)
44 KOG2660 Locus-specific chromos 95.6 0.0012 2.5E-08 56.1 -2.5 44 17-60 14-60 (331)
45 KOG0824 Predicted E3 ubiquitin 95.6 0.0048 1E-07 51.9 1.0 42 18-60 7-52 (324)
46 PF11789 zf-Nse: Zinc-finger o 95.5 0.0043 9.4E-08 39.8 0.5 41 15-55 8-53 (57)
47 KOG2879 Predicted E3 ubiquitin 95.4 0.0094 2E-07 49.6 2.2 45 16-60 237-286 (298)
48 COG5222 Uncharacterized conser 95.3 0.0075 1.6E-07 51.0 1.3 40 19-58 275-318 (427)
49 PF12861 zf-Apc11: Anaphase-pr 95.3 0.0066 1.4E-07 42.2 0.7 30 31-60 46-81 (85)
50 PF05290 Baculo_IE-1: Baculovi 95.1 0.006 1.3E-07 45.7 0.1 48 13-60 75-131 (140)
51 COG5175 MOT2 Transcriptional r 94.8 0.0062 1.4E-07 52.2 -0.7 45 15-60 12-63 (480)
52 KOG4265 Predicted E3 ubiquitin 94.2 0.015 3.2E-07 49.9 0.4 44 16-60 288-335 (349)
53 PLN03086 PRLI-interacting fact 94.0 0.082 1.8E-06 48.3 4.7 22 80-103 492-514 (567)
54 PF14447 Prok-RING_4: Prokaryo 93.8 0.037 8E-07 35.4 1.6 39 20-60 9-49 (55)
55 KOG4692 Predicted E3 ubiquitin 93.7 0.012 2.7E-07 50.7 -1.1 55 5-60 409-466 (489)
56 PF07191 zinc-ribbons_6: zinc- 93.2 0.031 6.6E-07 37.5 0.4 38 18-60 1-40 (70)
57 COG5540 RING-finger-containing 93.2 0.037 7.9E-07 46.9 0.9 43 18-60 323-371 (374)
58 KOG4367 Predicted Zn-finger pr 93.1 0.026 5.6E-07 50.1 -0.0 32 17-49 3-34 (699)
59 KOG1785 Tyrosine kinase negati 92.8 0.026 5.6E-07 49.5 -0.5 42 18-60 369-415 (563)
60 KOG0804 Cytoplasmic Zn-finger 92.1 0.049 1.1E-06 48.2 0.4 56 5-60 162-221 (493)
61 PF11793 FANCL_C: FANCL C-term 91.9 0.045 9.7E-07 36.4 -0.1 43 18-60 2-65 (70)
62 KOG4185 Predicted E3 ubiquitin 91.8 0.12 2.7E-06 42.8 2.4 42 17-60 2-54 (296)
63 COG5236 Uncharacterized conser 91.1 0.059 1.3E-06 46.5 -0.2 103 15-118 58-179 (493)
64 KOG1039 Predicted E3 ubiquitin 90.7 0.096 2.1E-06 45.1 0.7 45 16-60 159-220 (344)
65 KOG1812 Predicted E3 ubiquitin 90.0 0.067 1.5E-06 46.6 -0.8 92 15-110 143-252 (384)
66 PF13909 zf-H2C2_5: C2H2-type 90.0 0.23 5.1E-06 25.6 1.6 23 93-117 2-24 (24)
67 KOG1002 Nucleotide excision re 89.1 0.081 1.8E-06 48.0 -1.0 47 13-60 531-585 (791)
68 PF07975 C1_4: TFIIH C1-like d 89.0 0.25 5.5E-06 31.1 1.5 37 21-57 2-50 (51)
69 KOG1571 Predicted E3 ubiquitin 88.4 0.2 4.3E-06 43.2 0.9 44 15-60 302-346 (355)
70 KOG0825 PHD Zn-finger protein 88.3 0.057 1.2E-06 50.9 -2.5 41 20-60 125-170 (1134)
71 PRK11088 rrmA 23S rRNA methylt 88.1 0.27 5.8E-06 40.2 1.5 24 18-41 2-27 (272)
72 PF04641 Rtf2: Rtf2 RING-finge 88.0 0.42 9.2E-06 39.3 2.6 46 15-60 110-160 (260)
73 KOG1814 Predicted E3 ubiquitin 87.8 0.22 4.7E-06 43.8 0.8 33 16-48 182-216 (445)
74 PF10571 UPF0547: Uncharacteri 87.3 0.27 5.9E-06 26.6 0.7 22 20-41 2-24 (26)
75 KOG3161 Predicted E3 ubiquitin 87.1 0.14 3.1E-06 47.3 -0.8 38 16-54 9-51 (861)
76 KOG3800 Predicted E3 ubiquitin 87.0 0.2 4.4E-06 42.1 0.1 41 20-60 2-50 (300)
77 COG5219 Uncharacterized conser 85.7 0.13 2.8E-06 49.6 -1.8 46 15-60 1466-1522(1525)
78 KOG1001 Helicase-like transcri 83.0 0.31 6.7E-06 45.5 -0.5 40 19-60 455-499 (674)
79 PF10367 Vps39_2: Vacuolar sor 82.7 1.5 3.2E-05 30.3 3.0 35 13-48 74-109 (109)
80 KOG4628 Predicted E3 ubiquitin 82.7 1 2.2E-05 38.9 2.5 42 19-60 230-277 (348)
81 PF10083 DUF2321: Uncharacteri 82.5 0.3 6.5E-06 37.5 -0.7 20 41-60 30-49 (158)
82 PF01363 FYVE: FYVE zinc finge 81.9 0.9 1.9E-05 29.4 1.5 34 15-48 6-42 (69)
83 PRK04023 DNA polymerase II lar 81.9 1.6 3.5E-05 42.5 3.7 50 6-60 617-673 (1121)
84 PF05605 zf-Di19: Drought indu 81.0 1.3 2.7E-05 27.6 1.9 27 92-120 3-29 (54)
85 KOG1645 RING-finger-containing 80.2 0.79 1.7E-05 40.4 1.0 43 18-60 4-55 (463)
86 PRK14714 DNA polymerase II lar 80.1 3 6.4E-05 41.6 4.9 51 5-60 657-719 (1337)
87 KOG3039 Uncharacterized conser 78.0 1 2.3E-05 37.3 1.0 46 15-60 218-269 (303)
88 COG4306 Uncharacterized protei 77.9 0.7 1.5E-05 34.6 -0.0 39 33-72 8-60 (160)
89 PF12660 zf-TFIIIC: Putative z 76.3 1.4 3E-05 31.2 1.2 41 19-60 15-65 (99)
90 KOG3039 Uncharacterized conser 74.5 1.1 2.5E-05 37.1 0.4 30 18-48 43-72 (303)
91 COG5243 HRD1 HRD ubiquitin lig 74.5 1 2.2E-05 39.4 0.1 44 17-60 286-344 (491)
92 PF04216 FdhE: Protein involve 73.6 1.5 3.3E-05 36.5 0.9 43 18-60 172-221 (290)
93 smart00064 FYVE Protein presen 73.4 1.8 3.8E-05 27.9 1.0 35 15-49 7-44 (68)
94 smart00647 IBR In Between Ring 73.1 3.6 7.9E-05 25.6 2.4 35 16-50 16-59 (64)
95 PF06906 DUF1272: Protein of u 72.6 2.1 4.6E-05 27.4 1.2 41 20-60 7-51 (57)
96 PF02891 zf-MIZ: MIZ/SP-RING z 71.6 1.5 3.3E-05 27.1 0.4 42 18-59 2-50 (50)
97 PF10426 zf-RAG1: Recombinatio 70.2 2.7 5.9E-05 23.5 1.1 23 92-114 3-25 (30)
98 PF01485 IBR: IBR domain; Int 69.9 3 6.5E-05 25.9 1.5 37 14-50 14-59 (64)
99 PF14446 Prok-RING_1: Prokaryo 69.6 3.1 6.7E-05 26.5 1.4 40 15-55 2-44 (54)
100 PRK14892 putative transcriptio 69.3 4.2 9.1E-05 29.0 2.2 40 8-48 11-51 (99)
101 KOG2231 Predicted E3 ubiquitin 69.1 2 4.3E-05 40.1 0.7 40 20-60 2-51 (669)
102 TIGR01562 FdhE formate dehydro 67.8 3.8 8.3E-05 34.8 2.1 42 18-59 184-233 (305)
103 PF13834 DUF4193: Domain of un 66.8 4 8.7E-05 29.1 1.7 39 7-45 57-98 (99)
104 KOG2817 Predicted E3 ubiquitin 66.5 2.6 5.6E-05 37.0 0.8 43 17-60 333-384 (394)
105 KOG3608 Zn finger proteins [Ge 66.2 2.7 5.8E-05 36.7 0.9 101 16-116 205-345 (467)
106 PRK14559 putative protein seri 65.8 4.6 0.0001 37.7 2.4 34 19-59 2-36 (645)
107 COG2888 Predicted Zn-ribbon RN 65.5 6.3 0.00014 25.6 2.3 12 91-104 50-61 (61)
108 PF00412 LIM: LIM domain; Int 65.2 2.8 6E-05 25.7 0.6 34 15-48 23-56 (58)
109 cd00065 FYVE FYVE domain; Zinc 64.8 3.3 7E-05 25.5 0.9 31 19-49 3-36 (57)
110 KOG4218 Nuclear hormone recept 64.6 3.1 6.7E-05 36.2 0.9 24 20-47 17-40 (475)
111 COG3813 Uncharacterized protei 64.3 3.6 7.9E-05 27.9 1.0 29 32-60 22-51 (84)
112 PF14445 Prok-RING_2: Prokaryo 64.2 0.48 1E-05 29.9 -3.0 42 18-59 7-50 (57)
113 TIGR00622 ssl1 transcription f 64.0 6.1 0.00013 28.8 2.2 38 20-57 57-110 (112)
114 smart00734 ZnF_Rad18 Rad18-lik 63.9 6.1 0.00013 21.1 1.7 21 92-114 2-22 (26)
115 KOG4362 Transcriptional regula 63.7 1.6 3.5E-05 40.8 -1.0 43 17-60 20-68 (684)
116 KOG1100 Predicted E3 ubiquitin 63.2 6.1 0.00013 31.6 2.4 38 21-60 161-199 (207)
117 KOG2068 MOT2 transcription fac 63.2 4.9 0.00011 34.5 1.8 42 19-60 250-297 (327)
118 PF09297 zf-NADH-PPase: NADH p 61.4 2.4 5.2E-05 23.6 -0.2 21 38-58 2-29 (32)
119 smart00154 ZnF_AN1 AN1-like Zi 61.2 6.4 0.00014 23.1 1.6 25 21-46 1-27 (39)
120 PF10272 Tmpp129: Putative tra 61.2 3.5 7.6E-05 35.8 0.7 29 32-60 306-350 (358)
121 PRK14890 putative Zn-ribbon RN 60.5 8 0.00017 25.0 2.1 40 18-57 7-55 (59)
122 KOG0827 Predicted E3 ubiquitin 60.2 3 6.5E-05 36.7 0.1 52 19-72 5-71 (465)
123 PF13240 zinc_ribbon_2: zinc-r 60.1 4.3 9.4E-05 21.1 0.7 6 53-58 16-21 (23)
124 PF12773 DZR: Double zinc ribb 59.3 7.5 0.00016 23.4 1.8 14 16-29 10-23 (50)
125 COG4647 AcxC Acetone carboxyla 59.0 4.6 0.0001 30.4 0.9 21 23-44 62-82 (165)
126 COG1645 Uncharacterized Zn-fin 58.2 6.2 0.00013 29.5 1.5 25 18-47 28-52 (131)
127 KOG3579 Predicted E3 ubiquitin 58.1 4.7 0.0001 34.1 0.9 34 16-49 266-302 (352)
128 PRK03564 formate dehydrogenase 58.1 9.7 0.00021 32.4 2.8 43 17-59 186-235 (309)
129 KOG4621 Uncharacterized conser 57.4 5.3 0.00011 30.2 1.0 40 8-48 71-112 (167)
130 PF12907 zf-met2: Zinc-binding 57.2 6.5 0.00014 23.4 1.2 26 92-119 2-31 (40)
131 PF01428 zf-AN1: AN1-like Zinc 57.2 11 0.00023 22.3 2.2 33 21-54 1-36 (43)
132 PF08882 Acetone_carb_G: Aceto 56.7 6 0.00013 28.8 1.1 13 32-44 24-36 (112)
133 PF15616 TerY-C: TerY-C metal 56.7 7.5 0.00016 29.1 1.7 39 18-60 77-115 (131)
134 PHA00616 hypothetical protein 56.3 9.7 0.00021 23.2 1.8 33 91-125 1-34 (44)
135 KOG2462 C2H2-type Zn-finger pr 56.3 5.5 0.00012 33.4 1.0 13 52-64 217-230 (279)
136 KOG0826 Predicted E3 ubiquitin 55.9 3.8 8.2E-05 35.2 0.0 47 13-59 295-344 (357)
137 smart00301 DM Doublesex DNA-bi 55.6 7.4 0.00016 24.7 1.3 33 78-112 15-47 (54)
138 KOG1734 Predicted RING-contain 55.4 3.3 7.1E-05 34.9 -0.4 44 17-60 223-280 (328)
139 PF06677 Auto_anti-p27: Sjogre 55.3 11 0.00023 22.5 1.9 23 19-45 18-40 (41)
140 cd00350 rubredoxin_like Rubred 54.6 11 0.00024 21.0 1.8 9 51-59 18-26 (33)
141 PRK00420 hypothetical protein; 54.4 8.8 0.00019 27.9 1.7 27 19-49 24-50 (112)
142 PF13894 zf-C2H2_4: C2H2-type 53.6 13 0.00028 17.9 1.9 22 93-116 2-24 (24)
143 PF13248 zf-ribbon_3: zinc-rib 52.2 7.1 0.00015 20.7 0.7 6 21-26 5-10 (26)
144 COG5220 TFB3 Cdk activating ki 51.2 3.9 8.4E-05 33.9 -0.7 43 18-60 10-63 (314)
145 PF12756 zf-C2H2_2: C2H2 type 50.4 16 0.00035 24.2 2.5 29 88-118 47-77 (100)
146 KOG2114 Vacuolar assembly/sort 49.9 8.2 0.00018 37.1 1.2 42 19-60 841-882 (933)
147 PF01286 XPA_N: XPA protein N- 49.7 11 0.00024 21.7 1.3 32 17-48 2-33 (34)
148 PF14319 Zn_Tnp_IS91: Transpos 46.3 17 0.00036 26.2 2.1 25 32-59 42-69 (111)
149 PF06750 DiS_P_DiS: Bacterial 45.8 20 0.00044 24.9 2.4 33 38-70 32-78 (92)
150 PF02318 FYVE_2: FYVE-type zin 44.2 19 0.00041 25.9 2.1 42 17-58 53-102 (118)
151 PF14569 zf-UDP: Zinc-binding 42.6 6.8 0.00015 26.8 -0.4 46 15-60 6-61 (80)
152 TIGR00595 priA primosomal prot 41.9 30 0.00066 31.1 3.5 44 17-60 212-263 (505)
153 PF08271 TF_Zn_Ribbon: TFIIB z 41.6 23 0.0005 20.8 1.9 27 19-47 1-27 (43)
154 PF09237 GAGA: GAGA factor; I 41.3 22 0.00049 22.5 1.8 29 89-119 22-51 (54)
155 KOG0828 Predicted E3 ubiquitin 41.1 5.7 0.00012 36.1 -1.2 43 18-60 571-633 (636)
156 KOG2932 E3 ubiquitin ligase in 41.0 12 0.00026 32.2 0.7 80 18-117 90-172 (389)
157 COG5194 APC11 Component of SCF 40.6 8.2 0.00018 26.6 -0.2 43 18-60 20-80 (88)
158 COG1198 PriA Primosomal protei 40.5 21 0.00046 33.9 2.4 43 18-60 435-485 (730)
159 cd00729 rubredoxin_SM Rubredox 40.3 24 0.00051 19.9 1.7 9 51-59 19-27 (34)
160 KOG0298 DEAD box-containing he 39.9 4.7 0.0001 40.3 -2.0 42 17-60 1152-1198(1394)
161 PF08273 Prim_Zn_Ribbon: Zinc- 39.8 20 0.00044 21.2 1.4 27 19-45 4-32 (40)
162 PF00751 DM: DM DNA binding do 39.7 17 0.00036 22.4 1.1 29 77-107 14-42 (47)
163 PRK05580 primosome assembly pr 39.7 25 0.00053 32.9 2.7 55 18-72 381-444 (679)
164 PF10235 Cript: Microtubule-as 38.6 19 0.0004 25.3 1.3 34 20-60 46-79 (90)
165 KOG1701 Focal adhesion adaptor 38.4 9 0.0002 34.1 -0.4 52 15-72 299-350 (468)
166 KOG2807 RNA polymerase II tran 38.0 19 0.00041 31.2 1.4 37 21-57 333-374 (378)
167 PF03107 C1_2: C1 domain; Int 37.5 34 0.00074 18.5 2.0 18 19-36 1-19 (30)
168 COG1592 Rubrerythrin [Energy p 37.4 26 0.00057 27.2 2.1 24 32-59 134-158 (166)
169 PRK11595 DNA utilization prote 36.9 20 0.00042 28.7 1.4 8 21-28 8-15 (227)
170 PF00096 zf-C2H2: Zinc finger, 36.4 22 0.00047 17.5 1.0 20 93-114 2-22 (23)
171 KOG3899 Uncharacterized conser 36.1 8.7 0.00019 32.8 -0.8 26 35-60 323-364 (381)
172 PF13913 zf-C2HC_2: zinc-finge 35.3 43 0.00092 17.5 2.1 21 92-114 3-23 (25)
173 KOG1701 Focal adhesion adaptor 35.2 38 0.00083 30.3 2.9 44 5-48 410-461 (468)
174 KOG3576 Ovo and related transc 34.8 17 0.00037 29.6 0.7 100 10-120 109-240 (267)
175 KOG0297 TNF receptor-associate 33.7 25 0.00055 30.7 1.7 26 90-115 85-112 (391)
176 PF13453 zf-TFIIB: Transcripti 33.2 30 0.00066 20.0 1.5 11 20-30 1-11 (41)
177 PLN02189 cellulose synthase 32.6 29 0.00063 34.3 1.9 42 19-60 35-86 (1040)
178 KOG3268 Predicted E3 ubiquitin 32.5 13 0.00029 29.5 -0.3 43 18-60 165-227 (234)
179 PF03854 zf-P11: P-11 zinc fin 32.5 11 0.00023 23.5 -0.6 40 19-60 3-45 (50)
180 PF03145 Sina: Seven in absent 32.4 25 0.00054 27.4 1.3 28 90-117 13-42 (198)
181 smart00661 RPOL9 RNA polymeras 32.0 32 0.0007 20.5 1.5 25 21-46 3-27 (52)
182 cd02249 ZZ Zinc finger, ZZ typ 31.5 28 0.0006 20.7 1.1 30 19-48 1-32 (46)
183 COG2816 NPY1 NTP pyrophosphohy 31.4 24 0.00052 29.7 1.1 24 37-60 109-139 (279)
184 PF10262 Rdx: Rdx family; Int 31.4 65 0.0014 21.1 3.0 26 93-120 7-32 (76)
185 COG0675 Transposase and inacti 31.3 54 0.0012 26.5 3.1 20 7-26 296-317 (364)
186 PRK01343 zinc-binding protein; 31.2 32 0.00068 22.1 1.4 9 19-27 10-18 (57)
187 PF13717 zinc_ribbon_4: zinc-r 30.9 48 0.001 18.9 2.0 11 19-29 3-13 (36)
188 PF06827 zf-FPG_IleRS: Zinc fi 30.9 25 0.00054 18.9 0.8 26 20-46 3-28 (30)
189 TIGR02098 MJ0042_CXXC MJ0042 f 30.6 25 0.00053 19.9 0.7 30 19-48 3-34 (38)
190 PF13008 zf-Paramyx-P: Zinc-bi 30.4 36 0.00077 21.0 1.4 25 22-46 17-44 (47)
191 KOG3608 Zn finger proteins [Ge 30.2 30 0.00066 30.4 1.5 25 92-118 264-289 (467)
192 PF01754 zf-A20: A20-like zinc 29.8 39 0.00085 18.0 1.4 15 91-106 1-15 (25)
193 PF11781 RRN7: RNA polymerase 29.7 37 0.0008 19.5 1.4 25 19-47 9-33 (36)
194 PF02148 zf-UBP: Zn-finger in 29.4 45 0.00097 21.1 1.9 22 21-43 1-23 (63)
195 PF00868 Transglut_N: Transglu 28.8 94 0.002 22.3 3.7 38 100-138 7-44 (118)
196 PTZ00303 phosphatidylinositol 28.6 34 0.00073 33.2 1.6 30 19-48 461-498 (1374)
197 PF08792 A2L_zn_ribbon: A2L zi 28.4 68 0.0015 18.0 2.3 26 18-46 3-28 (33)
198 COG4357 Zinc finger domain con 28.2 30 0.00066 24.7 1.0 21 40-60 63-90 (105)
199 PLN02436 cellulose synthase A 28.2 38 0.00083 33.6 2.0 42 19-60 37-88 (1094)
200 smart00132 LIM Zinc-binding do 28.2 65 0.0014 17.2 2.3 25 21-45 2-27 (39)
201 PRK14873 primosome assembly pr 28.1 54 0.0012 30.8 2.9 55 18-72 383-445 (665)
202 PF03966 Trm112p: Trm112p-like 27.4 52 0.0011 21.2 2.0 14 15-28 4-17 (68)
203 PF04423 Rad50_zn_hook: Rad50 27.1 38 0.00083 20.8 1.2 9 52-60 22-30 (54)
204 KOG1815 Predicted E3 ubiquitin 27.0 19 0.00042 31.8 -0.2 36 14-49 66-101 (444)
205 KOG1705 Uncharacterized conser 26.9 42 0.0009 23.8 1.5 39 17-60 26-65 (110)
206 KOG1729 FYVE finger containing 26.9 19 0.00041 30.4 -0.3 36 13-48 163-202 (288)
207 PLN02195 cellulose synthase A 26.8 45 0.00098 32.8 2.2 47 14-60 2-58 (977)
208 PF04606 Ogr_Delta: Ogr/Delta- 26.4 20 0.00044 21.6 -0.2 15 91-105 25-39 (47)
209 PRK12286 rpmF 50S ribosomal pr 26.3 58 0.0013 20.7 2.0 25 13-45 22-46 (57)
210 PF14353 CpXC: CpXC protein 26.1 35 0.00075 24.6 1.0 16 19-34 2-17 (128)
211 PF07649 C1_3: C1-like domain; 26.0 28 0.0006 18.8 0.4 16 20-35 2-18 (30)
212 TIGR03826 YvyF flagellar opero 25.8 21 0.00046 26.8 -0.2 36 6-49 69-104 (137)
213 KOG2272 Focal adhesion protein 25.0 43 0.00093 28.1 1.5 43 17-60 162-205 (332)
214 PF10497 zf-4CXXC_R1: Zinc-fin 25.0 42 0.00091 23.9 1.3 16 20-35 9-24 (105)
215 PF03119 DNA_ligase_ZBD: NAD-d 24.7 37 0.0008 18.3 0.7 10 20-29 1-10 (28)
216 PF07754 DUF1610: Domain of un 23.5 48 0.001 17.5 1.0 6 52-57 18-23 (24)
217 PLN02400 cellulose synthase 23.1 84 0.0018 31.3 3.2 42 19-60 37-88 (1085)
218 KOG2789 Putative Zn-finger pro 22.9 42 0.00091 29.8 1.1 32 18-49 74-106 (482)
219 KOG1842 FYVE finger-containing 22.6 17 0.00037 32.6 -1.4 37 12-48 174-213 (505)
220 PLN02638 cellulose synthase A 22.5 55 0.0012 32.6 1.8 47 14-60 13-69 (1079)
221 PLN02248 cellulose synthase-li 22.4 32 0.00069 34.3 0.3 29 32-60 145-176 (1135)
222 PF04438 zf-HIT: HIT zinc fing 21.8 44 0.00095 18.4 0.6 10 51-60 14-23 (30)
223 PF08209 Sgf11: Sgf11 (transcr 21.5 64 0.0014 18.3 1.3 23 91-115 4-26 (33)
224 PF02150 RNA_POL_M_15KD: RNA p 21.3 55 0.0012 18.6 1.0 25 20-46 3-27 (35)
225 PF05253 zf-U11-48K: U11-48K-l 20.9 74 0.0016 16.9 1.4 22 92-114 3-24 (27)
226 KOG2857 Predicted MYND Zn-fing 20.6 60 0.0013 24.8 1.4 22 39-60 5-27 (157)
227 PF14326 DUF4384: Domain of un 20.2 2.7E+02 0.0058 18.3 4.7 31 123-153 3-35 (83)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=99.96 E-value=2e-30 Score=216.26 Aligned_cols=148 Identities=33% Similarity=0.682 Sum_probs=134.8
Q ss_pred EEeeCCCeeecccccccCCCceeeccCCceeccccccccCCCCCCCccCc-chhhHHHHHHHH--------------hhc
Q 042263 11 STISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVNNKCPACRSCV-MLRSRVMDIALE--------------KTM 75 (159)
Q Consensus 11 ~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~Cr~~~-~~rn~~le~~~~--------------~~~ 75 (159)
++..+.+.|+||||.+++.+||+||.+||..|++|..++.++||.||.++ ++|++++|++++ +++
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 67889999999999999999999999999999999988888999999999 999999999999 688
Q ss_pred cCCCchhhhccCCCCCCCCCCC--CCcceeChhHHHhHhhhhcCCceE-----EEEeCcEEEEEEeCC---CcEEEEEEc
Q 042263 76 SFGENKDHERNCQCAPCACPLL--DCNFLGSASQLYLYFSWKNGKTFV-----SFTYKKRVKVTLNVN---DSVFLFRQQ 145 (159)
Q Consensus 76 ~~~~~~~He~~C~~~p~~Cp~~--gC~~~g~~~~l~~H~~~~H~~~~~-----~~~~~~~~~~~~~~~---~~~~~l~~~ 145 (159)
+|++..+||+.|.|+|+.||.+ .|+|+|.+++|+.|+...|+..++ .|.|..+.+..+... ..+.++.+.
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 8999999999999999999998 999999999999999999999876 667766666666655 478888888
Q ss_pred CCCcEEEEEceec
Q 042263 146 KNGHLFSLKNVVA 158 (159)
Q Consensus 146 ~d~~lF~l~~~~~ 158 (159)
+++.+|+++++.+
T Consensus 201 ~~~~~~~~q~~~~ 213 (299)
T KOG3002|consen 201 EFGLLFEVQCFRE 213 (299)
T ss_pred EEeeeeeehhhcC
Confidence 9999999998765
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=99.62 E-value=3.9e-16 Score=123.17 Aligned_cols=95 Identities=23% Similarity=0.407 Sum_probs=58.0
Q ss_pred hhhHHHHHHHH--------------hhccCCCchhhhccCCCCCCCCCC--CCCcceeChhHHHhHhhhhcCCceEEEEe
Q 042263 62 LRSRVMDIALE--------------KTMSFGENKDHERNCQCAPCACPL--LDCNFLGSASQLYLYFSWKNGKTFVSFTY 125 (159)
Q Consensus 62 ~rn~~le~~~~--------------~~~~~~~~~~He~~C~~~p~~Cp~--~gC~~~g~~~~l~~H~~~~H~~~~~~~~~ 125 (159)
+||++||++++ ++++|.++.+||++|+|+|+.||. .+|+|+|+.++|..|+.+.|+|.++...+
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 48999999998 578999999999999999999999 79999999999999999999998865443
Q ss_pred Cc-EEEEEEeCC--CcEEEEEE-cCCCcEEEEEce
Q 042263 126 KK-RVKVTLNVN--DSVFLFRQ-QKNGHLFSLKNV 156 (159)
Q Consensus 126 ~~-~~~~~~~~~--~~~~~l~~-~~d~~lF~l~~~ 156 (159)
.+ .+....... ....++.+ +.+|++|+|.+.
T Consensus 81 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~F~l~~~ 115 (198)
T PF03145_consen 81 FSISFLHSDINSVESPDWVLVQFSCFGKLFLLYVQ 115 (198)
T ss_dssp -EEEEEECTTT-SSSEEEEEEE-EETTEEEEEEEE
T ss_pred ceEEEeeecccccCCceEEEeecccCCccEEEEEE
Confidence 22 222222221 23455554 689999999853
No 3
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=98.85 E-value=1.8e-09 Score=93.62 Aligned_cols=103 Identities=23% Similarity=0.471 Sum_probs=80.5
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc-chhhH-----HHHHHHH-------------h
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV-MLRSR-----VMDIALE-------------K 73 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~-~~rn~-----~le~~~~-------------~ 73 (159)
.+.+.|++|..++.+|+..-.|||.||..|+.++. ..||.|+..+ .+..+ ....+++ .
T Consensus 19 ~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~GC~~ 98 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASRGCRA 98 (391)
T ss_pred cccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCCCccc
Confidence 45689999999999997634779999999999874 5799998887 33222 1222222 3
Q ss_pred hccCCCchhhhccCCCCCCCCCCCCCcceeChhHHHhHhhhhcCCceE
Q 042263 74 TMSFGENKDHERNCQCAPCACPLLDCNFLGSASQLYLYFSWKNGKTFV 121 (159)
Q Consensus 74 ~~~~~~~~~He~~C~~~p~~Cp~~gC~~~g~~~~l~~H~~~~H~~~~~ 121 (159)
.+....+..|+..| .+..||.. |+..+...++..|++........
T Consensus 99 ~~~l~~~~~Hl~~c--~~~~C~~~-C~~~~~~~d~~~hl~~~C~~~~~ 143 (391)
T KOG0297|consen 99 DLELEALQGHLSTC--DPLKCPHR-CGVQVPRDDLEDHLEAECPRRSL 143 (391)
T ss_pred cccHHHHHhHhccC--CcccCccc-cccccchHHHHHHHhcccccccc
Confidence 56677899999999 99999975 99999999999999887766543
No 4
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.82 E-value=2.3e-09 Score=70.40 Aligned_cols=55 Identities=33% Similarity=0.730 Sum_probs=29.9
Q ss_pred CeeecccccccCCCceeeccCCceecccccccc-CCCCCCCccCc----chhhHHHHHHH
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAKV-NNKCPACRSCV----MLRSRVMDIAL 71 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~-~~~CP~Cr~~~----~~rn~~le~~~ 71 (159)
+.+.|++|.++|+.||..-.|.|.||+.|+.+. ...||.|.++. ...|+.++.++
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HHHHHHH
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhhhhccC
Confidence 367899999999999865578999999999875 36799999998 34588888764
No 5
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.78 E-value=1.3e-09 Score=66.06 Aligned_cols=35 Identities=46% Similarity=0.957 Sum_probs=27.3
Q ss_pred cccccccCCCceeeccCCceeccccccccC-------CCCCCC
Q 042263 21 CPIWYQALKVPVSQSINGHIICSSCLAKVN-------NKCPAC 56 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-------~~CP~C 56 (159)
||||+++|++||.. .|||+||.+|+.+++ ..||.|
T Consensus 1 CpiC~~~~~~Pv~l-~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSL-PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCcccc-CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999999875 889999999999864 258887
No 6
>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=98.64 E-value=7.9e-09 Score=61.33 Aligned_cols=36 Identities=42% Similarity=0.947 Sum_probs=29.9
Q ss_pred cccccccCCCceeeccCCceeccccccccC---CCCCCC
Q 042263 21 CPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPAC 56 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~C 56 (159)
|+||++.+.+|+....+||+||..|+.++. .+||.|
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 899999999997777899999999998863 679987
No 7
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.61 E-value=4e-09 Score=89.19 Aligned_cols=65 Identities=29% Similarity=0.614 Sum_probs=53.5
Q ss_pred CceEEEeeCCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc----chhhHHHHHHHH
Q 042263 7 GSITSTISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV----MLRSRVMDIALE 72 (159)
Q Consensus 7 ~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~----~~rn~~le~~~~ 72 (159)
++|-+...-.+.|.|.||+++|+.|+.. +|||.||+.|+.+.. ..||.|+.++ ...|+.++.+++
T Consensus 12 tsipslk~lD~lLRC~IC~eyf~ip~it-pCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~ 83 (442)
T KOG0287|consen 12 TSIPSLKTLDDLLRCGICFEYFNIPMIT-PCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVK 83 (442)
T ss_pred ccCchhhhhHHHHHHhHHHHHhcCceec-cccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHH
Confidence 3455555566789999999999999764 799999999999864 6899999998 445788888887
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.60 E-value=1.7e-08 Score=79.74 Aligned_cols=54 Identities=33% Similarity=0.727 Sum_probs=43.2
Q ss_pred CCceEEEeeCCCeeecccccccCCCceeeccCCceeccccccccC-------------------CCCCCCccCc
Q 042263 6 NGSITSTISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-------------------NKCPACRSCV 60 (159)
Q Consensus 6 ~~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-------------------~~CP~Cr~~~ 60 (159)
+.+=...+...+.++|+||++.+++|+. ..|||.||..|+.++. .+||.|+.++
T Consensus 6 ~~~~~~~~~~~~~~~CpICld~~~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 6 DEDDTTLVDSGGDFDCNICLDQVRDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred ccccceeccCCCccCCccCCCcCCCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 3334445556678999999999999977 4789999999997641 3699999987
No 9
>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=98.57 E-value=3.5e-08 Score=63.62 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=43.1
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc----chhhHHHHHHH
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV----MLRSRVMDIAL 71 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~----~~rn~~le~~~ 71 (159)
.+.||||+++|.+|+.. .+||+||..|+.++. ..||.|+.++ ...|..+.+.+
T Consensus 1 ~~~Cpi~~~~~~~Pv~~-~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i 60 (63)
T smart00504 1 EFLCPISLEVMKDPVIL-PSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAI 60 (63)
T ss_pred CcCCcCCCCcCCCCEEC-CCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHH
Confidence 36799999999999864 789999999999863 5799999988 34566666554
No 10
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.53 E-value=2.1e-08 Score=62.50 Aligned_cols=42 Identities=31% Similarity=0.740 Sum_probs=35.4
Q ss_pred eeecccccccCCCceeeccCCce-eccccccccC---CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHI-ICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~-~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
...|+||++...++++. +|||. ||..|+.++. .+||.||+++
T Consensus 2 ~~~C~iC~~~~~~~~~~-pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i 47 (50)
T PF13920_consen 2 DEECPICFENPRDVVLL-PCGHLCFCEECAERLLKRKKKCPICRQPI 47 (50)
T ss_dssp HSB-TTTSSSBSSEEEE-TTCEEEEEHHHHHHHHHTTSBBTTTTBB-
T ss_pred cCCCccCCccCCceEEe-CCCChHHHHHHhHHhcccCCCCCcCChhh
Confidence 46799999999998776 88999 9999999873 6899999986
No 11
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.52 E-value=3.3e-08 Score=85.82 Aligned_cols=56 Identities=27% Similarity=0.548 Sum_probs=47.3
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc----chhhHHHHHHHH
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV----MLRSRVMDIALE 72 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~----~~rn~~le~~~~ 72 (159)
.+.+.|+||.+++..|+. -.|||.||..|+..+. ..||.|+.++ ..+|..|+++++
T Consensus 24 e~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe 86 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVE 86 (397)
T ss_pred ccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHH
Confidence 357899999999999986 4899999999998753 4799999988 356888888887
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=98.34 E-value=1e-07 Score=57.80 Aligned_cols=38 Identities=34% Similarity=0.796 Sum_probs=31.2
Q ss_pred ecccccccCC--CceeeccCCceeccccccccC---CCCCCCc
Q 042263 20 DCPIWYQALK--VPVSQSINGHIICSSCLAKVN---NKCPACR 57 (159)
Q Consensus 20 ~C~iC~~~l~--~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr 57 (159)
+|+||++.+. ..+....|||.||.+|+.++. .+||.||
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 5999999994 456667899999999999873 6899997
No 13
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.33 E-value=1.5e-07 Score=78.37 Aligned_cols=45 Identities=27% Similarity=0.630 Sum_probs=38.9
Q ss_pred CCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
-...+.|-||..+++.|+. .+|||.||+.|+.... ..||.||.+.
T Consensus 22 LDs~lrC~IC~~~i~ip~~-TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 22 LDSMLRCRICDCRISIPCE-TTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred chhHHHhhhhhheeeccee-cccccchhHHHHHHHhcCCCCCccccccH
Confidence 3457899999999999975 4889999999999864 5799999987
No 14
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=3.4e-07 Score=73.80 Aligned_cols=46 Identities=37% Similarity=0.810 Sum_probs=40.2
Q ss_pred eCCCeeecccccccCCCceeeccCCceeccccccccC------CCCCCCccCc
Q 042263 14 SDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
.|...|+|.||++..++||.. -|||.||=.|+.+|. +.||+|+..+
T Consensus 43 ~~~~~FdCNICLd~akdPVvT-lCGHLFCWpClyqWl~~~~~~~~cPVCK~~V 94 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAKDPVVT-LCGHLFCWPCLYQWLQTRPNSKECPVCKAEV 94 (230)
T ss_pred CCCCceeeeeeccccCCCEEe-ecccceehHHHHHHHhhcCCCeeCCcccccc
Confidence 367799999999999999875 579999999999984 4689999876
No 15
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=1.6e-07 Score=73.10 Aligned_cols=44 Identities=34% Similarity=0.859 Sum_probs=35.7
Q ss_pred CeeecccccccCCCce-eeccCCceeccccccccC---CCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVPV-SQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv-~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
..+.||||++.+..-+ .-..|||+||+.|+.... .+||+|+..+
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkI 177 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKI 177 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence 3699999999986543 335789999999998763 6899999876
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.23 E-value=3.8e-07 Score=55.47 Aligned_cols=39 Identities=36% Similarity=0.845 Sum_probs=31.7
Q ss_pred ecccccccC--CCceeeccCCceeccccccccC---CCCCCCcc
Q 042263 20 DCPIWYQAL--KVPVSQSINGHIICSSCLAKVN---NKCPACRS 58 (159)
Q Consensus 20 ~C~iC~~~l--~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~ 58 (159)
+|++|++.+ ..+.+.-.|||+||..|+.++. ..||.|++
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 599999999 3344556789999999999875 57999984
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=98.23 E-value=3.8e-07 Score=54.18 Aligned_cols=36 Identities=42% Similarity=0.851 Sum_probs=31.1
Q ss_pred cccccccCCCceeeccCCceeccccccccC-----CCCCCC
Q 042263 21 CPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPAC 56 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~C 56 (159)
|+||.+.+..|+..-++||.||..|+.++. .+||.|
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 899999999998566889999999998863 469887
No 18
>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=98.17 E-value=8.6e-07 Score=59.56 Aligned_cols=56 Identities=27% Similarity=0.396 Sum_probs=41.5
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccccC----CCCCCCccCc----chhhHHHHHHHH
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPACRSCV----MLRSRVMDIALE 72 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~----~~rn~~le~~~~ 72 (159)
++.|.|||++++|.+||.. ..||+|+.+++.++. ..||.++.++ ...|..|.+.++
T Consensus 2 P~~f~CpIt~~lM~dPVi~-~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~ 65 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVIL-PSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIE 65 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEE-TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHH
T ss_pred CcccCCcCcCcHhhCceeC-CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHH
Confidence 5789999999999999875 789999999998874 4699999988 456777776665
No 19
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.16 E-value=6e-07 Score=73.22 Aligned_cols=45 Identities=24% Similarity=0.547 Sum_probs=35.9
Q ss_pred CCeeecccccccCCCc-e------eeccCCceeccccccccC---CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVP-V------SQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~P-v------~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.+..+|+||++.+.++ + ....|||.||..|+.++. ..||.||.++
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 4468999999987653 1 234689999999998874 6899999988
No 20
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.14 E-value=6.4e-07 Score=52.82 Aligned_cols=41 Identities=39% Similarity=0.914 Sum_probs=33.4
Q ss_pred ecccccccCCCceeeccCCceeccccccccC----CCCCCCccCc
Q 042263 20 DCPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
+|+||.+.+..++..-.+||.||..|+..+. ..||.|+..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4999999997776665589999999998653 4699998753
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.86 E-value=4.3e-06 Score=66.25 Aligned_cols=58 Identities=28% Similarity=0.557 Sum_probs=46.1
Q ss_pred eCCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc--chhhHHHHHHHH
Q 042263 14 SDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV--MLRSRVMDIALE 72 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~--~~rn~~le~~~~ 72 (159)
...+.+.||||++.|+.|.. =+|||+||..|+..++ ..||.||... ..+|..+++++.
T Consensus 9 ~~~~~~~C~iC~~~~~~p~~-l~C~H~~c~~C~~~~~~~~~~Cp~cr~~~~~~~~n~~l~~~~~ 71 (386)
T KOG2177|consen 9 VLQEELTCPICLEYFREPVL-LPCGHNFCRACLTRSWEGPLSCPVCRPPSRNLRPNVLLANLVE 71 (386)
T ss_pred hccccccChhhHHHhhcCcc-ccccchHhHHHHHHhcCCCcCCcccCCchhccCccHHHHHHHH
Confidence 45678999999999999943 3679999999999876 5899999622 346777777776
No 22
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.81 E-value=4.1e-06 Score=69.57 Aligned_cols=46 Identities=26% Similarity=0.587 Sum_probs=38.7
Q ss_pred eCCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 14 SDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
++....+|.+|++....|.- .+|||.||-+|+..+- ..||.||..+
T Consensus 235 i~~a~~kC~LCLe~~~~pSa-TpCGHiFCWsCI~~w~~ek~eCPlCR~~~ 283 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRSNPSA-TPCGHIFCWSCILEWCSEKAECPLCREKF 283 (293)
T ss_pred CCCCCCceEEEecCCCCCCc-CcCcchHHHHHHHHHHccccCCCcccccC
Confidence 34557899999999999954 4789999999998873 5799999987
No 23
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=97.77 E-value=5.5e-05 Score=58.05 Aligned_cols=28 Identities=21% Similarity=0.316 Sum_probs=25.6
Q ss_pred CCCCCCCCCcceeChhHHHhHhhhhcCC
Q 042263 91 PCACPLLDCNFLGSASQLYLYFSWKNGK 118 (159)
Q Consensus 91 p~~Cp~~gC~~~g~~~~l~~H~~~~H~~ 118 (159)
+-.|+..+|.|.|.+.+|.+|...+|+.
T Consensus 107 ~RsC~~e~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 107 KRSCSQESCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred CccCcccccccccCHHHHHHHHHhhCCC
Confidence 4488989999999999999999999986
No 24
>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=97.73 E-value=1.6e-05 Score=66.96 Aligned_cols=44 Identities=25% Similarity=0.585 Sum_probs=33.7
Q ss_pred Ceeecccccc--cCCCce--eeccCCceeccccccccC----CCCCCCccCc
Q 042263 17 DLFDCPIWYQ--ALKVPV--SQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~--~l~~Pv--~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
+...||+|.. ++.+-+ +.-.|||.||.+|+..++ ..||.|+.++
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence 4567999998 555431 222689999999999864 4799999987
No 25
>PHA02926 zinc finger-like protein; Provisional
Probab=97.71 E-value=6.4e-06 Score=66.47 Aligned_cols=44 Identities=25% Similarity=0.633 Sum_probs=34.0
Q ss_pred CCeeecccccccCCC---------ceeeccCCceeccccccccC---------CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKV---------PVSQSINGHIICSSCLAKVN---------NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~---------Pv~qC~~GH~~C~~C~~~~~---------~~CP~Cr~~~ 60 (159)
++..+|+||++.... ++. -.|+|.||-.|+.+|. ..||.||..+
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL-~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f 229 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLL-DSCNHIFCITCINIWHRTRRETGASDNCPICRTRF 229 (242)
T ss_pred cCCCCCccCcccccccccccccccccc-CCCCchHHHHHHHHHHHhccccCcCCcCCCCccee
Confidence 446889999988633 222 3789999999999874 2399999987
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=1.1e-05 Score=71.48 Aligned_cols=42 Identities=38% Similarity=0.852 Sum_probs=35.6
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC--------CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN--------NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~--------~~CP~Cr~~~ 60 (159)
...||||++...-|+.. .|||+||.+|+-..+ ..||.|+..|
T Consensus 186 ~~~CPICL~~~~~p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I 235 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTI 235 (513)
T ss_pred CCcCCcccCCCCccccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhc
Confidence 67899999999888664 589999999987643 5799999988
No 27
>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=97.65 E-value=1.3e-05 Score=45.39 Aligned_cols=35 Identities=49% Similarity=0.986 Sum_probs=28.6
Q ss_pred cccccccCCCceeeccCCceeccccccccC----CCCCCC
Q 042263 21 CPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPAC 56 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~C 56 (159)
|+||.+....++.. .+||.||..|+.++. .+||.|
T Consensus 1 C~iC~~~~~~~~~~-~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVL-PCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEe-cCCChHHHHHHHHHHHhCcCCCCCC
Confidence 78999998877664 789999999998652 469887
No 28
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.62 E-value=1.9e-05 Score=50.48 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=25.3
Q ss_pred ccCCCchhhhc-cCCCCCCCCCC--CCCcceeChhHHHhH
Q 042263 75 MSFGENKDHER-NCQCAPCACPL--LDCNFLGSASQLYLY 111 (159)
Q Consensus 75 ~~~~~~~~He~-~C~~~p~~Cp~--~gC~~~g~~~~l~~H 111 (159)
+.-.++.+|.+ .|+++++.||+ .||++.+.+.+|.+|
T Consensus 21 i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 21 IPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred eeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 55567778887 88888888887 388888888888776
No 29
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.58 E-value=1.6e-05 Score=48.44 Aligned_cols=28 Identities=36% Similarity=0.904 Sum_probs=18.1
Q ss_pred cccccccCCC----ceeeccCCceeccccccccC
Q 042263 21 CPIWYQALKV----PVSQSINGHIICSSCLAKVN 50 (159)
Q Consensus 21 C~iC~~~l~~----Pv~qC~~GH~~C~~C~~~~~ 50 (159)
||||.+ +.. |+.. .|||+||..|++++.
T Consensus 1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l~ 32 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKLS 32 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHHH
Confidence 899999 766 8765 589999999999874
No 30
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=2.3e-05 Score=64.45 Aligned_cols=44 Identities=32% Similarity=0.659 Sum_probs=37.0
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccc-cC----CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAK-VN----NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~-~~----~~CP~Cr~~~ 60 (159)
...++|++|.+....|++. +|||+||-+|+-. +. ..||.||...
T Consensus 213 ~~d~kC~lC~e~~~~ps~t-~CgHlFC~~Cl~~~~t~~k~~~CplCRak~ 261 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCT-PCGHLFCLSCLLISWTKKKYEFCPLCRAKV 261 (271)
T ss_pred ccccceeeeecccCCcccc-cccchhhHHHHHHHHHhhccccCchhhhhc
Confidence 3478899999999999864 7899999999877 42 3599999976
No 31
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.46 E-value=7e-05 Score=47.78 Aligned_cols=43 Identities=28% Similarity=0.389 Sum_probs=33.1
Q ss_pred hhccCCCCCCCCCCCCCcceeChhHHHhHhhhhcCCceEEEEe
Q 042263 83 HERNCQCAPCACPLLDCNFLGSASQLYLYFSWKNGKTFVSFTY 125 (159)
Q Consensus 83 He~~C~~~p~~Cp~~gC~~~g~~~~l~~H~~~~H~~~~~~~~~ 125 (159)
|+++|+++++.||+.+|.-...+.+|..|+....++..+.=.|
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 8889999999999988877788999999999988887654444
No 32
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=1e-05 Score=68.99 Aligned_cols=43 Identities=33% Similarity=0.624 Sum_probs=37.0
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC----CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
.+.||||+++++..+..=.|+|+||..|+-+.. +.||+||+..
T Consensus 43 ~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l 89 (381)
T KOG0311|consen 43 QVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKL 89 (381)
T ss_pred hhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhc
Confidence 678999999999876655689999999988753 6899999988
No 33
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=7.4e-05 Score=68.87 Aligned_cols=44 Identities=27% Similarity=0.742 Sum_probs=37.1
Q ss_pred CCeeecccccccCCCceeeccCCceecccccccc----CCCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
...|.||+|..=.++.|. -.|||.||..|+.+. ..+||.|..+|
T Consensus 641 K~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 641 KELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYETRQRKCPKCNAAF 688 (698)
T ss_pred HhceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHHhcCCCCCCCCCC
Confidence 358999999987888765 378999999999886 36899999988
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=97.01 E-value=0.00051 Score=46.12 Aligned_cols=44 Identities=32% Similarity=0.575 Sum_probs=31.6
Q ss_pred eCCCeeecccccccCCCc------------eeeccCCceeccccccccC---CCCCCCc
Q 042263 14 SDQDLFDCPIWYQALKVP------------VSQSINGHIICSSCLAKVN---NKCPACR 57 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~~P------------v~qC~~GH~~C~~C~~~~~---~~CP~Cr 57 (159)
.|...-.|.||++.|.+| +..=.|||.|-..|+.++. ..||+||
T Consensus 15 ~~~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 15 WDIADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp ESSCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred ecCcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 344444599999999443 3333589999999999863 6899997
No 35
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.95 E-value=0.00025 Score=44.16 Aligned_cols=39 Identities=28% Similarity=0.673 Sum_probs=21.0
Q ss_pred cccccccCC--C-ceeeccCCceeccccccccC----CCCCCCccC
Q 042263 21 CPIWYQALK--V-PVSQSINGHIICSSCLAKVN----NKCPACRSC 59 (159)
Q Consensus 21 C~iC~~~l~--~-Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~ 59 (159)
||+|.+.+. + -++.|+||..+|..|+.++. +.||.||.+
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 788988883 2 24569999999999988764 679999986
No 36
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.82 E-value=0.00029 Score=61.49 Aligned_cols=44 Identities=34% Similarity=0.739 Sum_probs=39.3
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.+.|+|.||...|.+||.. +|||.||..|+.+.. ..||.||.++
T Consensus 82 ~sef~c~vc~~~l~~pv~t-pcghs~c~~Cl~r~ld~~~~cp~Cr~~l 128 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVT-PCGHSFCLECLDRSLDQETECPLCRDEL 128 (398)
T ss_pred cchhhhhhhHhhcCCCccc-cccccccHHHHHHHhccCCCCccccccc
Confidence 6789999999999999876 999999999977653 5799999988
No 37
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.56 E-value=0.00067 Score=54.16 Aligned_cols=56 Identities=23% Similarity=0.452 Sum_probs=41.4
Q ss_pred CCeeecccccccCCCceeeccCCceecccccccc-C--CCCCCCccCc---chhhHHHHHHHH
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKV-N--NKCPACRSCV---MLRSRVMDIALE 72 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~-~--~~CP~Cr~~~---~~rn~~le~~~~ 72 (159)
.--|.|.||.+-+..||.. .|||.||+.|..+- . ..|-+|.... ..-...+++++.
T Consensus 194 ~IPF~C~iCKkdy~spvvt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 194 KIPFLCGICKKDYESPVVT-ECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred CCceeehhchhhccchhhh-hcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHHh
Confidence 3368899999999999864 78999999997653 2 5799998877 222344555543
No 38
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.51 E-value=0.0016 Score=54.53 Aligned_cols=48 Identities=27% Similarity=0.446 Sum_probs=38.6
Q ss_pred eeecccccccCCCceeeccCCceecccccccc-C--CCCCCCccCc-chhhHH
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKV-N--NKCPACRSCV-MLRSRV 66 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~-~--~~CP~Cr~~~-~~rn~~ 66 (159)
-+.|-||.+++..||.. .|||.||..|..+- . ..|.+|...+ .+-|.+
T Consensus 241 Pf~c~icr~~f~~pVvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~a 292 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVA 292 (313)
T ss_pred Cccccccccccccchhh-cCCceeehhhhccccccCCcceecccccccccchH
Confidence 45799999999999874 78999999997654 2 5799999998 444443
No 39
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.05 E-value=0.0098 Score=54.14 Aligned_cols=17 Identities=18% Similarity=0.239 Sum_probs=12.6
Q ss_pred eeCCCeeecccccccCC
Q 042263 13 ISDQDLFDCPIWYQALK 29 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~ 29 (159)
-.+.+...|+-|.....
T Consensus 402 s~~~~~V~C~NC~~~i~ 418 (567)
T PLN03086 402 SMDVDTVECRNCKHYIP 418 (567)
T ss_pred cCCCCeEECCCCCCccc
Confidence 35677788999987764
No 40
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.96 E-value=0.0047 Score=50.31 Aligned_cols=44 Identities=23% Similarity=0.652 Sum_probs=36.0
Q ss_pred CeeecccccccC-CCceeeccCCceeccccccccCC-CCCCCccCc
Q 042263 17 DLFDCPIWYQAL-KVPVSQSINGHIICSSCLAKVNN-KCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l-~~Pv~qC~~GH~~C~~C~~~~~~-~CP~Cr~~~ 60 (159)
+-..|..|+.-- .+|.|...|+|+||..|..-..+ .||.|+.++
T Consensus 2 ~~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~i 47 (233)
T KOG4739|consen 2 DFVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSI 47 (233)
T ss_pred ceEEeccccccCCCCceeeeechhhhhhhhcccCCcccccccccee
Confidence 456788888654 57788888999999999877654 899999987
No 41
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.75 E-value=0.00064 Score=43.49 Aligned_cols=41 Identities=29% Similarity=0.690 Sum_probs=32.6
Q ss_pred eecccccccCCCceeeccCCce-eccccccccC----CCCCCCccCc
Q 042263 19 FDCPIWYQALKVPVSQSINGHI-ICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~-~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
-+|.||++-..+.|.. .|||. .|-.|-.+++ +.||.||.++
T Consensus 8 dECTICye~pvdsVlY-tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLY-TCGHMCMCYACGLRLKKALHGCCPICRAPI 53 (62)
T ss_pred cceeeeccCcchHHHH-HcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence 5799999988777553 66995 8889976653 6899999987
No 42
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.002 Score=58.16 Aligned_cols=42 Identities=33% Similarity=0.582 Sum_probs=35.1
Q ss_pred eeecccccccCCC-----ceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 18 LFDCPIWYQALKV-----PVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~-----Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.-.|+||.+.|.. |... +|||.|+.+|+.+|. ..||.||..+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred CCeeeeechhhcccccccccee-ecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 5679999999977 4443 679999999999873 6899999965
No 43
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.64 E-value=0.002 Score=54.05 Aligned_cols=41 Identities=32% Similarity=0.642 Sum_probs=35.8
Q ss_pred eeecccccccCCCceeeccCCc-eeccccccccCCCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGH-IICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH-~~C~~C~~~~~~~CP~Cr~~~ 60 (159)
...|.||++...+-++. +||| ..|-.|-.+++ .||+||+-+
T Consensus 300 ~~LC~ICmDaP~DCvfL-eCGHmVtCt~CGkrm~-eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFL-ECGHMVTCTKCGKRMN-ECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEe-ecCcEEeehhhccccc-cCchHHHHH
Confidence 55699999999998776 8899 68999999886 999999876
No 44
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.63 E-value=0.0012 Score=56.06 Aligned_cols=44 Identities=23% Similarity=0.483 Sum_probs=38.2
Q ss_pred CeeecccccccCCCceeeccCCceecccccccc---CCCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAKV---NNKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~---~~~CP~Cr~~~ 60 (159)
....|.+|..+|.++...-.|=|+||.+|+-+. ...||.|...+
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVI 60 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence 367899999999999777778999999998774 36899999988
No 45
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.0048 Score=51.92 Aligned_cols=42 Identities=26% Similarity=0.531 Sum_probs=35.7
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC----CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
.-+|+||+....-|+.. .|+|.||--|+.... ..|+.||.+|
T Consensus 7 ~~eC~IC~nt~n~Pv~l-~C~HkFCyiCiKGsy~ndk~~CavCR~pi 52 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNL-YCFHKFCYICIKGSYKNDKKTCAVCRFPI 52 (324)
T ss_pred CCcceeeeccCCcCccc-cccchhhhhhhcchhhcCCCCCceecCCC
Confidence 34799999999999765 789999999998752 4699999998
No 46
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.55 E-value=0.0043 Score=39.85 Aligned_cols=41 Identities=24% Similarity=0.487 Sum_probs=28.2
Q ss_pred CCCeeecccccccCCCceeeccCCceeccccccccC-----CCCCC
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPA 55 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~ 55 (159)
..-.+.|||...+|.+||..-.|||+|-.+.+..+. .+||.
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 445689999999999998876789999999988754 35887
No 47
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.42 E-value=0.0094 Score=49.62 Aligned_cols=45 Identities=29% Similarity=0.617 Sum_probs=36.1
Q ss_pred CCeeecccccccCCCceeeccCCceeccccccccC-----CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~Cr~~~ 60 (159)
.+..+||+|.+....|...=.|||++|=.|+.+.. -.||.|.++.
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 34567999999999995533579999999998753 3799998876
No 48
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.32 E-value=0.0075 Score=51.00 Aligned_cols=40 Identities=30% Similarity=0.801 Sum_probs=34.5
Q ss_pred eecccccccCCCceeeccCCceeccccccccC----CCCCCCcc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKVN----NKCPACRS 58 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~ 58 (159)
|.||.|..+++.|+..=.|||.||..|++... ..||.|..
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 99999999999998753489999999998643 58999966
No 49
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.26 E-value=0.0066 Score=42.17 Aligned_cols=30 Identities=27% Similarity=0.507 Sum_probs=24.7
Q ss_pred ceeeccCCceeccccccccC------CCCCCCccCc
Q 042263 31 PVSQSINGHIICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 31 Pv~qC~~GH~~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
|+....|||.|=..|+.++. +.||.||++.
T Consensus 46 plv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 46 PLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred ceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 55556789999999998863 5799999976
No 50
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=95.10 E-value=0.006 Score=45.71 Aligned_cols=48 Identities=25% Similarity=0.562 Sum_probs=38.8
Q ss_pred eeCCCeeecccccccCCCceeec---cCCceeccccccccC------CCCCCCccCc
Q 042263 13 ISDQDLFDCPIWYQALKVPVSQS---INGHIICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~Pv~qC---~~GH~~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
-.|+..++|.||.+...++-+.= -||-.+|..|-..+| +.||.|++.+
T Consensus 75 F~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSF 131 (140)
T PF05290_consen 75 FLDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSF 131 (140)
T ss_pred ecCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccc
Confidence 44778999999999987654431 269999999998876 6799999988
No 51
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.77 E-value=0.0062 Score=52.25 Aligned_cols=45 Identities=29% Similarity=0.753 Sum_probs=35.7
Q ss_pred CCCeeecccccccCCC---ceeeccCCceecccccccc----CCCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALKV---PVSQSINGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~---Pv~qC~~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
|.+.+ ||.|.+.|.. -.+.|+||-.+|..|+..+ +++||.||...
T Consensus 12 deed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y 63 (480)
T COG5175 12 DEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKY 63 (480)
T ss_pred ccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhc
Confidence 44445 9999999852 2456999999999999765 47999999865
No 52
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.25 E-value=0.015 Score=49.91 Aligned_cols=44 Identities=27% Similarity=0.609 Sum_probs=36.3
Q ss_pred CCeeecccccccCCCceeeccCCce-eccccccccC---CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPVSQSINGHI-ICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~qC~~GH~-~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.+--+|-||+.=.++-+.. +|.|. .|++|-+.+. ++||+||+++
T Consensus 288 ~~gkeCVIClse~rdt~vL-PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi 335 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVL-PCRHLCLCSGCAKSLRYQTNNCPICRQPI 335 (349)
T ss_pred cCCCeeEEEecCCcceEEe-cchhhehhHhHHHHHHHhhcCCCccccch
Confidence 3467899999999886544 77995 9999988874 6899999998
No 53
>PLN03086 PRLI-interacting factor K; Provisional
Probab=93.99 E-value=0.082 Score=48.26 Aligned_cols=22 Identities=18% Similarity=0.463 Sum_probs=10.3
Q ss_pred chhhhc-cCCCCCCCCCCCCCccee
Q 042263 80 NKDHER-NCQCAPCACPLLDCNFLG 103 (159)
Q Consensus 80 ~~~He~-~C~~~p~~Cp~~gC~~~g 103 (159)
+..|.. .|+.+++.|++ |+...
T Consensus 492 L~~H~~thCp~Kpi~C~f--C~~~v 514 (567)
T PLN03086 492 MVQHQASTCPLRLITCRF--CGDMV 514 (567)
T ss_pred HHhhhhccCCCCceeCCC--CCCcc
Confidence 444432 35555555554 54443
No 54
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.85 E-value=0.037 Score=35.35 Aligned_cols=39 Identities=31% Similarity=0.572 Sum_probs=27.6
Q ss_pred ecccccccC-CCceeeccCCceeccccccccC-CCCCCCccCc
Q 042263 20 DCPIWYQAL-KVPVSQSINGHIICSSCLAKVN-NKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l-~~Pv~qC~~GH~~C~~C~~~~~-~~CP~Cr~~~ 60 (159)
.|-.|...- +.++. +|||.+|..|+.-.. +-||.|..++
T Consensus 9 ~~~~~~~~~~~~~~~--pCgH~I~~~~f~~~rYngCPfC~~~~ 49 (55)
T PF14447_consen 9 PCVFCGFVGTKGTVL--PCGHLICDNCFPGERYNGCPFCGTPF 49 (55)
T ss_pred eEEEccccccccccc--cccceeeccccChhhccCCCCCCCcc
Confidence 344455553 34443 559999999998764 5799999887
No 55
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.66 E-value=0.012 Score=50.70 Aligned_cols=55 Identities=25% Similarity=0.472 Sum_probs=41.1
Q ss_pred CCCceEEEeeCCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 5 KNGSITSTISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 5 ~~~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
+.-+....+-|.+.-.||||+--.-..|++ +|||.-|..|+.+.. +.|=.|...+
T Consensus 409 ~~~~~~~~lp~sEd~lCpICyA~pi~Avf~-PC~H~SC~~CI~qHlmN~k~CFfCktTv 466 (489)
T KOG4692|consen 409 KEESFNKDLPDSEDNLCPICYAGPINAVFA-PCSHRSCYGCITQHLMNCKRCFFCKTTV 466 (489)
T ss_pred hHHhhcCCCCCcccccCcceecccchhhcc-CCCCchHHHHHHHHHhcCCeeeEeccee
Confidence 333444456677888899999777777887 899999999999864 4576776665
No 56
>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=93.19 E-value=0.031 Score=37.47 Aligned_cols=38 Identities=29% Similarity=0.606 Sum_probs=22.9
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC--CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN--NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~--~~CP~Cr~~~ 60 (159)
++.||.|...|.. ..|+..|..|-.... +.||.|..++
T Consensus 1 e~~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 1 ENTCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp --B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred CCcCCCCCCccEE-----eCCEEECccccccceecccCCCcccHH
Confidence 3679999977643 338999999988754 6899999987
No 57
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.18 E-value=0.037 Score=46.94 Aligned_cols=43 Identities=26% Similarity=0.493 Sum_probs=35.3
Q ss_pred eeecccccccCC--CceeeccCCceeccccccccC----CCCCCCccCc
Q 042263 18 LFDCPIWYQALK--VPVSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~--~Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
-.+|.||++-+. +.+..-+|.|.|=.+|+++|. .+||+||+++
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 478999998874 334456789999999999984 6899999986
No 58
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.12 E-value=0.026 Score=50.06 Aligned_cols=32 Identities=19% Similarity=0.563 Sum_probs=28.2
Q ss_pred CeeecccccccCCCceeeccCCceecccccccc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAKV 49 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~ 49 (159)
++|.||||..++++||.. +|||..|..|-..+
T Consensus 3 eelkc~vc~~f~~epiil-~c~h~lc~~ca~~~ 34 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPIIL-PCSHNLCQACARNI 34 (699)
T ss_pred ccccCceehhhccCceEe-ecccHHHHHHHHhh
Confidence 689999999999999876 78999999997543
No 59
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.81 E-value=0.026 Score=49.49 Aligned_cols=42 Identities=36% Similarity=0.666 Sum_probs=35.0
Q ss_pred eeecccccccCCCceeeccCCceeccccccccC-----CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~Cr~~~ 60 (159)
.-.|-||-+-=++ |-.-+|||..|.+|+..|+ ..||.||-.|
T Consensus 369 FeLCKICaendKd-vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 369 FELCKICAENDKD-VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred HHHHHHhhccCCC-cccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 3459999998887 5555789999999999875 5799999887
No 60
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=92.13 E-value=0.049 Score=48.23 Aligned_cols=56 Identities=25% Similarity=0.557 Sum_probs=42.3
Q ss_pred CCCceEEEeeCCCeeecccccccCCCce---eeccCCceeccccccccC-CCCCCCccCc
Q 042263 5 KNGSITSTISDQDLFDCPIWYQALKVPV---SQSINGHIICSSCLAKVN-NKCPACRSCV 60 (159)
Q Consensus 5 ~~~~~~~~~~~~~~l~C~iC~~~l~~Pv---~qC~~GH~~C~~C~~~~~-~~CP~Cr~~~ 60 (159)
.+|+-+..+.-.+.-+||||++=|.+-+ ..-.|.|.|=.+|+.+|+ ..||.||-.-
T Consensus 162 ~d~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q 221 (493)
T KOG0804|consen 162 EDGASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQ 221 (493)
T ss_pred ccCCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhc
Confidence 4454445556667889999999997543 444579999999999986 6899998643
No 61
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=91.88 E-value=0.045 Score=36.40 Aligned_cols=43 Identities=26% Similarity=0.488 Sum_probs=19.0
Q ss_pred eeecccccccCC----Cceeec---cCCceeccccccccC--------------CCCCCCccCc
Q 042263 18 LFDCPIWYQALK----VPVSQS---INGHIICSSCLAKVN--------------NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~----~Pv~qC---~~GH~~C~~C~~~~~--------------~~CP~Cr~~~ 60 (159)
.++|+||+..+. .|...| .||..|=..|+.++. ++||.|+.++
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 468999998864 356667 367677778887651 4699999987
No 62
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.82 E-value=0.12 Score=42.75 Aligned_cols=42 Identities=33% Similarity=0.709 Sum_probs=33.2
Q ss_pred CeeecccccccCCC------c-eeeccCCceeccccccccC----CCCCCCccCc
Q 042263 17 DLFDCPIWYQALKV------P-VSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~------P-v~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
..+.|-||.+.+.. | +. .|||.+|..|..++. ..||.||.+.
T Consensus 2 ~~~~c~~c~~~~s~~~~~~~p~~l--~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 2 SFPECEICNEDYSSEDGDHIPRVL--KCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCCceeecCccccccCcccCCccc--ccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 46789999988753 4 33 369999999999974 3599999995
No 63
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.07 E-value=0.059 Score=46.53 Aligned_cols=103 Identities=20% Similarity=0.393 Sum_probs=59.9
Q ss_pred CCCeeecccccccCCCceeeccCCceeccccccccC-----CCCCCCccCc-----chh------hHHHHHHHHhh--cc
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPACRSCV-----MLR------SRVMDIALEKT--MS 76 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~Cr~~~-----~~r------n~~le~~~~~~--~~ 76 (159)
|.+.-.|-||-+-+..-. .-+|||..|.-|--++. +.||.||+.. ..+ ....-+.-++. +.
T Consensus 58 DEen~~C~ICA~~~TYs~-~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~~~~~DI~D~~~~k~~~EK~GI~ 136 (493)
T COG5236 58 DEENMNCQICAGSTTYSA-RYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDRRQWKGREEKVGIF 136 (493)
T ss_pred ccccceeEEecCCceEEE-eccCCchHHHHHHHHHHHHHhccCCCccccccceEEEecCCCCcchhHhhhcccccceeee
Confidence 455778999998876532 23679999999976652 6799999976 111 11111111111 22
Q ss_pred CCCchhhhccCCCCCCCCCCCCCcce-eChhHHHhHhhhhcCC
Q 042263 77 FGENKDHERNCQCAPCACPLLDCNFL-GSASQLYLYFSWKNGK 118 (159)
Q Consensus 77 ~~~~~~He~~C~~~p~~Cp~~gC~~~-g~~~~l~~H~~~~H~~ 118 (159)
|..-..-+++=.--...||...|..+ +...+|..|+...|..
T Consensus 137 y~~E~v~~E~~~LL~F~CP~skc~~~C~~~k~lk~H~K~~H~~ 179 (493)
T COG5236 137 YEGEDVRDEMEDLLSFKCPKSKCHRRCGSLKELKKHYKAQHGF 179 (493)
T ss_pred ecchHHHHHHHHHHHhcCCchhhhhhhhhHHHHHHHHHhhcCc
Confidence 22111111110111247887766544 3478999999999986
No 64
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.72 E-value=0.096 Score=45.09 Aligned_cols=45 Identities=22% Similarity=0.476 Sum_probs=36.2
Q ss_pred CCeeecccccccCCCce-----e--eccCCceeccccccccC----------CCCCCCccCc
Q 042263 16 QDLFDCPIWYQALKVPV-----S--QSINGHIICSSCLAKVN----------NKCPACRSCV 60 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv-----~--qC~~GH~~C~~C~~~~~----------~~CP~Cr~~~ 60 (159)
.....|.||++....+. + .-.|-|.||..|+.++. ..||.||...
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 44678999999987765 3 12579999999999874 5699999987
No 65
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.04 E-value=0.067 Score=46.59 Aligned_cols=92 Identities=22% Similarity=0.371 Sum_probs=49.8
Q ss_pred CCCeeeccccc-ccCCCc-ee-eccCCceeccccccccC---------CCCCC--CccCc-chhhHHH--HHHHHhhccC
Q 042263 15 DQDLFDCPIWY-QALKVP-VS-QSINGHIICSSCLAKVN---------NKCPA--CRSCV-MLRSRVM--DIALEKTMSF 77 (159)
Q Consensus 15 ~~~~l~C~iC~-~~l~~P-v~-qC~~GH~~C~~C~~~~~---------~~CP~--Cr~~~-~~rn~~l--e~~~~~~~~~ 77 (159)
+....+|.||. +..... .+ ...|||.||..|+.+.. ..||. |...+ ...+..+ -++.+ +
T Consensus 143 ~~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e----~ 218 (384)
T KOG1812|consen 143 KLPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTPKLRE----M 218 (384)
T ss_pred ccccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCHHHHH----H
Confidence 33477899999 544332 11 24579999999998642 35754 54444 1111111 11211 1
Q ss_pred CCchhhhccCCC-CCCCCCCCCCcceeChhHHHh
Q 042263 78 GENKDHERNCQC-APCACPLLDCNFLGSASQLYL 110 (159)
Q Consensus 78 ~~~~~He~~C~~-~p~~Cp~~gC~~~g~~~~l~~ 110 (159)
-+.+..++.-+- ...+||+++|.+.....+|..
T Consensus 219 ~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~ 252 (384)
T KOG1812|consen 219 WEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSS 252 (384)
T ss_pred HHHHHHHHhhhhhhcccCCCCCchHhhhhhhhcc
Confidence 111111111111 123899999999888888865
No 66
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.99 E-value=0.23 Score=25.62 Aligned_cols=23 Identities=26% Similarity=0.494 Sum_probs=17.8
Q ss_pred CCCCCCCcceeChhHHHhHhhhhcC
Q 042263 93 ACPLLDCNFLGSASQLYLYFSWKNG 117 (159)
Q Consensus 93 ~Cp~~gC~~~g~~~~l~~H~~~~H~ 117 (159)
.|+. |+|.....+|..|+...|+
T Consensus 2 ~C~~--C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCPH--CSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp E-SS--SS-EESHHHHHHHHHHHHS
T ss_pred CCCC--CCCcCCHHHHHHHHHhhCc
Confidence 5776 9999888899999998885
No 67
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.14 E-value=0.081 Score=48.00 Aligned_cols=47 Identities=19% Similarity=0.458 Sum_probs=38.3
Q ss_pred eeCCCeeecccccccCCCceeeccCCceecccccccc--------CCCCCCCccCc
Q 042263 13 ISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKV--------NNKCPACRSCV 60 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~--------~~~CP~Cr~~~ 60 (159)
..+.+...|.+|.++-.++|- ..|-|.||..|+..- +-+||.|...+
T Consensus 531 ~enk~~~~C~lc~d~aed~i~-s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAEDYIE-SSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred ccccCceeecccCChhhhhHh-hhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence 446678999999999999865 478999999999543 24799998876
No 68
>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=89.03 E-value=0.25 Score=31.07 Aligned_cols=37 Identities=16% Similarity=0.347 Sum_probs=20.4
Q ss_pred cccccccCCC--------ceeecc-CCceeccccccc---cCCCCCCCc
Q 042263 21 CPIWYQALKV--------PVSQSI-NGHIICSSCLAK---VNNKCPACR 57 (159)
Q Consensus 21 C~iC~~~l~~--------Pv~qC~-~GH~~C~~C~~~---~~~~CP~Cr 57 (159)
|--|...|.. ..|+|+ |++.||-.|-.= .+.+||-|.
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 5567777765 368887 799999999433 236899884
No 69
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.41 E-value=0.2 Score=43.21 Aligned_cols=44 Identities=25% Similarity=0.512 Sum_probs=33.1
Q ss_pred CCCeeecccccccCCCceeeccCCceec-cccccccCCCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIIC-SSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C-~~C~~~~~~~CP~Cr~~~ 60 (159)
++....|.||.+-.+..++. +|||.-| -.|...+ .+||.||..|
T Consensus 302 ~~~p~lcVVcl~e~~~~~fv-pcGh~ccct~cs~~l-~~CPvCR~rI 346 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSAVFV-PCGHVCCCTLCSKHL-PQCPVCRQRI 346 (355)
T ss_pred cCCCCceEEecCCccceeee-cCCcEEEchHHHhhC-CCCchhHHHH
Confidence 44467799999999988876 8899866 2333333 5799999987
No 70
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.33 E-value=0.057 Score=50.87 Aligned_cols=41 Identities=20% Similarity=0.545 Sum_probs=29.1
Q ss_pred ecccccccCCCceee--ccCCceeccccccccC---CCCCCCccCc
Q 042263 20 DCPIWYQALKVPVSQ--SINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~q--C~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.||+|..-+.+-... =.|+|.||..|+..|. .+||.||..+
T Consensus 125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF 170 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF 170 (1134)
T ss_pred hhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence 466666555443211 1579999999998874 6899999987
No 71
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=88.05 E-value=0.27 Score=40.22 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=20.2
Q ss_pred eeecccccccCC--CceeeccCCcee
Q 042263 18 LFDCPIWYQALK--VPVSQSINGHII 41 (159)
Q Consensus 18 ~l~C~iC~~~l~--~Pv~qC~~GH~~ 41 (159)
.|.||+|..+|. +..+.|.+||.|
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 378999999995 456789999987
No 72
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.03 E-value=0.42 Score=39.28 Aligned_cols=46 Identities=22% Similarity=0.429 Sum_probs=38.1
Q ss_pred CCCeeecccccccCCC---ceeeccCCceeccccccccC--CCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALKV---PVSQSINGHIICSSCLAKVN--NKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~---Pv~qC~~GH~~C~~C~~~~~--~~CP~Cr~~~ 60 (159)
....|.|||....|.. =|+.=+|||+|+..++..+. ..||.|..++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f 160 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPF 160 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcc
Confidence 4668999999999954 25555789999999999885 3799999997
No 73
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.84 E-value=0.22 Score=43.78 Aligned_cols=33 Identities=30% Similarity=0.602 Sum_probs=25.9
Q ss_pred CCeeecccccccCCCc--eeeccCCceeccccccc
Q 042263 16 QDLFDCPIWYQALKVP--VSQSINGHIICSSCLAK 48 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~P--v~qC~~GH~~C~~C~~~ 48 (159)
...++|.||++-.... ++.-+|+|.||.+|...
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kd 216 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKD 216 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHH
Confidence 3478999999988653 33348899999999875
No 74
>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=87.29 E-value=0.27 Score=26.58 Aligned_cols=22 Identities=14% Similarity=0.090 Sum_probs=12.1
Q ss_pred ecccccccCCCceeecc-CCcee
Q 042263 20 DCPIWYQALKVPVSQSI-NGHII 41 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~-~GH~~ 41 (159)
.||.|......-...|+ |||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 36666666544444555 56554
No 75
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.06 E-value=0.14 Score=47.33 Aligned_cols=38 Identities=37% Similarity=0.696 Sum_probs=29.2
Q ss_pred CCeeecccccccCC----CceeeccCCceecccccccc-CCCCC
Q 042263 16 QDLFDCPIWYQALK----VPVSQSINGHIICSSCLAKV-NNKCP 54 (159)
Q Consensus 16 ~~~l~C~iC~~~l~----~Pv~qC~~GH~~C~~C~~~~-~~~CP 54 (159)
.+.+.|+||.+.+. -|+.. .|||++|+.|.+++ +..||
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl-~cghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSL-QCGHTICGHCVQLLYNASCP 51 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccc-cccchHHHHHHHhHhhccCC
Confidence 45788999976653 46653 56999999999987 46788
No 76
>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=86.96 E-value=0.2 Score=42.07 Aligned_cols=41 Identities=27% Similarity=0.659 Sum_probs=29.8
Q ss_pred ecccccc--cCCCce--eeccCCceeccccccccC----CCCCCCccCc
Q 042263 20 DCPIWYQ--ALKVPV--SQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~--~l~~Pv--~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
.||+|.- ++.+.+ +.-+|||..|.+|...+- +.||.|....
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 4888873 343332 233789999999999873 6899998876
No 77
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.72 E-value=0.13 Score=49.58 Aligned_cols=46 Identities=28% Similarity=0.572 Sum_probs=35.1
Q ss_pred CCCeeecccccccCC-----Cceeecc-CCceecccccccc-----CCCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV-----NNKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~-----~~~CP~Cr~~~ 60 (159)
....-+|+||+.++. -|.-.|. |-|-|=.+|+-+| ..+||.||..+
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 344668999999985 3555664 7888888888887 26899999876
No 78
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=83.01 E-value=0.31 Score=45.49 Aligned_cols=40 Identities=33% Similarity=0.622 Sum_probs=32.5
Q ss_pred eecccccccCCCceeeccCCceeccccccccC-----CCCCCCccCc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKVN-----NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-----~~CP~Cr~~~ 60 (159)
+.|++|.+ ...++ .-.|||.+|.+|+.+.. ..||.||..+
T Consensus 455 ~~c~ic~~-~~~~~-it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-LDSFF-ITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-cccce-eecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 89999999 55554 45789999999998863 4699998875
No 79
>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=82.68 E-value=1.5 Score=30.32 Aligned_cols=35 Identities=17% Similarity=0.350 Sum_probs=25.7
Q ss_pred eeCCCeeecccccccCCCc-eeeccCCceeccccccc
Q 042263 13 ISDQDLFDCPIWYQALKVP-VSQSINGHIICSSCLAK 48 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~P-v~qC~~GH~~C~~C~~~ 48 (159)
+++.+.. |++|.+.+... +...++||.+-..|..+
T Consensus 74 ~i~~~~~-C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 74 VITESTK-CSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred EECCCCC-ccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 3444444 99999999755 44568899999999753
No 80
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.66 E-value=1 Score=38.92 Aligned_cols=42 Identities=17% Similarity=0.365 Sum_probs=34.3
Q ss_pred eecccccccCCC--ceeeccCCceeccccccccC----CCCCCCccCc
Q 042263 19 FDCPIWYQALKV--PVSQSINGHIICSSCLAKVN----NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~~--Pv~qC~~GH~~C~~C~~~~~----~~CP~Cr~~~ 60 (159)
..|.||+|-+.. -+..=+|+|.|=..|+.+|. ..||.|+.++
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 489999998863 35555789999999999984 3499999987
No 81
>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=82.53 E-value=0.3 Score=37.54 Aligned_cols=20 Identities=40% Similarity=0.947 Sum_probs=17.4
Q ss_pred eccccccccCCCCCCCccCc
Q 042263 41 ICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 41 ~C~~C~~~~~~~CP~Cr~~~ 60 (159)
||+.|-.+...+||.|..+|
T Consensus 30 fC~kCG~~tI~~Cp~C~~~I 49 (158)
T PF10083_consen 30 FCSKCGAKTITSCPNCSTPI 49 (158)
T ss_pred HHHHhhHHHHHHCcCCCCCC
Confidence 89999888767899999887
No 82
>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=81.89 E-value=0.9 Score=29.40 Aligned_cols=34 Identities=24% Similarity=0.532 Sum_probs=17.9
Q ss_pred CCCeeecccccccCCC--ceeecc-CCceeccccccc
Q 042263 15 DQDLFDCPIWYQALKV--PVSQSI-NGHIICSSCLAK 48 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~--Pv~qC~-~GH~~C~~C~~~ 48 (159)
|.+.-.|.+|...|.- .-+.|. ||++||+.|...
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 4556779999988742 235686 899999999865
No 83
>PRK04023 DNA polymerase II large subunit; Validated
Probab=81.88 E-value=1.6 Score=42.48 Aligned_cols=50 Identities=20% Similarity=0.392 Sum_probs=37.6
Q ss_pred CCceEEEeeCCCeeecccccccCCCceeecc-CCc-----eeccccccccC-CCCCCCccCc
Q 042263 6 NGSITSTISDQDLFDCPIWYQALKVPVSQSI-NGH-----IICSSCLAKVN-NKCPACRSCV 60 (159)
Q Consensus 6 ~~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~-~GH-----~~C~~C~~~~~-~~CP~Cr~~~ 60 (159)
.|.+++ +.....||-|.... +.+.|+ ||. .||..|..... ..||.|....
T Consensus 617 ~g~~eV---EVg~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 617 KGTIEV---EIGRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred CCceee---cccCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCC
Confidence 455544 44566799999886 456897 884 59999987765 5799999887
No 84
>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=81.03 E-value=1.3 Score=27.62 Aligned_cols=27 Identities=22% Similarity=0.165 Sum_probs=18.4
Q ss_pred CCCCCCCCcceeChhHHHhHhhhhcCCce
Q 042263 92 CACPLLDCNFLGSASQLYLYFSWKNGKTF 120 (159)
Q Consensus 92 ~~Cp~~gC~~~g~~~~l~~H~~~~H~~~~ 120 (159)
+.||+ |+......+|..|+.+.|....
T Consensus 3 f~CP~--C~~~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 3 FTCPY--CGKGFSESSLVEHCEDEHRSES 29 (54)
T ss_pred cCCCC--CCCccCHHHHHHHHHhHCcCCC
Confidence 46776 7775555678888888777643
No 85
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.15 E-value=0.79 Score=40.40 Aligned_cols=43 Identities=26% Similarity=0.526 Sum_probs=33.7
Q ss_pred eeecccccccCCCceeec----cCCceeccccccccC-----CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQS----INGHIICSSCLAKVN-----NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC----~~GH~~C~~C~~~~~-----~~CP~Cr~~~ 60 (159)
--.||||++-...|.-.| .|||.|=+.|++++. ..||.|...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 357999998877664333 579999999999974 4799998765
No 86
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=80.14 E-value=3 Score=41.63 Aligned_cols=51 Identities=24% Similarity=0.471 Sum_probs=37.4
Q ss_pred CCCceEEEeeCCCeeecccccccCCCceeecc-CCce-----eccccccccC------CCCCCCccCc
Q 042263 5 KNGSITSTISDQDLFDCPIWYQALKVPVSQSI-NGHI-----ICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 5 ~~~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~-~GH~-----~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
+.|.+.+-+ ..+.||-|...... ..|+ ||.. .|..|-.++. ..||.|..+.
T Consensus 657 ~~G~ieVEV---~~rkCPkCG~~t~~--~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 657 EGGVIEVEV---GRRRCPSCGTETYE--NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred cCCeEEEEE---EEEECCCCCCcccc--ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcc
Confidence 455665544 38999999986543 3687 8866 4999988763 2799999887
No 87
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.98 E-value=1 Score=37.31 Aligned_cols=46 Identities=17% Similarity=0.351 Sum_probs=37.1
Q ss_pred CCCeeecccccccCCCc---eeeccCCceeccccccccC---CCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALKVP---VSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~P---v~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
-...+.||+|.+.|... .+.=++||+||..|.+++. .-||.|..++
T Consensus 218 ~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~pl 269 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPL 269 (303)
T ss_pred hccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcC
Confidence 34789999999999753 2233789999999999986 4699998887
No 88
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.86 E-value=0.7 Score=34.59 Aligned_cols=39 Identities=26% Similarity=0.623 Sum_probs=25.7
Q ss_pred eeccCCce--------------eccccccccCCCCCCCccCcchhhHHHHHHHH
Q 042263 33 SQSINGHI--------------ICSSCLAKVNNKCPACRSCVMLRSRVMDIALE 72 (159)
Q Consensus 33 ~qC~~GH~--------------~C~~C~~~~~~~CP~Cr~~~~~rn~~le~~~~ 72 (159)
+.|.|||. ||+.|-+.-.-+||.|..+| .-...+|.++.
T Consensus 8 qic~ngh~attaadq~pel~eafcskcgeati~qcp~csasi-rgd~~vegvlg 60 (160)
T COG4306 8 QICLNGHVATTAADQSPELMEAFCSKCGEATITQCPICSASI-RGDYYVEGVLG 60 (160)
T ss_pred hhcCCCceeeccccCCHHHHHHHHhhhchHHHhcCCccCCcc-cccceeeeeec
Confidence 45788885 89999776445899998875 11234555543
No 89
>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=76.28 E-value=1.4 Score=31.18 Aligned_cols=41 Identities=27% Similarity=0.514 Sum_probs=15.3
Q ss_pred eecccccccC--CCc-eeeccCCceeccccccccC-------CCCCCCccCc
Q 042263 19 FDCPIWYQAL--KVP-VSQSINGHIICSSCLAKVN-------NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l--~~P-v~qC~~GH~~C~~C~~~~~-------~~CP~Cr~~~ 60 (159)
=.|++|...+ .++ +.+|.+||. -..|..... ..|+.|....
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~~GH~-w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCENGHV-WPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-TTS-E-EEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECCCCCE-EeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 4699999976 344 568999998 466655432 5799998776
No 90
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.53 E-value=1.1 Score=37.07 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=25.7
Q ss_pred eeecccccccCCCceeeccCCceeccccccc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAK 48 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~ 48 (159)
.-.|+.|+.+..+||. |+.||+||..|+-.
T Consensus 43 FdcCsLtLqPc~dPvi-t~~GylfdrEaILe 72 (303)
T KOG3039|consen 43 FDCCSLTLQPCRDPVI-TPDGYLFDREAILE 72 (303)
T ss_pred cceeeeecccccCCcc-CCCCeeeeHHHHHH
Confidence 3458899999999975 79999999999865
No 91
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=74.53 E-value=1 Score=39.44 Aligned_cols=44 Identities=27% Similarity=0.458 Sum_probs=32.5
Q ss_pred CeeecccccccCC-Ccee-----------eccCCceeccccccccC---CCCCCCccCc
Q 042263 17 DLFDCPIWYQALK-VPVS-----------QSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~-~Pv~-----------qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
+.-.|-||.+-|. +|-. .=+|||.+=-+|+..|. ..||.||.++
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence 4556999998753 3311 12689999999988763 6899999995
No 92
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=73.63 E-value=1.5 Score=36.46 Aligned_cols=43 Identities=26% Similarity=0.418 Sum_probs=20.3
Q ss_pred eeecccccccCCCceeeccC--C--ceeccccccccC---CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSIN--G--HIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~--G--H~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.-.||||+....--+..=.. | +.+|+.|-..|. ..||.|...-
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 45799999876544333222 4 469999998874 5899997754
No 93
>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 smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=73.06 E-value=3.6 Score=25.59 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=24.8
Q ss_pred CCeeecc--cccccCC------Cceeec-cCCceeccccccccC
Q 042263 16 QDLFDCP--IWYQALK------VPVSQS-INGHIICSSCLAKVN 50 (159)
Q Consensus 16 ~~~l~C~--iC~~~l~------~Pv~qC-~~GH~~C~~C~~~~~ 50 (159)
.+..-|| -|..++. .+..+| .||+.||..|...+.
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 3445588 7765543 345679 699999999988764
No 95
>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=72.57 E-value=2.1 Score=27.43 Aligned_cols=41 Identities=20% Similarity=0.460 Sum_probs=30.7
Q ss_pred ecccccccCCC---ceeeccCCceecccccccc-CCCCCCCccCc
Q 042263 20 DCPIWYQALKV---PVSQSINGHIICSSCLAKV-NNKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l~~---Pv~qC~~GH~~C~~C~~~~-~~~CP~Cr~~~ 60 (159)
.|-.|..-|-+ ..+.|.--..||..|.+.+ .+.||.|...+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcc
Confidence 36666666532 2467777779999999887 57999999876
No 96
>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=71.64 E-value=1.5 Score=27.13 Aligned_cols=42 Identities=26% Similarity=0.612 Sum_probs=21.4
Q ss_pred eeecccccccCCCceeeccCCceecccccccc-------CCCCCCCccC
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKV-------NNKCPACRSC 59 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~-------~~~CP~Cr~~ 59 (159)
.|.||+-+..+..|+.--.|-|.-|-.=..=+ ..+||.|.++
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 37899999999999997778998653211101 1479999764
No 97
>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=70.19 E-value=2.7 Score=23.55 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=15.6
Q ss_pred CCCCCCCCcceeChhHHHhHhhh
Q 042263 92 CACPLLDCNFLGSASQLYLYFSW 114 (159)
Q Consensus 92 ~~Cp~~gC~~~g~~~~l~~H~~~ 114 (159)
+.||..+|+-........+|+++
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 57999999999999999999875
No 98
>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=69.86 E-value=3 Score=25.92 Aligned_cols=37 Identities=19% Similarity=0.282 Sum_probs=21.1
Q ss_pred eCCCeeeccc--ccccCCC----c--eeecc-CCceeccccccccC
Q 042263 14 SDQDLFDCPI--WYQALKV----P--VSQSI-NGHIICSSCLAKVN 50 (159)
Q Consensus 14 ~~~~~l~C~i--C~~~l~~----P--v~qC~-~GH~~C~~C~~~~~ 50 (159)
.+.+..-||- |..++.. . ..+|. ||+.||..|...+.
T Consensus 14 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 14 SDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 4455568988 9988752 1 25798 99999999988764
No 99
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.58 E-value=3.1 Score=26.46 Aligned_cols=40 Identities=15% Similarity=0.284 Sum_probs=27.6
Q ss_pred CCCeeecccccccC--CCceeecc-CCceeccccccccCCCCCC
Q 042263 15 DQDLFDCPIWYQAL--KVPVSQSI-NGHIICSSCLAKVNNKCPA 55 (159)
Q Consensus 15 ~~~~l~C~iC~~~l--~~Pv~qC~-~GH~~C~~C~~~~~~~CP~ 55 (159)
+...-.|++|.+.| .+.|.+|+ ||-..=++|+.+.. .|-.
T Consensus 2 ~~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g-~C~~ 44 (54)
T PF14446_consen 2 NYEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAG-GCIN 44 (54)
T ss_pred CccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCC-ceEe
Confidence 34456799999999 67787876 67666667776653 5544
No 100
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=69.30 E-value=4.2 Score=28.97 Aligned_cols=40 Identities=20% Similarity=0.337 Sum_probs=25.7
Q ss_pred ceEEEeeCCCeeecccccccC-CCceeeccCCceeccccccc
Q 042263 8 SITSTISDQDLFDCPIWYQAL-KVPVSQSINGHIICSSCLAK 48 (159)
Q Consensus 8 ~~~~~~~~~~~l~C~iC~~~l-~~Pv~qC~~GH~~C~~C~~~ 48 (159)
.+......+..+.||-|.+.. .-|+-. .-+|+.|..|-..
T Consensus 11 ~~k~k~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y 51 (99)
T PRK14892 11 IIRPKPKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCGLY 51 (99)
T ss_pred CcccccCCCcEeECCCCCCeEeeeecCC-CcceEECCCCCCc
Confidence 344456678899999999532 223333 3477877777554
No 101
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.13 E-value=2 Score=40.15 Aligned_cols=40 Identities=30% Similarity=0.716 Sum_probs=30.6
Q ss_pred ecccccccCCCceeeccCCc-eeccccccccC---------CCCCCCccCc
Q 042263 20 DCPIWYQALKVPVSQSINGH-IICSSCLAKVN---------NKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH-~~C~~C~~~~~---------~~CP~Cr~~~ 60 (159)
.|+||-.-+.-+.+- .+|| .+|..|..++. ..||.|+..+
T Consensus 2 ~c~ic~~s~~~~~~~-s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~ 51 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRG-SCGHNEVCATCVVRLRFELNNRKCSNECPVCRREV 51 (669)
T ss_pred CcceeecCccccccc-cccccccchhhhhhhhhhcccccccccCcccccce
Confidence 488888777666553 6799 89999988763 3479999976
No 102
>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=67.85 E-value=3.8 Score=34.79 Aligned_cols=42 Identities=21% Similarity=0.430 Sum_probs=29.4
Q ss_pred eeecccccccCCCceeec---cCC--ceeccccccccC---CCCCCCccC
Q 042263 18 LFDCPIWYQALKVPVSQS---ING--HIICSSCLAKVN---NKCPACRSC 59 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC---~~G--H~~C~~C~~~~~---~~CP~Cr~~ 59 (159)
.-.||||.....--+..= ..| +..|+.|-..|. .+||.|...
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 447999998764332221 345 468999998875 589999764
No 103
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=66.75 E-value=4 Score=29.09 Aligned_cols=39 Identities=18% Similarity=0.533 Sum_probs=27.2
Q ss_pred CceEEEe--eCCCeeecccccccCCCc-eeeccCCceecccc
Q 042263 7 GSITSTI--SDQDLFDCPIWYQALKVP-VSQSINGHIICSSC 45 (159)
Q Consensus 7 ~~~~~~~--~~~~~l~C~iC~~~l~~P-v~qC~~GH~~C~~C 45 (159)
.+++|.+ ...++|+|..|+.+--.- +-.-..|+.+|..|
T Consensus 57 EEL~V~ViP~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 57 EELSVRVIPKQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CeEEEEEecCCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 3444444 467799999999887432 22335799999988
No 104
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.48 E-value=2.6 Score=36.96 Aligned_cols=43 Identities=30% Similarity=0.656 Sum_probs=32.7
Q ss_pred CeeecccccccC---CCceeeccCCceeccccccccC------CCCCCCccCc
Q 042263 17 DLFDCPIWYQAL---KVPVSQSINGHIICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l---~~Pv~qC~~GH~~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
..|.|||=.+-- .||+.. .|||+++..=+.++. -+||.|-...
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L-~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMML-ICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ceeecccchhhccCCCCCeee-eccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 478999977655 367654 789999999988873 3699996654
No 105
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=66.16 E-value=2.7 Score=36.69 Aligned_cols=101 Identities=15% Similarity=0.303 Sum_probs=58.6
Q ss_pred CCeeecccccccCCCce-------eec--cCCceeccccccccC---------------CCCCCCccCcch----hhHHH
Q 042263 16 QDLFDCPIWYQALKVPV-------SQS--INGHIICSSCLAKVN---------------NKCPACRSCVML----RSRVM 67 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv-------~qC--~~GH~~C~~C~~~~~---------------~~CP~Cr~~~~~----rn~~l 67 (159)
...+.||.|.++|..-. .|. ...|.-|+.|..+.. .+||.|...... ++...
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 34678999999986410 111 235788999987651 579999877611 12111
Q ss_pred HHHHH-----------hhccCCCchhhhccCCCCCCCCCCCCCcceeC-hhHHHhHhhhhc
Q 042263 68 DIALE-----------KTMSFGENKDHERNCQCAPCACPLLDCNFLGS-ASQLYLYFSWKN 116 (159)
Q Consensus 68 e~~~~-----------~~~~~~~~~~He~~C~~~p~~Cp~~gC~~~g~-~~~l~~H~~~~H 116 (159)
=+-.+ .-+...+|.+|...=..--+.|-.+.|.+... +.+|..|+...|
T Consensus 285 ~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 285 YRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred hhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 11111 12334466777653333345677667777654 357777777766
No 106
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=65.77 E-value=4.6 Score=37.65 Aligned_cols=34 Identities=24% Similarity=0.574 Sum_probs=16.4
Q ss_pred eecccccccCCCceeeccCCceeccccccccC-CCCCCCccC
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKVN-NKCPACRSC 59 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-~~CP~Cr~~ 59 (159)
..||-|.... +.|..||..|-.++. ..||.|...
T Consensus 2 ~~Cp~Cg~~n-------~~~akFC~~CG~~l~~~~Cp~CG~~ 36 (645)
T PRK14559 2 LICPQCQFEN-------PNNNRFCQKCGTSLTHKPCPQCGTE 36 (645)
T ss_pred CcCCCCCCcC-------CCCCccccccCCCCCCCcCCCCCCC
Confidence 4578787543 224445555544432 234444433
No 107
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=65.50 E-value=6.3 Score=25.59 Aligned_cols=12 Identities=50% Similarity=1.292 Sum_probs=8.3
Q ss_pred CCCCCCCCCcceeC
Q 042263 91 PCACPLLDCNFLGS 104 (159)
Q Consensus 91 p~~Cp~~gC~~~g~ 104 (159)
++.||. |+|.|+
T Consensus 50 ~Y~Cp~--CGF~GP 61 (61)
T COG2888 50 PYRCPK--CGFEGP 61 (61)
T ss_pred ceECCC--cCccCC
Confidence 667775 777774
No 108
>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=65.17 E-value=2.8 Score=25.71 Aligned_cols=34 Identities=21% Similarity=0.385 Sum_probs=26.0
Q ss_pred CCCeeecccccccCCCceeeccCCceeccccccc
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIICSSCLAK 48 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~ 48 (159)
-.+=+.|..|...|.+.-+.-..|..+|..|..+
T Consensus 23 H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 23 HPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp ETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred EccccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 4557889999999977645547889999988654
No 109
>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=64.80 E-value=3.3 Score=25.53 Aligned_cols=31 Identities=19% Similarity=0.349 Sum_probs=21.6
Q ss_pred eecccccccCCC--ceeecc-CCceecccccccc
Q 042263 19 FDCPIWYQALKV--PVSQSI-NGHIICSSCLAKV 49 (159)
Q Consensus 19 l~C~iC~~~l~~--Pv~qC~-~GH~~C~~C~~~~ 49 (159)
-.|++|...|.. .-..|. +|++||..|....
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 358888766542 234675 7999999998753
No 110
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=64.56 E-value=3.1 Score=36.22 Aligned_cols=24 Identities=25% Similarity=0.522 Sum_probs=17.2
Q ss_pred ecccccccCCCceeeccCCceecccccc
Q 042263 20 DCPIWYQALKVPVSQSINGHIICSSCLA 47 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH~~C~~C~~ 47 (159)
.||+|.+-... | ..|-..|.+|..
T Consensus 17 lCPVCGDkVSG--Y--HYGLLTCESCKG 40 (475)
T KOG4218|consen 17 LCPVCGDKVSG--Y--HYGLLTCESCKG 40 (475)
T ss_pred ccccccCcccc--c--eeeeeehhhhhh
Confidence 39999877665 2 348888888865
No 111
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.28 E-value=3.6 Score=27.85 Aligned_cols=29 Identities=17% Similarity=0.559 Sum_probs=24.4
Q ss_pred eeeccCCceecccccc-ccCCCCCCCccCc
Q 042263 32 VSQSINGHIICSSCLA-KVNNKCPACRSCV 60 (159)
Q Consensus 32 v~qC~~GH~~C~~C~~-~~~~~CP~Cr~~~ 60 (159)
-..|+--+.||..|.+ ++...||.|...+
T Consensus 22 A~ICtfEcTFCadCae~~l~g~CPnCGGel 51 (84)
T COG3813 22 ARICTFECTFCADCAENRLHGLCPNCGGEL 51 (84)
T ss_pred eeEEEEeeehhHhHHHHhhcCcCCCCCchh
Confidence 3568888899999988 4568999999988
No 112
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=64.24 E-value=0.48 Score=29.88 Aligned_cols=42 Identities=19% Similarity=0.560 Sum_probs=30.8
Q ss_pred eeecccccccCCC-ceeecc-CCceeccccccccCCCCCCCccC
Q 042263 18 LFDCPIWYQALKV-PVSQSI-NGHIICSSCLAKVNNKCPACRSC 59 (159)
Q Consensus 18 ~l~C~iC~~~l~~-Pv~qC~-~GH~~C~~C~~~~~~~CP~Cr~~ 59 (159)
.+.|..|...... -..||. ||-..|++||+.--..|..|..-
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 4678889877643 367886 89999999998754467666543
No 113
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.96 E-value=6.1 Score=28.81 Aligned_cols=38 Identities=21% Similarity=0.367 Sum_probs=27.4
Q ss_pred ecccccccCCCc------------eeecc-CCceecccccccc---CCCCCCCc
Q 042263 20 DCPIWYQALKVP------------VSQSI-NGHIICSSCLAKV---NNKCPACR 57 (159)
Q Consensus 20 ~C~iC~~~l~~P------------v~qC~-~GH~~C~~C~~~~---~~~CP~Cr 57 (159)
.|-.|...|..+ .|+|+ |++.||-.|-.-+ ..+||-|.
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 47786 7889999995443 35799885
No 114
>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=63.92 E-value=6.1 Score=21.10 Aligned_cols=21 Identities=14% Similarity=0.252 Sum_probs=17.6
Q ss_pred CCCCCCCCcceeChhHHHhHhhh
Q 042263 92 CACPLLDCNFLGSASQLYLYFSW 114 (159)
Q Consensus 92 ~~Cp~~gC~~~g~~~~l~~H~~~ 114 (159)
+.||. |.+..+..++..|+..
T Consensus 2 v~CPi--C~~~v~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLDS 22 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHHH
Confidence 57997 9999888899999864
No 115
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=63.74 E-value=1.6 Score=40.76 Aligned_cols=43 Identities=30% Similarity=0.669 Sum_probs=35.4
Q ss_pred CeeecccccccCCCceeeccCCceeccccccccC------CCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN------NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~------~~CP~Cr~~~ 60 (159)
-.++||||......|+.. .|-|.||..|+.... ..||.|+..+
T Consensus 20 k~lEc~ic~~~~~~p~~~-kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 20 KILECPICLEHVKEPSLL-KCDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hhccCCceeEEeeccchh-hhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 468999999999999654 679999999998752 4699998766
No 116
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.19 E-value=6.1 Score=31.62 Aligned_cols=38 Identities=26% Similarity=0.447 Sum_probs=28.4
Q ss_pred cccccccCCCceeeccCCc-eeccccccccCCCCCCCccCc
Q 042263 21 CPIWYQALKVPVSQSINGH-IICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH-~~C~~C~~~~~~~CP~Cr~~~ 60 (159)
|-.|.+--.. |..=+|.| .+|+.|-..+ ..||.|+.+.
T Consensus 161 Cr~C~~~~~~-VlllPCrHl~lC~~C~~~~-~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGEREAT-VLLLPCRHLCLCGICDESL-RICPICRSPK 199 (207)
T ss_pred ceecCcCCce-EEeecccceEecccccccC-ccCCCCcChh
Confidence 8888876655 34336676 7999998873 5899999875
No 117
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=63.18 E-value=4.9 Score=34.47 Aligned_cols=42 Identities=29% Similarity=0.680 Sum_probs=34.0
Q ss_pred eecccccccCC---CceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 19 FDCPIWYQALK---VPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~---~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
-.||+|.+.+. .+...|++|+..|-.|+..+. ..||.||.+.
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence 46999999872 344568999999999998864 6899999876
No 118
>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=61.36 E-value=2.4 Score=23.56 Aligned_cols=21 Identities=33% Similarity=0.950 Sum_probs=11.5
Q ss_pred CceeccccccccC-------CCCCCCcc
Q 042263 38 GHIICSSCLAKVN-------NKCPACRS 58 (159)
Q Consensus 38 GH~~C~~C~~~~~-------~~CP~Cr~ 58 (159)
-|.||+.|-.+.. ..||.|..
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcC
Confidence 4778888877652 35888864
No 119
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.19 E-value=6.4 Score=23.08 Aligned_cols=25 Identities=12% Similarity=0.340 Sum_probs=16.5
Q ss_pred cccccccCCC-ceeecc-CCceeccccc
Q 042263 21 CPIWYQALKV-PVSQSI-NGHIICSSCL 46 (159)
Q Consensus 21 C~iC~~~l~~-Pv~qC~-~GH~~C~~C~ 46 (159)
|.+|.....- | +.|. ||..||+.=.
T Consensus 1 C~~C~~~~~l~~-f~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLTG-FKCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCcccccC-eECCccCCccccccC
Confidence 5567655444 5 5788 8889987633
No 120
>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=61.16 E-value=3.5 Score=35.81 Aligned_cols=29 Identities=28% Similarity=0.609 Sum_probs=22.0
Q ss_pred eeeccCCceeccccccccC----------------CCCCCCccCc
Q 042263 32 VSQSINGHIICSSCLAKVN----------------NKCPACRSCV 60 (159)
Q Consensus 32 v~qC~~GH~~C~~C~~~~~----------------~~CP~Cr~~~ 60 (159)
-.+|-|.=..|-+|..++- ..||+||..+
T Consensus 306 C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 306 CQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred CccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 3356667778999998871 4699999987
No 121
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.46 E-value=8 Score=25.02 Aligned_cols=40 Identities=20% Similarity=0.403 Sum_probs=21.6
Q ss_pred eeecccccccCC----Cceeecc-CCce---eccccccccC-CCCCCCc
Q 042263 18 LFDCPIWYQALK----VPVSQSI-NGHI---ICSSCLAKVN-NKCPACR 57 (159)
Q Consensus 18 ~l~C~iC~~~l~----~Pv~qC~-~GH~---~C~~C~~~~~-~~CP~Cr 57 (159)
...|..|...+. ...|.|+ ||.. -|..|.+..+ ..||.|.
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCC
Confidence 335666665553 2234454 3443 3667766543 4687774
No 122
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.21 E-value=3 Score=36.71 Aligned_cols=52 Identities=25% Similarity=0.555 Sum_probs=34.3
Q ss_pred eecccccccCC-----CceeeccCCceeccccccccC------CCCCCCccCc----chhhHHHHHHHH
Q 042263 19 FDCPIWYQALK-----VPVSQSINGHIICSSCLAKVN------NKCPACRSCV----MLRSRVMDIALE 72 (159)
Q Consensus 19 l~C~iC~~~l~-----~Pv~qC~~GH~~C~~C~~~~~------~~CP~Cr~~~----~~rn~~le~~~~ 72 (159)
-.|.||-+..- .||. .|||+|=..|+..|- ..||+|+... .+...+.+.+++
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~--~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~N~~~~d~vvE 71 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIG--TCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVANPSTVDHVVE 71 (465)
T ss_pred ceeeEeccCCcccccccccc--chhhHHHHHHHHHHHccCCccCCCCceeecccceeeechhhhhhhhc
Confidence 46999954431 2444 359999999998872 4799999555 222345566555
No 123
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.07 E-value=4.3 Score=21.09 Aligned_cols=6 Identities=50% Similarity=1.708 Sum_probs=2.6
Q ss_pred CCCCcc
Q 042263 53 CPACRS 58 (159)
Q Consensus 53 CP~Cr~ 58 (159)
||.|..
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 124
>PF12773 DZR: Double zinc ribbon
Probab=59.27 E-value=7.5 Score=23.37 Aligned_cols=14 Identities=29% Similarity=0.292 Sum_probs=6.8
Q ss_pred CCeeecccccccCC
Q 042263 16 QDLFDCPIWYQALK 29 (159)
Q Consensus 16 ~~~l~C~iC~~~l~ 29 (159)
.+...|+.|...|.
T Consensus 10 ~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP 23 (50)
T ss_pred ccccCChhhcCChh
Confidence 33444555555554
No 125
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=59.02 E-value=4.6 Score=30.42 Aligned_cols=21 Identities=29% Similarity=0.170 Sum_probs=16.0
Q ss_pred cccccCCCceeeccCCceeccc
Q 042263 23 IWYQALKVPVSQSINGHIICSS 44 (159)
Q Consensus 23 iC~~~l~~Pv~qC~~GH~~C~~ 44 (159)
||...-.. |..|+|||.||..
T Consensus 62 i~qs~~~r-v~rcecghsf~d~ 82 (165)
T COG4647 62 ICQSAQKR-VIRCECGHSFGDY 82 (165)
T ss_pred EEeccccc-EEEEeccccccCh
Confidence 46665555 7789999999875
No 126
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=58.23 E-value=6.2 Score=29.54 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=18.7
Q ss_pred eeecccccccCCCceeeccCCceecccccc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLA 47 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~ 47 (159)
...||.|. .|.|+ ..|-+||-.|-.
T Consensus 28 ~~hCp~Cg----~PLF~-KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCG----TPLFR-KDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccC----Cccee-eCCeEECCCCCc
Confidence 45799999 55566 779998888763
No 127
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.14 E-value=4.7 Score=34.14 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=27.9
Q ss_pred CCeeecccccccCCCcee-ecc--CCceecccccccc
Q 042263 16 QDLFDCPIWYQALKVPVS-QSI--NGHIICSSCLAKV 49 (159)
Q Consensus 16 ~~~l~C~iC~~~l~~Pv~-qC~--~GH~~C~~C~~~~ 49 (159)
..-|.|-+|.+-|.|--| ||+ .+|-||-.|....
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRes 302 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRES 302 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHH
Confidence 345999999999988744 897 6999999997653
No 128
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=58.09 E-value=9.7 Score=32.43 Aligned_cols=43 Identities=23% Similarity=0.469 Sum_probs=29.8
Q ss_pred CeeecccccccCCCceee--ccCCc--eeccccccccC---CCCCCCccC
Q 042263 17 DLFDCPIWYQALKVPVSQ--SINGH--IICSSCLAKVN---NKCPACRSC 59 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~q--C~~GH--~~C~~C~~~~~---~~CP~Cr~~ 59 (159)
..-.||+|.....--+.. -..|+ ..|+.|-..|. .+||.|...
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 356799999876433221 13454 68999998875 589999763
No 129
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.39 E-value=5.3 Score=30.16 Aligned_cols=40 Identities=33% Similarity=0.562 Sum_probs=28.8
Q ss_pred ceEEEeeCCCeeecccccccCCCceeeccCCc-eecc-ccccc
Q 042263 8 SITSTISDQDLFDCPIWYQALKVPVSQSINGH-IICS-SCLAK 48 (159)
Q Consensus 8 ~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH-~~C~-~C~~~ 48 (159)
-|-.+++|+++|.|..|.++++.-.+ .++|| -||+ .|.+.
T Consensus 71 hiAIaLVdq~~Lhcdlceeplk~ccf-spnghhcfcrtp~YqG 112 (167)
T KOG4621|consen 71 HIAIALVDQDKLHCDLCEEPLKSCCF-SPNGHHCFCRTPCYQG 112 (167)
T ss_pred eEEEEEecCCceehHHHHhHHHHhcc-CCCCccccccCCcccc
Confidence 35557899999999999999977544 36775 5776 35443
No 130
>PF12907 zf-met2: Zinc-binding
Probab=57.22 E-value=6.5 Score=23.43 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=19.2
Q ss_pred CCCCCCCCc----ceeChhHHHhHhhhhcCCc
Q 042263 92 CACPLLDCN----FLGSASQLYLYFSWKNGKT 119 (159)
Q Consensus 92 ~~Cp~~gC~----~~g~~~~l~~H~~~~H~~~ 119 (159)
+.|+. |. -+.+...|.+|.+++|+..
T Consensus 2 i~C~i--C~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKI--CRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHH--hhHHHHhcCCHHHHHHHHHccCCCC
Confidence 45654 76 3455689999999999974
No 131
>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=57.16 E-value=11 Score=22.33 Aligned_cols=33 Identities=15% Similarity=0.332 Sum_probs=17.9
Q ss_pred ccc--ccccCCCceeecc-CCceeccccccccCCCCC
Q 042263 21 CPI--WYQALKVPVSQSI-NGHIICSSCLAKVNNKCP 54 (159)
Q Consensus 21 C~i--C~~~l~~Pv~qC~-~GH~~C~~C~~~~~~~CP 54 (159)
|.. |.....-| +.|. ||..||..=+..-...|+
T Consensus 1 C~~~~C~~~~~~~-~~C~~C~~~FC~~Hr~~e~H~C~ 36 (43)
T PF01428_consen 1 CSFPGCKKKDFLP-FKCKHCGKSFCLKHRLPEDHNCS 36 (43)
T ss_dssp -SSTTT--BCTSH-EE-TTTS-EE-TTTHSTTTCT-S
T ss_pred CccCcCcCccCCC-eECCCCCcccCccccCccccCCc
Confidence 445 88777766 5688 999999987765444453
No 132
>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=56.67 E-value=6 Score=28.79 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=11.6
Q ss_pred eeeccCCceeccc
Q 042263 32 VSQSINGHIICSS 44 (159)
Q Consensus 32 v~qC~~GH~~C~~ 44 (159)
+.+|.|||.||..
T Consensus 24 ~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 24 VVKCDCGHEFCDA 36 (112)
T ss_pred eeeccCCCeecCh
Confidence 7789999999986
No 133
>PF15616 TerY-C: TerY-C metal binding domain
Probab=56.66 E-value=7.5 Score=29.08 Aligned_cols=39 Identities=18% Similarity=0.317 Sum_probs=28.3
Q ss_pred eeecccccccCCCceeeccCCceeccccccccCCCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~Cr~~~ 60 (159)
.--||-|.+..-- -.|.||.++|-.=-. ...||.|....
T Consensus 77 ~PgCP~CGn~~~f--a~C~CGkl~Ci~g~~--~~~CPwCg~~g 115 (131)
T PF15616_consen 77 APGCPHCGNQYAF--AVCGCGKLFCIDGEG--EVTCPWCGNEG 115 (131)
T ss_pred CCCCCCCcChhcE--EEecCCCEEEeCCCC--CEECCCCCCee
Confidence 3689999987644 358899999843222 24899998876
No 134
>PHA00616 hypothetical protein
Probab=56.32 E-value=9.7 Score=23.16 Aligned_cols=33 Identities=9% Similarity=0.125 Sum_probs=25.0
Q ss_pred CCCCCCCCCcceeC-hhHHHhHhhhhcCCceEEEEe
Q 042263 91 PCACPLLDCNFLGS-ASQLYLYFSWKNGKTFVSFTY 125 (159)
Q Consensus 91 p~~Cp~~gC~~~g~-~~~l~~H~~~~H~~~~~~~~~ 125 (159)
|+.||. |+..-. .++|..|+...|+..-....|
T Consensus 1 pYqC~~--CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLR--CGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccch--hhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 467875 887655 478999999999987655554
No 135
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=56.25 E-value=5.5 Score=33.40 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=9.9
Q ss_pred CCCCCccCc-chhh
Q 042263 52 KCPACRSCV-MLRS 64 (159)
Q Consensus 52 ~CP~Cr~~~-~~rn 64 (159)
.||.|...| +.-|
T Consensus 217 ~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 217 SCPHCGKAFADRSN 230 (279)
T ss_pred cCCcccchhcchHH
Confidence 599999988 5445
No 136
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=55.92 E-value=3.8 Score=35.24 Aligned_cols=47 Identities=19% Similarity=0.462 Sum_probs=35.5
Q ss_pred eeCCCeeecccccccCCCceeeccCCceeccccccccC---CCCCCCccC
Q 042263 13 ISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSC 59 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~ 59 (159)
+..++.-.||+|...-..|...-..|-+||=.|+-+-. +.||.=..+
T Consensus 295 ~l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p 344 (357)
T KOG0826|consen 295 LLPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYP 344 (357)
T ss_pred cCCCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCc
Confidence 44566778999999998885544579999999987742 689875444
No 137
>smart00301 DM Doublesex DNA-binding motif.
Probab=55.63 E-value=7.4 Score=24.73 Aligned_cols=33 Identities=21% Similarity=0.480 Sum_probs=26.4
Q ss_pred CCchhhhccCCCCCCCCCCCCCcceeChhHHHhHh
Q 042263 78 GENKDHERNCQCAPCACPLLDCNFLGSASQLYLYF 112 (159)
Q Consensus 78 ~~~~~He~~C~~~p~~Cp~~gC~~~g~~~~l~~H~ 112 (159)
..++.|-..|+|+.+.|+. |..+..+..++...
T Consensus 15 ~~lKGHKr~C~~r~C~C~k--C~Li~~Rq~vma~q 47 (54)
T smart00301 15 VPLKGHKPECPFRDCECEK--CTLVEKRRALMALQ 47 (54)
T ss_pred eccCCcCCCCCCCCCcCCC--CcChHHHHHHHHHH
Confidence 4577899999999999975 98887777766543
No 138
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.45 E-value=3.3 Score=34.86 Aligned_cols=44 Identities=20% Similarity=0.412 Sum_probs=33.8
Q ss_pred CeeecccccccCCCc---------eeeccCCceecccccccc-----CCCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVP---------VSQSINGHIICSSCLAKV-----NNKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~P---------v~qC~~GH~~C~~C~~~~-----~~~CP~Cr~~~ 60 (159)
+.-.|.||.+-+... +|+-.|+|+|=..|+..+ .+.||-|++.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 344599998776543 466678999999998876 25799999887
No 139
>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=55.33 E-value=11 Score=22.54 Aligned_cols=23 Identities=35% Similarity=0.748 Sum_probs=16.6
Q ss_pred eecccccccCCCceeeccCCceecccc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSC 45 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C 45 (159)
-.||.|. .|.++-..|..+|-.|
T Consensus 18 ~~Cp~C~----~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCG----TPLMRDKDGKIYCVSC 40 (41)
T ss_pred CccCCCC----CeeEEecCCCEECCCC
Confidence 3599996 4555546788998887
No 140
>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=54.61 E-value=11 Score=21.04 Aligned_cols=9 Identities=33% Similarity=0.829 Sum_probs=6.6
Q ss_pred CCCCCCccC
Q 042263 51 NKCPACRSC 59 (159)
Q Consensus 51 ~~CP~Cr~~ 59 (159)
..||.|..+
T Consensus 18 ~~CP~Cg~~ 26 (33)
T cd00350 18 WVCPVCGAP 26 (33)
T ss_pred CcCcCCCCc
Confidence 478888764
No 141
>PRK00420 hypothetical protein; Validated
Probab=54.36 E-value=8.8 Score=27.94 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=18.7
Q ss_pred eecccccccCCCceeeccCCceecccccccc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKV 49 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~ 49 (159)
-.||+|..+|.. =..|..+|..|-...
T Consensus 24 ~~CP~Cg~pLf~----lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFE----LKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCccee----cCCCceECCCCCCee
Confidence 579999955543 255888887776643
No 142
>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=53.64 E-value=13 Score=17.93 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=15.1
Q ss_pred CCCCCCCcceeC-hhHHHhHhhhhc
Q 042263 93 ACPLLDCNFLGS-ASQLYLYFSWKN 116 (159)
Q Consensus 93 ~Cp~~gC~~~g~-~~~l~~H~~~~H 116 (159)
.|+. |+...+ ..+|..|+...|
T Consensus 2 ~C~~--C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCPI--CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-SS--TS-EESSHHHHHHHHHHHS
T ss_pred CCcC--CCCcCCcHHHHHHHHHhhC
Confidence 4665 877755 578999998876
No 143
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=52.19 E-value=7.1 Score=20.68 Aligned_cols=6 Identities=33% Similarity=0.617 Sum_probs=2.9
Q ss_pred cccccc
Q 042263 21 CPIWYQ 26 (159)
Q Consensus 21 C~iC~~ 26 (159)
||-|..
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444544
No 144
>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=51.19 E-value=3.9 Score=33.93 Aligned_cols=43 Identities=23% Similarity=0.580 Sum_probs=29.9
Q ss_pred eeeccccc--ccCCCcee--ec-cCCceeccccccccC----CCCC--CCccCc
Q 042263 18 LFDCPIWY--QALKVPVS--QS-INGHIICSSCLAKVN----NKCP--ACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~--~~l~~Pv~--qC-~~GH~~C~~C~~~~~----~~CP--~Cr~~~ 60 (159)
.-.||+|. .+|.+-|- .- +|=|+.|.+|..++- +.|| .|..-+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 34699998 35555433 22 378999999999873 6899 786543
No 145
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=50.39 E-value=16 Score=24.25 Aligned_cols=29 Identities=28% Similarity=0.264 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCCccee-ChhHHHhHhhhh-cCC
Q 042263 88 QCAPCACPLLDCNFLG-SASQLYLYFSWK-NGK 118 (159)
Q Consensus 88 ~~~p~~Cp~~gC~~~g-~~~~l~~H~~~~-H~~ 118 (159)
......|++ |+... +..+|..|+... |..
T Consensus 47 ~~~~~~C~~--C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 47 VKESFRCPY--CNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp --SSEEBSS--SS-EESSHHHHHHHHHHTTTTC
T ss_pred cCCCCCCCc--cCCCCcCHHHHHHHHcCccCCC
Confidence 333678986 88775 467899999986 444
No 146
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.89 E-value=8.2 Score=37.10 Aligned_cols=42 Identities=26% Similarity=0.585 Sum_probs=35.2
Q ss_pred eecccccccCCCceeeccCCceeccccccccCCCCCCCccCc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~Cr~~~ 60 (159)
-.|..|.-.|.-|+..=.|||.|=..|.+.-...||.|+...
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhccCcccCCccchhh
Confidence 589999999999965547799999999996556899998743
No 147
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=49.71 E-value=11 Score=21.67 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=16.3
Q ss_pred CeeecccccccCCCceeeccCCceeccccccc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAK 48 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~ 48 (159)
+...|--|.+.+.+.-+.-.-++.+|..|+.+
T Consensus 2 ~~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD~ 33 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLNNFDLPVCDKCRDK 33 (34)
T ss_dssp S-EE-TTT--EES-SSCCCCTS-S--TTT-ST
T ss_pred CCchHhHhCCHHHHHHHHHhCCccccccccCC
Confidence 45678889998888644445688999988653
No 148
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=46.30 E-value=17 Score=26.17 Aligned_cols=25 Identities=32% Similarity=0.792 Sum_probs=15.9
Q ss_pred eeecc-CCc--eeccccccccCCCCCCCccC
Q 042263 32 VSQSI-NGH--IICSSCLAKVNNKCPACRSC 59 (159)
Q Consensus 32 v~qC~-~GH--~~C~~C~~~~~~~CP~Cr~~ 59 (159)
++.|+ ||| .+..+|..+ .||.|...
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R---~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNR---HCPSCQAK 69 (111)
T ss_pred eeecCCCCceEEecCcccCc---CCCCCCCh
Confidence 44554 555 467777665 68888663
No 149
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=45.78 E-value=20 Score=24.88 Aligned_cols=33 Identities=15% Similarity=0.445 Sum_probs=24.2
Q ss_pred CceeccccccccC--------------CCCCCCccCcchhhHHHHHH
Q 042263 38 GHIICSSCLAKVN--------------NKCPACRSCVMLRSRVMDIA 70 (159)
Q Consensus 38 GH~~C~~C~~~~~--------------~~CP~Cr~~~~~rn~~le~~ 70 (159)
+.+.|..|..++. ++|..|++++..+-..+|-+
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~~y~l~El~ 78 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPPRYPLIELL 78 (92)
T ss_pred CCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCChHHHHHHHH
Confidence 5678888888762 68999999986655555543
No 150
>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=44.15 E-value=19 Score=25.92 Aligned_cols=42 Identities=14% Similarity=0.283 Sum_probs=26.9
Q ss_pred CeeecccccccCC---Cceeecc-CCceeccccccccC----CCCCCCcc
Q 042263 17 DLFDCPIWYQALK---VPVSQSI-NGHIICSSCLAKVN----NKCPACRS 58 (159)
Q Consensus 17 ~~l~C~iC~~~l~---~Pv~qC~-~GH~~C~~C~~~~~----~~CP~Cr~ 58 (159)
+.-.|.+|..+|. .+-..|. |+|.+|+.|..... ..|..|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 3457999987653 3334675 89999999976542 24777754
No 151
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=42.65 E-value=6.8 Score=26.81 Aligned_cols=46 Identities=17% Similarity=0.357 Sum_probs=16.7
Q ss_pred CCCeeecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 15 DQDLFDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
+.+.-.|.||.+-.- .+..-|. |+-.+|..|.+-- .+.||.|+++.
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 344456999987652 2322353 6888888887532 36799999876
No 152
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.88 E-value=30 Score=31.13 Aligned_cols=44 Identities=23% Similarity=0.387 Sum_probs=28.6
Q ss_pred CeeecccccccCCCc------eeeccCCceecccccccc--CCCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVP------VSQSINGHIICSSCLAKV--NNKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~P------v~qC~~GH~~C~~C~~~~--~~~CP~Cr~~~ 60 (159)
..+.|..|...++=| +|.=..+...|..|-.+. ...||.|....
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSED 263 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCe
Confidence 356677777776544 111124567899997664 36899998864
No 153
>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=41.61 E-value=23 Score=20.76 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=15.7
Q ss_pred eecccccccCCCceeeccCCceecccccc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLA 47 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~ 47 (159)
+.||.|.... -++--..|-.+|..|-.
T Consensus 1 m~Cp~Cg~~~--~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKE--IVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSE--EEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCc--eEEcCCCCeEECCCCCC
Confidence 3588888643 12222457788888844
No 154
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=41.26 E-value=22 Score=22.45 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCcceeCh-hHHHhHhhhhcCCc
Q 042263 89 CAPCACPLLDCNFLGSA-SQLYLYFSWKNGKT 119 (159)
Q Consensus 89 ~~p~~Cp~~gC~~~g~~-~~l~~H~~~~H~~~ 119 (159)
.-|-.||. |+-+.+. .+|..|++-.|...
T Consensus 22 ~~PatCP~--C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPI--CGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TT--T--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCCc--chhhccchhhHHHHHHHHhccc
Confidence 34668987 9988775 68999999999754
No 155
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.15 E-value=5.7 Score=36.07 Aligned_cols=43 Identities=26% Similarity=0.498 Sum_probs=30.9
Q ss_pred eeecccccccCCC-----c-----------eeeccCCceeccccccccCC----CCCCCccCc
Q 042263 18 LFDCPIWYQALKV-----P-----------VSQSINGHIICSSCLAKVNN----KCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~-----P-----------v~qC~~GH~~C~~C~~~~~~----~CP~Cr~~~ 60 (159)
.-+|+||.....- | -...+|.|.|=..|+.++.. .||.||.++
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pL 633 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPL 633 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCC
Confidence 4579999866421 0 01237899999999998752 799999875
No 156
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=40.96 E-value=12 Score=32.18 Aligned_cols=80 Identities=16% Similarity=0.298 Sum_probs=48.8
Q ss_pred eeecccccccCCCceeeccCCceecccccccc-CCCCCCCccCcchhhHHHHHHHHhhccCCCchhhhccCCCCCCCCCC
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCLAKV-NNKCPACRSCVMLRSRVMDIALEKTMSFGENKDHERNCQCAPCACPL 96 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~-~~~CP~Cr~~~~~rn~~le~~~~~~~~~~~~~~He~~C~~~p~~Cp~ 96 (159)
+-.|.-|..+...=-..=.|-|+||-.|-..- .+.||.|...+ .-+|.+..+.+ .-|-.
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V----qrIeq~~~g~i----------------FmC~~ 149 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV----QRIEQIMMGGI----------------FMCAA 149 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH----HHHHHhcccce----------------EEeec
Confidence 56688888665421011256999999996543 36899997765 22333322221 13333
Q ss_pred C-CCcce-eChhHHHhHhhhhcC
Q 042263 97 L-DCNFL-GSASQLYLYFSWKNG 117 (159)
Q Consensus 97 ~-gC~~~-g~~~~l~~H~~~~H~ 117 (159)
. ||.-+ .+..+|..|+...|.
T Consensus 150 ~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 150 PHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred chhHHHHHhhHHHHHHHhhhhhc
Confidence 3 67654 445789999999887
No 157
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=40.56 E-value=8.2 Score=26.64 Aligned_cols=43 Identities=16% Similarity=0.311 Sum_probs=29.0
Q ss_pred eeecccccccCCCceeec---------------cCCceeccccccccC---CCCCCCccCc
Q 042263 18 LFDCPIWYQALKVPVSQS---------------INGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC---------------~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
.-.|.||...+.++-.+| .|.|.|=..|+.++. +.||.+++++
T Consensus 20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w 80 (88)
T COG5194 20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTW 80 (88)
T ss_pred cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCcee
Confidence 445666666655543334 356777778888764 6799999987
No 158
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.52 E-value=21 Score=33.89 Aligned_cols=43 Identities=23% Similarity=0.440 Sum_probs=27.9
Q ss_pred eeecccccccCCCc------eeeccCCceecccccccc--CCCCCCCccCc
Q 042263 18 LFDCPIWYQALKVP------VSQSINGHIICSSCLAKV--NNKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~~P------v~qC~~GH~~C~~C~~~~--~~~CP~Cr~~~ 60 (159)
.+.|..|..+++=| ++.=..|...|..|-... ...||.|....
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~ 485 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEH 485 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCe
Confidence 45566666655433 121145778999997653 36899999985
No 159
>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=40.30 E-value=24 Score=19.95 Aligned_cols=9 Identities=44% Similarity=1.143 Sum_probs=6.2
Q ss_pred CCCCCCccC
Q 042263 51 NKCPACRSC 59 (159)
Q Consensus 51 ~~CP~Cr~~ 59 (159)
..||.|..+
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 478888664
No 160
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=39.95 E-value=4.7 Score=40.29 Aligned_cols=42 Identities=29% Similarity=0.600 Sum_probs=33.3
Q ss_pred CeeecccccccCC--CceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 17 DLFDCPIWYQALK--VPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~--~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
+...|+||.++++ .-|++| ||.+|..|...+. ..||.|....
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~c--gh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGC--GHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred cccchHHHHHHHHhcCCeeee--chhHhhhHHHHHHHHhccCcchhhhh
Confidence 3458999999997 346666 9999999988764 5799997654
No 161
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=39.79 E-value=20 Score=21.24 Aligned_cols=27 Identities=26% Similarity=0.466 Sum_probs=13.9
Q ss_pred eecccccccCCCceee--ccCCceecccc
Q 042263 19 FDCPIWYQALKVPVSQ--SINGHIICSSC 45 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~q--C~~GH~~C~~C 45 (159)
.-||+|..--+--|+. =..|+.+|..|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCC
Confidence 4599998754433332 12499999999
No 162
>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=39.74 E-value=17 Score=22.38 Aligned_cols=29 Identities=24% Similarity=0.633 Sum_probs=16.1
Q ss_pred CCCchhhhccCCCCCCCCCCCCCcceeChhH
Q 042263 77 FGENKDHERNCQCAPCACPLLDCNFLGSASQ 107 (159)
Q Consensus 77 ~~~~~~He~~C~~~p~~Cp~~gC~~~g~~~~ 107 (159)
...++.|...|+|+.+.|.. |.....+..
T Consensus 14 ~~~lKgHk~~C~~~~C~C~k--C~li~eRq~ 42 (47)
T PF00751_consen 14 IVPLKGHKRYCPFRDCQCDK--CALIAERQR 42 (47)
T ss_dssp --TTTT-GGG-TTTT--SHH--HHHHHHHH-
T ss_pred ccchhhhccccCcCCCcCCC--CcCcHHHHH
Confidence 34578999999999999964 765544433
No 163
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.68 E-value=25 Score=32.91 Aligned_cols=55 Identities=16% Similarity=0.266 Sum_probs=30.9
Q ss_pred eeecccccccCCCc------eeeccCCceecccccccc--CCCCCCCccCc-chhhHHHHHHHH
Q 042263 18 LFDCPIWYQALKVP------VSQSINGHIICSSCLAKV--NNKCPACRSCV-MLRSRVMDIALE 72 (159)
Q Consensus 18 ~l~C~iC~~~l~~P------v~qC~~GH~~C~~C~~~~--~~~CP~Cr~~~-~~rn~~le~~~~ 72 (159)
.+.|.-|...++-| ++.=..+-..|..|-.+. ...||.|.... .......|++.+
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e 444 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEE 444 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHH
Confidence 45566665555432 111134557899997664 36899998875 333333444433
No 164
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=38.58 E-value=19 Score=25.28 Aligned_cols=34 Identities=24% Similarity=0.557 Sum_probs=25.1
Q ss_pred ecccccccCCCceeeccCCceeccccccccCCCCCCCccCc
Q 042263 20 DCPIWYQALKVPVSQSINGHIICSSCLAKVNNKCPACRSCV 60 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~Cr~~~ 60 (159)
.|-+|..-+ . +.||.+|..|--+- +.|..|...+
T Consensus 46 ~C~~CK~~v----~--q~g~~YCq~CAYkk-GiCamCGKki 79 (90)
T PF10235_consen 46 KCKICKTKV----H--QPGAKYCQTCAYKK-GICAMCGKKI 79 (90)
T ss_pred ccccccccc----c--cCCCccChhhhccc-CcccccCCee
Confidence 677776332 2 23999999997664 4899999887
No 165
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=38.37 E-value=9 Score=34.10 Aligned_cols=52 Identities=23% Similarity=0.475 Sum_probs=40.2
Q ss_pred CCCeeecccccccCCCceeeccCCceeccccccccCCCCCCCccCcchhhHHHHHHHH
Q 042263 15 DQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVNNKCPACRSCVMLRSRVMDIALE 72 (159)
Q Consensus 15 ~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~~~CP~Cr~~~~~rn~~le~~~~ 72 (159)
..+-|+|..|..-|....|.-.+|-.+|..|.+....+|-.|... .+|+|+.
T Consensus 299 Hv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~------I~d~iLr 350 (468)
T KOG1701|consen 299 HVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEP------IMDRILR 350 (468)
T ss_pred cccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhH------HHHHHHH
Confidence 456789999999998765554789999999988766789888774 4566665
No 166
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=37.96 E-value=19 Score=31.15 Aligned_cols=37 Identities=19% Similarity=0.443 Sum_probs=26.1
Q ss_pred cccc-cccCCCceeecc-CCceecccccccc---CCCCCCCc
Q 042263 21 CPIW-YQALKVPVSQSI-NGHIICSSCLAKV---NNKCPACR 57 (159)
Q Consensus 21 C~iC-~~~l~~Pv~qC~-~GH~~C~~C~~~~---~~~CP~Cr 57 (159)
|-.| .+.+..+.|+|. |-+.||..|-.=+ ...||-|-
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 7778 444556788887 7888999985432 25788885
No 167
>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=37.46 E-value=34 Score=18.54 Aligned_cols=18 Identities=11% Similarity=0.148 Sum_probs=13.8
Q ss_pred eecccccccCCCc-eeecc
Q 042263 19 FDCPIWYQALKVP-VSQSI 36 (159)
Q Consensus 19 l~C~iC~~~l~~P-v~qC~ 36 (159)
+.|.+|.+.+... .|.|.
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~ 19 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCS 19 (30)
T ss_pred CCCCCCCCCcCCCEeEEeC
Confidence 3588898888877 77774
No 168
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=37.44 E-value=26 Score=27.22 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=14.5
Q ss_pred eeecc-CCceeccccccccCCCCCCCccC
Q 042263 32 VSQSI-NGHIICSSCLAKVNNKCPACRSC 59 (159)
Q Consensus 32 v~qC~-~GH~~C~~C~~~~~~~CP~Cr~~ 59 (159)
++.|. |||+ |...-...||+|..+
T Consensus 134 ~~vC~vCGy~----~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYT----HEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCc----ccCCCCCcCCCCCCh
Confidence 56665 5665 333223589999765
No 169
>PRK11595 DNA utilization protein GntX; Provisional
Probab=36.94 E-value=20 Score=28.68 Aligned_cols=8 Identities=25% Similarity=0.409 Sum_probs=5.0
Q ss_pred cccccccC
Q 042263 21 CPIWYQAL 28 (159)
Q Consensus 21 C~iC~~~l 28 (159)
|.+|..++
T Consensus 8 C~~C~~~~ 15 (227)
T PRK11595 8 CWLCRMPL 15 (227)
T ss_pred CccCCCcc
Confidence 66666554
No 170
>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=36.37 E-value=22 Score=17.47 Aligned_cols=20 Identities=30% Similarity=0.439 Sum_probs=14.8
Q ss_pred CCCCCCCcceeCh-hHHHhHhhh
Q 042263 93 ACPLLDCNFLGSA-SQLYLYFSW 114 (159)
Q Consensus 93 ~Cp~~gC~~~g~~-~~l~~H~~~ 114 (159)
.||. |+...+. .+|..|+..
T Consensus 2 ~C~~--C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPI--CGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETT--TTEEESSHHHHHHHHHH
T ss_pred CCCC--CCCccCCHHHHHHHHhH
Confidence 4664 8887664 679999876
No 171
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.11 E-value=8.7 Score=32.77 Aligned_cols=26 Identities=38% Similarity=0.943 Sum_probs=19.5
Q ss_pred ccCCceecccccccc----------------CCCCCCCccCc
Q 042263 35 SINGHIICSSCLAKV----------------NNKCPACRSCV 60 (159)
Q Consensus 35 C~~GH~~C~~C~~~~----------------~~~CP~Cr~~~ 60 (159)
|-|.-..|.+|+.++ ..+||+||+.+
T Consensus 323 c~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~f 364 (381)
T KOG3899|consen 323 CICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNF 364 (381)
T ss_pred cccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhce
Confidence 445667888898876 14699999987
No 172
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.29 E-value=43 Score=17.48 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=17.6
Q ss_pred CCCCCCCCcceeChhHHHhHhhh
Q 042263 92 CACPLLDCNFLGSASQLYLYFSW 114 (159)
Q Consensus 92 ~~Cp~~gC~~~g~~~~l~~H~~~ 114 (159)
+.||. |+-+.....|..|...
T Consensus 3 ~~C~~--CgR~F~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPI--CGRKFNPDRLEKHEKI 23 (25)
T ss_pred CcCCC--CCCEECHHHHHHHHHh
Confidence 57886 9999999999999764
No 173
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=35.19 E-value=38 Score=30.27 Aligned_cols=44 Identities=25% Similarity=0.539 Sum_probs=31.5
Q ss_pred CCCceEEEeeCCC----eeecccccccCC-Cceee-c--cCCceeccccccc
Q 042263 5 KNGSITSTISDQD----LFDCPIWYQALK-VPVSQ-S--INGHIICSSCLAK 48 (159)
Q Consensus 5 ~~~~~~~~~~~~~----~l~C~iC~~~l~-~Pv~q-C--~~GH~~C~~C~~~ 48 (159)
++.+|.|.-+|.+ -+.|--|...|. .+--| | -+||++|..|..+
T Consensus 410 ~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~ 461 (468)
T KOG1701|consen 410 KDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLK 461 (468)
T ss_pred CcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhh
Confidence 4556777777766 577888888887 44334 2 3799999999765
No 174
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=34.82 E-value=17 Score=29.57 Aligned_cols=100 Identities=21% Similarity=0.432 Sum_probs=55.0
Q ss_pred EEEeeCCCeeecccccccCCCceeeccCCcee---------ccccccccC-----------------CCCCCCccCcchh
Q 042263 10 TSTISDQDLFDCPIWYQALKVPVSQSINGHII---------CSSCLAKVN-----------------NKCPACRSCVMLR 63 (159)
Q Consensus 10 ~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~---------C~~C~~~~~-----------------~~CP~Cr~~~~~r 63 (159)
...-.|.+.+.|.||.+.|.-.-+ -+.|.- |..|-...+ .+|-.|.+.+..|
T Consensus 109 ~gsssd~d~ftCrvCgK~F~lQRm--lnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 109 IGSSSDQDSFTCRVCGKKFGLQRM--LNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred ccCCCCCCeeeeehhhhhhhHHHH--HHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh
Confidence 334457889999999998863211 123333 333332221 3577776665444
Q ss_pred hH---HHHHHHH--hhccCCCchhhhccCCCCCCCCCCCCCcceeChh-HHHhHhhhhcCCce
Q 042263 64 SR---VMDIALE--KTMSFGENKDHERNCQCAPCACPLLDCNFLGSAS-QLYLYFSWKNGKTF 120 (159)
Q Consensus 64 n~---~le~~~~--~~~~~~~~~~He~~C~~~p~~Cp~~gC~~~g~~~-~l~~H~~~~H~~~~ 120 (159)
+. .+.++-. ....|.++++- .+.|- .|++++... .++.|+...|+...
T Consensus 187 csleshl~kvhgv~~~yaykerr~k-------l~vce--dcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAK-------LYVCE--DCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhh-------eeeec--ccCCCCCChhHHHHHHHhcCCCCH
Confidence 32 1222221 22223333322 34564 589988765 57899999998764
No 175
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=33.75 E-value=25 Score=30.66 Aligned_cols=26 Identities=19% Similarity=0.107 Sum_probs=22.5
Q ss_pred CCCCCCCC--CCcceeChhHHHhHhhhh
Q 042263 90 APCACPLL--DCNFLGSASQLYLYFSWK 115 (159)
Q Consensus 90 ~p~~Cp~~--gC~~~g~~~~l~~H~~~~ 115 (159)
.++.|+++ ||.|.+...++..|+...
T Consensus 85 l~i~c~~~~~GC~~~~~l~~~~~Hl~~c 112 (391)
T KOG0297|consen 85 LPIRCIFASRGCRADLELEALQGHLSTC 112 (391)
T ss_pred cccccccCCCCccccccHHHHHhHhccC
Confidence 37888765 999999999999999875
No 176
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=33.17 E-value=30 Score=20.05 Aligned_cols=11 Identities=27% Similarity=0.473 Sum_probs=7.7
Q ss_pred ecccccccCCC
Q 042263 20 DCPIWYQALKV 30 (159)
Q Consensus 20 ~C~iC~~~l~~ 30 (159)
.||.|...|..
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 48888876654
No 177
>PLN02189 cellulose synthase
Probab=32.57 E-value=29 Score=34.27 Aligned_cols=42 Identities=19% Similarity=0.444 Sum_probs=31.6
Q ss_pred eecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 19 FDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
-.|.||.+-+- .|-.-|. ||--+|..|.+-- ++.||.|++..
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRY 86 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 37999998864 2433575 8999999998643 36799999886
No 178
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.54 E-value=13 Score=29.50 Aligned_cols=43 Identities=26% Similarity=0.463 Sum_probs=26.8
Q ss_pred eeecccccccCC---Cceeecc---CCceeccccccccC--------------CCCCCCccCc
Q 042263 18 LFDCPIWYQALK---VPVSQSI---NGHIICSSCLAKVN--------------NKCPACRSCV 60 (159)
Q Consensus 18 ~l~C~iC~~~l~---~Pv~qC~---~GH~~C~~C~~~~~--------------~~CP~Cr~~~ 60 (159)
...|.||+.+-- .|-+.|. ||..|=+-|+..|. +.||.|..++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi 227 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI 227 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence 445556655432 2444453 57677777776652 5799999988
No 179
>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=32.52 E-value=11 Score=23.54 Aligned_cols=40 Identities=25% Similarity=0.686 Sum_probs=21.9
Q ss_pred eecccccccCCCceeeccCCceeccccccccC---CCCCCCccCc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
+.|-.|--.-+. ...| ..|-.|-.|+..+. ..||.|..++
T Consensus 3 ~nCKsCWf~~k~-Li~C-~dHYLCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 3 YNCKSCWFANKG-LIKC-SDHYLCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp ----SS-S--SS-EEE--SS-EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred ccChhhhhcCCC-eeee-cchhHHHHHHHHHhccccCCCcccCcC
Confidence 345556555444 3344 48999999998874 5799999876
No 180
>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=32.36 E-value=25 Score=27.35 Aligned_cols=28 Identities=11% Similarity=-0.202 Sum_probs=16.2
Q ss_pred CCCCCCCC--CCcceeChhHHHhHhhhhcC
Q 042263 90 APCACPLL--DCNFLGSASQLYLYFSWKNG 117 (159)
Q Consensus 90 ~p~~Cp~~--gC~~~g~~~~l~~H~~~~H~ 117 (159)
..++|++. ||.+..++.+...|.+..--
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~ 42 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEECPF 42 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT-TT
T ss_pred ceecCCCCCCCCcccccccChhhHhccCCC
Confidence 45688875 89999999999999887543
No 181
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.05 E-value=32 Score=20.54 Aligned_cols=25 Identities=20% Similarity=0.425 Sum_probs=13.6
Q ss_pred cccccccCCCceeeccCCceeccccc
Q 042263 21 CPIWYQALKVPVSQSINGHIICSSCL 46 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC~~GH~~C~~C~ 46 (159)
||-|..+|..+-.. .+.+..|..|-
T Consensus 3 Cp~Cg~~l~~~~~~-~~~~~vC~~Cg 27 (52)
T smart00661 3 CPKCGNMLIPKEGK-EKRRFVCRKCG 27 (52)
T ss_pred CCCCCCccccccCC-CCCEEECCcCC
Confidence 88888877654211 11245555554
No 182
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=31.51 E-value=28 Score=20.73 Aligned_cols=30 Identities=23% Similarity=0.435 Sum_probs=20.3
Q ss_pred eecccccccCCCceeecc-C-Cceeccccccc
Q 042263 19 FDCPIWYQALKVPVSQSI-N-GHIICSSCLAK 48 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~-~-GH~~C~~C~~~ 48 (159)
+.|.+|..++...-+.|. | +-..|..|...
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCc
Confidence 358899988777666764 2 34667777654
No 183
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.39 E-value=24 Score=29.68 Aligned_cols=24 Identities=29% Similarity=0.682 Sum_probs=20.0
Q ss_pred CCceeccccccccC-------CCCCCCccCc
Q 042263 37 NGHIICSSCLAKVN-------NKCPACRSCV 60 (159)
Q Consensus 37 ~GH~~C~~C~~~~~-------~~CP~Cr~~~ 60 (159)
..|+||+.|-.+.. ..||.|+...
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 47999999998873 4699999876
No 184
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=31.36 E-value=65 Score=21.10 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=22.4
Q ss_pred CCCCCCCcceeChhHHHhHhhhhcCCce
Q 042263 93 ACPLLDCNFLGSASQLYLYFSWKNGKTF 120 (159)
Q Consensus 93 ~Cp~~gC~~~g~~~~l~~H~~~~H~~~~ 120 (159)
+|. +|+|...+.++.+.+....+..+
T Consensus 7 YC~--~C~~~~~a~~l~~~l~~~fp~~~ 32 (76)
T PF10262_consen 7 YCT--SCGYRPRALELAQELLQTFPDRI 32 (76)
T ss_dssp EET--TTTCHHHHHHHHHHHHHHSTTTC
T ss_pred ECC--CCCCHHHHHHHHHHHHHHCCCcc
Confidence 564 69999999999999999988844
No 185
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.28 E-value=54 Score=26.52 Aligned_cols=20 Identities=20% Similarity=0.311 Sum_probs=11.1
Q ss_pred CceEEEeeC--CCeeecccccc
Q 042263 7 GSITSTISD--QDLFDCPIWYQ 26 (159)
Q Consensus 7 ~~~~~~~~~--~~~l~C~iC~~ 26 (159)
|-+.|.+.+ +..-.||.|..
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~ 317 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH 317 (364)
T ss_pred CCeEEEECCCCCCcccccccCC
Confidence 445555554 33455776666
No 186
>PRK01343 zinc-binding protein; Provisional
Probab=31.22 E-value=32 Score=22.10 Aligned_cols=9 Identities=22% Similarity=0.345 Sum_probs=4.4
Q ss_pred eeccccccc
Q 042263 19 FDCPIWYQA 27 (159)
Q Consensus 19 l~C~iC~~~ 27 (159)
..||||...
T Consensus 10 ~~CP~C~k~ 18 (57)
T PRK01343 10 RPCPECGKP 18 (57)
T ss_pred CcCCCCCCc
Confidence 345555544
No 187
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.91 E-value=48 Score=18.90 Aligned_cols=11 Identities=18% Similarity=0.461 Sum_probs=6.9
Q ss_pred eecccccccCC
Q 042263 19 FDCPIWYQALK 29 (159)
Q Consensus 19 l~C~iC~~~l~ 29 (159)
+.||-|...+.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 46777776554
No 188
>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=30.89 E-value=25 Score=18.92 Aligned_cols=26 Identities=15% Similarity=0.539 Sum_probs=11.6
Q ss_pred ecccccccCCCceeeccCCceeccccc
Q 042263 20 DCPIWYQALKVPVSQSINGHIICSSCL 46 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH~~C~~C~ 46 (159)
.|+.|..++.+ +.+=..+..+|..|.
T Consensus 3 ~C~rC~~~~~~-~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIED-IGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEE-EEETTEEEEE-TTTC
T ss_pred cCccCCCcceE-eEecCCCCeECcCCc
Confidence 47777777654 233233445666663
No 189
>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=30.64 E-value=25 Score=19.85 Aligned_cols=30 Identities=27% Similarity=0.495 Sum_probs=16.2
Q ss_pred eecccccccCCCceeec--cCCceeccccccc
Q 042263 19 FDCPIWYQALKVPVSQS--INGHIICSSCLAK 48 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC--~~GH~~C~~C~~~ 48 (159)
+.||-|...++-+.-+- .-+...|..|...
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 67888888665442211 1234556655443
No 190
>PF13008 zf-Paramyx-P: Zinc-binding domain of Paramyxoviridae V protein; InterPro: IPR024279 The paramyxoviruses, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT []. The P mRNA encodes a variety of proteins beyond P. Protein V consists of PNT fused to a C-terminal zinc-binding region. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction []. In the Henipavirus family, which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation [].; GO: 0046872 metal ion binding; PDB: 2HYE_B 2B5L_D.
Probab=30.42 E-value=36 Score=20.99 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=10.5
Q ss_pred ccccccCCCcee-eccCCc--eeccccc
Q 042263 22 PIWYQALKVPVS-QSINGH--IICSSCL 46 (159)
Q Consensus 22 ~iC~~~l~~Pv~-qC~~GH--~~C~~C~ 46 (159)
|+|.-+-..|.+ .|.||. .+|+.|.
T Consensus 17 P~CspIt~~p~r~~C~CG~CP~~C~~C~ 44 (47)
T PF13008_consen 17 PICSPITATPRREKCTCGECPRICSLCE 44 (47)
T ss_dssp ETTS---SS-EEE--SSTTS-S--SSST
T ss_pred CcCcccccccEEeeEECCCCcchhhhhc
Confidence 678777777755 576666 4555553
No 191
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=30.20 E-value=30 Score=30.36 Aligned_cols=25 Identities=36% Similarity=0.728 Sum_probs=13.6
Q ss_pred CCCCCCCCcce-eChhHHHhHhhhhcCC
Q 042263 92 CACPLLDCNFL-GSASQLYLYFSWKNGK 118 (159)
Q Consensus 92 ~~Cp~~gC~~~-g~~~~l~~H~~~~H~~ 118 (159)
+.||. |+.+ +.+.+|..|+...|+.
T Consensus 264 ykCpl--Cdmtc~~~ssL~~H~r~rHs~ 289 (467)
T KOG3608|consen 264 YKCPL--CDMTCSSASSLTTHIRYRHSK 289 (467)
T ss_pred ccccc--cccCCCChHHHHHHHHhhhcc
Confidence 45554 4443 3345666666666654
No 192
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=29.76 E-value=39 Score=17.99 Aligned_cols=15 Identities=40% Similarity=0.955 Sum_probs=9.6
Q ss_pred CCCCCCCCCcceeChh
Q 042263 91 PCACPLLDCNFLGSAS 106 (159)
Q Consensus 91 p~~Cp~~gC~~~g~~~ 106 (159)
|..| ..||+|.|+..
T Consensus 1 ~~~C-~~gCgf~Gs~~ 15 (25)
T PF01754_consen 1 PSLC-ANGCGFYGSPA 15 (25)
T ss_dssp SSB--TTTSSSB-BGG
T ss_pred CCcc-cCCCCCccccc
Confidence 4578 67999999854
No 193
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=29.70 E-value=37 Score=19.50 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=16.8
Q ss_pred eecccccccCCCceeeccCCceecccccc
Q 042263 19 FDCPIWYQALKVPVSQSINGHIICSSCLA 47 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~ 47 (159)
..|++|...+ +.-..|-.+|..|-.
T Consensus 9 ~~C~~C~~~~----~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRW----FYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeE----eEccCCEEEhhhCce
Confidence 4599999873 233567777777754
No 194
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=29.37 E-value=45 Score=21.11 Aligned_cols=22 Identities=14% Similarity=0.292 Sum_probs=11.9
Q ss_pred cccccccCCCceeec-cCCceecc
Q 042263 21 CPIWYQALKVPVSQS-INGHIICS 43 (159)
Q Consensus 21 C~iC~~~l~~Pv~qC-~~GH~~C~ 43 (159)
|.+|... ...++.| .||+.+|.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~ 23 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCG 23 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEET
T ss_pred CCCCCCc-CCceEEeCCCCccccc
Confidence 5566655 4445666 36777776
No 195
>PF00868 Transglut_N: Transglutaminase family; InterPro: IPR001102 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) (TGase) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ]. Transglutaminases are widely distributed in various organs, tissues and body fluids. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. There are commonly three domains: N-terminal, middle (IPR013808 from INTERPRO) and C-terminal (IPR013807 from INTERPRO). This entry represents the N-terminal domain found in transglutaminases.; GO: 0018149 peptide cross-linking; PDB: 1L9N_B 1NUF_A 1NUD_A 1NUG_B 1L9M_A 1KV3_C 3S3S_A 2Q3Z_A 3LY6_A 3S3P_A ....
Probab=28.85 E-value=94 Score=22.32 Aligned_cols=38 Identities=8% Similarity=0.032 Sum_probs=22.3
Q ss_pred cceeChhHHHhHhhhhcCCceEEEEeCcEEEEEEeCCCc
Q 042263 100 NFLGSASQLYLYFSWKNGKTFVSFTYKKRVKVTLNVNDS 138 (159)
Q Consensus 100 ~~~g~~~~l~~H~~~~H~~~~~~~~~~~~~~~~~~~~~~ 138 (159)
+|.-..+. .+|-.+.-..+..-++.|++|.+.|..+.+
T Consensus 7 Dl~~~~N~-~~HhT~~y~~~~LVVRRGQ~F~i~l~f~r~ 44 (118)
T PF00868_consen 7 DLQSEENA-RAHHTDEYESPRLVVRRGQPFTITLRFNRP 44 (118)
T ss_dssp EE-HHHHH-HHTT-TTTSSSSEEEETTSEEEEEEEESSS
T ss_pred EeEehHhh-hhhCccccCCCCEEEECCCEEEEEEEEcCC
Confidence 33333333 344444433444558999999999987644
No 196
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=28.64 E-value=34 Score=33.25 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=23.2
Q ss_pred eecccccccCCC-------ceeecc-CCceeccccccc
Q 042263 19 FDCPIWYQALKV-------PVSQSI-NGHIICSSCLAK 48 (159)
Q Consensus 19 l~C~iC~~~l~~-------Pv~qC~-~GH~~C~~C~~~ 48 (159)
-.|..|...|.. --..|. ||.+||..|..+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSn 498 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITK 498 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCC
Confidence 569999999853 123486 899999999864
No 197
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.43 E-value=68 Score=18.05 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=15.6
Q ss_pred eeecccccccCCCceeeccCCceeccccc
Q 042263 18 LFDCPIWYQALKVPVSQSINGHIICSSCL 46 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~ 46 (159)
...|+.|...+ +++-..+..+|..|-
T Consensus 3 ~~~C~~C~~~~---i~~~~~~~~~C~~Cg 28 (33)
T PF08792_consen 3 LKKCSKCGGNG---IVNKEDDYEVCIFCG 28 (33)
T ss_pred ceEcCCCCCCe---EEEecCCeEEcccCC
Confidence 44577777544 443456777777764
No 198
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=28.24 E-value=30 Score=24.66 Aligned_cols=21 Identities=38% Similarity=0.914 Sum_probs=17.7
Q ss_pred eeccccccccC-------CCCCCCccCc
Q 042263 40 IICSSCLAKVN-------NKCPACRSCV 60 (159)
Q Consensus 40 ~~C~~C~~~~~-------~~CP~Cr~~~ 60 (159)
++|+-|...+. ..||.|+.++
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCC
Confidence 78999988763 5799999998
No 199
>PLN02436 cellulose synthase A
Probab=28.22 E-value=38 Score=33.59 Aligned_cols=42 Identities=21% Similarity=0.542 Sum_probs=31.3
Q ss_pred eecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 19 FDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
-.|.||.+-.- .|-.-|. ||--+|..|.+-- ++.||.|++..
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRY 88 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 37999998752 2433575 8999999998643 36799999886
No 200
>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=28.19 E-value=65 Score=17.24 Aligned_cols=25 Identities=12% Similarity=0.258 Sum_probs=13.3
Q ss_pred cccccccCCCc-eeeccCCceecccc
Q 042263 21 CPIWYQALKVP-VSQSINGHIICSSC 45 (159)
Q Consensus 21 C~iC~~~l~~P-v~qC~~GH~~C~~C 45 (159)
|..|.+.+.+. ...-..|..|-..|
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~C 27 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPEC 27 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccC
Confidence 77788877653 22223445444444
No 201
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.12 E-value=54 Score=30.81 Aligned_cols=55 Identities=18% Similarity=0.242 Sum_probs=29.7
Q ss_pred eeecccccccCCCc-----e-eeccCCceecccccccc-CCCCCCCccCc-chhhHHHHHHHH
Q 042263 18 LFDCPIWYQALKVP-----V-SQSINGHIICSSCLAKV-NNKCPACRSCV-MLRSRVMDIALE 72 (159)
Q Consensus 18 ~l~C~iC~~~l~~P-----v-~qC~~GH~~C~~C~~~~-~~~CP~Cr~~~-~~rn~~le~~~~ 72 (159)
.+.|.-|...++=| + +.=..+-..|..|-... ...||.|.... ...-...|++.+
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~Gter~ee 445 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVGARRTAE 445 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeeccHHHHHH
Confidence 45566666555422 1 11123457799996543 35899998874 333333344433
No 202
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=27.42 E-value=52 Score=21.19 Aligned_cols=14 Identities=21% Similarity=0.560 Sum_probs=10.1
Q ss_pred CCCeeecccccccC
Q 042263 15 DQDLFDCPIWYQAL 28 (159)
Q Consensus 15 ~~~~l~C~iC~~~l 28 (159)
..+.|.||+|..+|
T Consensus 4 llniL~Cp~ck~pL 17 (68)
T PF03966_consen 4 LLNILACPVCKGPL 17 (68)
T ss_dssp GCGTBB-TTTSSBE
T ss_pred HHhhhcCCCCCCcc
Confidence 35688999999855
No 203
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=27.14 E-value=38 Score=20.78 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=5.4
Q ss_pred CCCCCccCc
Q 042263 52 KCPACRSCV 60 (159)
Q Consensus 52 ~CP~Cr~~~ 60 (159)
.||.|..++
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 799999988
No 204
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.04 E-value=19 Score=31.78 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=27.1
Q ss_pred eCCCeeecccccccCCCceeeccCCceecccccccc
Q 042263 14 SDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKV 49 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~ 49 (159)
.+....+|.||.+.....+..=.|||.||..|+...
T Consensus 66 ~~~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~y 101 (444)
T KOG1815|consen 66 KKKGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGY 101 (444)
T ss_pred CCCccccCCcccCCCcchhhhcCCCcHHHHHHHHHH
Confidence 356678999999988652222357999999999873
No 205
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=26.91 E-value=42 Score=23.78 Aligned_cols=39 Identities=18% Similarity=0.270 Sum_probs=25.6
Q ss_pred CeeecccccccCCCceeeccCCceecccccc-ccCCCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLA-KVNNKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~-~~~~~CP~Cr~~~ 60 (159)
-.-.||||-.+.++-... ++|..|-- +...+|-+|..+-
T Consensus 26 CDgkC~ICDS~VRP~tlV-----RiC~eC~~Gs~q~~ciic~~~g 65 (110)
T KOG1705|consen 26 CDGKCVICDSYVRPCTLV-----RICDECNYGSYQGRCVICGGVG 65 (110)
T ss_pred cCCcccccccccccceee-----eeehhcCCccccCceEEecCCc
Confidence 345799998888764332 67778843 3346788887643
No 206
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=26.87 E-value=19 Score=30.40 Aligned_cols=36 Identities=17% Similarity=0.369 Sum_probs=26.7
Q ss_pred eeCCCeeecccccccCCCce---eecc-CCceeccccccc
Q 042263 13 ISDQDLFDCPIWYQALKVPV---SQSI-NGHIICSSCLAK 48 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~Pv---~qC~-~GH~~C~~C~~~ 48 (159)
+-|.+.-.|.+|..+-...+ ..|. ||++||..|...
T Consensus 163 ~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n 202 (288)
T KOG1729|consen 163 LPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRN 202 (288)
T ss_pred cCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcC
Confidence 45778899999998533322 2475 799999999876
No 207
>PLN02195 cellulose synthase A
Probab=26.85 E-value=45 Score=32.76 Aligned_cols=47 Identities=13% Similarity=0.229 Sum_probs=33.2
Q ss_pred eCCCeeecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 14 SDQDLFDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
++...-.|.||.+-+- .|-.-|. ||--+|+.|.+=- ++.||+|.+..
T Consensus 2 ~~~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Y 58 (977)
T PLN02195 2 MESGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPY 58 (977)
T ss_pred CcCCCccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCcc
Confidence 4555567999998653 3433464 8999999997532 35799998875
No 208
>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=26.41 E-value=20 Score=21.59 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=10.3
Q ss_pred CCCCCCCCCcceeCh
Q 042263 91 PCACPLLDCNFLGSA 105 (159)
Q Consensus 91 p~~Cp~~gC~~~g~~ 105 (159)
-+.|.+..|++....
T Consensus 25 Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 25 YCQCTNPECGHTFVA 39 (47)
T ss_pred EEEECCCcCCCEEEE
Confidence 457777778877643
No 209
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.26 E-value=58 Score=20.69 Aligned_cols=25 Identities=28% Similarity=0.652 Sum_probs=16.4
Q ss_pred eeCCCeeecccccccCCCceeeccCCceecccc
Q 042263 13 ISDQDLFDCPIWYQALKVPVSQSINGHIICSSC 45 (159)
Q Consensus 13 ~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C 45 (159)
+.-++...||.|.++-.+ |.+|..|
T Consensus 22 l~~~~l~~C~~CG~~~~~--------H~vC~~C 46 (57)
T PRK12286 22 LKAPGLVECPNCGEPKLP--------HRVCPSC 46 (57)
T ss_pred ccCCcceECCCCCCccCC--------eEECCCC
Confidence 455677788888876544 5555555
No 210
>PF14353 CpXC: CpXC protein
Probab=26.13 E-value=35 Score=24.61 Aligned_cols=16 Identities=19% Similarity=0.355 Sum_probs=9.6
Q ss_pred eecccccccCCCceee
Q 042263 19 FDCPIWYQALKVPVSQ 34 (159)
Q Consensus 19 l~C~iC~~~l~~Pv~q 34 (159)
++||.|...+...++.
T Consensus 2 itCP~C~~~~~~~v~~ 17 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWT 17 (128)
T ss_pred cCCCCCCCeeEEEEEe
Confidence 4577777666655543
No 211
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=26.04 E-value=28 Score=18.79 Aligned_cols=16 Identities=6% Similarity=0.029 Sum_probs=5.9
Q ss_pred ecccccccCCC-ceeec
Q 042263 20 DCPIWYQALKV-PVSQS 35 (159)
Q Consensus 20 ~C~iC~~~l~~-Pv~qC 35 (159)
.|.+|.+.... +.|.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C 18 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRC 18 (30)
T ss_dssp --TTTS----S--EEE-
T ss_pred cCCcCCCcCCCCceEEC
Confidence 57788877766 66665
No 212
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.82 E-value=21 Score=26.83 Aligned_cols=36 Identities=17% Similarity=0.396 Sum_probs=17.4
Q ss_pred CCceEEEeeCCCeeecccccccCCCceeeccCCceecccccccc
Q 042263 6 NGSITSTISDQDLFDCPIWYQALKVPVSQSINGHIICSSCLAKV 49 (159)
Q Consensus 6 ~~~~~~~~~~~~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~ 49 (159)
.|.++..-...-.+.|..|+. ||.. | .||.+|...+
T Consensus 69 eGRL~~~~~~nl~~~CE~CG~----~I~~---G-r~C~~C~~~l 104 (137)
T TIGR03826 69 EGRLQLKHFPNLGYPCERCGT----SIRE---G-RLCDSCAGEL 104 (137)
T ss_pred cCCeeccCCCCCcCcccccCC----cCCC---C-CccHHHHHHH
Confidence 444444444444556666663 2221 3 5566665544
No 213
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.02 E-value=43 Score=28.11 Aligned_cols=43 Identities=26% Similarity=0.580 Sum_probs=28.6
Q ss_pred CeeecccccccCCCceeeccCCceeccccccccC-CCCCCCccCc
Q 042263 17 DLFDCPIWYQALKVPVSQSINGHIICSSCLAKVN-NKCPACRSCV 60 (159)
Q Consensus 17 ~~l~C~iC~~~l~~Pv~qC~~GH~~C~~C~~~~~-~~CP~Cr~~~ 60 (159)
..+.|..|...|..... --.|-.+|-.|..++. .-|-.|+.+|
T Consensus 162 yHFkCt~C~keL~sdaR-evk~eLyClrChD~mgipiCgaC~rpI 205 (332)
T KOG2272|consen 162 YHFKCTTCGKELTSDAR-EVKGELYCLRCHDKMGIPICGACRRPI 205 (332)
T ss_pred cceecccccccccchhh-hhccceeccccccccCCcccccccCch
Confidence 36778888888765433 2568888888888863 3444455554
No 214
>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=24.95 E-value=42 Score=23.89 Aligned_cols=16 Identities=13% Similarity=-0.083 Sum_probs=8.5
Q ss_pred ecccccccCCCceeec
Q 042263 20 DCPIWYQALKVPVSQS 35 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC 35 (159)
.|..|..--.+....|
T Consensus 9 ~CHqCrqKt~~~~~~C 24 (105)
T PF10497_consen 9 TCHQCRQKTLDFKTIC 24 (105)
T ss_pred CchhhcCCCCCCceEc
Confidence 4666665444444455
No 215
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=24.68 E-value=37 Score=18.35 Aligned_cols=10 Identities=30% Similarity=0.643 Sum_probs=4.5
Q ss_pred ecccccccCC
Q 042263 20 DCPIWYQALK 29 (159)
Q Consensus 20 ~C~iC~~~l~ 29 (159)
.||+|...+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4788876653
No 216
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=23.53 E-value=48 Score=17.51 Aligned_cols=6 Identities=50% Similarity=1.591 Sum_probs=3.5
Q ss_pred CCCCCc
Q 042263 52 KCPACR 57 (159)
Q Consensus 52 ~CP~Cr 57 (159)
.||.|.
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 466664
No 217
>PLN02400 cellulose synthase
Probab=23.10 E-value=84 Score=31.32 Aligned_cols=42 Identities=17% Similarity=0.356 Sum_probs=30.5
Q ss_pred eecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 19 FDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 19 l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
-.|.||.+-.- .|-.-|. ||--+|+.|.+=- ++.||+|++..
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrY 88 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRY 88 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcc
Confidence 37999998753 2433464 7889999997532 36799999986
No 218
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=22.90 E-value=42 Score=29.84 Aligned_cols=32 Identities=22% Similarity=0.479 Sum_probs=22.2
Q ss_pred eeecccccccCCCceeec-cCCceecccccccc
Q 042263 18 LFDCPIWYQALKVPVSQS-INGHIICSSCLAKV 49 (159)
Q Consensus 18 ~l~C~iC~~~l~~Pv~qC-~~GH~~C~~C~~~~ 49 (159)
..+||||+.+.-.....- .|.-.+|+.|+..+
T Consensus 74 ~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 74 KTECPICFLYYPSAKNLVRCCSETICGECFAPF 106 (482)
T ss_pred cccCceeeeecccccchhhhhccchhhhheecc
Confidence 468999997764321111 25889999999876
No 219
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=22.56 E-value=17 Score=32.59 Aligned_cols=37 Identities=16% Similarity=0.388 Sum_probs=28.1
Q ss_pred EeeCCCeeecccccccCCCc--eeecc-CCceeccccccc
Q 042263 12 TISDQDLFDCPIWYQALKVP--VSQSI-NGHIICSSCLAK 48 (159)
Q Consensus 12 ~~~~~~~l~C~iC~~~l~~P--v~qC~-~GH~~C~~C~~~ 48 (159)
-..|.++.-||+|.+.|.-- -..|. ||-+.|..|..-
T Consensus 174 W~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~ 213 (505)
T KOG1842|consen 174 WLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKF 213 (505)
T ss_pred ccCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHh
Confidence 45688899999999988532 23576 899999999654
No 220
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.51 E-value=55 Score=32.56 Aligned_cols=47 Identities=19% Similarity=0.397 Sum_probs=32.7
Q ss_pred eCCCeeecccccccCC-----Cceeecc-CCceecccccccc----CCCCCCCccCc
Q 042263 14 SDQDLFDCPIWYQALK-----VPVSQSI-NGHIICSSCLAKV----NNKCPACRSCV 60 (159)
Q Consensus 14 ~~~~~l~C~iC~~~l~-----~Pv~qC~-~GH~~C~~C~~~~----~~~CP~Cr~~~ 60 (159)
...+.-.|.||.+-.- .|-.-|. ||--+|+.|.+=- ++.||+|++..
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCch
Confidence 3444457999998753 2433464 8999999997532 36799999876
No 221
>PLN02248 cellulose synthase-like protein
Probab=22.39 E-value=32 Score=34.26 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=24.4
Q ss_pred eeeccCCceeccccccccC---CCCCCCccCc
Q 042263 32 VSQSINGHIICSSCLAKVN---NKCPACRSCV 60 (159)
Q Consensus 32 v~qC~~GH~~C~~C~~~~~---~~CP~Cr~~~ 60 (159)
+..|+|+..+|..|..... ..||-|+.+.
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 176 (1135)
T PLN02248 145 LLPCECGFKICRDCYIDAVKSGGICPGCKEPY 176 (1135)
T ss_pred CCcccccchhHHhHhhhhhhcCCCCCCCcccc
Confidence 5669999999999987653 6899998875
No 222
>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=21.76 E-value=44 Score=18.39 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=3.5
Q ss_pred CCCCCCccCc
Q 042263 51 NKCPACRSCV 60 (159)
Q Consensus 51 ~~CP~Cr~~~ 60 (159)
.+||.|+.+.
T Consensus 14 Y~Cp~C~~~~ 23 (30)
T PF04438_consen 14 YRCPRCGARY 23 (30)
T ss_dssp EE-TTT--EE
T ss_pred EECCCcCCce
Confidence 3566655543
No 223
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.55 E-value=64 Score=18.28 Aligned_cols=23 Identities=22% Similarity=0.212 Sum_probs=18.1
Q ss_pred CCCCCCCCCcceeChhHHHhHhhhh
Q 042263 91 PCACPLLDCNFLGSASQLYLYFSWK 115 (159)
Q Consensus 91 p~~Cp~~gC~~~g~~~~l~~H~~~~ 115 (159)
.+.||+ |+-......+..|++..
T Consensus 4 ~~~C~n--C~R~v~a~RfA~HLekC 26 (33)
T PF08209_consen 4 YVECPN--CGRPVAASRFAPHLEKC 26 (33)
T ss_dssp EEE-TT--TSSEEEGGGHHHHHHHH
T ss_pred eEECCC--CcCCcchhhhHHHHHHH
Confidence 357886 99888889999999864
No 224
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=21.34 E-value=55 Score=18.57 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=14.9
Q ss_pred ecccccccCCCceeeccCCceeccccc
Q 042263 20 DCPIWYQALKVPVSQSINGHIICSSCL 46 (159)
Q Consensus 20 ~C~iC~~~l~~Pv~qC~~GH~~C~~C~ 46 (159)
-||-|.++|.+.-- ..+...|..|-
T Consensus 3 FCp~C~nlL~p~~~--~~~~~~C~~C~ 27 (35)
T PF02150_consen 3 FCPECGNLLYPKED--KEKRVACRTCG 27 (35)
T ss_dssp BETTTTSBEEEEEE--TTTTEEESSSS
T ss_pred eCCCCCccceEcCC--CccCcCCCCCC
Confidence 38888888865321 23334666664
No 225
>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=20.88 E-value=74 Score=16.87 Aligned_cols=22 Identities=23% Similarity=0.153 Sum_probs=14.3
Q ss_pred CCCCCCCCcceeChhHHHhHhhh
Q 042263 92 CACPLLDCNFLGSASQLYLYFSW 114 (159)
Q Consensus 92 ~~Cp~~gC~~~g~~~~l~~H~~~ 114 (159)
+.||+. =.-+.+..+|..|+..
T Consensus 3 v~CPyn-~~H~v~~~~l~~Hi~~ 24 (27)
T PF05253_consen 3 VRCPYN-PSHRVPASELQKHIKK 24 (27)
T ss_dssp EE-TTT-SS-EEEGGGHHHHHHH
T ss_pred eeCCCC-CCcCcCHHHHHHHHHH
Confidence 467763 4567788899999864
No 226
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=20.65 E-value=60 Score=24.81 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=13.7
Q ss_pred ceecccccccc-CCCCCCCccCc
Q 042263 39 HIICSSCLAKV-NNKCPACRSCV 60 (159)
Q Consensus 39 H~~C~~C~~~~-~~~CP~Cr~~~ 60 (159)
-..|.-|..+. ..+||.|+.+.
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vPY 27 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVPY 27 (157)
T ss_pred eeeehhhhcchhhccCCCCCCcc
Confidence 45666666654 35677776665
No 227
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=20.22 E-value=2.7e+02 Score=18.32 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=20.2
Q ss_pred EEeCcEEEEEEeCCCc--EEEEEEcCCCcEEEE
Q 042263 123 FTYKKRVKVTLNVNDS--VFLFRQQKNGHLFSL 153 (159)
Q Consensus 123 ~~~~~~~~~~~~~~~~--~~~l~~~~d~~lF~l 153 (159)
+.-|+.+.+.++.+.+ ..++.-+.||.+-+|
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEEE
Confidence 5667888888887765 333444577777555
Done!