Query 043224
Match_columns 516
No_of_seqs 358 out of 1491
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 02:44:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 2.6E-74 5.6E-79 614.0 26.0 421 44-490 1-437 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 2.1E-36 4.7E-41 315.0 10.4 262 72-356 85-374 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 1E-34 2.2E-39 291.6 12.8 192 120-316 182-403 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 3.4E-26 7.3E-31 222.4 8.5 191 119-318 218-436 (446)
5 smart00647 IBR In Between Ring 99.4 6.6E-13 1.4E-17 103.6 6.1 62 196-258 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 1.1E-12 2.5E-17 102.2 1.0 62 196-258 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.3 4.3E-07 9.3E-12 64.9 2.7 41 125-171 1-41 (42)
8 smart00647 IBR In Between Ring 98.2 2E-06 4.2E-11 66.8 4.3 43 276-318 10-59 (64)
9 PF13639 zf-RING_2: Ring finge 98.1 1.7E-06 3.8E-11 62.3 2.7 40 124-171 2-42 (44)
10 PF01485 IBR: IBR domain; Int 98.1 1.1E-06 2.4E-11 68.1 1.4 38 281-318 17-59 (64)
11 PF13923 zf-C3HC4_2: Zinc fing 98.1 2.8E-06 6.1E-11 59.6 3.0 38 125-171 1-38 (39)
12 PF00097 zf-C3HC4: Zinc finger 98.0 5.3E-06 1.1E-10 58.7 3.4 40 125-171 1-40 (41)
13 KOG0320 Predicted E3 ubiquitin 97.9 6.9E-06 1.5E-10 75.5 3.5 55 119-183 128-182 (187)
14 PLN03208 E3 ubiquitin-protein 97.8 1.4E-05 3E-10 75.3 3.5 66 119-188 15-88 (193)
15 cd00162 RING RING-finger (Real 97.8 2.6E-05 5.6E-10 55.3 3.6 44 124-177 1-44 (45)
16 PF13445 zf-RING_UBOX: RING-ty 97.7 2.4E-05 5.2E-10 56.1 2.8 41 125-170 1-43 (43)
17 PF14634 zf-RING_5: zinc-RING 97.7 3E-05 6.5E-10 55.9 2.9 42 124-175 1-43 (44)
18 PF13920 zf-C3HC4_3: Zinc fing 97.7 4.5E-05 9.7E-10 56.5 3.6 46 122-179 2-48 (50)
19 KOG0823 Predicted E3 ubiquitin 97.5 5.3E-05 1.2E-09 72.8 2.2 60 120-188 45-104 (230)
20 smart00184 RING Ring finger. E 97.4 0.00013 2.9E-09 49.6 3.0 30 125-156 1-30 (39)
21 PHA02926 zinc finger-like prot 97.4 0.00013 2.8E-09 69.7 3.5 57 119-179 167-230 (242)
22 PHA02929 N1R/p28-like protein; 97.3 0.00022 4.7E-09 70.1 3.7 50 120-179 172-227 (238)
23 smart00504 Ubox Modified RING 97.2 0.00045 9.8E-09 53.3 4.0 49 123-183 2-50 (63)
24 KOG2164 Predicted E3 ubiquitin 97.0 0.00026 5.7E-09 75.1 1.8 60 122-188 186-245 (513)
25 KOG0317 Predicted E3 ubiquitin 97.0 0.0004 8.6E-09 68.8 2.3 51 121-183 238-288 (293)
26 KOG2177 Predicted E3 ubiquitin 96.9 0.00058 1.3E-08 68.3 2.5 43 121-175 12-54 (386)
27 TIGR00599 rad18 DNA repair pro 96.8 0.0015 3.2E-08 68.8 5.3 50 120-181 24-73 (397)
28 PF14555 UBA_4: UBA-like domai 96.5 0.0062 1.3E-07 43.6 5.2 39 56-94 1-39 (43)
29 PF11789 zf-Nse: Zinc-finger o 96.4 0.0027 5.8E-08 48.5 2.5 48 121-175 10-57 (57)
30 KOG0287 Postreplication repair 96.3 0.0017 3.8E-08 65.4 1.9 52 121-184 22-73 (442)
31 TIGR00570 cdk7 CDK-activating 96.1 0.0041 8.9E-08 63.0 3.3 54 123-185 4-60 (309)
32 COG5540 RING-finger-containing 96.1 0.0042 9.1E-08 61.9 2.9 53 119-180 320-373 (374)
33 KOG1814 Predicted E3 ubiquitin 96.1 0.01 2.3E-07 61.5 5.9 40 279-318 270-312 (445)
34 KOG0978 E3 ubiquitin ligase in 96.0 0.0022 4.8E-08 71.3 0.5 57 119-186 640-696 (698)
35 KOG4628 Predicted E3 ubiquitin 95.7 0.0058 1.3E-07 62.9 2.4 47 123-178 230-277 (348)
36 PF12678 zf-rbx1: RING-H2 zinc 95.5 0.013 2.9E-07 47.0 3.4 42 122-171 19-71 (73)
37 KOG1812 Predicted E3 ubiquitin 95.2 0.019 4E-07 60.8 4.0 102 122-256 238-345 (384)
38 PF04564 U-box: U-box domain; 95.1 0.017 3.6E-07 46.3 2.7 50 121-181 3-52 (73)
39 KOG1002 Nucleotide excision re 95.1 0.011 2.4E-07 62.8 1.9 111 64-181 453-588 (791)
40 COG5574 PEX10 RING-finger-cont 95.0 0.016 3.5E-07 57.0 2.7 53 121-183 214-266 (271)
41 PF11793 FANCL_C: FANCL C-term 94.7 0.014 3.1E-07 46.4 1.2 57 122-180 2-67 (70)
42 PF14835 zf-RING_6: zf-RING of 94.6 0.0048 1E-07 47.7 -1.5 44 122-179 7-51 (65)
43 KOG2879 Predicted E3 ubiquitin 94.6 0.11 2.4E-06 51.4 7.3 54 117-179 234-287 (298)
44 PF10571 UPF0547: Uncharacteri 93.8 0.027 5.8E-07 35.8 0.9 23 283-309 1-24 (26)
45 KOG4367 Predicted Zn-finger pr 93.7 0.1 2.2E-06 54.5 5.3 35 121-157 3-37 (699)
46 COG5243 HRD1 HRD ubiquitin lig 93.7 0.057 1.2E-06 55.4 3.4 50 120-179 285-345 (491)
47 KOG1039 Predicted E3 ubiquitin 93.1 0.081 1.8E-06 54.8 3.6 55 119-176 158-218 (344)
48 KOG2660 Locus-specific chromos 92.5 0.11 2.4E-06 52.8 3.4 48 121-179 14-61 (331)
49 KOG4185 Predicted E3 ubiquitin 92.4 0.21 4.6E-06 50.9 5.5 58 122-188 3-66 (296)
50 PF14570 zf-RING_4: RING/Ubox 92.4 0.098 2.1E-06 38.3 2.1 44 125-177 1-46 (48)
51 KOG0824 Predicted E3 ubiquitin 92.2 0.077 1.7E-06 53.2 1.9 53 121-184 6-58 (324)
52 KOG0006 E3 ubiquitin-protein l 91.9 0.4 8.6E-06 48.4 6.4 94 141-256 341-439 (446)
53 COG5432 RAD18 RING-finger-cont 91.8 0.079 1.7E-06 52.6 1.4 45 121-177 24-68 (391)
54 KOG4159 Predicted E3 ubiquitin 91.7 0.22 4.8E-06 52.7 4.7 71 120-208 82-153 (398)
55 KOG0826 Predicted E3 ubiquitin 90.9 0.65 1.4E-05 47.2 6.8 49 121-178 299-347 (357)
56 TIGR00570 cdk7 CDK-activating 90.7 0.17 3.6E-06 51.6 2.6 53 215-296 5-57 (309)
57 KOG1428 Inhibitor of type V ad 90.3 0.48 1E-05 56.2 5.9 75 121-201 3485-3562(3738)
58 KOG1645 RING-finger-containing 90.2 0.21 4.6E-06 52.0 2.9 54 122-183 4-60 (463)
59 smart00744 RINGv The RING-vari 89.8 0.36 7.9E-06 35.5 3.1 42 124-171 1-47 (49)
60 COG5152 Uncharacterized conser 89.6 0.13 2.8E-06 48.4 0.7 33 121-155 195-227 (259)
61 PRK00420 hypothetical protein; 88.6 1.3 2.8E-05 38.5 6.1 28 281-317 22-50 (112)
62 PF05883 Baculo_RING: Baculovi 88.3 0.21 4.6E-06 44.5 1.1 35 121-155 25-66 (134)
63 KOG2817 Predicted E3 ubiquitin 88.1 0.74 1.6E-05 48.1 5.0 125 44-185 255-391 (394)
64 KOG0802 E3 ubiquitin ligase [P 87.9 0.29 6.3E-06 54.3 2.1 46 121-176 290-338 (543)
65 PF12861 zf-Apc11: Anaphase-pr 87.5 0.61 1.3E-05 38.4 3.2 50 122-178 21-81 (85)
66 PHA00626 hypothetical protein 87.5 0.36 7.7E-06 36.3 1.7 27 284-310 2-34 (59)
67 KOG0311 Predicted E3 ubiquitin 87.5 0.099 2.1E-06 53.5 -1.7 49 120-178 41-89 (381)
68 smart00661 RPOL9 RNA polymeras 87.3 0.38 8.3E-06 35.4 1.8 27 283-309 1-30 (52)
69 PF13920 zf-C3HC4_3: Zinc fing 87.0 0.4 8.6E-06 35.2 1.7 33 236-294 16-49 (50)
70 KOG1734 Predicted RING-contain 86.8 0.45 9.8E-06 47.1 2.4 53 121-181 223-283 (328)
71 KOG4265 Predicted E3 ubiquitin 86.4 0.68 1.5E-05 47.7 3.6 48 120-179 288-336 (349)
72 KOG1815 Predicted E3 ubiquitin 86.0 0.39 8.4E-06 52.0 1.8 37 282-318 158-197 (444)
73 PRK14559 putative protein seri 85.9 0.47 1E-05 53.5 2.4 23 283-316 28-50 (645)
74 PF13240 zinc_ribbon_2: zinc-r 85.8 0.38 8.2E-06 29.7 0.9 13 284-296 1-13 (23)
75 PRK00432 30S ribosomal protein 85.7 0.35 7.7E-06 35.8 0.9 29 279-309 17-47 (50)
76 PF14952 zf-tcix: Putative tre 83.6 0.68 1.5E-05 33.0 1.5 30 276-309 5-37 (44)
77 PF00627 UBA: UBA/TS-N domain; 83.0 4.1 8.9E-05 27.8 5.3 34 56-90 3-36 (37)
78 KOG4692 Predicted E3 ubiquitin 82.9 0.91 2E-05 46.5 2.6 51 118-180 418-468 (489)
79 PF09297 zf-NADH-PPase: NADH p 82.7 1.3 2.7E-05 29.5 2.5 28 281-308 2-30 (32)
80 PF13248 zf-ribbon_3: zinc-rib 82.3 0.69 1.5E-05 29.3 1.0 14 282-295 2-15 (26)
81 KOG0828 Predicted E3 ubiquitin 82.0 0.73 1.6E-05 49.2 1.7 51 120-179 569-634 (636)
82 KOG4739 Uncharacterized protei 82.0 0.42 9.1E-06 46.7 -0.1 47 122-180 3-49 (233)
83 KOG1001 Helicase-like transcri 81.1 0.68 1.5E-05 52.5 1.2 48 123-181 455-502 (674)
84 PF02845 CUE: CUE domain; Int 79.9 6.3 0.00014 27.7 5.5 38 56-93 2-40 (42)
85 KOG0317 Predicted E3 ubiquitin 79.9 0.37 8.1E-06 48.2 -1.2 35 278-318 235-270 (293)
86 TIGR02098 MJ0042_CXXC MJ0042 f 79.7 0.96 2.1E-05 31.1 1.1 26 283-309 3-35 (38)
87 KOG4172 Predicted E3 ubiquitin 79.5 0.7 1.5E-05 34.6 0.4 45 123-178 8-53 (62)
88 PF13719 zinc_ribbon_5: zinc-r 78.6 2 4.3E-05 29.7 2.4 28 214-244 3-35 (37)
89 PF02150 RNA_POL_M_15KD: RNA p 77.9 1.3 2.7E-05 30.3 1.2 28 213-243 1-29 (35)
90 PF13717 zinc_ribbon_4: zinc-r 77.7 2.2 4.7E-05 29.3 2.4 28 214-244 3-35 (36)
91 PRK00398 rpoP DNA-directed RNA 77.6 1.7 3.7E-05 31.4 1.9 28 283-310 4-32 (46)
92 COG5220 TFB3 Cdk activating ki 76.8 0.72 1.6E-05 44.9 -0.3 49 123-178 11-63 (314)
93 KOG1493 Anaphase-promoting com 76.6 0.86 1.9E-05 36.5 0.2 48 123-177 21-79 (84)
94 PRK14559 putative protein seri 76.2 2 4.3E-05 48.6 2.9 15 280-294 39-53 (645)
95 PLN03086 PRLI-interacting fact 75.5 4.1 9E-05 45.1 5.1 57 165-244 406-463 (567)
96 PF08274 PhnA_Zn_Ribbon: PhnA 75.4 1.9 4.1E-05 28.4 1.5 26 283-309 3-29 (30)
97 KOG0320 Predicted E3 ubiquitin 74.7 1.3 2.8E-05 41.4 0.8 30 239-294 150-179 (187)
98 KOG1952 Transcription factor N 74.5 2.4 5.3E-05 48.3 3.0 50 121-171 190-241 (950)
99 KOG1785 Tyrosine kinase negati 73.8 1.5 3.2E-05 45.7 1.1 47 121-175 368-414 (563)
100 PF05320 Pox_RNA_Pol_19: Poxvi 73.7 1.4 3.1E-05 40.0 0.8 32 121-157 125-156 (167)
101 PLN03208 E3 ubiquitin-protein 73.7 1.1 2.3E-05 42.7 0.0 32 281-317 17-48 (193)
102 KOG0978 E3 ubiquitin ligase in 72.3 1.3 2.8E-05 49.9 0.3 31 239-294 660-690 (698)
103 KOG0823 Predicted E3 ubiquitin 71.7 1.1 2.3E-05 43.7 -0.5 14 305-318 65-78 (230)
104 KOG0804 Cytoplasmic Zn-finger 71.4 2.7 5.8E-05 44.7 2.3 121 44-177 84-220 (493)
105 KOG0827 Predicted E3 ubiquitin 71.2 2.5 5.3E-05 44.1 1.9 51 122-179 4-56 (465)
106 KOG4275 Predicted E3 ubiquitin 71.1 3 6.6E-05 41.9 2.5 29 122-152 300-329 (350)
107 smart00546 CUE Domain that may 70.3 15 0.00033 25.8 5.4 37 56-92 3-40 (43)
108 cd00194 UBA Ubiquitin Associat 69.9 15 0.00033 24.8 5.2 35 57-92 3-37 (38)
109 smart00165 UBA Ubiquitin assoc 69.7 13 0.00028 25.0 4.8 33 58-91 4-36 (37)
110 PF09538 FYDLN_acid: Protein o 69.5 2.6 5.6E-05 36.5 1.4 26 283-309 10-36 (108)
111 TIGR02098 MJ0042_CXXC MJ0042 f 68.6 5 0.00011 27.5 2.5 27 215-244 4-35 (38)
112 PF10367 Vps39_2: Vacuolar sor 68.3 2.1 4.6E-05 36.2 0.7 32 121-152 77-108 (109)
113 COG1645 Uncharacterized Zn-fin 68.2 3 6.5E-05 37.2 1.6 25 282-315 28-52 (131)
114 PF04641 Rtf2: Rtf2 RING-finge 68.2 5 0.00011 40.2 3.4 60 119-189 110-171 (260)
115 PF13639 zf-RING_2: Ring finge 68.0 1.4 3.1E-05 31.2 -0.4 33 284-318 2-34 (44)
116 PHA03096 p28-like protein; Pro 68.0 3.2 6.9E-05 42.1 2.0 38 123-160 179-222 (284)
117 COG1998 RPS31 Ribosomal protei 67.8 3.3 7.1E-05 30.4 1.4 27 281-307 18-45 (51)
118 KOG1813 Predicted E3 ubiquitin 67.6 1.9 4.1E-05 43.4 0.2 44 122-177 241-284 (313)
119 PF07282 OrfB_Zn_ribbon: Putat 66.5 3.8 8.3E-05 32.0 1.8 28 281-308 27-55 (69)
120 PRK04023 DNA polymerase II lar 66.2 4.6 0.0001 47.1 3.0 33 209-251 622-660 (1121)
121 KOG0297 TNF receptor-associate 66.1 3.3 7.2E-05 44.0 1.8 37 120-157 19-55 (391)
122 KOG4445 Uncharacterized conser 65.8 3.8 8.1E-05 41.4 1.9 39 121-159 114-153 (368)
123 COG5574 PEX10 RING-finger-cont 65.8 1.6 3.4E-05 43.3 -0.7 34 283-322 216-252 (271)
124 smart00661 RPOL9 RNA polymeras 65.8 5.6 0.00012 29.1 2.4 26 214-242 1-28 (52)
125 TIGR03655 anti_R_Lar restricti 65.3 4.6 0.0001 30.1 1.9 28 283-310 2-37 (53)
126 COG4647 AcxC Acetone carboxyla 64.6 12 0.00026 33.1 4.6 111 178-294 17-132 (165)
127 PF14369 zf-RING_3: zinc-finge 64.6 5.9 0.00013 27.0 2.1 28 214-244 3-31 (35)
128 KOG3039 Uncharacterized conser 64.0 4.5 9.8E-05 39.7 2.1 55 121-185 220-276 (303)
129 PF10446 DUF2457: Protein of u 64.0 5.1 0.00011 42.6 2.6 17 115-131 187-203 (458)
130 KOG3579 Predicted E3 ubiquitin 63.3 5.3 0.00012 40.0 2.4 63 121-188 267-341 (352)
131 KOG3002 Zn finger protein [Gen 63.1 13 0.00027 38.2 5.2 77 121-230 47-124 (299)
132 PRK05654 acetyl-CoA carboxylas 63.0 2 4.2E-05 43.9 -0.7 28 282-309 27-56 (292)
133 KOG2807 RNA polymerase II tran 62.8 3 6.6E-05 42.5 0.7 84 143-253 275-364 (378)
134 PF07975 C1_4: TFIIH C1-like d 62.6 3.8 8.2E-05 30.5 1.0 35 221-255 4-42 (51)
135 COG1997 RPL43A Ribosomal prote 62.1 5.4 0.00012 32.9 1.9 28 282-309 35-63 (89)
136 PF14569 zf-UDP: Zinc-binding 62.0 6.7 0.00014 31.7 2.3 55 221-300 14-69 (80)
137 PF06677 Auto_anti-p27: Sjogre 60.9 6.4 0.00014 27.9 1.8 23 282-306 17-41 (41)
138 PF14835 zf-RING_6: zf-RING of 60.5 5.5 0.00012 31.1 1.6 21 283-303 8-31 (65)
139 KOG3970 Predicted E3 ubiquitin 60.3 7.3 0.00016 37.7 2.7 54 123-178 51-104 (299)
140 KOG1941 Acetylcholine receptor 60.0 3.5 7.6E-05 43.0 0.5 48 121-176 364-413 (518)
141 PRK14714 DNA polymerase II lar 59.6 7.5 0.00016 46.6 3.2 39 465-507 846-892 (1337)
142 PRK08665 ribonucleotide-diphos 59.4 5.3 0.00011 46.2 1.9 26 283-310 725-751 (752)
143 PF14803 Nudix_N_2: Nudix N-te 59.3 7.6 0.00016 26.4 1.9 27 214-243 1-31 (34)
144 PRK00398 rpoP DNA-directed RNA 59.1 10 0.00022 27.2 2.7 27 215-245 5-32 (46)
145 PRK09710 lar restriction allev 57.8 8.1 0.00017 30.1 2.1 27 281-307 5-35 (64)
146 COG5175 MOT2 Transcriptional r 57.4 4.9 0.00011 41.1 1.1 53 122-183 14-68 (480)
147 TIGR00515 accD acetyl-CoA carb 57.4 2.8 6.1E-05 42.6 -0.7 28 282-309 26-55 (285)
148 TIGR01384 TFS_arch transcripti 57.0 6.4 0.00014 33.5 1.6 24 283-308 1-25 (104)
149 KOG2177 Predicted E3 ubiquitin 56.6 5.3 0.00012 39.4 1.2 16 299-314 96-112 (386)
150 KOG3130 Uncharacterized conser 56.5 6.2 0.00014 41.3 1.7 6 127-132 396-401 (514)
151 COG1198 PriA Primosomal protei 56.0 8.1 0.00018 44.3 2.6 35 282-316 444-484 (730)
152 KOG2034 Vacuolar sorting prote 55.8 7.3 0.00016 44.9 2.2 39 121-159 816-854 (911)
153 PF07191 zinc-ribbons_6: zinc- 55.1 8.6 0.00019 30.5 1.9 33 284-318 3-41 (70)
154 CHL00174 accD acetyl-CoA carbo 54.8 3.2 6.9E-05 42.3 -0.7 28 282-309 38-67 (296)
155 COG5219 Uncharacterized conser 54.1 5 0.00011 46.4 0.5 53 119-179 1466-1523(1525)
156 KOG2906 RNA polymerase III sub 53.3 7.2 0.00016 32.9 1.2 26 284-309 3-31 (105)
157 PF01599 Ribosomal_S27: Riboso 52.9 9.4 0.0002 27.9 1.6 27 281-307 17-46 (47)
158 PF03943 TAP_C: TAP C-terminal 52.8 16 0.00035 27.1 2.9 37 57-93 2-38 (51)
159 KOG1464 COP9 signalosome, subu 52.6 7.7 0.00017 39.1 1.5 17 1-17 1-19 (440)
160 PF14447 Prok-RING_4: Prokaryo 52.2 5.7 0.00012 30.0 0.4 46 122-181 7-52 (55)
161 smart00804 TAP_C C-terminal do 51.9 50 0.0011 25.7 5.7 40 53-92 10-49 (63)
162 COG5222 Uncharacterized conser 50.9 9.7 0.00021 38.4 1.9 44 123-176 275-318 (427)
163 PF14149 YhfH: YhfH-like prote 50.4 1.3 2.9E-05 30.5 -2.9 26 280-305 11-37 (37)
164 PRK14892 putative transcriptio 50.2 10 0.00022 32.3 1.7 29 280-308 19-51 (99)
165 PF12773 DZR: Double zinc ribb 50.2 9.2 0.0002 27.8 1.3 13 212-227 11-23 (50)
166 PF12861 zf-Apc11: Anaphase-pr 48.8 6.4 0.00014 32.5 0.3 33 283-318 33-65 (85)
167 KOG2114 Vacuolar assembly/sort 48.7 25 0.00055 40.5 4.9 40 123-176 841-880 (933)
168 PF04931 DNA_pol_phi: DNA poly 48.4 38 0.00081 39.5 6.6 20 72-91 764-783 (784)
169 TIGR00686 phnA alkylphosphonat 47.6 13 0.00028 32.0 1.9 26 283-309 3-29 (109)
170 TIGR02300 FYDLN_acid conserved 47.5 11 0.00023 33.5 1.4 27 282-309 9-36 (129)
171 PHA02929 N1R/p28-like protein; 47.3 7.8 0.00017 38.3 0.7 38 281-318 173-213 (238)
172 KOG3800 Predicted E3 ubiquitin 47.3 13 0.00029 37.4 2.3 49 124-181 2-53 (300)
173 COG1594 RPB9 DNA-directed RNA 47.2 13 0.00028 32.5 1.9 28 282-309 2-32 (113)
174 COG0777 AccD Acetyl-CoA carbox 46.1 6.8 0.00015 39.3 0.0 28 282-309 28-57 (294)
175 COG2888 Predicted Zn-ribbon RN 46.0 7.9 0.00017 29.6 0.4 9 281-289 49-57 (61)
176 PF09889 DUF2116: Uncharacteri 45.5 5.9 0.00013 30.4 -0.4 14 283-296 4-17 (59)
177 PF14445 Prok-RING_2: Prokaryo 44.5 4.2 9.1E-05 30.0 -1.2 33 121-153 6-39 (57)
178 PF03119 DNA_ligase_ZBD: NAD-d 44.1 20 0.00043 23.2 2.0 20 284-303 1-20 (28)
179 KOG3268 Predicted E3 ubiquitin 43.9 22 0.00048 33.3 3.0 56 122-179 165-228 (234)
180 KOG2932 E3 ubiquitin ligase in 43.3 9.4 0.0002 38.8 0.5 54 209-298 86-139 (389)
181 KOG0825 PHD Zn-finger protein 42.9 7.4 0.00016 44.1 -0.3 40 122-161 96-140 (1134)
182 PRK10220 hypothetical protein; 42.0 18 0.0004 31.1 2.0 27 282-309 3-30 (111)
183 PF12906 RINGv: RING-variant d 41.8 23 0.00049 25.7 2.2 33 125-157 1-38 (47)
184 COG2051 RPS27A Ribosomal prote 41.3 25 0.00053 27.6 2.4 30 214-246 20-50 (67)
185 TIGR00993 3a0901s04IAP86 chlor 41.2 43 0.00093 38.2 5.2 42 41-86 411-452 (763)
186 KOG1832 HIV-1 Vpr-binding prot 40.2 16 0.00034 42.3 1.7 9 4-12 1405-1413(1516)
187 PF08938 HBS1_N: HBS1 N-termin 40.1 1.7 3.8E-05 35.3 -4.3 48 45-93 19-69 (79)
188 PF13453 zf-TFIIB: Transcripti 39.6 16 0.00035 25.5 1.1 29 284-317 1-29 (41)
189 PF14569 zf-UDP: Zinc-binding 39.1 39 0.00085 27.4 3.3 47 121-176 8-59 (80)
190 KOG2906 RNA polymerase III sub 39.1 28 0.00061 29.4 2.6 26 214-242 2-29 (105)
191 KOG3161 Predicted E3 ubiquitin 39.1 9.9 0.00022 42.2 -0.0 34 123-156 12-47 (861)
192 KOG1991 Nuclear transport rece 39.0 33 0.00072 40.2 4.0 34 44-80 953-986 (1010)
193 cd07621 BAR_SNX5_6 The Bin/Amp 38.7 1.6E+02 0.0035 28.8 8.2 60 429-488 156-215 (219)
194 PRK11827 hypothetical protein; 38.2 25 0.00054 27.1 2.0 27 282-308 8-35 (60)
195 KOG2463 Predicted RNA-binding 37.9 17 0.00037 37.3 1.4 83 45-145 183-266 (376)
196 PRK14714 DNA polymerase II lar 37.7 19 0.0004 43.5 1.8 59 430-489 796-858 (1337)
197 PHA02926 zinc finger-like prot 37.4 12 0.00026 36.4 0.3 41 277-318 165-210 (242)
198 PF00098 zf-CCHC: Zinc knuckle 37.1 19 0.0004 20.8 0.9 16 244-259 2-17 (18)
199 TIGR00595 priA primosomal prot 36.6 25 0.00054 38.8 2.6 34 283-316 223-262 (505)
200 PF13834 DUF4193: Domain of un 36.4 14 0.00031 31.2 0.5 33 118-150 66-98 (99)
201 KOG0943 Predicted ubiquitin-pr 36.4 22 0.00048 42.5 2.1 19 428-446 2418-2436(3015)
202 PF06254 DUF1019: Protein of u 36.0 1.9E+02 0.004 24.2 7.0 66 422-491 7-75 (89)
203 PF08746 zf-RING-like: RING-li 35.2 29 0.00062 24.7 1.9 41 125-171 1-42 (43)
204 PF03884 DUF329: Domain of unk 35.1 14 0.00029 28.3 0.2 16 282-297 2-17 (57)
205 PLN02189 cellulose synthase 35.0 34 0.00073 40.6 3.4 59 215-301 36-95 (1040)
206 PRK08115 ribonucleotide-diphos 34.7 19 0.00041 42.1 1.3 24 283-308 828-853 (858)
207 KOG2164 Predicted E3 ubiquitin 34.1 19 0.00041 39.1 1.1 34 240-294 204-237 (513)
208 PF14471 DUF4428: Domain of un 34.0 33 0.00072 25.4 2.1 30 124-154 1-30 (51)
209 PF14446 Prok-RING_1: Prokaryo 33.9 47 0.001 25.1 2.8 32 122-153 5-38 (54)
210 PF04931 DNA_pol_phi: DNA poly 33.9 45 0.00098 38.9 4.3 7 62-68 708-714 (784)
211 PF08792 A2L_zn_ribbon: A2L zi 33.7 35 0.00077 22.9 2.0 29 281-309 2-31 (33)
212 PF06827 zf-FPG_IleRS: Zinc fi 33.7 25 0.00055 22.7 1.3 23 283-305 2-27 (30)
213 COG5151 SSL1 RNA polymerase II 33.2 12 0.00026 38.0 -0.5 88 143-253 307-407 (421)
214 KOG1824 TATA-binding protein-i 33.2 53 0.0012 38.6 4.4 34 71-105 373-406 (1233)
215 KOG3130 Uncharacterized conser 33.0 27 0.00058 36.8 1.9 8 16-23 283-290 (514)
216 PF05605 zf-Di19: Drought indu 33.0 39 0.00086 25.0 2.4 46 122-184 2-47 (54)
217 PF02891 zf-MIZ: MIZ/SP-RING z 33.0 31 0.00067 25.4 1.8 47 123-176 3-49 (50)
218 PRK14811 formamidopyrimidine-D 32.6 29 0.00063 35.0 2.1 25 282-306 235-262 (269)
219 PF01363 FYVE: FYVE zinc finge 32.2 18 0.0004 28.0 0.5 34 281-316 8-42 (69)
220 PF02318 FYVE_2: FYVE-type zin 32.1 66 0.0014 28.0 4.1 35 281-316 53-88 (118)
221 PRK00415 rps27e 30S ribosomal 32.1 44 0.00095 25.7 2.5 30 214-246 12-42 (59)
222 PF14354 Lar_restr_allev: Rest 31.9 29 0.00063 26.2 1.6 11 282-292 3-13 (61)
223 KOG0309 Conserved WD40 repeat- 31.1 35 0.00075 38.9 2.5 48 122-178 1028-1075(1081)
224 PF12677 DUF3797: Domain of un 31.1 36 0.00078 25.0 1.8 27 282-308 13-47 (49)
225 KOG2879 Predicted E3 ubiquitin 31.1 21 0.00045 35.9 0.7 30 281-316 238-269 (298)
226 PLN02638 cellulose synthase A 31.0 41 0.00088 40.1 3.2 53 221-298 22-75 (1079)
227 PF06844 DUF1244: Protein of u 30.5 34 0.00073 26.8 1.6 18 145-162 11-28 (68)
228 PF06056 Terminase_5: Putative 30.5 66 0.0014 24.5 3.3 32 58-89 15-46 (58)
229 PRK12495 hypothetical protein; 30.4 63 0.0014 31.5 3.8 27 281-316 41-67 (226)
230 cd07662 BAR_SNX6 The Bin/Amphi 30.1 2.7E+02 0.0059 27.2 8.2 58 429-486 155-212 (218)
231 PHA02825 LAP/PHD finger-like p 30.0 53 0.0012 30.4 3.1 50 121-179 7-59 (162)
232 KOG2979 Protein involved in DN 30.0 40 0.00087 33.5 2.5 47 123-176 177-223 (262)
233 PF05129 Elf1: Transcription e 29.9 23 0.00049 29.0 0.7 29 281-309 21-56 (81)
234 PRK01103 formamidopyrimidine/5 29.9 33 0.00071 34.6 2.0 25 282-306 245-272 (274)
235 KOG1940 Zn-finger protein [Gen 29.9 39 0.00084 34.2 2.4 47 120-176 156-204 (276)
236 TIGR00577 fpg formamidopyrimid 29.4 34 0.00074 34.5 2.0 22 282-303 245-268 (272)
237 COG0266 Nei Formamidopyrimidin 29.4 34 0.00073 34.6 1.9 25 282-306 245-272 (273)
238 PRK10445 endonuclease VIII; Pr 29.3 34 0.00074 34.3 2.0 25 282-306 235-262 (263)
239 PRK14873 primosome assembly pr 29.2 36 0.00078 38.9 2.3 26 283-308 393-419 (665)
240 cd07630 BAR_SNX_like The Bin/A 29.2 5.2E+02 0.011 24.8 13.0 63 423-485 131-193 (198)
241 PRK05580 primosome assembly pr 29.1 38 0.00082 38.8 2.5 34 283-316 391-430 (679)
242 COG2816 NPY1 NTP pyrophosphohy 29.0 47 0.001 33.6 2.9 34 275-309 105-139 (279)
243 PF01667 Ribosomal_S27e: Ribos 28.9 51 0.0011 25.0 2.3 30 214-246 8-38 (55)
244 PRK14810 formamidopyrimidine-D 28.8 35 0.00076 34.4 2.0 22 282-303 244-267 (272)
245 PRK09521 exosome complex RNA-b 28.7 35 0.00075 32.4 1.8 24 284-308 151-175 (189)
246 TIGR02443 conserved hypothetic 28.7 41 0.00088 25.8 1.8 26 283-308 10-40 (59)
247 PRK13945 formamidopyrimidine-D 28.7 35 0.00077 34.6 2.0 25 282-306 254-281 (282)
248 smart00659 RPOLCX RNA polymera 28.6 40 0.00087 24.2 1.7 10 283-292 20-29 (44)
249 COG1623 Predicted nucleic-acid 28.2 2.7E+02 0.0059 28.5 7.9 30 327-356 151-180 (349)
250 PLN02915 cellulose synthase A 28.2 51 0.0011 39.2 3.3 55 221-300 20-75 (1044)
251 PRK04023 DNA polymerase II lar 28.1 30 0.00065 40.8 1.4 33 279-317 623-661 (1121)
252 TIGR01206 lysW lysine biosynth 27.9 63 0.0014 24.3 2.7 27 215-244 4-32 (54)
253 PF08882 Acetone_carb_G: Aceto 27.9 25 0.00054 30.5 0.6 14 299-312 23-36 (112)
254 PF10122 Mu-like_Com: Mu-like 27.8 23 0.00051 26.3 0.4 24 283-306 5-31 (51)
255 PRK00241 nudC NADH pyrophospha 27.7 39 0.00084 33.8 2.0 31 276-307 94-125 (256)
256 PF09526 DUF2387: Probable met 27.5 41 0.00089 26.8 1.7 26 283-308 9-39 (71)
257 PF12760 Zn_Tnp_IS1595: Transp 26.7 92 0.002 22.3 3.3 27 281-307 17-45 (46)
258 TIGR00622 ssl1 transcription f 26.6 52 0.0011 28.7 2.3 38 214-254 56-101 (112)
259 PLN02436 cellulose synthase A 26.4 60 0.0013 38.7 3.5 56 221-301 41-97 (1094)
260 PF06044 DRP: Dam-replacing fa 26.2 36 0.00079 33.6 1.4 35 274-309 24-63 (254)
261 PF14353 CpXC: CpXC protein 25.9 13 0.00028 32.8 -1.6 51 167-230 2-52 (128)
262 PRK06369 nac nascent polypepti 25.9 1.5E+02 0.0033 25.9 5.1 36 56-91 77-112 (115)
263 KOG2930 SCF ubiquitin ligase, 25.7 49 0.0011 28.3 1.9 23 141-171 80-102 (114)
264 COG5243 HRD1 HRD ubiquitin lig 25.5 54 0.0012 34.3 2.6 12 282-293 334-345 (491)
265 PHA02325 hypothetical protein 25.3 32 0.0007 26.7 0.7 12 281-292 2-13 (72)
266 PLN03086 PRLI-interacting fact 25.3 37 0.0008 37.9 1.5 30 280-309 431-463 (567)
267 COG1594 RPB9 DNA-directed RNA 25.2 62 0.0014 28.2 2.6 28 213-243 2-31 (113)
268 cd07663 BAR_SNX5 The Bin/Amphi 25.2 3.7E+02 0.008 26.3 8.2 58 429-486 155-212 (218)
269 TIGR00264 alpha-NAC-related pr 25.2 1.6E+02 0.0035 25.8 5.1 34 56-89 79-112 (116)
270 PTZ00083 40S ribosomal protein 24.8 62 0.0014 26.7 2.3 31 214-247 36-67 (85)
271 PF01428 zf-AN1: AN1-like Zinc 24.8 35 0.00077 24.1 0.8 26 220-251 4-30 (43)
272 PLN00209 ribosomal protein S27 24.7 63 0.0014 26.7 2.4 30 214-246 37-67 (86)
273 COG1096 Predicted RNA-binding 24.6 43 0.00094 31.8 1.6 23 283-307 150-173 (188)
274 COG2824 PhnA Uncharacterized Z 24.5 47 0.001 28.6 1.6 26 282-309 3-30 (112)
275 PF03604 DNA_RNApol_7kD: DNA d 24.4 45 0.00097 22.3 1.2 22 285-307 3-25 (32)
276 TIGR00373 conserved hypothetic 24.3 84 0.0018 29.0 3.5 32 209-243 105-137 (158)
277 PF08580 KAR9: Yeast cortical 24.3 1.1E+03 0.025 27.1 13.3 104 380-488 230-337 (683)
278 KOG4362 Transcriptional regula 24.1 24 0.00051 40.0 -0.3 56 121-185 20-75 (684)
279 smart00531 TFIIE Transcription 23.9 92 0.002 28.2 3.6 19 60-78 19-37 (147)
280 PLN02400 cellulose synthase 23.9 65 0.0014 38.5 3.2 55 221-300 41-96 (1085)
281 PF03833 PolC_DP2: DNA polymer 23.9 26 0.00056 40.5 0.0 76 428-507 776-874 (900)
282 COG1579 Zn-ribbon protein, pos 23.9 61 0.0013 32.1 2.6 56 184-242 166-229 (239)
283 PF07754 DUF1610: Domain of un 23.7 53 0.0011 20.5 1.3 8 282-289 16-23 (24)
284 PRK13182 racA polar chromosome 23.4 6.2E+02 0.014 23.8 9.9 60 425-485 86-145 (175)
285 COG1645 Uncharacterized Zn-fin 23.3 53 0.0011 29.4 1.8 23 214-242 29-52 (131)
286 COG5194 APC11 Component of SCF 23.0 61 0.0013 26.4 1.9 17 141-157 53-69 (88)
287 PRK11426 hypothetical protein; 23.0 1.3E+02 0.0029 27.0 4.3 46 43-91 58-104 (132)
288 COG4640 Predicted membrane pro 23.0 41 0.00089 35.5 1.2 23 283-309 2-25 (465)
289 PF06906 DUF1272: Protein of u 23.0 59 0.0013 24.7 1.7 43 124-178 7-51 (57)
290 KOG1701 Focal adhesion adaptor 22.9 69 0.0015 34.2 2.8 25 282-306 427-459 (468)
291 PF14319 Zn_Tnp_IS91: Transpos 22.8 1.9E+02 0.004 25.1 5.1 23 239-269 57-79 (111)
292 KOG0801 Predicted E3 ubiquitin 22.6 32 0.00069 31.8 0.3 29 119-147 174-203 (205)
293 PRK12286 rpmF 50S ribosomal pr 22.5 48 0.001 25.2 1.2 24 279-307 24-48 (57)
294 PF15616 TerY-C: TerY-C metal 22.4 50 0.0011 29.6 1.5 24 214-247 78-101 (131)
295 KOG3053 Uncharacterized conser 22.3 62 0.0013 32.2 2.2 54 121-176 19-79 (293)
296 KOG4234 TPR repeat-containing 22.2 3.2E+02 0.007 26.7 6.9 47 428-481 177-223 (271)
297 KOG2807 RNA polymerase II tran 22.2 54 0.0012 33.8 1.8 36 124-160 332-368 (378)
298 PF10112 Halogen_Hydrol: 5-bro 22.0 6.7E+02 0.015 23.6 13.9 104 364-482 81-185 (199)
299 PF11781 RRN7: RNA polymerase 21.9 48 0.001 22.7 1.0 30 277-308 3-34 (36)
300 COG3024 Uncharacterized protei 21.7 43 0.00094 26.1 0.8 14 281-294 6-19 (65)
301 PRK00420 hypothetical protein; 21.6 2E+02 0.0042 25.2 4.9 19 379-397 93-111 (112)
302 KOG0994 Extracellular matrix g 21.5 1.6E+03 0.035 27.8 15.3 132 343-493 1166-1303(1758)
303 cd00065 FYVE FYVE domain; Zinc 21.5 63 0.0014 23.8 1.7 35 123-157 3-39 (57)
304 PRK06266 transcription initiat 21.4 1E+02 0.0022 29.0 3.5 31 209-242 113-144 (178)
305 KOG3800 Predicted E3 ubiquitin 21.3 67 0.0014 32.6 2.3 53 215-296 2-54 (300)
306 cd07666 BAR_SNX7 The Bin/Amphi 21.2 8.2E+02 0.018 24.3 14.0 98 377-485 141-238 (243)
307 smart00834 CxxC_CXXC_SSSS Puta 21.1 56 0.0012 22.3 1.2 14 282-295 26-39 (41)
308 COG1198 PriA Primosomal protei 21.0 74 0.0016 36.7 2.9 13 282-294 475-487 (730)
309 PF05715 zf-piccolo: Piccolo Z 20.9 40 0.00087 25.8 0.5 34 283-316 3-39 (61)
310 PF05957 DUF883: Bacterial pro 20.8 2.1E+02 0.0045 23.6 4.9 27 459-485 40-66 (94)
311 KOG0824 Predicted E3 ubiquitin 20.7 33 0.00072 34.9 0.0 26 282-316 7-36 (324)
312 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.6 61 0.0013 29.8 1.8 24 282-306 34-58 (166)
313 PF03115 Astro_capsid: Astrovi 20.5 33 0.00073 39.7 0.0 7 67-73 721-727 (787)
314 PF07227 DUF1423: Protein of u 20.4 52 0.0011 35.4 1.4 32 215-249 99-130 (446)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-74 Score=614.04 Aligned_cols=421 Identities=33% Similarity=0.653 Sum_probs=380.2
Q ss_pred cccCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHhhhChhHHHHHhCcccccCCCCCCCCCCCCcc
Q 043224 44 MVIPKESLLAAQMGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLVEEGKDKLFAQAGVTVVENDHQVPLSQCSSTF 123 (516)
Q Consensus 44 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~e~~~~~~~~~~gl~~~~~~~~~~~~~~~~~~ 123 (516)
.|+|.+++...|.++|.+|+++|.++..+|++||.||.|+.+++++.|+ .+++.++..+|+.... ......
T Consensus 1 ~vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~-~~~~~~~~~~g~~~~~--------~~~~~~ 71 (444)
T KOG1815|consen 1 EVLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWV-EDEETGCFFVGLLLWP--------KKKGDV 71 (444)
T ss_pred CCCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHH-hcCcchhhhccccccC--------CCCccc
Confidence 3789999999999999999999999999999999999999999999999 5678888888876543 123568
Q ss_pred cccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHHHHHHH
Q 043224 124 CCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFLL 203 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~~ 203 (516)
.|.||++.++. .+..+.|||.||..||..||..+|.+|....|+||.++|...++.++|..+++. ++...+|.++++
T Consensus 72 ~c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~--~~~~~ky~~~i~ 148 (444)
T KOG1815|consen 72 QCGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSD--KEDKEKYQRYIL 148 (444)
T ss_pred cCCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCC--HHHHHHHHHHHH
Confidence 99999999865 788889999999999999999999998755599999999999999999999983 368999999999
Q ss_pred HHhhhcCCCcccCCCCCCCCceEeecCCCcceeeccCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcc
Q 043224 204 ESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTK 283 (516)
Q Consensus 204 ~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK 283 (516)
++||+.+..++|||+ |+|++++.........|.|.||+.|||+|+.+||.|.+|..+..|+++..+++++.+||..|||
T Consensus 149 ~syve~~~~lkwCP~-~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk 227 (444)
T KOG1815|consen 149 RSYVEDNVPLKWCPA-PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTK 227 (444)
T ss_pred HHHHhcCCccccCCC-CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCc
Confidence 999999999999995 9999999975555667999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCccceecCCCCceee-c--cccccccccccccc---------c-cccCCCCcc-hhhhhhhhhhhhhhHHHHHhh
Q 043224 284 PCPKCCKPIEKNGGCNMVRC-K--CGITFNWISGLEYS---------N-GYIEVSEER-PEHGKWRLESYYHCHKLYKAH 349 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC-~--C~~~FCw~C~~~w~---------C-~y~~~~~~~-~~~~~~~l~ry~hy~~r~~~h 349 (516)
+||+|.++|||++|||||+| . |+++|||+|++.|. | +|+...... ...++..|.||.|||+||++|
T Consensus 228 ~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~~~ 307 (444)
T KOG1815|consen 228 ECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWMEH 307 (444)
T ss_pred cCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHHhh
Confidence 99999999999999999999 4 99999999999986 8 998766544 778888999999999999999
Q ss_pred hHHHHHHHHHHHHHHHH-HHHhh-ccCCCCchhhHHHHHHHHHHHHHHHHhhhhhhhhcccccchhhhhhcHHHHHHHHH
Q 043224 350 TESFRLEYEMKEDIQDK-IKILG-EKDTSSKDFGWIKDGLNKLFRARRILSFSYPFAFYMFADDLLKNEMTREERKIKQN 427 (516)
Q Consensus 350 ~~s~k~e~~l~~~~~~k-~~~~~-~~~~~~~~~~fl~~a~~~l~~~R~~L~~sY~~~yyl~~~~~~~~~~~~~~~~~~~~ 427 (516)
+.|++++.++...++++ +..+. ...+++++++|+.+|+.+|++||+||+|||+||||+.. +++++
T Consensus 308 q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~-------------~~~~~ 374 (444)
T KOG1815|consen 308 QVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSE-------------NNKRN 374 (444)
T ss_pred hhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhcc-------------cchhh
Confidence 99999998877777543 33333 33467999999999999999999999999999999973 24568
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 043224 428 FFEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIETDLLG 490 (516)
Q Consensus 428 lFe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~~l~~ 490 (516)
+||++|.+||..+|+||..+++++...+.+++..+|+++.++|.++++++++++..+++||..
T Consensus 375 ~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 437 (444)
T KOG1815|consen 375 LFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLED 437 (444)
T ss_pred hhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccchhhhhHHHHHHHHHHhcccc
Confidence 999999999999999999999987777778899999999999999999999999999999874
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-36 Score=315.03 Aligned_cols=262 Identities=25% Similarity=0.494 Sum_probs=204.5
Q ss_pred HHHHHHHHhCCChHHHHHHHhhhChhHHHHHhCcccccC-CC----------CC-CCCCCCCcccccccccccCC-CCee
Q 043224 72 HARTLLIHYRWDVEKVFAVLVEEGKDKLFAQAGVTVVEN-DH----------QV-PLSQCSSTFCCNICCDDVSP-QEVT 138 (516)
Q Consensus 72 ~a~~LL~~~~W~~~~l~e~~~e~~~~~~~~~~gl~~~~~-~~----------~~-~~~~~~~~~~C~IC~e~~~~-~~~~ 138 (516)
.+......+.|+...|.+.+. ....++.....+..+.. +. .. ..+......+|.||+.+.+. ..++
T Consensus 85 v~~~~~~~~~~~~~~l~~~v~-~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s~~~~~~~~~~C~iC~~e~~~~~~~f 163 (384)
T KOG1812|consen 85 VAGREKPEQHRKIVLLVELVQ-RIREQLTSSEPILVPKNADIKFAYKLAREAIVSQLPSKLPKEECGICFVEDPEAEDMF 163 (384)
T ss_pred HhhhhhHHHHHHHHHHHHHHH-HHHHHhhcccceecccchhhHHHHHHHHHhhccccccccccccCccCccccccHhhhH
Confidence 455556666676666666664 23333333333332221 00 00 01112246789999955443 3555
Q ss_pred e-cCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHHHHHHHHHhhhcCCCcccCC
Q 043224 139 T-MDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFLLESYIDDNRRVKWCP 217 (516)
Q Consensus 139 ~-l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP 217 (516)
. ..|+|.||.+||++|++.+...| ..|+||..+|+..++.+....+|+ +.+.++|.+++.+.++.....+ +||
T Consensus 164 ~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt---~kl~e~~e~~~~e~~i~~~~~~-ycp 237 (384)
T KOG1812|consen 164 SVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLT---PKLREMWEQRLKEEVIPSLDRV-YCP 237 (384)
T ss_pred HHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcC---HHHHHHHHHHHHHHhhhhhhcc-cCC
Confidence 4 58999999999999999994444 589999999999999999999999 7899999999999999999888 999
Q ss_pred CCCCCCceEeecC----CCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccc
Q 043224 218 SVPHCGNAIQVEA----DELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPI 292 (516)
Q Consensus 218 ~~p~C~~~i~~~~----~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~I 292 (516)
.|+|...+.... .......|. ||..||.+|+.+||.+.+|+.+++|......++.+++|+..+++.||+|+..|
T Consensus 238 -~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~i 316 (384)
T KOG1812|consen 238 -YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMI 316 (384)
T ss_pred -CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceee
Confidence 599999887544 223345676 99999999999999999999999999877788899999999999999999999
Q ss_pred eecCCCCceeeccccccccccccccc--------c-cccCCCCcchhhhhhhhhhhhhhHHHHHhhhHHHHHH
Q 043224 293 EKNGGCNMVRCKCGITFNWISGLEYS--------N-GYIEVSEERPEHGKWRLESYYHCHKLYKAHTESFRLE 356 (516)
Q Consensus 293 EKn~GCnhMtC~C~~~FCw~C~~~w~--------C-~y~~~~~~~~~~~~~~l~ry~hy~~r~~~h~~s~k~e 356 (516)
++++|||||+|+|||+|||.|+++|. | |++.. ++||.++.+|..+..++
T Consensus 317 e~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~~r~~~~---------------~~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 317 ELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYECCRYKES---------------THYFEDDENHDKSIQLE 374 (384)
T ss_pred eecCCcceEEeeccccchhhcCcchhhCCccccCccccccc---------------ccccccccccccccccc
Confidence 99999999999999999999999996 3 55432 88888888887776655
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-34 Score=291.59 Aligned_cols=192 Identities=29% Similarity=0.688 Sum_probs=168.7
Q ss_pred CCcccccccccccCC-CCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHH
Q 043224 120 SSTFCCNICCDDVSP-QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKF 198 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y 198 (516)
.+.+.|.|||++..+ ..+..++|+|.||+.|++.|++..|.+|.+..++||+++|+...+...++++|. .++++||
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg---~EL~arY 258 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVG---DELFARY 258 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHH---HHHHHHH
Confidence 467899999999877 456778999999999999999999999999999999999999999999999998 6899999
Q ss_pred HHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhH--------HHHhH---
Q 043224 199 ERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMW--------ELWSK--- 266 (516)
Q Consensus 199 ~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~--------~~w~~--- 266 (516)
+++++++.++...++++||+ +.|...+..++ +...+.|+ |+..||+.|+..||+..+|..- ..|..
T Consensus 259 e~l~lqk~l~~msdv~yCPr-~~Cq~p~~~d~-~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCPR-ACCQLPVKQDP-GRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE 336 (445)
T ss_pred HHHHHHHHHHhhcccccCCh-hhccCccccCc-hhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence 99999999999999999994 89999984443 44568997 9999999999999999999753 22321
Q ss_pred ----------------HhHHHHHHHHHHhcCcccCCCCCccceecCCCCceee-ccccccccccccc
Q 043224 267 ----------------KFEVESLSLNWISSHTKPCPKCCKPIEKNGGCNMVRC-KCGITFNWISGLE 316 (516)
Q Consensus 267 ----------------k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~ 316 (516)
...++-.+..|+..|.|+||+|+++|||++|||+|+| +|++.|||+|+..
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~ 403 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAEL 403 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhh
Confidence 1113445678999999999999999999999999999 8999999999985
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.4e-26 Score=222.36 Aligned_cols=191 Identities=30% Similarity=0.673 Sum_probs=148.5
Q ss_pred CCCcccccccccccCCCCeeecCCC--CcccHHHHHHHHHhhhhcCCc-------ccccccccccccccCHH-HHHHhhC
Q 043224 119 CSSTFCCNICCDDVSPQEVTTMDCG--HCFCNNCWTEHFIVKINDGQS-------RRIKCMALKCNVVCDEA-KIRCLVS 188 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~I~~g~~-------~~i~CP~~~C~~~i~~~-~i~~ll~ 188 (516)
+....+|..|-+.- +.+..+.|. |..|.+|++.|....+++.+. ..+.||. +|...+-.+ .--++|.
T Consensus 218 N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg 294 (446)
T KOG0006|consen 218 NSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 55778999998763 345556887 999999999999999987653 3578886 787643332 2335566
Q ss_pred CCChHHHHHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcceeecc--CCcccccccccccCCCC----------
Q 043224 189 ARDSNIADKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECA--CGFQFCFSCSSVAHSPC---------- 256 (516)
Q Consensus 189 ~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--Cg~~fC~~C~~~~H~p~---------- 256 (516)
.+.+.+|+++..+.+|-....+ -|| .|+||..+..+++. ..|+|. ||..||..|.+.+|.+.
T Consensus 295 ---~e~Y~rYQr~atEe~vlq~gGV-lCP-~pgCG~gll~EPD~-rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t 368 (446)
T KOG0006|consen 295 ---EEQYNRYQRYATEECVLQMGGV-LCP-RPGCGAGLLPEPDQ-RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGT 368 (446)
T ss_pred ---hhHHHHHHHhhhhhheeecCCE-ecC-CCCCCcccccCCCC-CcccCCCCchhHhHHHHHhhhccccceeeeccccc
Confidence 6799999999999999888765 699 59999999887743 469996 99999999999999863
Q ss_pred -CchhH--HHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCCCceee-c--cccccccccccccc
Q 043224 257 -SCLMW--ELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGCNMVRC-K--CGITFNWISGLEYS 318 (516)
Q Consensus 257 -~C~~~--~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCnhMtC-~--C~~~FCw~C~~~w~ 318 (516)
+|..- ..-.....-|..+..-|+..||+||+|++|.||||||+||.| + ||.+|||.|+-.|.
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~ 436 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWN 436 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhh
Confidence 24310 000111222445556688999999999999999999999999 5 99999999999997
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.38 E-value=6.6e-13 Score=103.61 Aligned_cols=62 Identities=52% Similarity=1.165 Sum_probs=55.8
Q ss_pred HHHHHHHHHHhhhcCCCcccCCCCCCCCceEeec-CCCcceeecc-CCcccccccccccCCCCCc
Q 043224 196 DKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVE-ADELCEVECA-CGFQFCFSCSSVAHSPCSC 258 (516)
Q Consensus 196 ~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C 258 (516)
++|++++++++|+.+++++||| +|+|+.++... +.....|.|+ ||+.||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP-~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCP-APDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCC-CCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4799999999999999999999 69999999987 3455679995 9999999999999999988
No 6
>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=99.26 E-value=1.1e-12 Score=102.19 Aligned_cols=62 Identities=34% Similarity=0.971 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcc-eeecc-CCcccccccccccCCCCCc
Q 043224 196 DKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELC-EVECA-CGFQFCFSCSSVAHSPCSC 258 (516)
Q Consensus 196 ~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-Cg~~fC~~C~~~~H~p~~C 258 (516)
++|++++++.||+.++.++||| .|+|+.++........ .|.|+ |++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp-~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCP-NPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--T-TSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCC-CCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 5799999999999899999999 5999999998775544 49998 9999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.30 E-value=4.3e-07 Score=64.89 Aligned_cols=41 Identities=27% Similarity=0.741 Sum_probs=29.8
Q ss_pred ccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 125 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
|+||++-+ .++++++|||.||..|+..+....-. ..+.||.
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSG----SGFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSS----ST---SS
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCC----cCCCCcC
Confidence 89999987 68999999999999999999866422 2278886
No 8
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.18 E-value=2e-06 Score=66.83 Aligned_cols=43 Identities=35% Similarity=0.833 Sum_probs=37.3
Q ss_pred HHHhc--CcccCC--CCCccceecC--CCCceee-ccccccccccccccc
Q 043224 276 NWISS--HTKPCP--KCCKPIEKNG--GCNMVRC-KCGITFNWISGLEYS 318 (516)
Q Consensus 276 ~wi~~--ntK~CP--kC~~~IEKn~--GCnhMtC-~C~~~FCw~C~~~w~ 318 (516)
.+|.. +.+.|| +|...|+..+ |.++|+| .|++.|||.|+.+|.
T Consensus 10 ~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 10 SYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred HHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 34544 578899 9999999964 9999999 899999999999985
No 9
>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=98.12 E-value=1.7e-06 Score=62.29 Aligned_cols=40 Identities=28% Similarity=0.692 Sum_probs=33.1
Q ss_pred cccccccccC-CCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 124 CCNICCDDVS-PQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 124 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
+|+||++++. ...++.++|||.||.+|+..|+... .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 6999999995 4667788999999999999999763 27886
No 10
>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=98.10 E-value=1.1e-06 Score=68.15 Aligned_cols=38 Identities=39% Similarity=0.892 Sum_probs=28.8
Q ss_pred CcccCCC--CCccceecCCCCc--eee-ccccccccccccccc
Q 043224 281 HTKPCPK--CCKPIEKNGGCNM--VRC-KCGITFNWISGLEYS 318 (516)
Q Consensus 281 ntK~CPk--C~~~IEKn~GCnh--MtC-~C~~~FCw~C~~~w~ 318 (516)
+.+.||+ |...|++..|.++ |+| .|++.|||.|+++|.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 4589988 9999999999999 999 599999999999985
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.07 E-value=2.8e-06 Score=59.60 Aligned_cols=38 Identities=34% Similarity=0.853 Sum_probs=29.1
Q ss_pred ccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 125 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
|+||++.+. +.++.++|||.||.+||.+|+... .+||.
T Consensus 1 C~iC~~~~~-~~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR-DPVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-S-SEEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCccc-CcCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 899999864 233678999999999999998863 47775
No 12
>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=98.01 E-value=5.3e-06 Score=58.69 Aligned_cols=40 Identities=30% Similarity=0.801 Sum_probs=31.9
Q ss_pred ccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 125 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
|+||++.+.. ....++|||.||..|+.+++.. . ..++||.
T Consensus 1 C~iC~~~~~~-~~~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFED-PVILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBCSS-EEEETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCccccC-CCEEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 8999998642 2347899999999999999998 2 3467886
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.93 E-value=6.9e-06 Score=75.53 Aligned_cols=55 Identities=29% Similarity=0.669 Sum_probs=43.7
Q ss_pred CCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 119 CSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
..+.+-|+||++.+....+++..|||.||..|++.-+... -+||. |...|+..++
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~--------~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT--------NKCPT--CRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhC--------CCCCC--cccccchhhh
Confidence 3456889999999987777889999999999998877643 58998 7766665544
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.81 E-value=1.4e-05 Score=75.32 Aligned_cols=66 Identities=29% Similarity=0.556 Sum_probs=48.5
Q ss_pred CCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhc--------CCcccccccccccccccCHHHHHHhhC
Q 043224 119 CSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKIND--------GQSRRIKCMALKCNVVCDEAKIRCLVS 188 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~--------g~~~~i~CP~~~C~~~i~~~~i~~ll~ 188 (516)
..+.++|+||++.+ .+.+.+.|||.||..|+..|+...-.. ......+||. |...+....+..+..
T Consensus 15 ~~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 15 SGGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 34578999999986 556778999999999999998643110 0113579998 999998776655554
No 15
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.77 E-value=2.6e-05 Score=55.27 Aligned_cols=44 Identities=27% Similarity=0.767 Sum_probs=33.1
Q ss_pred cccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 124 CCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
+|+||++.+ .......+|||.||..|+..|+.. ...+||. |+..
T Consensus 1 ~C~iC~~~~-~~~~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEF-REPVVLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhh-hCceEecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 599999987 233444469999999999999876 2357987 7653
No 16
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.72 E-value=2.4e-05 Score=56.06 Aligned_cols=41 Identities=32% Similarity=0.746 Sum_probs=22.6
Q ss_pred ccccccccCC--CCeeecCCCCcccHHHHHHHHHhhhhcCCccccccc
Q 043224 125 CNICCDDVSP--QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCM 170 (516)
Q Consensus 125 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP 170 (516)
|+||.+ +.. ..+..|.|||.||.+|+.+.+.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 632 2356789999999999999988543 1357887
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.69 E-value=3e-05 Score=55.90 Aligned_cols=42 Identities=33% Similarity=0.876 Sum_probs=33.5
Q ss_pred cccccccccC-CCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccc
Q 043224 124 CCNICCDDVS-PQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCN 175 (516)
Q Consensus 124 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~ 175 (516)
.|+||++.+. ...+..++|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 4999999993 3456677999999999999887 14678997 65
No 18
>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=97.66 E-value=4.5e-05 Score=56.50 Aligned_cols=46 Identities=30% Similarity=0.767 Sum_probs=36.3
Q ss_pred cccccccccccCCCCeeecCCCCc-ccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHC-FCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
...|.||++.. .++..++|||. ||..|+..++. ...+||. |...|.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 45799999985 45777899999 99999999998 2368998 887664
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=5.3e-05 Score=72.76 Aligned_cols=60 Identities=27% Similarity=0.550 Sum_probs=47.4
Q ss_pred CCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhC
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVS 188 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~ 188 (516)
...++|.||++.. .+++...|||.||..|+-+|+....+. -.||. |+..|+.+.|--|..
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeeec
Confidence 5689999999974 567777899999999999999887443 34787 999888776655543
No 20
>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=97.40 E-value=0.00013 Score=49.64 Aligned_cols=30 Identities=30% Similarity=0.947 Sum_probs=26.2
Q ss_pred ccccccccCCCCeeecCCCCcccHHHHHHHHH
Q 043224 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTEHFI 156 (516)
Q Consensus 125 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~ 156 (516)
|+||++. ...+..++|||.||..|+..|+.
T Consensus 1 C~iC~~~--~~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEE--LKDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccC--CCCcEEecCCChHHHHHHHHHHH
Confidence 7899988 35677789999999999999988
No 21
>PHA02926 zinc finger-like protein; Provisional
Probab=97.38 E-value=0.00013 Score=69.74 Aligned_cols=57 Identities=23% Similarity=0.443 Sum_probs=40.2
Q ss_pred CCCcccccccccccC-----CCCee--ecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 119 CSSTFCCNICCDDVS-----PQEVT--TMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~-----~~~~~--~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.+...+|+||++..- ....+ ..+|+|.||..|++.|-..+-..| ..-.||. |...+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Ccceee
Confidence 345789999999752 22223 339999999999999998754322 2457998 887543
No 22
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.26 E-value=0.00022 Score=70.05 Aligned_cols=50 Identities=26% Similarity=0.497 Sum_probs=37.3
Q ss_pred CCcccccccccccCCCC------eeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 120 SSTFCCNICCDDVSPQE------VTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
+...+|+||++.+.... ....+|+|.||.+|+..|+.. ...||. |...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 34679999999865332 234589999999999999863 247998 887554
No 23
>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=97.18 E-value=0.00045 Score=53.31 Aligned_cols=49 Identities=8% Similarity=0.180 Sum_probs=38.7
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
+.|+||.+.+ .+++.++|||.||+.|+..|+.. . ..||. |+..++.+.+
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~---~-----~~cP~--~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS---H-----GTDPV--TGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH---C-----CCCCC--CcCCCChhhc
Confidence 5799999986 45677899999999999999976 1 36887 7777765443
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.04 E-value=0.00026 Score=75.06 Aligned_cols=60 Identities=20% Similarity=0.443 Sum_probs=47.1
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhC
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVS 188 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~ 188 (516)
...|+||++..+. ...+.|||.||..|+-+|+...... ....||. |...|...++..+..
T Consensus 186 ~~~CPICL~~~~~--p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSV--PVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCc--ccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 6789999998532 3345699999999999999987332 3578998 999888877766655
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.0004 Score=68.79 Aligned_cols=51 Identities=27% Similarity=0.641 Sum_probs=41.9
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
...-|.+|++.. .++...+|||.||..|+..|+.++- .||. |...+.+..|
T Consensus 238 a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 456899999984 5677889999999999999998762 3998 9988776544
No 26
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.00058 Score=68.26 Aligned_cols=43 Identities=28% Similarity=0.788 Sum_probs=36.6
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCN 175 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~ 175 (516)
...+|+||++.+.. +..++|||.||..|+...+. ..+.||. |.
T Consensus 12 ~~~~C~iC~~~~~~--p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFRE--PVLLPCGHNFCRACLTRSWE--------GPLSCPV--CR 54 (386)
T ss_pred ccccChhhHHHhhc--CccccccchHhHHHHHHhcC--------CCcCCcc--cC
Confidence 56899999999853 37779999999999999988 3489998 87
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.83 E-value=0.0015 Score=68.80 Aligned_cols=50 Identities=26% Similarity=0.584 Sum_probs=39.6
Q ss_pred CCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
...+.|+||.+.+ ..++.++|||.||..|+..|+... ..||. |...+...
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~~--------~~CP~--Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSNQ--------PKCPL--CRAEDQES 73 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhCC--------CCCCC--CCCccccc
Confidence 3568999999987 455678999999999999998642 37987 88876653
No 28
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.52 E-value=0.0062 Score=43.60 Aligned_cols=39 Identities=18% Similarity=0.316 Sum_probs=33.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHhhh
Q 043224 56 MGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLVEE 94 (516)
Q Consensus 56 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~e~ 94 (516)
++.|...++++|+++..|+.+|..++||.+..++.||+.
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 357889999999999999999999999999999999953
No 29
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.35 E-value=0.0027 Score=48.47 Aligned_cols=48 Identities=21% Similarity=0.458 Sum_probs=30.8
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCN 175 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~ 175 (516)
..+.|+|....+. +.+.+..|||.|.++.+.+||. ....++||..||+
T Consensus 10 ~~~~CPiT~~~~~-~PV~s~~C~H~fek~aI~~~i~------~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFE-DPVKSKKCGHTFEKEAILQYIQ------RNGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-S-SEEEESSS--EEEHHHHHHHCT------TTS-EE-SCCC-S
T ss_pred eccCCCCcCChhh-CCcCcCCCCCeecHHHHHHHHH------hcCCCCCCCCCCC
Confidence 4578999999863 3445569999999999999992 1246899999995
No 30
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.34 E-value=0.0017 Score=65.36 Aligned_cols=52 Identities=27% Similarity=0.645 Sum_probs=42.0
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIR 184 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~ 184 (516)
...-|.||++-|. -+...+|+|.||.=|++.|+..+ ..||. |...+.+..++
T Consensus 22 ~lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~~--------p~CP~--C~~~~~Es~Lr 73 (442)
T KOG0287|consen 22 DLLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSYK--------PQCPT--CCVTVTESDLR 73 (442)
T ss_pred HHHHHhHHHHHhc--CceeccccchHHHHHHHHHhccC--------CCCCc--eecccchhhhh
Confidence 3467999999874 34455799999999999999764 57998 99988887665
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.13 E-value=0.0041 Score=63.02 Aligned_cols=54 Identities=22% Similarity=0.533 Sum_probs=37.8
Q ss_pred ccccccccccCCC-Ce--eecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHH
Q 043224 123 FCCNICCDDVSPQ-EV--TTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRC 185 (516)
Q Consensus 123 ~~C~IC~e~~~~~-~~--~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ 185 (516)
..||||..+...+ .+ ....|||.||..|+...+. .| +..||. |...+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~---~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG---SGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC---CCCCCC--CCCccchhhccc
Confidence 5799999963322 22 1127999999999999873 22 348996 998877665443
No 32
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.07 E-value=0.0042 Score=61.87 Aligned_cols=53 Identities=19% Similarity=0.476 Sum_probs=42.7
Q ss_pred CCCcccccccccccCC-CCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCH
Q 043224 119 CSSTFCCNICCDDVSP-QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDE 180 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~ 180 (516)
.....+|.||++++.. +....++|.|.|...|+.+|+.. ...+||. |...+++
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 3456899999999865 45667899999999999999864 2468998 9988764
No 33
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.06 E-value=0.01 Score=61.52 Aligned_cols=40 Identities=28% Similarity=0.694 Sum_probs=37.0
Q ss_pred hcCcccCCC--CCccceecCCCCceee-ccccccccccccccc
Q 043224 279 SSHTKPCPK--CCKPIEKNGGCNMVRC-KCGITFNWISGLEYS 318 (516)
Q Consensus 279 ~~ntK~CPk--C~~~IEKn~GCnhMtC-~C~~~FCw~C~~~w~ 318 (516)
.++.+-||+ |..|+-...|++-..| +|.+.||-+|...|.
T Consensus 270 msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H 312 (445)
T KOG1814|consen 270 MSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH 312 (445)
T ss_pred hcccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc
Confidence 457899999 9999977899999999 899999999999998
No 34
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.96 E-value=0.0022 Score=71.27 Aligned_cols=57 Identities=21% Similarity=0.646 Sum_probs=46.1
Q ss_pred CCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHh
Q 043224 119 CSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCL 186 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~l 186 (516)
.....+|++|..- ..+++...|||.||.+|++..+.+. .-+||. |+..++..+|..+
T Consensus 640 yK~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 640 YKELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETR-------QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HHhceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHh-------cCCCCC--CCCCCCccccccc
Confidence 3457899999954 3567778999999999999999875 458997 9999998877654
No 35
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.72 E-value=0.0058 Score=62.93 Aligned_cols=47 Identities=26% Similarity=0.543 Sum_probs=38.4
Q ss_pred ccccccccccCCC-CeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 123 FCCNICCDDVSPQ-EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 123 ~~C~IC~e~~~~~-~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
.+|.||+|++..+ .+..|+|+|.|...|+..||... .-.||. |+.-+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-------CccCCC--CCCcC
Confidence 6999999998654 56678999999999999999875 235998 77633
No 36
>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=95.54 E-value=0.013 Score=46.96 Aligned_cols=42 Identities=21% Similarity=0.473 Sum_probs=29.7
Q ss_pred cccccccccccCCC-----------CeeecCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 122 TFCCNICCDDVSPQ-----------EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 122 ~~~C~IC~e~~~~~-----------~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
...|.||++.+... .+....|||.|...|+.+|+... -.||.
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~ 71 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL 71 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC
Confidence 34599999998211 12334899999999999999653 27886
No 37
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.18 E-value=0.019 Score=60.81 Aligned_cols=102 Identities=20% Similarity=0.506 Sum_probs=64.1
Q ss_pred cccccccccccCCC---Ce---eecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHH
Q 043224 122 TFCCNICCDDVSPQ---EV---TTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIA 195 (516)
Q Consensus 122 ~~~C~IC~e~~~~~---~~---~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~ 195 (516)
...|+.|+...... .. .-..|+-.||.+|-..|-. ++.| ++++++.+..
T Consensus 238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~---------~~sC-----------~eykk~~~~~----- 292 (384)
T KOG1812|consen 238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA---------NLSC-----------EEYKKLNPEE----- 292 (384)
T ss_pred CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC---------CCCH-----------HHHHHhCCcc-----
Confidence 44577777654321 11 1236777888888555421 2334 5566665421
Q ss_pred HHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcceeeccCCcccccccccccCCCC
Q 043224 196 DKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVAHSPC 256 (516)
Q Consensus 196 ~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~ 256 (516)
+....+..++. ...+.|| .|+..|....+ -..++|.||+.||+.|+.+|+...
T Consensus 293 --~~d~~~~~~la--~~wr~Cp---kC~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 293 --YVDDITLKYLA--KRWRQCP---KCKFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred --cccHHHHHHHH--HhcCcCc---ccceeeeecCC-cceEEeeccccchhhcCcchhhCC
Confidence 11222333333 5677899 79999987765 556999999999999999886543
No 38
>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=95.13 E-value=0.017 Score=46.34 Aligned_cols=50 Identities=12% Similarity=0.141 Sum_probs=37.0
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
..+.|+|+.+-+ .+++.+++||.|++.++..|+.. ....||. |+..+..+
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcc
Confidence 568999999986 67888999999999999999987 2357887 66666654
No 39
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.06 E-value=0.011 Score=62.85 Aligned_cols=111 Identities=19% Similarity=0.412 Sum_probs=68.8
Q ss_pred HHcCCCHHHHHHHHHHhCCChHHHHHHHhhhChhHH--HHHhCcccccC--------------CCC--------CC-CCC
Q 043224 64 DLLSLKEKHARTLLIHYRWDVEKVFAVLVEEGKDKL--FAQAGVTVVEN--------------DHQ--------VP-LSQ 118 (516)
Q Consensus 64 ~~l~i~~~~a~~LL~~~~W~~~~l~e~~~e~~~~~~--~~~~gl~~~~~--------------~~~--------~~-~~~ 118 (516)
+-||+||-...+==-.|+=...++.+.++.....++ +.++|+.+... +++ .. ...
T Consensus 453 dDLgLPPRiv~vRrD~fn~eE~D~YeSLY~dSkrkfntyieeGvvlNNYAnIF~LitRmRQ~aDHP~LVl~S~~~n~~~e 532 (791)
T KOG1002|consen 453 DDLGLPPRIVTVRRDFFNEEEKDLYESLYKDSKRKFNTYIEEGVVLNNYANIFTLITRMRQAADHPDLVLYSANANLPDE 532 (791)
T ss_pred cccCCCccceeeehhhhhhHHHHHHHHHHHhhHHhhhhHHhhhhhhhhHHHHHHHHHHHHHhccCcceeeehhhcCCCcc
Confidence 567888865544333444445566776663222222 33455543210 000 00 112
Q ss_pred CCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 119 CSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
+.+..+|.+|-++ ..+.+..+|.|.||+-|++.|+....... .+.||. |...++.+
T Consensus 533 nk~~~~C~lc~d~--aed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 533 NKGEVECGLCHDP--AEDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred ccCceeecccCCh--hhhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 4467899999886 36677789999999999999998876543 389998 98877655
No 40
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.01 E-value=0.016 Score=56.98 Aligned_cols=53 Identities=23% Similarity=0.577 Sum_probs=39.9
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
....|.||++.. ..+....|||.||..|+-..++.+ ..-.||. |...+.+..|
T Consensus 214 ~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeeccc--CCcccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 367899999974 566777999999999999853332 2346998 9887776655
No 41
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.69 E-value=0.014 Score=46.40 Aligned_cols=57 Identities=25% Similarity=0.391 Sum_probs=27.1
Q ss_pred cccccccccccC-CCCeee-----cCCCCcccHHHHHHHHHhhhhcCCcc-c--ccccccccccccCH
Q 043224 122 TFCCNICCDDVS-PQEVTT-----MDCGHCFCNNCWTEHFIVKINDGQSR-R--IKCMALKCNVVCDE 180 (516)
Q Consensus 122 ~~~C~IC~e~~~-~~~~~~-----l~CgH~fC~~C~~~yl~~~I~~g~~~-~--i~CP~~~C~~~i~~ 180 (516)
..+|.||+.... .+.... ..|++.|...|+.+|+...-+....+ + =.||. |...|..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 467999999864 222222 26899999999999998766544322 2 26987 9887654
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=94.64 E-value=0.0048 Score=47.70 Aligned_cols=44 Identities=27% Similarity=0.698 Sum_probs=21.3
Q ss_pred cccccccccccCCCCeeec-CCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 122 TFCCNICCDDVSPQEVTTM-DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
..-|++|.+-+ ..++.+ .|.|.||..|++..+. ..||. |..+.-
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw 51 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAW 51 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-S
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC----------CCCCC--cCChHH
Confidence 35699999986 456555 9999999999866332 24998 887543
No 43
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.58 E-value=0.11 Score=51.40 Aligned_cols=54 Identities=20% Similarity=0.491 Sum_probs=39.4
Q ss_pred CCCCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 117 SQCSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 117 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
+..+...+|++|.+. |........|||.||--|+..-+... ..++||. |+..+.
T Consensus 234 s~~t~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 234 STGTSDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred ccccCCceeeccCCC-CCCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 334567899999986 33344445799999999998776543 3579997 987655
No 44
>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=93.83 E-value=0.027 Score=35.84 Aligned_cols=23 Identities=35% Similarity=0.999 Sum_probs=17.0
Q ss_pred ccCCCCCccceecCCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
|.||.|+..|-.+. +.| .|||.|
T Consensus 1 K~CP~C~~~V~~~~----~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESA----KFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhc----CcCCCCCCCC
Confidence 67999998885533 677 588877
No 45
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.70 E-value=0.1 Score=54.49 Aligned_cols=35 Identities=20% Similarity=0.587 Sum_probs=28.6
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHh
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIV 157 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~ 157 (516)
++..|+||..-+ .+++.|+|+|..|..|-+.-+..
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhccc
Confidence 356799998876 67889999999999998875543
No 46
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=93.68 E-value=0.057 Score=55.36 Aligned_cols=50 Identities=24% Similarity=0.563 Sum_probs=38.5
Q ss_pred CCcccccccccc-cCCC----------CeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 120 SSTFCCNICCDD-VSPQ----------EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 120 ~~~~~C~IC~e~-~~~~----------~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.+...|.||+++ +..+ .+..++|||.+...|++.|++.+ -.||- |..++-
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~i 345 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVI 345 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCccc
Confidence 456789999999 3222 23578999999999999999864 47988 887643
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.15 E-value=0.081 Score=54.83 Aligned_cols=55 Identities=25% Similarity=0.510 Sum_probs=37.2
Q ss_pred CCCcccccccccccCCCC-----eee-cCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 119 CSSTFCCNICCDDVSPQE-----VTT-MDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
.+...+|.||++...... .-. .+|.|.||..|++.|=...=. +....-.||. |..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv 218 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRV 218 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccC
Confidence 356789999999864322 112 479999999999998644322 2213457988 775
No 48
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=92.46 E-value=0.11 Score=52.79 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=37.5
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
...+|.+|-.-+- +.+....|-|.||+.|+-.|++.. ..||. |+..|.
T Consensus 14 ~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~~--------~~CP~--C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEES--------KYCPT--CDIVIH 61 (331)
T ss_pred cceehhhccceee-cchhHHHHHHHHHHHHHHHHHHHh--------ccCCc--cceecc
Confidence 5679999988763 344456899999999999999972 47987 776554
No 49
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.44 E-value=0.21 Score=50.85 Aligned_cols=58 Identities=28% Similarity=0.631 Sum_probs=43.2
Q ss_pred cccccccccccCCCC----eeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc--cCHHHHHHhhC
Q 043224 122 TFCCNICCDDVSPQE----VTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV--CDEAKIRCLVS 188 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~----~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~--i~~~~i~~ll~ 188 (516)
...|.||-++++..+ +..|.|||.+|..|....+.. ..|.||. |... ++...++.+-.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l~k 66 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSLQK 66 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhhhh
Confidence 357999999987642 455789999999999988764 3577876 8887 56666666543
No 50
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.35 E-value=0.098 Score=38.32 Aligned_cols=44 Identities=18% Similarity=0.663 Sum_probs=21.3
Q ss_pred ccccccccCCC--CeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 125 CNICCDDVSPQ--EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 125 C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
|++|.+++... ++....||+.+|..||..-++. . .=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~----~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---E----GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S-----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---c----CCCCCC--CCCC
Confidence 78999987443 3445589999999999886652 1 236987 8754
No 51
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.23 E-value=0.077 Score=53.19 Aligned_cols=53 Identities=21% Similarity=0.391 Sum_probs=40.4
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIR 184 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~ 184 (516)
..-+|.||+.+- ..++.|.|+|.||.-|++.-+.. +. ..|+. |...|+...+.
T Consensus 6 ~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 6 KKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred cCCcceeeeccC--CcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchhc
Confidence 456899999984 45688999999999999875443 22 35988 99988876543
No 52
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.89 E-value=0.4 Score=48.38 Aligned_cols=94 Identities=21% Similarity=0.538 Sum_probs=58.1
Q ss_pred CCCCcccHHHHHHHHHhhhhcCC--cccccccccccccccCHHHHHHhhCCCChHHHHHHHHHHHHHhhhcCCCcccCCC
Q 043224 141 DCGHCFCNNCWTEHFIVKINDGQ--SRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFLLESYIDDNRRVKWCPS 218 (516)
Q Consensus 141 ~CgH~fC~~C~~~yl~~~I~~g~--~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~ 218 (516)
.||-.||++|+..|-.-.-..+- +.. ..|...+++.. ...+||+...- ..| ....+.||
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t-----~tc~y~vde~~----------a~~arwd~as~-~TI--k~tTkpCP- 401 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGT-----TTCAYRVDERA----------AEQARWDAASK-ETI--KKTTKPCP- 401 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccc-----cceeeecChhh----------hhhhhhhhhhh-hhh--hhccCCCC-
Confidence 59999999999988543322221 111 12555555422 13344544332 222 23557798
Q ss_pred CCCCCceEeecCCCcceeecc---CCcccccccccccCCCC
Q 043224 219 VPHCGNAIQVEADELCEVECA---CGFQFCFSCSSVAHSPC 256 (516)
Q Consensus 219 ~p~C~~~i~~~~~~~~~v~C~---Cg~~fC~~C~~~~H~p~ 256 (516)
.|......+++ -..+.|+ ||..+||+|+.+|.+.+
T Consensus 402 --kChvptErnGG-CmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 402 --KCHVPTERNGG-CMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred --CccCccccCCc-eEEeecCCCCCCceeEeccCChhhhhh
Confidence 79888876664 3458894 99999999999987653
No 53
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=91.77 E-value=0.079 Score=52.64 Aligned_cols=45 Identities=31% Similarity=0.643 Sum_probs=34.2
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
...-|.||-+-+. -+....|||.||.=|++.|+.++ .-||. |...
T Consensus 24 s~lrC~IC~~~i~--ip~~TtCgHtFCslCIR~hL~~q--------p~CP~--Cr~~ 68 (391)
T COG5432 24 SMLRCRICDCRIS--IPCETTCGHTFCSLCIRRHLGTQ--------PFCPV--CRED 68 (391)
T ss_pred hHHHhhhhhheee--cceecccccchhHHHHHHHhcCC--------CCCcc--cccc
Confidence 3567999988763 34556999999999999999764 45776 6653
No 54
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.72 E-value=0.22 Score=52.72 Aligned_cols=71 Identities=20% Similarity=0.536 Sum_probs=45.8
Q ss_pred CCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCH-HHHHHhhCCCChHHHHHH
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDE-AKIRCLVSARDSNIADKF 198 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~-~~i~~ll~~~~~e~~~~y 198 (516)
.+.+.|.||+..+ -.+++++|||.||..|+.. .+. ..-.||. |...+.. ......+ ...++
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r----~ld----~~~~cp~--Cr~~l~e~~~~~~~~------~~~r~ 143 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDR----SLD----QETECPL--CRDELVELPALEQAL------SLNRL 143 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHH----Hhc----cCCCCcc--cccccccchHHHHHH------HHHHH
Confidence 4689999999886 4567779999999999666 222 2346887 8876653 2222221 13455
Q ss_pred HHHHHHHhhh
Q 043224 199 ERFLLESYID 208 (516)
Q Consensus 199 ~~~~~~~~v~ 208 (516)
...++..|++
T Consensus 144 ~~~li~~F~~ 153 (398)
T KOG4159|consen 144 LCKLITKFLE 153 (398)
T ss_pred HHHHHHHhhh
Confidence 5566655544
No 55
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=90.88 E-value=0.65 Score=47.23 Aligned_cols=49 Identities=16% Similarity=0.337 Sum_probs=34.7
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
....|+||.-... ++.+..--|-.||-.|.-.|+.. .| +||..+|+..+
T Consensus 299 ~~~~CpvClk~r~-Nptvl~vSGyVfCY~Ci~~Yv~~---~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ-NPTVLEVSGYVFCYPCIFSYVVN---YG-----HCPVTGYPASV 347 (357)
T ss_pred ccccChhHHhccC-CCceEEecceEEeHHHHHHHHHh---cC-----CCCccCCcchH
Confidence 4568999998753 22232345889999999999983 33 58887777543
No 56
>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=90.71 E-value=0.17 Score=51.57 Aligned_cols=53 Identities=28% Similarity=0.676 Sum_probs=36.7
Q ss_pred cCCCCCCCCceEeecCCCcceeeccCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 215 WCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
-|| .|..-....+.-...|. +|||.||..|-.. .| ..+..+||.|+.++-|
T Consensus 5 ~CP---~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~------------------------l~-~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCP---RCKTTKYRNPSLKLMVN-VCGHTLCESCVDL------------------------LF-VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCC---cCCCCCccCcccccccC-CCCCcccHHHHHH------------------------Hh-cCCCCCCCCCCCccch
Confidence 488 68886665554333455 8999999999511 12 2345689999999988
Q ss_pred cC
Q 043224 295 NG 296 (516)
Q Consensus 295 n~ 296 (516)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 75
No 57
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=90.33 E-value=0.48 Score=56.20 Aligned_cols=75 Identities=20% Similarity=0.398 Sum_probs=57.1
Q ss_pred Cccccccccccc-CCCCeeecCCCCcccHHHHHHHHHhhhhcCCc--ccccccccccccccCHHHHHHhhCCCChHHHHH
Q 043224 121 STFCCNICCDDV-SPQEVTTMDCGHCFCNNCWTEHFIVKINDGQS--RRIKCMALKCNVVCDEAKIRCLVSARDSNIADK 197 (516)
Q Consensus 121 ~~~~C~IC~e~~-~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~--~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~ 197 (516)
..-.|.|||.+- .....+.|.|+|.|...|-+.-++..-..-.+ ..|.||. |...|....++.||. .+.+.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLld----PiKel 3558 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLD----PIKEL 3558 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHH----HHHHH
Confidence 345799999874 44566789999999999999999887654332 4589998 999999998998886 24455
Q ss_pred HHHH
Q 043224 198 FERF 201 (516)
Q Consensus 198 y~~~ 201 (516)
|+..
T Consensus 3559 ~edV 3562 (3738)
T KOG1428|consen 3559 YEDV 3562 (3738)
T ss_pred HHHH
Confidence 5443
No 58
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.24 E-value=0.21 Score=52.01 Aligned_cols=54 Identities=22% Similarity=0.637 Sum_probs=40.0
Q ss_pred cccccccccccCC---CCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 122 TFCCNICCDDVSP---QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 122 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
..+|+||++.+.. ..+.++.|||.|=.+|+.+|+. +....+||. |...-....|
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~katkr~i 60 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGKATKRQI 60 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCChhHHHHH
Confidence 4689999998643 2467889999999999999993 224578998 8764443333
No 59
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=89.81 E-value=0.36 Score=35.54 Aligned_cols=42 Identities=17% Similarity=0.364 Sum_probs=31.0
Q ss_pred cccccccccCCCCeeecCCC-----CcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 124 CCNICCDDVSPQEVTTMDCG-----HCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
.|.||++....++....+|. |.+...|+..|+..+- ..+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG------NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence 48999984444556666774 8899999999998763 236775
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=89.56 E-value=0.13 Score=48.45 Aligned_cols=33 Identities=33% Similarity=0.895 Sum_probs=27.0
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHF 155 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl 155 (516)
-.+.|.||-.++ ..++...|||.||..|...-+
T Consensus 195 IPF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 195 IPFLCGICKKDY--ESPVVTECGHSFCSLCAIRKY 227 (259)
T ss_pred Cceeehhchhhc--cchhhhhcchhHHHHHHHHHh
Confidence 357899999997 457778999999999976543
No 61
>PRK00420 hypothetical protein; Validated
Probab=88.61 E-value=1.3 Score=38.53 Aligned_cols=28 Identities=29% Similarity=0.544 Sum_probs=21.9
Q ss_pred CcccCCCCCcccee-cCCCCceeecccccccccccccc
Q 043224 281 HTKPCPKCCKPIEK-NGGCNMVRCKCGITFNWISGLEY 317 (516)
Q Consensus 281 ntK~CPkC~~~IEK-n~GCnhMtC~C~~~FCw~C~~~w 317 (516)
-...||.|+.|..+ ++| ..||-.|+...
T Consensus 22 l~~~CP~Cg~pLf~lk~g---------~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG---------EVVCPVHGKVY 50 (112)
T ss_pred ccCCCCCCCCcceecCCC---------ceECCCCCCee
Confidence 34899999999998 665 56777777754
No 62
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=88.28 E-value=0.21 Score=44.54 Aligned_cols=35 Identities=29% Similarity=0.602 Sum_probs=28.0
Q ss_pred CcccccccccccCC-CCeeecCCC------CcccHHHHHHHH
Q 043224 121 STFCCNICCDDVSP-QEVTTMDCG------HCFCNNCWTEHF 155 (516)
Q Consensus 121 ~~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~yl 155 (516)
...+|.||++.+.. +-++.+.|| |.||.+|++.|-
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 36899999999876 345566775 789999999994
No 63
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.09 E-value=0.74 Score=48.06 Aligned_cols=125 Identities=15% Similarity=0.201 Sum_probs=72.3
Q ss_pred cccCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCChH-------HHHHH----HhhhChhHHHHHhCcccccCCC
Q 043224 44 MVIPKESLLAAQMGDLLRVMDLLSLKEKHARTLLIHYRWDVE-------KVFAV----LVEEGKDKLFAQAGVTVVENDH 112 (516)
Q Consensus 44 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~-------~l~e~----~~e~~~~~~~~~~gl~~~~~~~ 112 (516)
..|++......-.+-+.+-..+||+|..-...++...+--.= .+++. |. ..+.+-.++-|..
T Consensus 255 ~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~v~v~aG~~Alp~Llk~~~v~~~~~~~W~--~~deLPveIeL~~----- 327 (394)
T KOG2817|consen 255 EILSPKLWKELTEEFTREYCALLGISVESPLSVLVNAGCIALPQLLKYKSVMELKHGEWN--TKDELPVEIELGK----- 327 (394)
T ss_pred HHhCHHHHHHHHHHHHHHHHHHcCCCccCcHHHHHHhhHHHHHHHHHHHHHHHHhccCcc--ccccCccceeccc-----
Confidence 556667777777777899999999988655444443332211 11111 21 1111111111110
Q ss_pred CCCCCCCCCcccccccccccCC-CCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHH
Q 043224 113 QVPLSQCSSTFCCNICCDDVSP-QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRC 185 (516)
Q Consensus 113 ~~~~~~~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ 185 (516)
.-...+.|.|||=-+.-+. +.+..|.|||..|++=+.... ++|. ..++||- |+.....+..++
T Consensus 328 ---~~~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS----~ng~-~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 328 ---EYHFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLS----KNGS-QSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred ---cccccceeecccchhhccCCCCCeeeeccceecHHHHHHHh----hCCC-eeeeCCC--CCcccCHHhccc
Confidence 1124467899997665443 456778999999998665543 3344 4789997 987666554443
No 64
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.89 E-value=0.29 Score=54.35 Aligned_cols=46 Identities=26% Similarity=0.662 Sum_probs=36.4
Q ss_pred CcccccccccccCCC---CeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 121 STFCCNICCDDVSPQ---EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~---~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
....|.||.++.... ....+.|+|.||..|++.|++.+ -.||. |..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--------qtCP~--CR~ 338 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--------QTCPT--CRT 338 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--------CcCCc--chh
Confidence 367899999997532 15678999999999999999972 36887 665
No 65
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=87.54 E-value=0.61 Score=38.43 Aligned_cols=50 Identities=18% Similarity=0.393 Sum_probs=33.7
Q ss_pred cccccccccccCC---------CC--eeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 122 TFCCNICCDDVSP---------QE--VTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 122 ~~~C~IC~e~~~~---------~~--~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
...|+||...+.. ++ ++.-.|+|.|...|+.+++.++-.+ -.||. |....
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~-----~~CPm--CR~~w 81 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSK-----GQCPM--CRQPW 81 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCC-----CCCCC--cCCee
Confidence 4467777666442 22 1223799999999999999986222 37998 87654
No 66
>PHA00626 hypothetical protein
Probab=87.52 E-value=0.36 Score=36.26 Aligned_cols=27 Identities=33% Similarity=0.696 Sum_probs=21.1
Q ss_pred cCCCCCc-cceecCCCCc----eee-ccccccc
Q 043224 284 PCPKCCK-PIEKNGGCNM----VRC-KCGITFN 310 (516)
Q Consensus 284 ~CPkC~~-~IEKn~GCnh----MtC-~C~~~FC 310 (516)
.||+|+. -|-|++-|+. -.| .|||.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5999998 5889887765 678 6888773
No 67
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.46 E-value=0.099 Score=53.49 Aligned_cols=49 Identities=27% Similarity=0.586 Sum_probs=35.3
Q ss_pred CCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
...+.|+||++-+. .-+....|.|.||.+|+-.-+.. |. -.||. |...+
T Consensus 41 ~~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS----GN---NECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhhc
Confidence 45789999999864 34566799999999998765543 22 36876 76533
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.34 E-value=0.38 Score=35.44 Aligned_cols=27 Identities=33% Similarity=0.621 Sum_probs=20.1
Q ss_pred ccCCCCCccceecC--CCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNG--GCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~--GCnhMtC-~C~~~F 309 (516)
+.||.|+.++.... +-++..| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46999998887543 3468999 799764
No 69
>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=87.02 E-value=0.4 Score=35.17 Aligned_cols=33 Identities=39% Similarity=0.908 Sum_probs=23.5
Q ss_pred eeccCCcc-cccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 236 VECACGFQ-FCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 236 v~C~Cg~~-fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
+.=+|||. ||..|... |+. +.+.||-|+.+|++
T Consensus 16 ~~~pCgH~~~C~~C~~~-------------------------~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 16 VLLPCGHLCFCEECAER-------------------------LLK-RKKKCPICRQPIES 49 (50)
T ss_dssp EEETTCEEEEEHHHHHH-------------------------HHH-TTSBBTTTTBB-SE
T ss_pred EEeCCCChHHHHHHhHH-------------------------hcc-cCCCCCcCChhhcC
Confidence 34479999 99999521 222 56899999999975
No 70
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.76 E-value=0.45 Score=47.05 Aligned_cols=53 Identities=23% Similarity=0.535 Sum_probs=41.0
Q ss_pred CcccccccccccCCC--------CeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 121 STFCCNICCDDVSPQ--------EVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
+...|.||...+..+ +++.|+|+|.|...|++.|...- ..-.||- |+..++..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG------KkqtCPY--CKekVdl~ 283 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG------KKQTCPY--CKEKVDLK 283 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec------CCCCCch--HHHHhhHh
Confidence 456899999876432 57889999999999999997542 2357997 99877654
No 71
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.35 E-value=0.68 Score=47.70 Aligned_cols=48 Identities=21% Similarity=0.528 Sum_probs=36.0
Q ss_pred CCcccccccccccCCCCeeecCCCCc-ccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHC-FCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.+..+|-||+.+. .++..|+|.|. .|.+|-+..- +. .=+||. |...|.
T Consensus 288 ~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr---~q-----~n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR---YQ-----TNNCPI--CRQPIE 336 (349)
T ss_pred cCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH---Hh-----hcCCCc--cccchH
Confidence 3467999999984 67888999998 8999977643 11 126998 987654
No 72
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.03 E-value=0.39 Score=51.97 Aligned_cols=37 Identities=30% Similarity=0.522 Sum_probs=32.9
Q ss_pred cccCC--CCCcccee-cCCCCceeeccccccccccccccc
Q 043224 282 TKPCP--KCCKPIEK-NGGCNMVRCKCGITFNWISGLEYS 318 (516)
Q Consensus 282 tK~CP--kC~~~IEK-n~GCnhMtC~C~~~FCw~C~~~w~ 318 (516)
.|-|| .|+..|.- .+.+.-+.|.|++.|||.|+.+|.
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH 197 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence 56676 59998887 889999999999999999999987
No 73
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.91 E-value=0.47 Score=53.52 Aligned_cols=23 Identities=30% Similarity=0.593 Sum_probs=15.0
Q ss_pred ccCCCCCccceecCCCCceeeccccccccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRCKCGITFNWISGLE 316 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~ 316 (516)
+.||+|+..+... ..||-.||.+
T Consensus 28 ~~Cp~CG~~~~~~-----------~~fC~~CG~~ 50 (645)
T PRK14559 28 KPCPQCGTEVPVD-----------EAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCCCCcc-----------cccccccCCc
Confidence 4566666665543 3488888877
No 74
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.79 E-value=0.38 Score=29.67 Aligned_cols=13 Identities=38% Similarity=0.928 Sum_probs=9.1
Q ss_pred cCCCCCccceecC
Q 043224 284 PCPKCCKPIEKNG 296 (516)
Q Consensus 284 ~CPkC~~~IEKn~ 296 (516)
.||+|+..|+.+.
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 3788888887543
No 75
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.73 E-value=0.35 Score=35.81 Aligned_cols=29 Identities=31% Similarity=0.663 Sum_probs=21.2
Q ss_pred hcCcccCCCCCc-cceecCCCCceee-cccccc
Q 043224 279 SSHTKPCPKCCK-PIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 279 ~~ntK~CPkC~~-~IEKn~GCnhMtC-~C~~~F 309 (516)
..+.+.||+|+. ...... +.++| +||+.+
T Consensus 17 ~~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 17 KRKNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred EEccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 345679999998 443333 68999 899875
No 76
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=83.58 E-value=0.68 Score=32.99 Aligned_cols=30 Identities=30% Similarity=0.592 Sum_probs=23.4
Q ss_pred HHHhcCcccCCCCCccceecCCCCceeec---ccccc
Q 043224 276 NWISSHTKPCPKCCKPIEKNGGCNMVRCK---CGITF 309 (516)
Q Consensus 276 ~wi~~ntK~CPkC~~~IEKn~GCnhMtC~---C~~~F 309 (516)
.|+....|.||+|++.- |+--+.|+ |++.|
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchhh
Confidence 46778899999999864 77778883 77665
No 77
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=83.01 E-value=4.1 Score=27.82 Aligned_cols=34 Identities=18% Similarity=0.275 Sum_probs=28.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHH
Q 043224 56 MGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAV 90 (516)
Q Consensus 56 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~ 90 (516)
.+.|..+.++ |.+...|+.-|+..+||.+..++.
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 3567888888 999999999999999999987753
No 78
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.88 E-value=0.91 Score=46.54 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=36.9
Q ss_pred CCCCcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCH
Q 043224 118 QCSSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDE 180 (516)
Q Consensus 118 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~ 180 (516)
+.++...|+||+-. + ...+..+|+|.-|.+|+.+|+... -+|-. |+..+..
T Consensus 418 p~sEd~lCpICyA~-p-i~Avf~PC~H~SC~~CI~qHlmN~--------k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG-P-INAVFAPCSHRSCYGCITQHLMNC--------KRCFF--CKTTVID 468 (489)
T ss_pred CCcccccCcceecc-c-chhhccCCCCchHHHHHHHHHhcC--------CeeeE--ecceeee
Confidence 34567789999975 1 233446999999999999998642 36766 8876554
No 79
>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=82.68 E-value=1.3 Score=29.49 Aligned_cols=28 Identities=29% Similarity=0.686 Sum_probs=18.1
Q ss_pred CcccCCCCCccceecCCCCceee-ccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
+.+-||+|+.+.....|=--|.| .|+++
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 46889999999998887677899 78875
No 80
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.30 E-value=0.69 Score=29.29 Aligned_cols=14 Identities=29% Similarity=0.750 Sum_probs=9.8
Q ss_pred cccCCCCCccceec
Q 043224 282 TKPCPKCCKPIEKN 295 (516)
Q Consensus 282 tK~CPkC~~~IEKn 295 (516)
++.||+|+..|...
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 2 EMFCPNCGAEIDPD 15 (26)
T ss_pred cCCCcccCCcCCcc
Confidence 36788888876654
No 81
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.03 E-value=0.73 Score=49.21 Aligned_cols=51 Identities=20% Similarity=0.432 Sum_probs=37.1
Q ss_pred CCcccccccccccCCCC---------------eeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 120 SSTFCCNICCDDVSPQE---------------VTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~---------------~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.....|.||+.+++.-. ....+|.|.|...|+.+|+... .+.||. |..+++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y-------kl~CPv--CR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY-------KLICPV--CRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh-------cccCCc--cCCCCC
Confidence 45678999999865311 1123899999999999999742 477988 766655
No 82
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=82.00 E-value=0.42 Score=46.72 Aligned_cols=47 Identities=23% Similarity=0.458 Sum_probs=34.4
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCH
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDE 180 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~ 180 (516)
.+.|..|+---+...++.++|+|.||..|.+.- .+-.||. |+..|-.
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir~ 49 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSIRI 49 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccC----------Ccccccc--ccceeee
Confidence 357999988766566667799999999997642 1227987 9886543
No 83
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=81.08 E-value=0.68 Score=52.49 Aligned_cols=48 Identities=33% Similarity=0.757 Sum_probs=37.0
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
..|.||.+ .+..+...|+|.||.+||..++...-. ..||. |...+...
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKEK 502 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC------CCCcH--HHHHHHHH
Confidence 89999999 367778899999999999999876422 26766 76655443
No 84
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=79.91 E-value=6.3 Score=27.72 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=33.1
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHhCCChHHHHHHHhh
Q 043224 56 MGDLLRVMDLL-SLKEKHARTLLIHYRWDVEKVFAVLVE 93 (516)
Q Consensus 56 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~e~~~e 93 (516)
.+.|..+.+++ +++++.....|..+++|.+..++.+.+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 35788999999 899999999999999999999988773
No 85
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=79.91 E-value=0.37 Score=48.18 Aligned_cols=35 Identities=29% Similarity=0.594 Sum_probs=24.8
Q ss_pred HhcCcccCCCCCccceecCCCCceee-ccccccccccccccc
Q 043224 278 ISSHTKPCPKCCKPIEKNGGCNMVRC-KCGITFNWISGLEYS 318 (516)
Q Consensus 278 i~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~w~ 318 (516)
+..++.+|-=|--..+ |-+| .|||-|||-|...|-
T Consensus 235 i~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHH
Confidence 3345566655554433 4577 699999999999995
No 86
>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=79.67 E-value=0.96 Score=31.12 Aligned_cols=26 Identities=38% Similarity=0.930 Sum_probs=17.3
Q ss_pred ccCCCCCccceec------CCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKN------GGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn------~GCnhMtC-~C~~~F 309 (516)
-.||+|+..+.-. .| ..++| +||+.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 3689998855432 22 37888 788766
No 87
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.53 E-value=0.7 Score=34.60 Aligned_cols=45 Identities=22% Similarity=0.452 Sum_probs=31.0
Q ss_pred ccccccccccCCCCeeecCCCCc-ccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHC-FCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
-+|.||++.- .+.+.--|||. .|.+|-.+..+. -. -.||. |..+|
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~--~~-----g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA--LH-----GCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc--cC-----CcCcc--hhhHH
Confidence 6899999962 33344489998 899998776654 12 25776 77654
No 88
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.63 E-value=2 Score=29.66 Aligned_cols=28 Identities=32% Similarity=0.748 Sum_probs=21.6
Q ss_pred ccCCCCCCCCceEeecC----CCcceeecc-CCccc
Q 043224 214 KWCPSVPHCGNAIQVEA----DELCEVECA-CGFQF 244 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-Cg~~f 244 (516)
.-|| +|+....+++ .....|.|+ |++.|
T Consensus 3 i~CP---~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP---NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC---CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4688 7999998776 234579998 99876
No 89
>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=77.85 E-value=1.3 Score=30.29 Aligned_cols=28 Identities=36% Similarity=1.052 Sum_probs=17.7
Q ss_pred cccCCCCCCCCceEeecCCCcceeecc-CCcc
Q 043224 213 VKWCPSVPHCGNAIQVEADELCEVECA-CGFQ 243 (516)
Q Consensus 213 ~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 243 (516)
+++|| .|++.+.+..+....+.|. |++.
T Consensus 1 m~FCp---~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 1 MRFCP---ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp --BET---TTTSBEEEEEETTTTEEESSSS-E
T ss_pred CeeCC---CCCccceEcCCCccCcCCCCCCCc
Confidence 36898 7999999776444334675 7654
No 90
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.73 E-value=2.2 Score=29.30 Aligned_cols=28 Identities=29% Similarity=0.786 Sum_probs=21.2
Q ss_pred ccCCCCCCCCceEeecC----CCcceeecc-CCccc
Q 043224 214 KWCPSVPHCGNAIQVEA----DELCEVECA-CGFQF 244 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-Cg~~f 244 (516)
.-|| +|+....+++ .....|.|+ ||+.|
T Consensus 3 i~Cp---~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP---NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC---CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 3588 7999988775 344579997 99876
No 91
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.58 E-value=1.7 Score=31.38 Aligned_cols=28 Identities=29% Similarity=0.634 Sum_probs=19.6
Q ss_pred ccCCCCCccceecCCCCceee-ccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITFN 310 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~FC 310 (516)
-.||+|+..++-+.+=..++| .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 368999988876544337888 6887653
No 92
>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=76.79 E-value=0.72 Score=44.86 Aligned_cols=49 Identities=20% Similarity=0.498 Sum_probs=35.7
Q ss_pred ccccccccccCCC-Ceee---cCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 123 FCCNICCDDVSPQ-EVTT---MDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 123 ~~C~IC~e~~~~~-~~~~---l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
..||||-.+.-.+ ++.. ..|-|..|-+|...-++. .+-.||-++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence 4699998873222 2322 259999999999887764 35789999998654
No 93
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=76.65 E-value=0.86 Score=36.51 Aligned_cols=48 Identities=23% Similarity=0.515 Sum_probs=34.9
Q ss_pred ccccccccccCC---------CCeeec--CCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 123 FCCNICCDDVSP---------QEVTTM--DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 123 ~~C~IC~e~~~~---------~~~~~l--~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
.+|.||-..|.. ++...+ .|.|.|-.-|+.+++.+.-++|+ ||. |...
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~-----CPm--cRq~ 79 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQ-----CPM--CRQT 79 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccccc-----CCc--chhe
Confidence 378888877543 222222 68999999999999998877765 887 7654
No 94
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.22 E-value=2 Score=48.62 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=11.1
Q ss_pred cCcccCCCCCcccee
Q 043224 280 SHTKPCPKCCKPIEK 294 (516)
Q Consensus 280 ~ntK~CPkC~~~IEK 294 (516)
.+.|.||+|+.+..+
T Consensus 39 ~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 39 VDEAHCPNCGAETGT 53 (645)
T ss_pred cccccccccCCcccc
Confidence 345889999887654
No 95
>PLN03086 PRLI-interacting factor K; Provisional
Probab=75.50 E-value=4.1 Score=45.15 Aligned_cols=57 Identities=28% Similarity=0.605 Sum_probs=36.5
Q ss_pred ccccccccccccccCHHHHHHhhCCCChHHHHHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcceeecc-CCcc
Q 043224 165 RRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECA-CGFQ 243 (516)
Q Consensus 165 ~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 243 (516)
..+.|+. |...++...+...+. + -....+-||+ .+|+..+....... .+.|+ ||..
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~-----------------~--C~r~~V~Cp~-~~Cg~v~~r~el~~-H~~C~~Cgk~ 462 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEA-----------------Y--CSRHNVVCPH-DGCGIVLRVEEAKN-HVHCEKCGQA 462 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHh-----------------h--CCCcceeCCc-ccccceeecccccc-CccCCCCCCc
Confidence 3578997 998888665543322 1 1234456994 68999997665332 36787 8776
Q ss_pred c
Q 043224 244 F 244 (516)
Q Consensus 244 f 244 (516)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 6
No 96
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=75.36 E-value=1.9 Score=28.42 Aligned_cols=26 Identities=27% Similarity=0.836 Sum_probs=13.5
Q ss_pred ccCCCCCccceecCCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
-+||+|+....-.+| ..|.| .|+++|
T Consensus 3 p~Cp~C~se~~y~D~-~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDG-ELLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-S-SSEEETTTTEEE
T ss_pred CCCCCCCCcceeccC-CEEeCCcccccC
Confidence 379999988877776 45889 799876
No 97
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.65 E-value=1.3 Score=41.38 Aligned_cols=30 Identities=37% Similarity=0.840 Sum_probs=22.1
Q ss_pred cCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 239 ACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 239 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
.|||.||..|-+. ...++..||-|++.|-+
T Consensus 150 kCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 150 KCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccchhHHHHHHHH--------------------------HHHhCCCCCCcccccch
Confidence 5999999999421 13467899999986643
No 98
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=74.50 E-value=2.4 Score=48.26 Aligned_cols=50 Identities=26% Similarity=0.498 Sum_probs=39.1
Q ss_pred CcccccccccccCCC-Ceeec-CCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 121 STFCCNICCDDVSPQ-EVTTM-DCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
..++|.||++.+... .+.+. .|-|.|...|++.|....-+.|. ...+||.
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~ 241 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA 241 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc
Confidence 578999999998653 45554 79999999999999998545554 5678886
No 99
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=73.77 E-value=1.5 Score=45.70 Aligned_cols=47 Identities=28% Similarity=0.726 Sum_probs=33.7
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCN 175 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~ 175 (516)
.-..|.||-+.- .++..-+|||..|..|+..|-.+. +|+ .||...|.
T Consensus 368 TFeLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~sd--~gq----~CPFCRcE 414 (563)
T KOG1785|consen 368 TFELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDSD--EGQ----TCPFCRCE 414 (563)
T ss_pred hHHHHHHhhccC--CCcccccccchHHHHHHHhhcccC--CCC----CCCceeeE
Confidence 345799999873 455556999999999999985442 244 68884443
No 100
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 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. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=73.73 E-value=1.4 Score=39.96 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=14.6
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHh
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIV 157 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~ 157 (516)
...+|||=-+.- +++.++ .-|=+.|++.|+.-
T Consensus 125 eEg~CPIVIeKN--GElLS~---~DFD~~gl~~HLdY 156 (167)
T PF05320_consen 125 EEGTCPIVIEKN--GELLSI---NDFDKKGLKYHLDY 156 (167)
T ss_pred hcCCCcEEEeeC--CeEccc---cccCHHHHHHHHHH
Confidence 345676654431 222222 23455566655543
No 101
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=73.67 E-value=1.1 Score=42.71 Aligned_cols=32 Identities=22% Similarity=0.477 Sum_probs=23.8
Q ss_pred CcccCCCCCccceecCCCCceeecccccccccccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRCKCGITFNWISGLEY 317 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~w 317 (516)
..-.||-|.-.+..- +.=.|||.|||.|+..|
T Consensus 17 ~~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 17 GDFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKW 48 (193)
T ss_pred CccCCccCCCcCCCc-----EEcCCCchhHHHHHHHH
Confidence 346799998765321 23379999999999988
No 102
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=72.31 E-value=1.3 Score=49.90 Aligned_cols=31 Identities=29% Similarity=0.810 Sum_probs=22.6
Q ss_pred cCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 239 ACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 239 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
.|||.||+.|-.. .+....+.||+|+.+.--
T Consensus 660 kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-------------------------RYETRQRKCPKCNAAFGA 690 (698)
T ss_pred hcchHHHHHHHHH-------------------------HHHHhcCCCCCCCCCCCc
Confidence 4999999999411 233456999999987643
No 103
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.66 E-value=1.1 Score=43.70 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=13.5
Q ss_pred cccccccccccccc
Q 043224 305 CGITFNWISGLEYS 318 (516)
Q Consensus 305 C~~~FCw~C~~~w~ 318 (516)
|||-|||=|+-.|.
T Consensus 65 CGHLFCWpClyqWl 78 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWL 78 (230)
T ss_pred cccceehHHHHHHH
Confidence 99999999999996
No 104
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=71.43 E-value=2.7 Score=44.66 Aligned_cols=121 Identities=16% Similarity=0.348 Sum_probs=69.9
Q ss_pred cccCHHHHHHHHHHHHHHHHHHcCCCH--HHHHHHHHHhCCChHHH--HHHHhhh-----ChhHHHHHhCcc---cccCC
Q 043224 44 MVIPKESLLAAQMGDLLRVMDLLSLKE--KHARTLLIHYRWDVEKV--FAVLVEE-----GKDKLFAQAGVT---VVEND 111 (516)
Q Consensus 44 ~vlt~~~i~~~~~~~i~~v~~~l~i~~--~~a~~LL~~~~W~~~~l--~e~~~e~-----~~~~~~~~~gl~---~~~~~ 111 (516)
.-+|.-||..-+-.-+..|++|.-|-. ..-..+|++|+=..+.. .+.|.-. +++ +..-+-+. .....
T Consensus 84 ~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Chll~V~~ve~~~s~ 162 (493)
T KOG0804|consen 84 AYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCHLLYVDRVEVTESE 162 (493)
T ss_pred ccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-ceeEEEEEEEEEEecc
Confidence 457899999999988888988876642 23345666676554432 2222100 111 11111111 11111
Q ss_pred CCC--CCCCCCCcccccccccccCCCC--eeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 112 HQV--PLSQCSSTFCCNICCDDVSPQE--VTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 112 ~~~--~~~~~~~~~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
+.+ +.....+..+|+||++-+..+- +.+..|.|.|.-.|+..|- ...||. |...
T Consensus 163 d~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~----------~~scpv--cR~~ 220 (493)
T KOG0804|consen 163 DGASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW----------DSSCPV--CRYC 220 (493)
T ss_pred cCCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc----------cCcChh--hhhh
Confidence 111 1222335569999999876432 3556899999999998873 467987 7653
No 105
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.23 E-value=2.5 Score=44.09 Aligned_cols=51 Identities=27% Similarity=0.621 Sum_probs=35.0
Q ss_pred cccccccccccCCC-Ceeec-CCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 122 TFCCNICCDDVSPQ-EVTTM-DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 122 ~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.-.|.||-+-+|.+ ++... .|||.|...|+.+|+...-.. -.||. |...++
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ik~~ 56 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQIKLQ 56 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eeeccc
Confidence 45799996655543 34455 499999999999999875332 35776 664333
No 106
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.12 E-value=3 Score=41.87 Aligned_cols=29 Identities=34% Similarity=0.939 Sum_probs=23.9
Q ss_pred cccccccccccCCCCeeecCCCCc-ccHHHHH
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHC-FCNNCWT 152 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~ 152 (516)
...|.||++. +.+.+.|.|||. -|..|=+
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhcc
Confidence 5689999996 367899999997 6888843
No 107
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=70.31 E-value=15 Score=25.81 Aligned_cols=37 Identities=22% Similarity=0.259 Sum_probs=33.3
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHhCCChHHHHHHHh
Q 043224 56 MGDLLRVMDLL-SLKEKHARTLLIHYRWDVEKVFAVLV 92 (516)
Q Consensus 56 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~e~~~ 92 (516)
.+.+..+.+++ +++...++..|+.+++|.+..++.+.
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45788899999 89999999999999999999998876
No 108
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=69.93 E-value=15 Score=24.82 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=28.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHh
Q 043224 57 GDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLV 92 (516)
Q Consensus 57 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~ 92 (516)
+.|+.+.+ +|.+...++..|...+||.++.++.++
T Consensus 3 ~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 34555555 599999999999999999999887654
No 109
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=69.73 E-value=13 Score=25.03 Aligned_cols=33 Identities=15% Similarity=0.224 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHH
Q 043224 58 DLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVL 91 (516)
Q Consensus 58 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~ 91 (516)
.|..+.++ |.+...|+..|+..+||.++.++-+
T Consensus 4 ~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 44555443 9999999999999999999887643
No 110
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.45 E-value=2.6 Score=36.48 Aligned_cols=26 Identities=31% Similarity=0.841 Sum_probs=18.9
Q ss_pred ccCCCCCccceecCCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
+.||+|++..---.- +.++| +||..|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 679999987764222 77889 788765
No 111
>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=68.64 E-value=5 Score=27.48 Aligned_cols=27 Identities=30% Similarity=0.807 Sum_probs=19.4
Q ss_pred cCCCCCCCCceEeecCC----Ccceeecc-CCccc
Q 043224 215 WCPSVPHCGNAIQVEAD----ELCEVECA-CGFQF 244 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~----~~~~v~C~-Cg~~f 244 (516)
-|| +|+..+.+..+ ....|.|+ ||+.|
T Consensus 4 ~CP---~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCP---NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECC---CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 588 79999887642 23368997 88765
No 112
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=68.30 E-value=2.1 Score=36.18 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=26.4
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWT 152 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 152 (516)
+...|+||...+..+.+...+|||.|+..|.+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 45679999999877666667999999999975
No 113
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=68.22 E-value=3 Score=37.20 Aligned_cols=25 Identities=36% Similarity=0.781 Sum_probs=20.1
Q ss_pred cccCCCCCccceecCCCCceeecccccccccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRCKCGITFNWISGL 315 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~ 315 (516)
.+.||.|+.|..+-.| .-||-+|+.
T Consensus 28 ~~hCp~Cg~PLF~KdG---------~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDG---------EVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCC---------eEECCCCCc
Confidence 4799999999988666 677777774
No 114
>PF04641 Rtf2: Rtf2 RING-finger
Probab=68.21 E-value=5 Score=40.24 Aligned_cols=60 Identities=20% Similarity=0.398 Sum_probs=44.2
Q ss_pred CCCcccccccccccCCC-Ceeec-CCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCC
Q 043224 119 CSSTFCCNICCDDVSPQ-EVTTM-DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSA 189 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~ 189 (516)
....+.|||...++... .++.+ +|||.|+..+++..= .+ -.||. |+..+...+|-.|.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNPP 171 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecCC
Confidence 35678999999998543 34444 999999999999871 11 24988 9998887776666553
No 115
>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=67.99 E-value=1.4 Score=31.22 Aligned_cols=33 Identities=27% Similarity=0.587 Sum_probs=23.3
Q ss_pred cCCCCCccceecCCCCceeeccccccccccccccc
Q 043224 284 PCPKCCKPIEKNGGCNMVRCKCGITFNWISGLEYS 318 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~w~ 318 (516)
.||-|...++... .-+...|||.||+.|+..|-
T Consensus 2 ~C~IC~~~~~~~~--~~~~l~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 2 ECPICLEEFEDGE--KVVKLPCGHVFHRSCIKEWL 34 (44)
T ss_dssp CETTTTCBHHTTS--CEEEETTSEEEEHHHHHHHH
T ss_pred CCcCCChhhcCCC--eEEEccCCCeeCHHHHHHHH
Confidence 4777777776522 22344799999999999883
No 116
>PHA03096 p28-like protein; Provisional
Probab=67.96 E-value=3.2 Score=42.15 Aligned_cols=38 Identities=16% Similarity=0.361 Sum_probs=29.6
Q ss_pred ccccccccccCC----CCeee-c-CCCCcccHHHHHHHHHhhhh
Q 043224 123 FCCNICCDDVSP----QEVTT-M-DCGHCFCNNCWTEHFIVKIN 160 (516)
Q Consensus 123 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~C~~~yl~~~I~ 160 (516)
.+|.||++..-. +..++ | .|.|.||..|.+.|..++..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 789999998542 22333 3 89999999999999998763
No 117
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=67.75 E-value=3.3 Score=30.42 Aligned_cols=27 Identities=26% Similarity=0.641 Sum_probs=16.6
Q ss_pred CcccCCCCCccceecCCCCceee-cccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~ 307 (516)
..+.||+|+--+.--.-=+...| +||+
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccc
Confidence 45889999953332111136788 7886
No 118
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.62 E-value=1.9 Score=43.41 Aligned_cols=44 Identities=30% Similarity=0.681 Sum_probs=33.3
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccc
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVV 177 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~ 177 (516)
.+-|.||-..+ ..++...|+|.||..|....+.. .-+|+. |...
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk--------~~~c~v--C~~~ 284 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK--------GEKCYV--CSQQ 284 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc--------CCccee--cccc
Confidence 46799999987 56777899999999998766543 236766 7653
No 119
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=66.49 E-value=3.8 Score=31.99 Aligned_cols=28 Identities=25% Similarity=0.788 Sum_probs=21.9
Q ss_pred CcccCCCCCccceecCCCCceee-ccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
.++.||.|+....++..=..++| .||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 57999999999999544457888 58865
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.18 E-value=4.6 Score=47.12 Aligned_cols=33 Identities=27% Similarity=0.631 Sum_probs=22.0
Q ss_pred cCCCcccCCCCCCCCceEeecCCCcceeecc-CCc-----ccccccccc
Q 043224 209 DNRRVKWCPSVPHCGNAIQVEADELCEVECA-CGF-----QFCFSCSSV 251 (516)
Q Consensus 209 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~-----~fC~~C~~~ 251 (516)
.....+.|| .|+... ....|+ ||. .||..|+..
T Consensus 622 VEVg~RfCp---sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 622 VEIGRRKCP---SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ecccCccCC---CCCCcC-------CcccCCCCCCCCCcceeCccccCc
Confidence 334567898 698773 236787 885 478888643
No 121
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=66.08 E-value=3.3 Score=44.04 Aligned_cols=37 Identities=32% Similarity=0.749 Sum_probs=29.1
Q ss_pred CCcccccccccccCCCCeeecCCCCcccHHHHHHHHHh
Q 043224 120 SSTFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIV 157 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~ 157 (516)
..+..|++|...+. +.+.+..|||.||..|+..++..
T Consensus 19 ~~~l~C~~C~~vl~-~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 19 DENLLCPICMSVLR-DPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred cccccCcccccccc-CCCCCCCCCCcccccccchhhcc
Confidence 45688999998864 23333699999999999998876
No 122
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=65.84 E-value=3.8 Score=41.37 Aligned_cols=39 Identities=18% Similarity=0.343 Sum_probs=31.1
Q ss_pred CcccccccccccCCCC-eeecCCCCcccHHHHHHHHHhhh
Q 043224 121 STFCCNICCDDVSPQE-VTTMDCGHCFCNNCWTEHFIVKI 159 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yl~~~I 159 (516)
....|.||+--|..++ +....|.|+|...|+..||+...
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 3567888887776665 55679999999999999998754
No 123
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.78 E-value=1.6 Score=43.33 Aligned_cols=34 Identities=26% Similarity=0.457 Sum_probs=25.2
Q ss_pred ccCCCCCccceecCCCCceee-ccccccccccccc-ccc-ccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITFNWISGLE-YSN-GYI 322 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~-w~C-~y~ 322 (516)
..|+=|--.++. -.| .|||-|||.|+-. |.+ +|.
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~~k~~ 252 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTKKKYE 252 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHHHHHhhccc
Confidence 567777766654 346 5999999999988 985 554
No 124
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=65.76 E-value=5.6 Score=29.11 Aligned_cols=26 Identities=35% Similarity=0.986 Sum_probs=17.7
Q ss_pred ccCCCCCCCCceEeecCCCc-ceeecc-CCc
Q 043224 214 KWCPSVPHCGNAIQVEADEL-CEVECA-CGF 242 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~ 242 (516)
++|| .||..+....... ....|+ ||+
T Consensus 1 ~FCp---~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCP---KCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCC---CCCCccccccCCCCCEEECCcCCC
Confidence 3688 7999888765332 356776 775
No 125
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=65.32 E-value=4.6 Score=30.07 Aligned_cols=28 Identities=29% Similarity=0.513 Sum_probs=17.7
Q ss_pred ccCCCCCccce------ecCCCCcee-e-ccccccc
Q 043224 283 KPCPKCCKPIE------KNGGCNMVR-C-KCGITFN 310 (516)
Q Consensus 283 K~CPkC~~~IE------Kn~GCnhMt-C-~C~~~FC 310 (516)
|+||.|+..-+ .+.+..++. | .||+...
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 89999986544 244555554 6 5666543
No 126
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=64.61 E-value=12 Score=33.09 Aligned_cols=111 Identities=17% Similarity=0.208 Sum_probs=51.2
Q ss_pred cCHHHHHHhhCC-CChHHHHHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecCCCcceeeccCCccccccccccc--CC
Q 043224 178 CDEAKIRCLVSA-RDSNIADKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVA--HS 254 (516)
Q Consensus 178 i~~~~i~~ll~~-~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~--H~ 254 (516)
++....+++++. +|-+.+.+|...+....--+.+-+ =| -=...+.........+.|.||++||-- .+.| |.
T Consensus 17 l~w~qt~r~msa~kdhdrf~kylavlqdrv~~~dpil--lp---vg~hlfi~qs~~~rv~rcecghsf~d~-r~nwkl~a 90 (165)
T COG4647 17 LPWPQTRRMMSAYKDHDRFFKYLAVLQDRVDWDDPIL--LP---VGDHLFICQSAQKRVIRCECGHSFGDY-RENWKLHA 90 (165)
T ss_pred CCcHHHHHHHhccccHHHHHHHHHHHHhhcccCCCee--ee---cCCcEEEEecccccEEEEeccccccCh-hhCceeee
Confidence 455566777764 233445555444333211122222 12 122233333333346899999999853 2223 22
Q ss_pred CCCchhH-HHHhHHh-HHHHHHHHHHhcCcccCCCCCcccee
Q 043224 255 PCSCLMW-ELWSKKF-EVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 255 p~~C~~~-~~w~~k~-~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
...-... .+..+.. ..+...-+|+...---||.|+...+-
T Consensus 91 ~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~ev 132 (165)
T COG4647 91 NIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHEV 132 (165)
T ss_pred EEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceeee
Confidence 2111100 0000000 01122346777667789999987764
No 127
>PF14369 zf-RING_3: zinc-finger
Probab=64.58 E-value=5.9 Score=27.03 Aligned_cols=28 Identities=25% Similarity=0.791 Sum_probs=19.7
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQF 244 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~f 244 (516)
-||- .|...|.+.......+.|| |+..|
T Consensus 3 ywCh---~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH---QCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCc---cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 4897 7999999765433446687 87655
No 128
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.05 E-value=4.5 Score=39.69 Aligned_cols=55 Identities=11% Similarity=0.232 Sum_probs=39.1
Q ss_pred CcccccccccccCCCC-eeec-CCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHH
Q 043224 121 STFCCNICCDDVSPQE-VTTM-DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRC 185 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ 185 (516)
..+.|+||-+.+...- ...| +|||.||.+|....|.. ...||. |...+.+.+|-.
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdiI~ 276 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDIIG 276 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccceEe
Confidence 5678999999986432 2334 89999999999888753 345666 777666655543
No 129
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=63.95 E-value=5.1 Score=42.62 Aligned_cols=17 Identities=29% Similarity=0.471 Sum_probs=9.2
Q ss_pred CCCCCCCcccccccccc
Q 043224 115 PLSQCSSTFCCNICCDD 131 (516)
Q Consensus 115 ~~~~~~~~~~C~IC~e~ 131 (516)
|..+-+..|.|.-==++
T Consensus 187 P~LPDSTDFVCGTLDED 203 (458)
T PF10446_consen 187 PELPDSTDFVCGTLDED 203 (458)
T ss_pred CCCCCcccccCCCcCCc
Confidence 34455666777653333
No 130
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.29 E-value=5.3 Score=39.98 Aligned_cols=63 Identities=24% Similarity=0.620 Sum_probs=44.1
Q ss_pred CcccccccccccCCCCeeecCC----CCcccHHHHHHHHHhhhhcCCcccccccc-ccccc---ccCHH----HHHHhhC
Q 043224 121 STFCCNICCDDVSPQEVTTMDC----GHCFCNNCWTEHFIVKINDGQSRRIKCMA-LKCNV---VCDEA----KIRCLVS 188 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~C----gH~fC~~C~~~yl~~~I~~g~~~~i~CP~-~~C~~---~i~~~----~i~~ll~ 188 (516)
....|.+|-+.+. ++....| .|.||.-|-++.|+.+-..| .+.||. .+|.. .|+.. +|..+|.
T Consensus 267 apLcCTLC~ERLE--DTHFVQCPSVp~HKFCFPCSResIK~Qg~sg---evYCPSGdkCPLvgS~vPWAFMQGEIatILa 341 (352)
T KOG3579|consen 267 APLCCTLCHERLE--DTHFVQCPSVPSHKFCFPCSRESIKQQGASG---EVYCPSGDKCPLVGSNVPWAFMQGEIATILA 341 (352)
T ss_pred Cceeehhhhhhhc--cCceeecCCCcccceecccCHHHHHhhcCCC---ceeCCCCCcCcccCCcccHHHhhhhHHHHhc
Confidence 4578999999874 4444555 69999999999999875555 478886 45664 44444 4455554
No 131
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=63.12 E-value=13 Score=38.18 Aligned_cols=77 Identities=25% Similarity=0.540 Sum_probs=48.9
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFER 200 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~ 200 (516)
.-.+||||++.+.. .++..+=||..|..|-.. ..-+||. |...++ .|+.+.- +
T Consensus 47 ~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g--~~R~~am-----------E 99 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG--NIRCRAM-----------E 99 (299)
T ss_pred hhccCchhhccCcc-cceecCCCcEehhhhhhh-----------hcccCCc--cccccc--cHHHHHH-----------H
Confidence 56799999998742 333444489999999762 3468998 998888 3454432 1
Q ss_pred HHHHHhhhcCCCcccCCCC-CCCCceEeecC
Q 043224 201 FLLESYIDDNRRVKWCPSV-PHCGNAIQVEA 230 (516)
Q Consensus 201 ~~~~~~v~~~~~~~~CP~~-p~C~~~i~~~~ 230 (516)
.++++ .+..||++ -+|...+....
T Consensus 100 kV~e~------~~vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 100 KVAEA------VLVPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred HHHHh------ceecccccccCCceeecccc
Confidence 22222 23457742 47877776544
No 132
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=62.96 E-value=2 Score=43.90 Aligned_cols=28 Identities=29% Similarity=0.687 Sum_probs=22.7
Q ss_pred cccCCCCCcccee-cCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEK-NGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 309 (516)
+..||+|+..|-+ .-.=|.+.| +|+|+|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 5899999998875 445577899 899988
No 133
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=62.84 E-value=3 Score=42.49 Aligned_cols=84 Identities=21% Similarity=0.627 Sum_probs=46.6
Q ss_pred CCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHHHHHH-HHHhhh----cCCCcccCC
Q 043224 143 GHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFL-LESYID----DNRRVKWCP 217 (516)
Q Consensus 143 gH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~-~~~~v~----~~~~~~~CP 217 (516)
|-+||..|-..+.. .++.||. |+..+- +. +.+...|..+. ++.|.+ .+.....|-
T Consensus 275 ~Gy~CP~CkakvCs--------LP~eCpi--C~ltLV--------ss--~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf 334 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCS--------LPIECPI--CSLTLV--------SS--PHLARSYHHLFPLKPFVEIPETEYNGSRFCF 334 (378)
T ss_pred CceeCCcccCeeec--------CCccCCc--cceeEe--------cc--hHHHHHHHhhcCCcchhhccccccCCCccee
Confidence 34577777555543 5788987 776432 11 33444444332 223333 223444575
Q ss_pred CCCCCCceEeecCCCcceeecc-CCcccccccccccC
Q 043224 218 SVPHCGNAIQVEADELCEVECA-CGFQFCFSCSSVAH 253 (516)
Q Consensus 218 ~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H 253 (516)
.|+.-. .....+.|. |...||..|..-.|
T Consensus 335 ---~C~~~~----~~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 335 ---ACQGEL----LSSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred ---eecccc----CCCCcEEchhccceeeccchHHHH
Confidence 562221 223458996 99999999975544
No 134
>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=62.58 E-value=3.8 Score=30.50 Aligned_cols=35 Identities=20% Similarity=0.644 Sum_probs=17.1
Q ss_pred CCCceEeecCC---Ccceeecc-CCcccccccccccCCC
Q 043224 221 HCGNAIQVEAD---ELCEVECA-CGFQFCFSCSSVAHSP 255 (516)
Q Consensus 221 ~C~~~i~~~~~---~~~~v~C~-Cg~~fC~~C~~~~H~p 255 (516)
+|...+..... ......|+ |+..||+.|-.=.|.-
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 46655553321 23568998 9999999997666643
No 135
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.07 E-value=5.4 Score=32.91 Aligned_cols=28 Identities=32% Similarity=0.781 Sum_probs=22.1
Q ss_pred cccCCCCCccceecCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
--.||.|+.+.-|..+=---.| +||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 4689999999998877666777 677665
No 136
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=62.03 E-value=6.7 Score=31.68 Aligned_cols=55 Identities=22% Similarity=0.594 Sum_probs=21.5
Q ss_pred CCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCCC
Q 043224 221 HCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGCN 299 (516)
Q Consensus 221 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCn 299 (516)
-|+--|-.......-|-|. |+.-.|..|. .+ -++..++.||.|+.+..+..|+-
T Consensus 14 iCGD~VGl~~~Ge~FVAC~eC~fPvCr~Cy----------EY---------------Erkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 14 ICGDDVGLTENGEVFVACHECAFPVCRPCY----------EY---------------ERKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp SS--B--B-SSSSB--S-SSS-----HHHH----------HH---------------HHHTS-SB-TTT--B----TT--
T ss_pred cccCccccCCCCCEEEEEcccCCccchhHH----------HH---------------HhhcCcccccccCCCcccccCCC
Confidence 5887777766666778997 9998888774 11 13456799999999998887764
Q ss_pred c
Q 043224 300 M 300 (516)
Q Consensus 300 h 300 (516)
.
T Consensus 69 ~ 69 (80)
T PF14569_consen 69 R 69 (80)
T ss_dssp -
T ss_pred C
Confidence 3
No 137
>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=60.94 E-value=6.4 Score=27.91 Aligned_cols=23 Identities=35% Similarity=1.122 Sum_probs=17.2
Q ss_pred cccCCCCCcccee-cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK-NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK-n~GCnhMtC-~C~ 306 (516)
...||.|+.|+-+ .+| .+.| .|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3789999999988 455 5667 563
No 138
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=60.51 E-value=5.5 Score=31.06 Aligned_cols=21 Identities=29% Similarity=0.879 Sum_probs=8.8
Q ss_pred ccCCCCCccceec---CCCCceee
Q 043224 283 KPCPKCCKPIEKN---GGCNMVRC 303 (516)
Q Consensus 283 K~CPkC~~~IEKn---~GCnhMtC 303 (516)
-+|++|....... |||.|+.|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fC 31 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFC 31 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-
T ss_pred cCCcHHHHHhcCCceeccCccHHH
Confidence 5799998776553 67766666
No 139
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.31 E-value=7.3 Score=37.75 Aligned_cols=54 Identities=19% Similarity=0.392 Sum_probs=41.4
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
..|..|-.++...+.+.|.|-|.|.-+|+...-..--....-..-+||. |...|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 4599999999889999999999999999998765433322213468987 88744
No 140
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=59.97 E-value=3.5 Score=43.00 Aligned_cols=48 Identities=19% Similarity=0.589 Sum_probs=36.9
Q ss_pred CcccccccccccCC--CCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 121 STFCCNICCDDVSP--QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 121 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
....|..|.+.+.. +....|+|.|.|...|+..|+.. + .+-.||. |..
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n---~~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---N---GTRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---C---CCCCCcc--HHH
Confidence 35679999998643 45677899999999999999943 2 3457987 773
No 141
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.55 E-value=7.5 Score=46.57 Aligned_cols=39 Identities=33% Similarity=0.416 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHH--------HHHhhhhhhhcccccccCCCCCchh
Q 043224 465 RVITQSVTADYLCRNLYE--------WIETDLLGSLKHSVHKIAPFNSAAV 507 (516)
Q Consensus 465 ~~~~~t~~~~~~~~~l~~--------~~e~~l~~~~~~~~~~~~~~~~~~~ 507 (516)
-+...++.|+..+.++|. ..| +|.|-|. ..+||-.|.|+
T Consensus 846 yl~~va~fiDdLL~k~Ygl~~fYn~~~~e-DLiGhLv---iGlAPHTSagv 892 (1337)
T PRK14714 846 YLLKVAKFVDDLLEKFYGLPRFYNVEKRE-DLVGHLV---IGLAPHTSAGV 892 (1337)
T ss_pred HHHHHHHHHHHHHHHhhCCCcccCCCChh-hccceee---eccCCccccce
Confidence 345567777777777642 233 6766443 45667666654
No 142
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=59.44 E-value=5.3 Score=46.16 Aligned_cols=26 Identities=35% Similarity=0.934 Sum_probs=22.9
Q ss_pred ccCCCCCccceecCCCCceee-ccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITFN 310 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~FC 310 (516)
..||.|+.++...+||. +| .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 36999999999999996 99 6998766
No 143
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=59.30 E-value=7.6 Score=26.36 Aligned_cols=27 Identities=41% Similarity=1.110 Sum_probs=14.1
Q ss_pred ccCCCCCCCCceEee---cCCCcceeecc-CCcc
Q 043224 214 KWCPSVPHCGNAIQV---EADELCEVECA-CGFQ 243 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~---~~~~~~~v~C~-Cg~~ 243 (516)
++|| .|+..+.. .++......|+ ||..
T Consensus 1 kfC~---~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP---QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T---TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc---cccChhhhhcCCCCCccceECCCCCCE
Confidence 4798 79998774 34566778887 8863
No 144
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=59.13 E-value=10 Score=27.24 Aligned_cols=27 Identities=26% Similarity=0.872 Sum_probs=20.0
Q ss_pred cCCCCCCCCceEeecCCCcceeecc-CCcccc
Q 043224 215 WCPSVPHCGNAIQVEADELCEVECA-CGFQFC 245 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC 245 (516)
-|| +|+..+....... .+.|+ ||..+=
T Consensus 5 ~C~---~CG~~~~~~~~~~-~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCA---RCGREVELDEYGT-GVRCPYCGYRIL 32 (46)
T ss_pred ECC---CCCCEEEECCCCC-ceECCCCCCeEE
Confidence 487 7999988776443 68898 887654
No 145
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=57.83 E-value=8.1 Score=30.08 Aligned_cols=27 Identities=33% Similarity=0.756 Sum_probs=17.2
Q ss_pred CcccCCCCCcccee---cCCCCceee-cccc
Q 043224 281 HTKPCPKCCKPIEK---NGGCNMVRC-KCGI 307 (516)
Q Consensus 281 ntK~CPkC~~~IEK---n~GCnhMtC-~C~~ 307 (516)
+.|+||.|+..+.. .+|=-...| +|+.
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 57999999976654 444333455 4554
No 146
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=57.38 E-value=4.9 Score=41.13 Aligned_cols=53 Identities=19% Similarity=0.562 Sum_probs=38.0
Q ss_pred cccccccccccCC--CCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHH
Q 043224 122 TFCCNICCDDVSP--QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKI 183 (516)
Q Consensus 122 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i 183 (516)
.-.|+.|.+++.. .+++..+||-..|.-||.. |...+ .=+||. |....+++-|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~l------ngrcpa--crr~y~denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNL------NGRCPA--CRRKYDDENV 68 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhc------cCCChH--hhhhccccce
Confidence 3459999998765 3567779999999999975 33332 337998 9876655544
No 147
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=57.38 E-value=2.8 Score=42.61 Aligned_cols=28 Identities=29% Similarity=0.586 Sum_probs=22.0
Q ss_pred cccCCCCCccceec-CCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEKN-GGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEKn-~GCnhMtC-~C~~~F 309 (516)
+..||+|+..|-+. -.=|.+.| +|+|+|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 57899999988763 44567899 799986
No 148
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=57.03 E-value=6.4 Score=33.47 Aligned_cols=24 Identities=38% Similarity=0.916 Sum_probs=18.2
Q ss_pred ccCCCCCccceecCCCCceee-ccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
+.||+|+.++...+| .+.| .|++.
T Consensus 1 ~fC~~Cg~~l~~~~~--~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKNG--VYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCCC--eEECcCCCCc
Confidence 369999998876553 7888 68864
No 149
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.62 E-value=5.3 Score=39.41 Aligned_cols=16 Identities=6% Similarity=-0.018 Sum_probs=14.4
Q ss_pred Cceee-ccccccccccc
Q 043224 299 NMVRC-KCGITFNWISG 314 (516)
Q Consensus 299 nhMtC-~C~~~FCw~C~ 314 (516)
.++.| .|+...|+.|.
T Consensus 96 ~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 96 LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred ceEEecccccccCCCCC
Confidence 67999 79999999998
No 150
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.49 E-value=6.2 Score=41.32 Aligned_cols=6 Identities=50% Similarity=1.071 Sum_probs=4.0
Q ss_pred cccccc
Q 043224 127 ICCDDV 132 (516)
Q Consensus 127 IC~e~~ 132 (516)
||+..-
T Consensus 396 Ic~~ts 401 (514)
T KOG3130|consen 396 ICSDTS 401 (514)
T ss_pred ccccCC
Confidence 777664
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.00 E-value=8.1 Score=44.32 Aligned_cols=35 Identities=29% Similarity=0.607 Sum_probs=29.8
Q ss_pred cccCCCCCccceecCCCCceee-ccccc-----cccccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCGIT-----FNWISGLE 316 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~ 316 (516)
+-.||+|..+..-..+=|.|.| .||++ .|-.||+.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3589999988876666699999 79998 89999997
No 152
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.83 E-value=7.3 Score=44.85 Aligned_cols=39 Identities=23% Similarity=0.652 Sum_probs=32.4
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhh
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKI 159 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I 159 (516)
+...|.+|.-.+-....+..+|||.|..+|+..++..-.
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHccc
Confidence 567899999998777667779999999999998876543
No 153
>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=55.13 E-value=8.6 Score=30.54 Aligned_cols=33 Identities=30% Similarity=0.627 Sum_probs=21.3
Q ss_pred cCCCCCccceecCCCCceee-ccccc-----cccccccccc
Q 043224 284 PCPKCCKPIEKNGGCNMVRC-KCGIT-----FNWISGLEYS 318 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~w~ 318 (516)
.||.|..+++.++ .+..| .|+.. +|--|+.+-.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHH
Confidence 6999999999988 68888 68654 5888888754
No 154
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=54.82 E-value=3.2 Score=42.33 Aligned_cols=28 Identities=25% Similarity=0.427 Sum_probs=19.7
Q ss_pred cccCCCCCcccee-cCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEK-NGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 309 (516)
+.+||+|+..|.+ .-.=|.+.| +|+|+|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3678888887764 334566788 688865
No 155
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=54.10 E-value=5 Score=46.38 Aligned_cols=53 Identities=21% Similarity=0.410 Sum_probs=37.6
Q ss_pred CCCcccccccccccCCCC---e--eecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 119 CSSTFCCNICCDDVSPQE---V--TTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~---~--~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
.++..+|.|||.-+...+ + ....|.|.|...|+-.|+.+. ..-+||. |...++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss------~~s~CPl--CRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS------ARSNCPL--CRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc------CCCCCCc--cccccc
Confidence 345678999998754211 1 112689999999999999875 2358998 886554
No 156
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=53.29 E-value=7.2 Score=32.87 Aligned_cols=26 Identities=35% Similarity=0.915 Sum_probs=20.2
Q ss_pred cCCCCCcc--ceecCCCCceee-cccccc
Q 043224 284 PCPKCCKP--IEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 284 ~CPkC~~~--IEKn~GCnhMtC-~C~~~F 309 (516)
.||.|+.. |++.+-||...| .|+|.|
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCcee
Confidence 59999864 456666999999 699876
No 157
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=52.93 E-value=9.4 Score=27.91 Aligned_cols=27 Identities=30% Similarity=0.632 Sum_probs=19.0
Q ss_pred CcccCC--CCCccceecCCCCceee-cccc
Q 043224 281 HTKPCP--KCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 281 ntK~CP--kC~~~IEKn~GCnhMtC-~C~~ 307 (516)
.-+.|| .|+.-|.--.--+..+| +|++
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 458999 99997755444578999 8985
No 158
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=52.77 E-value=16 Score=27.07 Aligned_cols=37 Identities=14% Similarity=0.232 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHhh
Q 043224 57 GDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLVE 93 (516)
Q Consensus 57 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~e 93 (516)
+.|..++...|++..-+...|...+||-++.+..|.+
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5688899999999999999999999999999988873
No 159
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=52.62 E-value=7.7 Score=39.06 Aligned_cols=17 Identities=41% Similarity=0.362 Sum_probs=12.6
Q ss_pred CCCCCCCCCCCC--CCCCC
Q 043224 1 MEDYGNSDDEHQ--YLDDD 17 (516)
Q Consensus 1 ~~~~~~~~~~~~--~~~~~ 17 (516)
|+|++++||+|| .|+||
T Consensus 1 m~D~~MdddEDYg~EYsdd 19 (440)
T KOG1464|consen 1 MSDDFMDDDEDYGFEYSDD 19 (440)
T ss_pred CCccccccchhcCceeccc
Confidence 888899888888 44444
No 160
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=52.21 E-value=5.7 Score=29.98 Aligned_cols=46 Identities=26% Similarity=0.558 Sum_probs=31.1
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
...|-.|... ......++|||..|..||-.- ..--||. |...+..+
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChh----------hccCCCC--CCCcccCC
Confidence 4456666554 244567899999999999642 2235888 88776543
No 161
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=51.90 E-value=50 Score=25.66 Aligned_cols=40 Identities=13% Similarity=0.194 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHh
Q 043224 53 AAQMGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLV 92 (516)
Q Consensus 53 ~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~ 92 (516)
..|.+.|..++...|++..-+..+|...+||-++.+..|-
T Consensus 10 ~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 10 PEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3567788999999999999999999999999999988876
No 162
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.88 E-value=9.7 Score=38.40 Aligned_cols=44 Identities=27% Similarity=0.705 Sum_probs=32.6
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
.-|+.|-.-+ ...+.+-.|+|.||.+|+..-|.. ....||. |..
T Consensus 275 LkCplc~~Ll-rnp~kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLL-RNPMKTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhh-hCcccCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 6799998754 234445589999999998876654 3578997 875
No 163
>PF14149 YhfH: YhfH-like protein
Probab=50.40 E-value=1.3 Score=30.50 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=21.9
Q ss_pred cCcccCCCCCccceecCCCCceee-cc
Q 043224 280 SHTKPCPKCCKPIEKNGGCNMVRC-KC 305 (516)
Q Consensus 280 ~ntK~CPkC~~~IEKn~GCnhMtC-~C 305 (516)
...|.||.|+..|+--.-|-.++| +|
T Consensus 11 Lp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 357999999999998888888888 66
No 164
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=50.24 E-value=10 Score=32.27 Aligned_cols=29 Identities=24% Similarity=0.769 Sum_probs=19.1
Q ss_pred cCcccCCCCCcc---ceecCCCCceee-ccccc
Q 043224 280 SHTKPCPKCCKP---IEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 280 ~ntK~CPkC~~~---IEKn~GCnhMtC-~C~~~ 308 (516)
.+.-.||+|+.. |....|=-|..| .||+.
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 345689999932 223346668999 78854
No 165
>PF12773 DZR: Double zinc ribbon
Probab=50.23 E-value=9.2 Score=27.77 Aligned_cols=13 Identities=46% Similarity=1.362 Sum_probs=8.4
Q ss_pred CcccCCCCCCCCceEe
Q 043224 212 RVKWCPSVPHCGNAIQ 227 (516)
Q Consensus 212 ~~~~CP~~p~C~~~i~ 227 (516)
..++|| .|+..+.
T Consensus 11 ~~~fC~---~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCP---HCGTPLP 23 (50)
T ss_pred cccCCh---hhcCChh
Confidence 445677 5777766
No 166
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=48.77 E-value=6.4 Score=32.51 Aligned_cols=33 Identities=30% Similarity=0.641 Sum_probs=27.2
Q ss_pred ccCCCCCccceecCCCCceeeccccccccccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRCKCGITFNWISGLEYS 318 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~w~ 318 (516)
..||.|+.| ...|--+.++|+|.|=..|...|-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl 65 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWL 65 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHH
Confidence 468888887 467888888999999999999884
No 167
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.67 E-value=25 Score=40.47 Aligned_cols=40 Identities=25% Similarity=0.597 Sum_probs=30.4
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
..|..|--++. -.++...|||.|...|+. ++ .-.||. |..
T Consensus 841 skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~---~~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK---EDKCPK--CLP 880 (933)
T ss_pred eeecccCCccc-cceeeeecccHHHHHhhc--------cC---cccCCc--cch
Confidence 57999988764 245567899999999988 32 357987 875
No 168
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=48.39 E-value=38 Score=39.54 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCChHHHHHHH
Q 043224 72 HARTLLIHYRWDVEKVFAVL 91 (516)
Q Consensus 72 ~a~~LL~~~~W~~~~l~e~~ 91 (516)
.++..++||+-.+=+|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 57777778877776676655
No 169
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=47.59 E-value=13 Score=32.02 Aligned_cols=26 Identities=31% Similarity=0.820 Sum_probs=18.0
Q ss_pred ccCCCCCccceecCCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
-+||+|..-.-=..| +.+.| -|+|+|
T Consensus 3 p~CP~C~seytY~dg-~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDG-TQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecC-CeeECccccccc
Confidence 579999886665555 34777 577664
No 170
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=47.53 E-value=11 Score=33.52 Aligned_cols=27 Identities=15% Similarity=0.208 Sum_probs=19.0
Q ss_pred cccCCCCCccceecCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
-+.||+|++..---.- +-++| +||..|
T Consensus 9 Kr~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCccccccCC-CCccCCCcCCcc
Confidence 3679999987664222 77888 788664
No 171
>PHA02929 N1R/p28-like protein; Provisional
Probab=47.33 E-value=7.8 Score=38.33 Aligned_cols=38 Identities=16% Similarity=0.207 Sum_probs=27.7
Q ss_pred CcccCCCCCccceecCCCC---ceeeccccccccccccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCN---MVRCKCGITFNWISGLEYS 318 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCn---hMtC~C~~~FCw~C~~~w~ 318 (516)
....||-|.-.+.....-+ -+.-.|+|.||..|...|.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl 213 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWK 213 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHH
Confidence 4578999999877544222 1334689999999999996
No 172
>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=47.29 E-value=13 Score=37.42 Aligned_cols=49 Identities=27% Similarity=0.691 Sum_probs=32.2
Q ss_pred cccccccccCC-CCeeec--CCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHH
Q 043224 124 CCNICCDDVSP-QEVTTM--DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEA 181 (516)
Q Consensus 124 ~C~IC~e~~~~-~~~~~l--~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~ 181 (516)
.|++|-.+.-. .++..+ .|+|..|.+|+-.-+.. .+-.|| +|..++-..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cp--eC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCP--ECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCC--cccchhhhc
Confidence 48888766321 122222 89999999999887654 234698 598765433
No 173
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=47.18 E-value=13 Score=32.46 Aligned_cols=28 Identities=29% Similarity=0.641 Sum_probs=18.8
Q ss_pred cccCCCCCcccee--cCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~~~F 309 (516)
.+.||+|+..+.- .++=+-+.| +||+++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 3689999987764 112237888 688653
No 174
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=46.13 E-value=6.8 Score=39.30 Aligned_cols=28 Identities=29% Similarity=0.678 Sum_probs=23.1
Q ss_pred cccCCCCCcccee-cCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEK-NGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEK-n~GCnhMtC-~C~~~F 309 (516)
+.+||+|+..+-+ .-+=|.+.| +|+|+|
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 5789999998875 557788899 899887
No 175
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.98 E-value=7.9 Score=29.63 Aligned_cols=9 Identities=44% Similarity=1.114 Sum_probs=4.6
Q ss_pred CcccCCCCC
Q 043224 281 HTKPCPKCC 289 (516)
Q Consensus 281 ntK~CPkC~ 289 (516)
|+=.||+|+
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 444555554
No 176
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=45.50 E-value=5.9 Score=30.44 Aligned_cols=14 Identities=50% Similarity=1.049 Sum_probs=12.0
Q ss_pred ccCCCCCccceecC
Q 043224 283 KPCPKCCKPIEKNG 296 (516)
Q Consensus 283 K~CPkC~~~IEKn~ 296 (516)
|.||.||.+|.-+.
T Consensus 4 kHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 4 KHCPVCGKPIPPDE 17 (59)
T ss_pred CcCCcCCCcCCcch
Confidence 78999999999753
No 177
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=44.51 E-value=4.2 Score=29.95 Aligned_cols=33 Identities=30% Similarity=0.915 Sum_probs=27.9
Q ss_pred CcccccccccccCCCCeeec-CCCCcccHHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTM-DCGHCFCNNCWTE 153 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~ 153 (516)
+.++|..|-...|..++... -||.-.|..||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 56899999999887776654 7999999999984
No 178
>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=44.13 E-value=20 Score=23.15 Aligned_cols=20 Identities=30% Similarity=0.798 Sum_probs=12.8
Q ss_pred cCCCCCccceecCCCCceee
Q 043224 284 PCPKCCKPIEKNGGCNMVRC 303 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC 303 (516)
.||.|+..+.+..|=-+..|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999887666666
No 179
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.92 E-value=22 Score=33.25 Aligned_cols=56 Identities=25% Similarity=0.425 Sum_probs=38.5
Q ss_pred cccccccccccCC-----CCeeecCCCCcccHHHHHHHHHhhhhcCCcccc---cccccccccccC
Q 043224 122 TFCCNICCDDVSP-----QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRI---KCMALKCNVVCD 179 (516)
Q Consensus 122 ~~~C~IC~e~~~~-----~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i---~CP~~~C~~~i~ 179 (516)
...|.||+--.-. ...-...||..|..-|+..|+..-+-..+++.| .||- |..+|.
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 4567777754211 112235899999999999999988877765544 5886 877654
No 180
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=43.28 E-value=9.4 Score=38.76 Aligned_cols=54 Identities=24% Similarity=0.632 Sum_probs=39.0
Q ss_pred cCCCcccCCCCCCCCceEeecCCCcceeeccCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCC
Q 043224 209 DNRRVKWCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKC 288 (516)
Q Consensus 209 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC 288 (516)
.++.+-+|- .|+..|.+-+.- + +|.+.||..|-.. ...|.||.|
T Consensus 86 l~p~VHfCd---~Cd~PI~IYGRm---I--PCkHvFCl~CAr~----------------------------~~dK~Cp~C 129 (389)
T KOG2932|consen 86 LGPRVHFCD---RCDFPIAIYGRM---I--PCKHVFCLECARS----------------------------DSDKICPLC 129 (389)
T ss_pred cCcceEeec---ccCCcceeeecc---c--ccchhhhhhhhhc----------------------------CccccCcCc
Confidence 356677786 799887754421 2 5899999999521 114899999
Q ss_pred CccceecCCC
Q 043224 289 CKPIEKNGGC 298 (516)
Q Consensus 289 ~~~IEKn~GC 298 (516)
.-+|+|.+-|
T Consensus 130 ~d~VqrIeq~ 139 (389)
T KOG2932|consen 130 DDRVQRIEQI 139 (389)
T ss_pred ccHHHHHHHh
Confidence 9999998765
No 181
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=42.92 E-value=7.4 Score=44.12 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=24.3
Q ss_pred cccccccccccCC--CCeeec---CCCCcccHHHHHHHHHhhhhc
Q 043224 122 TFCCNICCDDVSP--QEVTTM---DCGHCFCNNCWTEHFIVKIND 161 (516)
Q Consensus 122 ~~~C~IC~e~~~~--~~~~~l---~CgH~fC~~C~~~yl~~~I~~ 161 (516)
..+|.||.-++.. +....+ .|+|.+|..|+..+...-+..
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~ 140 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEES 140 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhcc
Confidence 3455555555433 112222 488889999988887776654
No 182
>PRK10220 hypothetical protein; Provisional
Probab=42.02 E-value=18 Score=31.12 Aligned_cols=27 Identities=26% Similarity=0.671 Sum_probs=18.0
Q ss_pred cccCCCCCccceecCCCCceee-cccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
.-+||+|..-.-=..| +.+.| -|+|+|
T Consensus 3 lP~CP~C~seytY~d~-~~~vCpeC~hEW 30 (111)
T PRK10220 3 LPHCPKCNSEYTYEDN-GMYICPECAHEW 30 (111)
T ss_pred CCcCCCCCCcceEcCC-CeEECCcccCcC
Confidence 3589999886665555 34667 566664
No 183
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=41.77 E-value=23 Score=25.73 Aligned_cols=33 Identities=18% Similarity=0.412 Sum_probs=22.6
Q ss_pred ccccccccCCCCeeecCCC--C---cccHHHHHHHHHh
Q 043224 125 CNICCDDVSPQEVTTMDCG--H---CFCNNCWTEHFIV 157 (516)
Q Consensus 125 C~IC~e~~~~~~~~~l~Cg--H---~fC~~C~~~yl~~ 157 (516)
|-||+++...+.....+|+ - ....+|+..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 7899998765553444553 3 5788999999988
No 184
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=41.34 E-value=25 Score=27.62 Aligned_cols=30 Identities=33% Similarity=0.638 Sum_probs=23.1
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQFCF 246 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~ 246 (516)
.-|| +|++.-.+-+.....|.|. ||...+.
T Consensus 20 VkCp---dC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP---DCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECC---CCCCEEEEeccCceEEEecccccEEEe
Confidence 4698 8999877666566779997 9987764
No 185
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=41.22 E-value=43 Score=38.21 Aligned_cols=42 Identities=12% Similarity=0.076 Sum_probs=26.6
Q ss_pred CCccccCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCChHH
Q 043224 41 ASSMVIPKESLLAAQMGDLLRVMDLLSLKEKHARTLLIHYRWDVEK 86 (516)
Q Consensus 41 ~~~~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~ 86 (516)
..++.|++.++.+..++.-..--+- .+.-..||++-+|..+.
T Consensus 411 ppf~~l~ksq~~kl~k~q~k~y~de----~dyr~kl~~kkq~ke~~ 452 (763)
T TIGR00993 411 PPFKPLTKAQMAKLSKEQRKAYLEE----YDYRVKLLQKKQWREEL 452 (763)
T ss_pred CCCccccHHHHHHHhHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence 4567888888777766554433332 24556788888887554
No 186
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=40.18 E-value=16 Score=42.32 Aligned_cols=9 Identities=11% Similarity=0.335 Sum_probs=3.6
Q ss_pred CCCCCCCCC
Q 043224 4 YGNSDDEHQ 12 (516)
Q Consensus 4 ~~~~~~~~~ 12 (516)
+|+|++||+
T Consensus 1405 dd~DeeeD~ 1413 (1516)
T KOG1832|consen 1405 DDSDEEEDD 1413 (1516)
T ss_pred cccCccccc
Confidence 344444433
No 187
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=40.05 E-value=1.7 Score=35.28 Aligned_cols=48 Identities=27% Similarity=0.365 Sum_probs=35.0
Q ss_pred ccCHHHHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHhCCChHHHHHHHhh
Q 043224 45 VIPKESLLAAQMGDLLRVMDLLSL---KEKHARTLLIHYRWDVEKVFAVLVE 93 (516)
Q Consensus 45 vlt~~~i~~~~~~~i~~v~~~l~i---~~~~a~~LL~~~~W~~~~l~e~~~e 93 (516)
-||+++-.+ |.+-+.+|.++||= +.....-.|.||.|++++.+..+.+
T Consensus 19 ~Ls~ed~~~-L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 19 ELSPEDQAQ-LYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp H-TCHHHHH-HCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred cCCHHHHHH-HHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 366766544 67778889999974 5567788899999999999987763
No 188
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=39.61 E-value=16 Score=25.54 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=16.4
Q ss_pred cCCCCCccceecCCCCceeecccccccccccccc
Q 043224 284 PCPKCCKPIEKNGGCNMVRCKCGITFNWISGLEY 317 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~w 317 (516)
.||+|+...+...- ..+.- .-|-.|+|.|
T Consensus 1 ~CP~C~~~l~~~~~-~~~~i----d~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDVEI----DVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEE-CCEEE----EECCCCCeEE
Confidence 59999987775433 22322 2233566666
No 189
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=39.14 E-value=39 Score=27.38 Aligned_cols=47 Identities=30% Similarity=0.697 Sum_probs=19.9
Q ss_pred CcccccccccccCC---CCeeec--CCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 121 STFCCNICCDDVSP---QEVTTM--DCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 121 ~~~~C~IC~e~~~~---~~~~~l--~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
....|.||.+++.. .++|.. .|+-..|+.|+.- .+++|. -.||. |+.
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY----Erkeg~---q~Cpq--Ckt 59 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY----ERKEGN---QVCPQ--CKT 59 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH----HHHTS----SB-TT--T--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHH----HhhcCc---ccccc--cCC
Confidence 46789999999753 344443 7888899999754 445665 35877 764
No 190
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=39.11 E-value=28 Score=29.43 Aligned_cols=26 Identities=38% Similarity=0.985 Sum_probs=17.1
Q ss_pred ccCCCCCCCCceEeecCCCc-ceeecc-CCc
Q 043224 214 KWCPSVPHCGNAIQVEADEL-CEVECA-CGF 242 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-Cg~ 242 (516)
.+|| .|++.+.+..+.. ..+.|+ |++
T Consensus 2 ~FCP---~Cgn~Live~g~~~~rf~C~tCpY 29 (105)
T KOG2906|consen 2 LFCP---TCGNMLIVESGESCNRFSCRTCPY 29 (105)
T ss_pred cccC---CCCCEEEEecCCeEeeEEcCCCCc
Confidence 4798 7999999876543 344453 443
No 191
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.05 E-value=9.9 Score=42.22 Aligned_cols=34 Identities=29% Similarity=0.761 Sum_probs=26.7
Q ss_pred ccccccccccCCC--CeeecCCCCcccHHHHHHHHH
Q 043224 123 FCCNICCDDVSPQ--EVTTMDCGHCFCNNCWTEHFI 156 (516)
Q Consensus 123 ~~C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yl~ 156 (516)
..|+||+..+... .++++.|||..|..|...-..
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 4699998876443 467889999999999886543
No 192
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=38.97 E-value=33 Score=40.20 Aligned_cols=34 Identities=6% Similarity=-0.005 Sum_probs=14.9
Q ss_pred cccCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Q 043224 44 MVIPKESLLAAQMGDLLRVMDLLSLKEKHARTLLIHY 80 (516)
Q Consensus 44 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~ 80 (516)
+.|++-|..+..++.+..++ +-.+.....|.++-
T Consensus 953 t~LD~VD~f~~f~~~i~~lq---~~d~~~yq~l~~~L 986 (1010)
T KOG1991|consen 953 TPLDQVDPFQLFKEAITNLQ---SSDAVRYQKLISTL 986 (1010)
T ss_pred CcccccchHHHHHHHHHhhh---ccChHHHHHHHhcC
Confidence 33455555555554444333 23334444444433
No 193
>cd07621 BAR_SNX5_6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Members of this subfamily include SNX5, SNX6, the mammalian SNX32, and similar proteins. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. The function of SNX32 is still unknown. BAR domain
Probab=38.73 E-value=1.6e+02 Score=28.81 Aligned_cols=60 Identities=13% Similarity=0.166 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043224 429 FEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIETDL 488 (516)
Q Consensus 429 Fe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~~l 488 (516)
=|..|.+.+..-|++|....+.+..+....+.+||.-|+.++..--++-+..+..+.+-|
T Consensus 156 AE~~~~~a~~~Fe~iS~~~k~El~rF~~~Rv~~fk~~lve~aE~~ik~Ak~~~~~l~~~~ 215 (219)
T cd07621 156 AEAAQQEACEKFESMSESAKQELLDFKTRRVAAFRKNLVELAELEIKHAKAQIQLLKNCL 215 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566788899999999999999988888888999999999988888888888888777544
No 194
>PRK11827 hypothetical protein; Provisional
Probab=38.16 E-value=25 Score=27.14 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=19.8
Q ss_pred cccCCCCCccceecCCCCceee-ccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
.-.||.|+.+.+-+.+=+...| .|+-.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 3579999999887665567888 57643
No 195
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=37.92 E-value=17 Score=37.35 Aligned_cols=83 Identities=17% Similarity=0.129 Sum_probs=42.7
Q ss_pred ccCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHHhhhChhHHHHHhCcccccCCCCCCCCCCCCccc
Q 043224 45 VIPKESLLAAQMGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVLVEEGKDKLFAQAGVTVVENDHQVPLSQCSSTFC 124 (516)
Q Consensus 45 vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~~e~~~~~~~~~~gl~~~~~~~~~~~~~~~~~~~ 124 (516)
|+|++.|.+.+.+.- .|.++...--.+| -..| ....|+...||.+....--......+=..-
T Consensus 183 witp~ni~~~~~e~~-----al~~pe~~~Vac~----------TtDf---amQNVlLqm~L~l~~~~G~~Ir~~r~~iLR 244 (376)
T KOG2463|consen 183 WITPSNITEAIIELG-----ALNRPENQLVACL----------TTDF---AMQNVLLQMNLNLLAMSGMKIRSVRSYILR 244 (376)
T ss_pred ccccchHHHHHHhhh-----cccccccceeeee----------cccH---HHHHHHHHhcccccCccchhhhhhhhheeE
Confidence 799999988877654 3444333211111 1111 145667777776544111000011122457
Q ss_pred ccccccccCCC-CeeecCCCCc
Q 043224 125 CNICCDDVSPQ-EVTTMDCGHC 145 (516)
Q Consensus 125 C~IC~e~~~~~-~~~~l~CgH~ 145 (516)
|--||..++.. ..|-..|||.
T Consensus 245 Ch~Cfsit~~m~k~FCp~CG~~ 266 (376)
T KOG2463|consen 245 CHGCFSITSEMPKDFCPSCGHK 266 (376)
T ss_pred eeeeeEecCccchhcccccCCC
Confidence 99999987532 3344467765
No 196
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.71 E-value=19 Score=43.45 Aligned_cols=59 Identities=17% Similarity=0.270 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHH-HHhhcc---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 043224 430 EDQQQQFETNIERLSLIL-EENFEK---YSEHQLKDFRMRVITQSVTADYLCRNLYEWIETDLL 489 (516)
Q Consensus 430 e~~Q~~le~~~E~Ls~~l-e~~~~~---~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~~l~ 489 (516)
.+.=.++--.+|+|.++= ++++.. ..++++.++|.+=+-++.-...|+-+..+.|. +||
T Consensus 796 hfrp~Eigvs~eklreLGY~~Di~G~pL~~~dQivELk~QDiil~~~aa~yl~~va~fiD-dLL 858 (1337)
T PRK14714 796 HFRPREIGVSVEKLRELGYTQDIHGDPLVHEDQVVELKVQDIVLSDGAAEYLLKVAKFVD-DLL 858 (1337)
T ss_pred cccHHHcCCCHHHHHHcCCccccCCCCCCCccceEEeecccEEcchHHHHHHHHHHHHHH-HHH
Confidence 344445666677776652 222211 12344666666656666666666666666665 444
No 197
>PHA02926 zinc finger-like protein; Provisional
Probab=37.44 E-value=12 Score=36.43 Aligned_cols=41 Identities=20% Similarity=0.190 Sum_probs=25.9
Q ss_pred HHhcCcccCCCCCccc-eecCCCCce-ee---ccccccccccccccc
Q 043224 277 WISSHTKPCPKCCKPI-EKNGGCNMV-RC---KCGITFNWISGLEYS 318 (516)
Q Consensus 277 wi~~ntK~CPkC~~~I-EKn~GCnhM-tC---~C~~~FCw~C~~~w~ 318 (516)
|....-+.|+=|--.+ +|.. .+-- .- .|+|.||+.|...|.
T Consensus 165 ~~~SkE~eCgICmE~I~eK~~-~~eRrFGIL~~CnHsFCl~CIr~Wr 210 (242)
T PHA02926 165 YRVSKEKECGICYEVVYSKRL-ENDRYFGLLDSCNHIFCITCINIWH 210 (242)
T ss_pred HhccCCCCCccCccccccccc-cccccccccCCCCchHHHHHHHHHH
Confidence 3445568999998665 4421 1111 11 488888888888886
No 198
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=37.08 E-value=19 Score=20.76 Aligned_cols=16 Identities=31% Similarity=0.810 Sum_probs=13.3
Q ss_pred cccccccccCCCCCch
Q 043224 244 FCFSCSSVAHSPCSCL 259 (516)
Q Consensus 244 fC~~C~~~~H~p~~C~ 259 (516)
.||+|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5999999999877764
No 199
>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=36.60 E-value=25 Score=38.81 Aligned_cols=34 Identities=26% Similarity=0.470 Sum_probs=24.3
Q ss_pred ccCCCCCccceecCCCCceee-ccccc-----cccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGIT-----FNWISGLE 316 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~ 316 (516)
-.||+|..+..--..=|.+.| .||+. .|-.|++.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 479999887763333358999 79877 57777764
No 200
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=36.40 E-value=14 Score=31.24 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=24.8
Q ss_pred CCCCcccccccccccCCCCeeecCCCCcccHHH
Q 043224 118 QCSSTFCCNICCDDVSPQEVTTMDCGHCFCNNC 150 (516)
Q Consensus 118 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 150 (516)
.....|+|.-||--...+.+..-.=|+.+|.+|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 345789999999876655555545588899988
No 201
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=36.35 E-value=22 Score=42.46 Aligned_cols=19 Identities=26% Similarity=0.475 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 043224 428 FFEDQQQQFETNIERLSLI 446 (516)
Q Consensus 428 lFe~~Q~~le~~~E~Ls~~ 446 (516)
-||--|....+++|+|..-
T Consensus 2418 ~FEtKer~Fnka~EK~RnQ 2436 (3015)
T KOG0943|consen 2418 GFETKERKFNKAMEKLRNQ 2436 (3015)
T ss_pred ccchHHHHHHHHHHHHHhc
Confidence 3888999999999987643
No 202
>PF06254 DUF1019: Protein of unknown function (DUF1019); InterPro: IPR009364 This entry is represented by Bacteriophage phi-80, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3C4R_C.
Probab=35.97 E-value=1.9e+02 Score=24.22 Aligned_cols=66 Identities=14% Similarity=0.102 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhhhhhh
Q 043224 422 RKIKQNFFEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVI---TQSVTADYLCRNLYEWIETDLLGS 491 (516)
Q Consensus 422 ~~~~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~---~~t~~~~~~~~~l~~~~e~~l~~~ 491 (516)
.+++++||..+.++=....++...++--.+..++.+ +|.++. ..+.++-..-+.+.+..+..|+|.
T Consensus 7 ~~N~Q~iFRwl~~ds~~~~~~~~~L~PAI~aAlP~E----~rarl~~~~~~~~~la~~~kE~~eA~~avlL~a 75 (89)
T PF06254_consen 7 NNNRQKIFRWLDNDSPAYREKIMQLSPAILAALPPE----RRARLSSGDSTMYLLASAAKECSEAKQAVLLGA 75 (89)
T ss_dssp HHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHS-HH----HHHHHHCTT-HHH------HHHHHHHHHH----
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCHH----HHhhccCCCCchhhhhHhHHHHHHHHHHHHhhh
Confidence 367899999999999999998888776555555443 556665 111123333377788888777763
No 203
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=35.22 E-value=29 Score=24.73 Aligned_cols=41 Identities=22% Similarity=0.544 Sum_probs=19.3
Q ss_pred ccccccccCCCCeee-cCCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 125 CNICCDDVSPQEVTT-MDCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 125 C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
|.+|-+-+..+..-. ..|+=.+...|+..|+...- ..+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 566766543322221 25888899999999998752 226875
No 204
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=35.10 E-value=14 Score=28.25 Aligned_cols=16 Identities=44% Similarity=0.816 Sum_probs=8.9
Q ss_pred cccCCCCCccceecCC
Q 043224 282 TKPCPKCCKPIEKNGG 297 (516)
Q Consensus 282 tK~CPkC~~~IEKn~G 297 (516)
+..||.|+++++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 4689999999987444
No 205
>PLN02189 cellulose synthase
Probab=35.04 E-value=34 Score=40.65 Aligned_cols=59 Identities=32% Similarity=0.712 Sum_probs=43.1
Q ss_pred cCCCCCCCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccce
Q 043224 215 WCPSVPHCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIE 293 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IE 293 (516)
-|. -|+--+-....+..-|-|. |+.-.|..|-+ +. .+..++.||.|+.+..
T Consensus 36 ~C~---iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye----------ye---------------r~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCE---ICGDEIGLTVDGDLFVACNECGFPVCRPCYE----------YE---------------RREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccc---ccccccCcCCCCCEEEeeccCCCccccchhh----------hh---------------hhcCCccCcccCCchh
Confidence 476 6888887766666779998 99999998851 10 1345689999999988
Q ss_pred ecCCCCce
Q 043224 294 KNGGCNMV 301 (516)
Q Consensus 294 Kn~GCnhM 301 (516)
+--|++.+
T Consensus 88 r~kgs~~v 95 (1040)
T PLN02189 88 RLKGSPRV 95 (1040)
T ss_pred hccCCCCc
Confidence 76675543
No 206
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=34.69 E-value=19 Score=42.09 Aligned_cols=24 Identities=46% Similarity=1.275 Sum_probs=19.5
Q ss_pred ccCCCCCc-cceecCCCCceee-ccccc
Q 043224 283 KPCPKCCK-PIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 283 K~CPkC~~-~IEKn~GCnhMtC-~C~~~ 308 (516)
-.||-|+. .||..|||| || .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999985 789999998 67 67654
No 207
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.06 E-value=19 Score=39.11 Aligned_cols=34 Identities=29% Similarity=0.728 Sum_probs=22.5
Q ss_pred CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 240 CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 240 Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
|||.||+.|.- +-|..- .....+.||=|+..|-.
T Consensus 204 CGHiFC~~CiL-----------qy~~~s----------~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 204 CGHIFCGPCIL-----------QYWNYS----------AIKGPCSCPICRSTITL 237 (513)
T ss_pred cCceeeHHHHH-----------HHHhhh----------cccCCccCCchhhhccc
Confidence 99999999952 222210 12345889999888765
No 208
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=34.04 E-value=33 Score=25.44 Aligned_cols=30 Identities=20% Similarity=0.558 Sum_probs=23.1
Q ss_pred cccccccccCCCCeeecCCCCcccHHHHHHH
Q 043224 124 CCNICCDDVSPQEVTTMDCGHCFCNNCWTEH 154 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~y 154 (516)
.|.||...+..-..+.+.=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999998765444557777 8999999875
No 209
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.91 E-value=47 Score=25.06 Aligned_cols=32 Identities=19% Similarity=0.770 Sum_probs=25.5
Q ss_pred cccccccccccC-CCCeeec-CCCCcccHHHHHH
Q 043224 122 TFCCNICCDDVS-PQEVTTM-DCGHCFCNNCWTE 153 (516)
Q Consensus 122 ~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~C~~~ 153 (516)
...|++|-+.+. .++++.. .||-.+.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 457999999985 4555554 8999999999975
No 210
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=33.87 E-value=45 Score=38.87 Aligned_cols=7 Identities=14% Similarity=0.041 Sum_probs=3.2
Q ss_pred HHHHcCC
Q 043224 62 VMDLLSL 68 (516)
Q Consensus 62 v~~~l~i 68 (516)
++..||.
T Consensus 708 l~~aL~~ 714 (784)
T PF04931_consen 708 LAKALGD 714 (784)
T ss_pred HHHHhcc
Confidence 4444554
No 211
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.69 E-value=35 Score=22.93 Aligned_cols=29 Identities=31% Similarity=0.529 Sum_probs=16.8
Q ss_pred CcccCCCCCccceecCCCCceee-cccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
+-+.|++|+....-+.-=..+.| .|+..|
T Consensus 2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 34789999875543222235677 566543
No 212
>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=33.67 E-value=25 Score=22.71 Aligned_cols=23 Identities=35% Similarity=0.918 Sum_probs=12.1
Q ss_pred ccCCCCCccceec--CCCCceee-cc
Q 043224 283 KPCPKCCKPIEKN--GGCNMVRC-KC 305 (516)
Q Consensus 283 K~CPkC~~~IEKn--~GCnhMtC-~C 305 (516)
++||.|+.+|++. +|=+...| +|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CcCccCCCcceEeEecCCCCeECcCC
Confidence 6899999999763 44444455 44
No 213
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.18 E-value=12 Score=38.02 Aligned_cols=88 Identities=23% Similarity=0.556 Sum_probs=47.7
Q ss_pred CCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHHhhCCCChHHHHHHHHH-HHHHhhhc----CCCcccCC
Q 043224 143 GHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRCLVSARDSNIADKFERF-LLESYIDD----NRRVKWCP 217 (516)
Q Consensus 143 gH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~-~~~~~v~~----~~~~~~CP 217 (516)
|-++|..|-..-. +.+|.||. |...+ +++ -.+...|..+ =++.|++. ++....|-
T Consensus 307 gGy~CP~CktkVC--------sLPi~CP~--Csl~L-------ils---thLarSyhhL~PLk~f~E~p~~~~~ks~~Cf 366 (421)
T COG5151 307 GGYECPVCKTKVC--------SLPISCPI--CSLQL-------ILS---THLARSYHHLYPLKPFVEKPEGTNPKSTHCF 366 (421)
T ss_pred CceeCCcccceee--------cCCccCcc--hhHHH-------HHH---HHHHHHHHhhccCcccccccCCCCCCCccce
Confidence 4567777744322 26788986 65422 222 1233444433 24445553 33444564
Q ss_pred CCCCCCceEeecC-------CCcceeecc-CCcccccccccccC
Q 043224 218 SVPHCGNAIQVEA-------DELCEVECA-CGFQFCFSCSSVAH 253 (516)
Q Consensus 218 ~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H 253 (516)
.|+..+.... .......|. |...||..|..-.|
T Consensus 367 ---~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 367 ---VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred ---eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 4666544322 123457897 99999999965444
No 214
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=33.15 E-value=53 Score=38.57 Aligned_cols=34 Identities=18% Similarity=0.119 Sum_probs=16.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHhhhChhHHHHHhCc
Q 043224 71 KHARTLLIHYRWDVEKVFAVLVEEGKDKLFAQAGV 105 (516)
Q Consensus 71 ~~a~~LL~~~~W~~~~l~e~~~e~~~~~~~~~~gl 105 (516)
..+..|..+|+=..|.+--.-+ .---.+++..+.
T Consensus 373 ~l~p~lI~RfkEREEnVk~dvf-~~yi~ll~qt~~ 406 (1233)
T KOG1824|consen 373 TLGPALISRFKEREENVKADVF-HAYIALLKQTRP 406 (1233)
T ss_pred HhCHHHHHHHHHHhhhHHHHHH-HHHHHHHHcCCC
Confidence 3445666666665555444433 122334444443
No 215
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.01 E-value=27 Score=36.79 Aligned_cols=8 Identities=75% Similarity=1.111 Sum_probs=2.9
Q ss_pred CCCCCCCC
Q 043224 16 DDEVDIDD 23 (516)
Q Consensus 16 ~~e~~~~~ 23 (516)
|||+.+||
T Consensus 283 DdeeN~dd 290 (514)
T KOG3130|consen 283 DDEENIDD 290 (514)
T ss_pred chhhcccc
Confidence 33333333
No 216
>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=33.00 E-value=39 Score=25.01 Aligned_cols=46 Identities=22% Similarity=0.457 Sum_probs=25.6
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHH
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIR 184 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~ 184 (516)
.+.||.|...++.. =+..++...=.... ..+.||. |...+....+.
T Consensus 2 ~f~CP~C~~~~~~~--------------~L~~H~~~~H~~~~-~~v~CPi--C~~~~~~~l~~ 47 (54)
T PF05605_consen 2 SFTCPYCGKGFSES--------------SLVEHCEDEHRSES-KNVVCPI--CSSRVTDNLIR 47 (54)
T ss_pred CcCCCCCCCccCHH--------------HHHHHHHhHCcCCC-CCccCCC--chhhhhhHHHH
Confidence 57899998854321 13444444322222 3689998 88755543333
No 217
>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=32.97 E-value=31 Score=25.39 Aligned_cols=47 Identities=19% Similarity=0.422 Sum_probs=24.8
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
..|+|.+..+. ....+..|.|.-|.| +..||......+. .+||. |+.
T Consensus 3 L~CPls~~~i~-~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~---W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR-IPVRGKNCKHLQCFD-LESFLESNQRTPK---WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-S-SEEEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEE-eCccCCcCcccceEC-HHHHHHHhhccCC---eECcC--CcC
Confidence 45788776653 245567999998876 7788888766544 78987 764
No 218
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.56 E-value=29 Score=34.96 Aligned_cols=25 Identities=48% Similarity=1.128 Sum_probs=17.8
Q ss_pred cccCCCCCcccee--cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 306 (516)
.++||.|+.+|+| .+|=.--.| .|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 4799999999997 466444455 454
No 219
>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=32.23 E-value=18 Score=28.05 Aligned_cols=34 Identities=18% Similarity=0.275 Sum_probs=18.4
Q ss_pred CcccCCCCCccceecCCCCceee-ccccccccccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGITFNWISGLE 316 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~ 316 (516)
....|+.|++.. +-.-..-.| .||.-||-.|...
T Consensus 8 ~~~~C~~C~~~F--~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKF--SLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B---BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcC--CCceeeEccCCCCCEECCchhCC
Confidence 468999999988 334556789 6999999999874
No 220
>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=32.13 E-value=66 Score=28.05 Aligned_cols=35 Identities=20% Similarity=0.351 Sum_probs=25.4
Q ss_pred CcccCCCCCccceecCCCCceee-ccccccccccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRC-KCGITFNWISGLE 316 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC-~C~~~FCw~C~~~ 316 (516)
+.+.|..|+.+.---++.. ..| .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 5789999998765544444 788 6999999999874
No 221
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=32.09 E-value=44 Score=25.68 Aligned_cols=30 Identities=33% Similarity=0.632 Sum_probs=21.5
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQFCF 246 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~ 246 (516)
..|| +|++...+-......|.|. ||+..+.
T Consensus 12 VkCp---~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCP---DCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECC---CCCCeEEEEecCCcEEECcccCCCccc
Confidence 4688 8999876655555678997 8887653
No 222
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=31.87 E-value=29 Score=26.22 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=8.6
Q ss_pred cccCCCCCccc
Q 043224 282 TKPCPKCCKPI 292 (516)
Q Consensus 282 tK~CPkC~~~I 292 (516)
.|+||.|+...
T Consensus 3 LkPCPFCG~~~ 13 (61)
T PF14354_consen 3 LKPCPFCGSAD 13 (61)
T ss_pred CcCCCCCCCcc
Confidence 58999998544
No 223
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=31.14 E-value=35 Score=38.89 Aligned_cols=48 Identities=31% Similarity=0.603 Sum_probs=35.6
Q ss_pred cccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 122 TFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 122 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
.+.|.||.-.+.....+-..|+|....+|.+.|+... . .||. ||+...
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~g----d----~Cps-GCGC~C 1075 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTG----D----VCPS-GCGCHC 1075 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcC----C----cCCC-CCCcCc
Confidence 4568888777766666667899999999999999863 2 6875 555443
No 224
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=31.14 E-value=36 Score=25.01 Aligned_cols=27 Identities=37% Similarity=0.744 Sum_probs=19.1
Q ss_pred cccCCCCCccceecCCCC--------ceeeccccc
Q 043224 282 TKPCPKCCKPIEKNGGCN--------MVRCKCGIT 308 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCn--------hMtC~C~~~ 308 (516)
.-.||+|+.-.--|++=+ +=+|+||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 468999998776665433 357888865
No 225
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.11 E-value=21 Score=35.87 Aligned_cols=30 Identities=30% Similarity=0.651 Sum_probs=21.6
Q ss_pred CcccCCCCCcc--ceecCCCCceeeccccccccccccc
Q 043224 281 HTKPCPKCCKP--IEKNGGCNMVRCKCGITFNWISGLE 316 (516)
Q Consensus 281 ntK~CPkC~~~--IEKn~GCnhMtC~C~~~FCw~C~~~ 316 (516)
.++.||-|+.+ |--..| +|||-|||.|...
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~------~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIG------KCGHIYCYYCIAT 269 (298)
T ss_pred CCceeeccCCCCCCCeeec------cccceeehhhhhh
Confidence 46899999874 334455 4777888888775
No 226
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.04 E-value=41 Score=40.14 Aligned_cols=53 Identities=26% Similarity=0.678 Sum_probs=39.5
Q ss_pred CCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCC
Q 043224 221 HCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGC 298 (516)
Q Consensus 221 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GC 298 (516)
-||--|-...++..-|-|. |+.-.|..|- ++. .+..++.||.|+....+--||
T Consensus 22 ICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY----------EYE---------------r~eG~q~CPqCktrYkr~kgs 75 (1079)
T PLN02638 22 ICGDNVGKTVDGEPFVACDVCAFPVCRPCY----------EYE---------------RKDGNQSCPQCKTKYKRHKGS 75 (1079)
T ss_pred ecccccCcCCCCCEEEEeccCCCccccchh----------hhh---------------hhcCCccCCccCCchhhhcCC
Confidence 5888877776666779998 9999999885 111 134568999999988876664
No 227
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=30.48 E-value=34 Score=26.82 Aligned_cols=18 Identities=22% Similarity=0.658 Sum_probs=13.0
Q ss_pred cccHHHHHHHHHhhhhcC
Q 043224 145 CFCNNCWTEHFIVKINDG 162 (516)
Q Consensus 145 ~fC~~C~~~yl~~~I~~g 162 (516)
-||++|+..|+..+-.+.
T Consensus 11 gFCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEER 28 (68)
T ss_dssp S--HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 499999999998886643
No 228
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=30.46 E-value=66 Score=24.49 Aligned_cols=32 Identities=13% Similarity=0.265 Sum_probs=27.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCChHHHHH
Q 043224 58 DLLRVMDLLSLKEKHARTLLIHYRWDVEKVFA 89 (516)
Q Consensus 58 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e 89 (516)
.+.+|++.||++......-...++|+...-++
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~~ 46 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLPIE 46 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCchh
Confidence 47899999999999999999999999755443
No 229
>PRK12495 hypothetical protein; Provisional
Probab=30.45 E-value=63 Score=31.47 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=21.1
Q ss_pred CcccCCCCCccceecCCCCceeeccccccccccccc
Q 043224 281 HTKPCPKCCKPIEKNGGCNMVRCKCGITFNWISGLE 316 (516)
Q Consensus 281 ntK~CPkC~~~IEKn~GCnhMtC~C~~~FCw~C~~~ 316 (516)
..+.||.|+.||.+..|| .||-.|...
T Consensus 41 sa~hC~~CG~PIpa~pG~---------~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ---------EFCPTCQQP 67 (226)
T ss_pred chhhcccccCcccCCCCe---------eECCCCCCc
Confidence 468999999999988885 566666654
No 230
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=30.10 E-value=2.7e+02 Score=27.19 Aligned_cols=58 Identities=12% Similarity=0.185 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043224 429 FEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIET 486 (516)
Q Consensus 429 Fe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~ 486 (516)
-|..|.+.+..-|++|....+.+..+....+.+||.-|+.++..--.+-++-+..+.+
T Consensus 155 aE~~~~~a~~~Fe~IS~~aK~El~rF~~~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~~~ 212 (218)
T cd07662 155 AETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQLLQS 212 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3888999999999999999998888877788888888877777766666666666653
No 231
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=30.00 E-value=53 Score=30.36 Aligned_cols=50 Identities=22% Similarity=0.506 Sum_probs=34.4
Q ss_pred CcccccccccccCCCCeeecCCCC---cccHHHHHHHHHhhhhcCCcccccccccccccccC
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGH---CFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCD 179 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH---~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~ 179 (516)
....|-||.++-. .......|.. ....+|+..|+... ...+|+. |+....
T Consensus 7 ~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYN 59 (162)
T ss_pred CCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEE
Confidence 4568999999853 2223335554 45899999999864 3568987 887544
No 232
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=29.97 E-value=40 Score=33.55 Aligned_cols=47 Identities=19% Similarity=0.347 Sum_probs=35.2
Q ss_pred ccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 123 FCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 123 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
..|+|=+-.+. ..+.+-.|||.|=++=+..++... ..|+||..+|..
T Consensus 177 ~rdPis~~~I~-nPviSkkC~HvydrDsI~~~l~~~------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 177 NRDPISKKPIV-NPVISKKCGHVYDRDSIMQILCDE------ITIRCPVLGCEN 223 (262)
T ss_pred ccCchhhhhhh-chhhhcCcCcchhhhhHHHHhccC------ceeecccccCCc
Confidence 46777655542 455677999999999888877652 579999999993
No 233
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=29.93 E-value=23 Score=29.01 Aligned_cols=29 Identities=34% Similarity=0.843 Sum_probs=13.9
Q ss_pred CcccCCCCC----c--cceecCCCCceee-cccccc
Q 043224 281 HTKPCPKCC----K--PIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 281 ntK~CPkC~----~--~IEKn~GCnhMtC-~C~~~F 309 (516)
.+=.||.|+ + .|.|..|=-+++| .||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 456899998 2 2334566667888 576554
No 234
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=29.91 E-value=33 Score=34.60 Aligned_cols=25 Identities=44% Similarity=1.100 Sum_probs=17.4
Q ss_pred cccCCCCCcccee--cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 306 (516)
.++||.|+.+|+| .+|=.-..| .|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 4799999999997 455444444 454
No 235
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=29.86 E-value=39 Score=34.18 Aligned_cols=47 Identities=28% Similarity=0.666 Sum_probs=35.9
Q ss_pred CCcccccccccccCC--CCeeecCCCCcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 120 SSTFCCNICCDDVSP--QEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 120 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
+....||||.+.+.. ..+..+.|||..-..|+..++-. . .+||. |..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 445669999998643 34556799999999999988754 2 68998 887
No 236
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.42 E-value=34 Score=34.48 Aligned_cols=22 Identities=45% Similarity=0.967 Sum_probs=16.0
Q ss_pred cccCCCCCcccee--cCCCCceee
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC 303 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC 303 (516)
.++||.|+.+|+| .+|=.-..|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~C 268 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFC 268 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEEC
Confidence 4699999999997 466444444
No 237
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.36 E-value=34 Score=34.60 Aligned_cols=25 Identities=44% Similarity=1.011 Sum_probs=19.0
Q ss_pred cccCCCCCcccee--cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 306 (516)
.++|+.|+.+|+| -+|=+--.| .|.
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4899999999998 467666666 554
No 238
>PRK10445 endonuclease VIII; Provisional
Probab=29.29 E-value=34 Score=34.33 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=18.2
Q ss_pred cccCCCCCcccee--cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 306 (516)
.++||.|+.+|++ .+|=.-..| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 5899999999997 466444555 453
No 239
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.16 E-value=36 Score=38.92 Aligned_cols=26 Identities=27% Similarity=0.671 Sum_probs=20.3
Q ss_pred ccCCCCCccceecCCCCceee-ccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
-.||+|..+..-..+=+.|.| .||+.
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCC
Confidence 589999988875445578999 79985
No 240
>cd07630 BAR_SNX_like The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of uncharacterized proteins with similarity to sorting nexins (SNXs), which are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=29.16 E-value=5.2e+02 Score=24.75 Aligned_cols=63 Identities=11% Similarity=0.222 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 423 KIKQNFFEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIE 485 (516)
Q Consensus 423 ~~~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e 485 (516)
..++..-|..|..++..-|.+|......+..|....+.++|.-|+.++..--.+-+..++.+.
T Consensus 131 ~~k~~~ae~~~~~a~~~fe~iS~~~k~EL~rF~~~Rv~~fk~~l~~~~E~~i~~ak~~~~~~~ 193 (198)
T cd07630 131 PQKKEQAEEAKKKAETEFEEISSLAKKELERFHRQRVLELQSALVCYAESQIKNAKEAAAVLT 193 (198)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567888899999999999999999888887777888887777766665555555555544
No 241
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.13 E-value=38 Score=38.82 Aligned_cols=34 Identities=24% Similarity=0.468 Sum_probs=24.8
Q ss_pred ccCCCCCccceecCCCCceee-ccccc-----cccccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGIT-----FNWISGLE 316 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~ 316 (516)
-.||+|..+..-...=|.++| .||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 379999988763333367999 79987 48888774
No 242
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.02 E-value=47 Score=33.62 Aligned_cols=34 Identities=26% Similarity=0.594 Sum_probs=25.5
Q ss_pred HHHHhcCcccCCCCCccceecCCCCceee-cccccc
Q 043224 275 LNWISSHTKPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 275 ~~wi~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
..|.. +.+-||+|+.+.+-..|=-.|.| .||+.+
T Consensus 105 ~~w~~-~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 105 LEWYR-SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHh-hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 35544 45899999999988777777888 677654
No 243
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=28.91 E-value=51 Score=24.97 Aligned_cols=30 Identities=30% Similarity=0.541 Sum_probs=18.6
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQFCF 246 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~ 246 (516)
..|| +|++.-.+-......|.|. ||...|.
T Consensus 8 VkCp---~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP---GCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T---TT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECC---CCCCeeEEEecCCeEEEcccCCCEecC
Confidence 3588 8999877655555679997 9998775
No 244
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.78 E-value=35 Score=34.43 Aligned_cols=22 Identities=32% Similarity=0.774 Sum_probs=16.1
Q ss_pred cccCCCCCcccee--cCCCCceee
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC 303 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC 303 (516)
.++||+|+.+|++ .+|=.--.|
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~C 267 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYC 267 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEEC
Confidence 5899999999997 466444444
No 245
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=28.70 E-value=35 Score=32.37 Aligned_cols=24 Identities=38% Similarity=0.985 Sum_probs=19.4
Q ss_pred cCCCCCccceecCCCCceee-ccccc
Q 043224 284 PCPKCCKPIEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 284 ~CPkC~~~IEKn~GCnhMtC-~C~~~ 308 (516)
.||+|+.+..+. +.|+|.| .|++.
T Consensus 151 ~~~~~g~~~~~~-~~~~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVKK-GENELKCPNCGNI 175 (189)
T ss_pred EccccCCceEEC-CCCEEECCCCCCE
Confidence 699999999884 4499999 79853
No 246
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=28.68 E-value=41 Score=25.83 Aligned_cols=26 Identities=31% Similarity=0.860 Sum_probs=18.8
Q ss_pred ccCCCCCcc----ceecCCCCceee-ccccc
Q 043224 283 KPCPKCCKP----IEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 283 K~CPkC~~~----IEKn~GCnhMtC-~C~~~ 308 (516)
-.||+|+.. .-+..|=.++.| .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 469999863 334566688999 79964
No 247
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.66 E-value=35 Score=34.56 Aligned_cols=25 Identities=44% Similarity=0.965 Sum_probs=18.2
Q ss_pred cccCCCCCcccee--cCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEK--NGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEK--n~GCnhMtC-~C~ 306 (516)
.++||.|+.+|+| .+|=.-..| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 4799999999987 466555555 453
No 248
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.63 E-value=40 Score=24.21 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=5.0
Q ss_pred ccCCCCCccc
Q 043224 283 KPCPKCCKPI 292 (516)
Q Consensus 283 K~CPkC~~~I 292 (516)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 4555555444
No 249
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=28.21 E-value=2.7e+02 Score=28.49 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=22.9
Q ss_pred cchhhhhhhhhhhhhhHHHHHhhhHHHHHH
Q 043224 327 ERPEHGKWRLESYYHCHKLYKAHTESFRLE 356 (516)
Q Consensus 327 ~~~~~~~~~l~ry~hy~~r~~~h~~s~k~e 356 (516)
.++.+|-+.|++|.+-++|-.+....+.+|
T Consensus 151 ~ranQAi~TLEkYk~~Ld~~~~~L~~lEle 180 (349)
T COG1623 151 SRANQAIQTLEKYKTVLDRVLNQLNLLELE 180 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhHHHh
Confidence 355678888999999999877766666655
No 250
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=28.16 E-value=51 Score=39.21 Aligned_cols=55 Identities=33% Similarity=0.795 Sum_probs=39.1
Q ss_pred CCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCCC
Q 043224 221 HCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGCN 299 (516)
Q Consensus 221 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCn 299 (516)
-||--|-...++..-|-|. |+.-.|..|-+ +. .+..++.||.|+.+..+--|++
T Consensus 20 iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye----------ye---------------~~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 20 VCGDEVGVKEDGQPFVACHVCGFPVCKPCYE----------YE---------------RSEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred ccccccCcCCCCCEEEEeccCCCccccchhh----------hh---------------hhcCCccCCccCCchhhhcCCC
Confidence 5777777666666779998 99999998851 10 1345689999999888655654
Q ss_pred c
Q 043224 300 M 300 (516)
Q Consensus 300 h 300 (516)
.
T Consensus 75 ~ 75 (1044)
T PLN02915 75 R 75 (1044)
T ss_pred C
Confidence 3
No 251
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.12 E-value=30 Score=40.81 Aligned_cols=33 Identities=30% Similarity=0.547 Sum_probs=25.1
Q ss_pred hcCcccCCCCCccceecCCCCceee-ccccc-----ccccccccc
Q 043224 279 SSHTKPCPKCCKPIEKNGGCNMVRC-KCGIT-----FNWISGLEY 317 (516)
Q Consensus 279 ~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~~-----FCw~C~~~w 317 (516)
....+.||.|+... ..-.| .||.. ||-.|+..-
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcC
Confidence 34578999999885 55788 69854 899998764
No 252
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=27.92 E-value=63 Score=24.35 Aligned_cols=27 Identities=37% Similarity=0.759 Sum_probs=19.7
Q ss_pred cCCCCCCCCceEeecCC-Ccceeecc-CCccc
Q 043224 215 WCPSVPHCGNAIQVEAD-ELCEVECA-CGFQF 244 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~-~~~~v~C~-Cg~~f 244 (516)
-|| .|+.-|.+++. ..-.|.|+ ||..+
T Consensus 4 ~CP---~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP---DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC---CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 588 79999987652 23468897 88765
No 253
>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=27.88 E-value=25 Score=30.46 Aligned_cols=14 Identities=36% Similarity=0.845 Sum_probs=11.4
Q ss_pred Cceeeccccccccc
Q 043224 299 NMVRCKCGITFNWI 312 (516)
Q Consensus 299 nhMtC~C~~~FCw~ 312 (516)
.-+.|.|||+||-.
T Consensus 23 k~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 23 KVVKCDCGHEFCDA 36 (112)
T ss_pred ceeeccCCCeecCh
Confidence 37899999999843
No 254
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=27.78 E-value=23 Score=26.27 Aligned_cols=24 Identities=29% Similarity=0.764 Sum_probs=13.1
Q ss_pred ccCCCCCccceecCCC--Cceee-ccc
Q 043224 283 KPCPKCCKPIEKNGGC--NMVRC-KCG 306 (516)
Q Consensus 283 K~CPkC~~~IEKn~GC--nhMtC-~C~ 306 (516)
-+|++|+..+-+-++= -.+.| +||
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCC
Confidence 3566666666664322 24566 565
No 255
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=27.66 E-value=39 Score=33.79 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=22.9
Q ss_pred HHHhcCcccCCCCCccceecCCCCceee-cccc
Q 043224 276 NWISSHTKPCPKCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 276 ~wi~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~ 307 (516)
.| ..+.+-||+|+.++....|=..+.| .|+.
T Consensus 94 ~w-~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 94 EF-YRSHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred HH-hhcCccccccCCCCeecCCceeEECCCCCC
Confidence 44 3457999999999887555467888 7874
No 256
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=27.51 E-value=41 Score=26.83 Aligned_cols=26 Identities=38% Similarity=0.926 Sum_probs=19.0
Q ss_pred ccCCCCCcc----ceecCCCCceee-ccccc
Q 043224 283 KPCPKCCKP----IEKNGGCNMVRC-KCGIT 308 (516)
Q Consensus 283 K~CPkC~~~----IEKn~GCnhMtC-~C~~~ 308 (516)
-.||+|+.. .-+..|=.++.| .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 369999863 234566789999 79964
No 257
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=26.70 E-value=92 Score=22.26 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=16.2
Q ss_pred CcccCCCCCcc-ceecCCCCceee-cccc
Q 043224 281 HTKPCPKCCKP-IEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 281 ntK~CPkC~~~-IEKn~GCnhMtC-~C~~ 307 (516)
+.-.||+|+.. +-+..+=....| .|++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 44669999974 333344345666 4665
No 258
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.56 E-value=52 Score=28.66 Aligned_cols=38 Identities=24% Similarity=0.668 Sum_probs=25.6
Q ss_pred ccCCCCCCCCceEeecC-------CCcceeecc-CCcccccccccccCC
Q 043224 214 KWCPSVPHCGNAIQVEA-------DELCEVECA-CGFQFCFSCSSVAHS 254 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~-------~~~~~v~C~-Cg~~fC~~C~~~~H~ 254 (516)
+.|- +|+..+.... .......|+ |+..||..|..-+|.
T Consensus 56 ~~C~---~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF---GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc---CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4575 6887665321 123357897 999999999766664
No 259
>PLN02436 cellulose synthase A
Probab=26.44 E-value=60 Score=38.75 Aligned_cols=56 Identities=29% Similarity=0.674 Sum_probs=40.3
Q ss_pred CCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCCC
Q 043224 221 HCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGCN 299 (516)
Q Consensus 221 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCn 299 (516)
-||--|-...++..-|-|. |+.-.|..|-+ +. .+..++.||.|+.+..+--|++
T Consensus 41 ICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye----------ye---------------r~eg~~~Cpqckt~Y~r~kgs~ 95 (1094)
T PLN02436 41 ICGDEIELTVDGEPFVACNECAFPVCRPCYE----------YE---------------RREGNQACPQCKTRYKRIKGSP 95 (1094)
T ss_pred ccccccCcCCCCCEEEeeccCCCccccchhh----------hh---------------hhcCCccCcccCCchhhccCCC
Confidence 5887777666666779998 99999998851 10 1345689999999888766654
Q ss_pred ce
Q 043224 300 MV 301 (516)
Q Consensus 300 hM 301 (516)
.+
T Consensus 96 ~~ 97 (1094)
T PLN02436 96 RV 97 (1094)
T ss_pred Cc
Confidence 43
No 260
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=26.17 E-value=36 Score=33.62 Aligned_cols=35 Identities=23% Similarity=0.705 Sum_probs=0.0
Q ss_pred HHHHHhcCcccCCCCCcc-cee---cCCCCceee-cccccc
Q 043224 274 SLNWISSHTKPCPKCCKP-IEK---NGGCNMVRC-KCGITF 309 (516)
Q Consensus 274 ~~~wi~~ntK~CPkC~~~-IEK---n~GCnhMtC-~C~~~F 309 (516)
|..|+..| -.||+|+.. +.+ |.-=--..| .|+.+|
T Consensus 24 tE~Wv~~n-~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 24 TEDWVAEN-MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp HHHHHHHH----TTT--SS-EE--------EEE-TTT--EE
T ss_pred HHHHHHHC-CcCCCCCChhHhhccCCCccceeECCCCchHH
No 261
>PF14353 CpXC: CpXC protein
Probab=25.87 E-value=13 Score=32.81 Aligned_cols=51 Identities=22% Similarity=0.427 Sum_probs=31.1
Q ss_pred ccccccccccccCHHHHHHhhCCCChHHHHHHHHHHHHHhhhcCCCcccCCCCCCCCceEeecC
Q 043224 167 IKCMALKCNVVCDEAKIRCLVSARDSNIADKFERFLLESYIDDNRRVKWCPSVPHCGNAIQVEA 230 (516)
Q Consensus 167 i~CP~~~C~~~i~~~~i~~ll~~~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~ 230 (516)
|+||. |+.....+....+-...+|++.++.. +..-...-|| .||..+.+..
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~il--------~g~l~~~~CP---~Cg~~~~~~~ 52 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEKIL--------DGSLFSFTCP---SCGHKFRLEY 52 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHHHH--------cCCcCEEECC---CCCCceecCC
Confidence 78997 99877665554444444566555422 2222445688 6998877643
No 262
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=25.87 E-value=1.5e+02 Score=25.94 Aligned_cols=36 Identities=22% Similarity=0.200 Sum_probs=30.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHH
Q 043224 56 MGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVL 91 (516)
Q Consensus 56 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~ 91 (516)
.++|.-|++..|+|...|+..|...+||.-..+-.+
T Consensus 77 ~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L 112 (115)
T PRK06369 77 EEDIELVAEQTGVSEEEARKALEEANGDLAEAILKL 112 (115)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHH
Confidence 467889999999999999999999999976655443
No 263
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=25.72 E-value=49 Score=28.33 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=20.0
Q ss_pred CCCCcccHHHHHHHHHhhhhcCCcccccccc
Q 043224 141 DCGHCFCNNCWTEHFIVKINDGQSRRIKCMA 171 (516)
Q Consensus 141 ~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~ 171 (516)
.|+|.|..-|+..+|.+. -.||.
T Consensus 80 ~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc--------CcCCC
Confidence 699999999999999874 46886
No 264
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=25.47 E-value=54 Score=34.34 Aligned_cols=12 Identities=33% Similarity=1.071 Sum_probs=9.7
Q ss_pred cccCCCCCccce
Q 043224 282 TKPCPKCCKPIE 293 (516)
Q Consensus 282 tK~CPkC~~~IE 293 (516)
.+.||-|+.|+-
T Consensus 334 qQTCPICr~p~i 345 (491)
T COG5243 334 QQTCPICRRPVI 345 (491)
T ss_pred ccCCCcccCccc
Confidence 378999999954
No 265
>PHA02325 hypothetical protein
Probab=25.34 E-value=32 Score=26.69 Aligned_cols=12 Identities=50% Similarity=0.894 Sum_probs=9.7
Q ss_pred CcccCCCCCccc
Q 043224 281 HTKPCPKCCKPI 292 (516)
Q Consensus 281 ntK~CPkC~~~I 292 (516)
++|.||+|++.-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 579999998754
No 266
>PLN03086 PRLI-interacting factor K; Provisional
Probab=25.27 E-value=37 Score=37.85 Aligned_cols=30 Identities=37% Similarity=0.804 Sum_probs=23.2
Q ss_pred cCcccCCC--CCccceecCCCCceee-cccccc
Q 043224 280 SHTKPCPK--CCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 280 ~ntK~CPk--C~~~IEKn~GCnhMtC-~C~~~F 309 (516)
.+...||+ |+..+.+...=+|..| .|+..|
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCcc
Confidence 35678885 8888888888888888 687554
No 267
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.25 E-value=62 Score=28.18 Aligned_cols=28 Identities=32% Similarity=1.003 Sum_probs=18.2
Q ss_pred cccCCCCCCCCceEeecCC-Ccceeecc-CCcc
Q 043224 213 VKWCPSVPHCGNAIQVEAD-ELCEVECA-CGFQ 243 (516)
Q Consensus 213 ~~~CP~~p~C~~~i~~~~~-~~~~v~C~-Cg~~ 243 (516)
+++|| .|+..+.+..+ ......|+ ||+.
T Consensus 2 m~FCp---~Cgsll~p~~~~~~~~l~C~kCgye 31 (113)
T COG1594 2 MRFCP---KCGSLLYPKKDDEGGKLVCRKCGYE 31 (113)
T ss_pred ccccC---CccCeeEEeEcCCCcEEECCCCCcc
Confidence 56898 79999987532 22246665 6653
No 268
>cd07663 BAR_SNX5 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It
Probab=25.24 E-value=3.7e+02 Score=26.30 Aligned_cols=58 Identities=17% Similarity=0.233 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043224 429 FEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIET 486 (516)
Q Consensus 429 Fe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~ 486 (516)
-|..|.+.+..-|++|....+.+..+....+.+||.-++.++..-=++-+.-+..+.+
T Consensus 155 aE~~~~ea~~~Fe~IS~~~k~El~rF~~~Rv~~Fk~~lve~~E~~ik~ak~~~~~~~~ 212 (218)
T cd07663 155 AEAHQQECCQKFEKLSESAKQELISFKRRRVAAFRKNLIEMTELEIKHAKNNVSLLQS 212 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677888999999999999988888877788888887777777666666666665553
No 269
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=25.23 E-value=1.6e+02 Score=25.83 Aligned_cols=34 Identities=21% Similarity=0.211 Sum_probs=29.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhCCChHHHHH
Q 043224 56 MGDLLRVMDLLSLKEKHARTLLIHYRWDVEKVFA 89 (516)
Q Consensus 56 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e 89 (516)
.++|.-|++..|+|...|+..|...+||.-..+-
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~ 112 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEECGGDLAEAIM 112 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHH
Confidence 4678999999999999999999999999765543
No 270
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.84 E-value=62 Score=26.68 Aligned_cols=31 Identities=29% Similarity=0.607 Sum_probs=23.5
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCcccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQFCFS 247 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~ 247 (516)
+-|| +|++.-.+-......|.|. ||...|.-
T Consensus 36 VkCp---~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 36 VKCP---GCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred EECC---CCCCeeEEEecCceEEEccccCCEeecc
Confidence 4698 8999877655556679997 99988753
No 271
>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=24.78 E-value=35 Score=24.12 Aligned_cols=26 Identities=27% Similarity=0.657 Sum_probs=15.0
Q ss_pred CCCCceEeecCCCcceeecc-CCcccccccccc
Q 043224 220 PHCGNAIQVEADELCEVECA-CGFQFCFSCSSV 251 (516)
Q Consensus 220 p~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~ 251 (516)
++|+.... ..+.|+ |+..||...+.+
T Consensus 4 ~~C~~~~~------~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 4 PGCKKKDF------LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp TTT--BCT------SHEE-TTTS-EE-TTTHST
T ss_pred CcCcCccC------CCeECCCCCcccCccccCc
Confidence 56765544 248998 999999988753
No 272
>PLN00209 ribosomal protein S27; Provisional
Probab=24.67 E-value=63 Score=26.70 Aligned_cols=30 Identities=27% Similarity=0.465 Sum_probs=23.0
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGFQFCF 246 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~fC~ 246 (516)
+-|| +|++.-.+-......|.|. ||...|.
T Consensus 37 VkCp---~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ---GCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC---CCCCeeEEEecCceEEEccccCCEeec
Confidence 4698 8999877655556679997 9988875
No 273
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.64 E-value=43 Score=31.79 Aligned_cols=23 Identities=43% Similarity=1.152 Sum_probs=17.2
Q ss_pred ccCCCCCccceecCCCCceee-cccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~ 307 (516)
-.|++|+.+.++ .| +.|+| +||+
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCCC
Confidence 478888888888 33 77888 7874
No 274
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=24.50 E-value=47 Score=28.58 Aligned_cols=26 Identities=35% Similarity=0.928 Sum_probs=18.1
Q ss_pred cccCCCCCc-cceecCCCCceee-cccccc
Q 043224 282 TKPCPKCCK-PIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 282 tK~CPkC~~-~IEKn~GCnhMtC-~C~~~F 309 (516)
.-+||+|.. ..-.++| +|.| -|.++|
T Consensus 3 lp~cp~c~sEytYed~~--~~~cpec~~ew 30 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG--QLICPECAHEW 30 (112)
T ss_pred CCCCCccCCceEEecCc--eEeCchhcccc
Confidence 358999965 5556666 7887 577654
No 275
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=24.40 E-value=45 Score=22.30 Aligned_cols=22 Identities=36% Similarity=1.004 Sum_probs=8.7
Q ss_pred CCCCCccceecCCCCceee-cccc
Q 043224 285 CPKCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 285 CPkC~~~IEKn~GCnhMtC-~C~~ 307 (516)
|..|+..++-..+ .-+.| .||+
T Consensus 3 C~~Cg~~~~~~~~-~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPG-DPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTS-STSSBSSSS-
T ss_pred CCcCCCeeEcCCC-CcEECCcCCC
Confidence 4455554443222 33455 3554
No 276
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.35 E-value=84 Score=28.99 Aligned_cols=32 Identities=19% Similarity=0.365 Sum_probs=19.3
Q ss_pred cCCCcccCCCCCCCCceEeecCCCcceeecc-CCcc
Q 043224 209 DNRRVKWCPSVPHCGNAIQVEADELCEVECA-CGFQ 243 (516)
Q Consensus 209 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~~ 243 (516)
.++.+-.|| .|+.-+.....-...+.|| ||..
T Consensus 105 ~~~~~Y~Cp---~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICP---NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECC---CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 445666799 5886665544323357777 7753
No 277
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=24.29 E-value=1.1e+03 Score=27.09 Aligned_cols=104 Identities=11% Similarity=0.041 Sum_probs=51.9
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhhhcccccchhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc----c
Q 043224 380 FGWIKDGLNKLFRARRILSFSYPFAFYMFADDLLKNEMTREERKIKQNFFEDQQQQFETNIERLSLILEENFEKY----S 455 (516)
Q Consensus 380 ~~fl~~a~~~l~~~R~~L~~sY~~~yyl~~~~~~~~~~~~~~~~~~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~----~ 455 (516)
..++..|.+.|..-|..|+-.|=|- ..+-+.+|.++-+.+ =-.+|.+.=.++...+|.|...+.+--... .
T Consensus 230 ~~~fp~a~e~L~~r~~~L~~k~~~L--~~e~~~LK~ELiedR---W~~vFr~l~~q~~~m~esver~~~kl~~~~~~~~~ 304 (683)
T PF08580_consen 230 ESIFPSACEELEDRYERLEKKWKKL--EKEAESLKKELIEDR---WNIVFRNLGRQAQKMCESVERSLSKLQEAIDSGIH 304 (683)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHhhhhh---HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 4556677777777777776666421 111112222222111 124677777777777777766665432211 0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043224 456 EHQLKDFRMRVITQSVTADYLCRNLYEWIETDL 488 (516)
Q Consensus 456 ~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~~l 488 (516)
...-..+-.+|.++.+.+.+++..++++++..+
T Consensus 305 ~~~~~~l~~~i~s~~~k~~~~~~~I~ka~~~sI 337 (683)
T PF08580_consen 305 LDNPSKLSKQIESKEKKKSHYFPAIYKARVLSI 337 (683)
T ss_pred ccchHHHHHHHHHHHHHHhccHHHHHHHHHHHh
Confidence 011112334555555555555555555544443
No 278
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=24.06 E-value=24 Score=39.99 Aligned_cols=56 Identities=25% Similarity=0.557 Sum_probs=40.4
Q ss_pred CcccccccccccCCCCeeecCCCCcccHHHHHHHHHhhhhcCCcccccccccccccccCHHHHHH
Q 043224 121 STFCCNICCDDVSPQEVTTMDCGHCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVCDEAKIRC 185 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i~~~~i~~ 185 (516)
...+|+||+..+. ....+.|.|.||..||..-+...-. ...||. |+..++...++.
T Consensus 20 k~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 20 KILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred hhccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhhhccc
Confidence 3568999999863 3467899999999999887765422 467877 876665544443
No 279
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.93 E-value=92 Score=28.25 Aligned_cols=19 Identities=32% Similarity=0.543 Sum_probs=13.7
Q ss_pred HHHHHHcCCCHHHHHHHHH
Q 043224 60 LRVMDLLSLKEKHARTLLI 78 (516)
Q Consensus 60 ~~v~~~l~i~~~~a~~LL~ 78 (516)
.+++..||++....+.+|.
T Consensus 19 edLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 19 EDLAELLGIKQKQLRKILY 37 (147)
T ss_pred HHHHHHhCCCHHHHHHHHH
Confidence 3456777888888777775
No 280
>PLN02400 cellulose synthase
Probab=23.90 E-value=65 Score=38.53 Aligned_cols=55 Identities=27% Similarity=0.649 Sum_probs=38.5
Q ss_pred CCCceEeecCCCcceeecc-CCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCccceecCCCC
Q 043224 221 HCGNAIQVEADELCEVECA-CGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEKNGGCN 299 (516)
Q Consensus 221 ~C~~~i~~~~~~~~~v~C~-Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEKn~GCn 299 (516)
-||--|-...+...-|-|. |+.-.|.-|-+ +. .+..++.||.|+....+--||.
T Consensus 41 ICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE----------YE---------------RkeGnq~CPQCkTrYkR~Kgsp 95 (1085)
T PLN02400 41 ICGDDVGVTETGDVFVACNECAFPVCRPCYE----------YE---------------RKDGTQCCPQCKTRYRRHKGSP 95 (1085)
T ss_pred ecccccCcCCCCCEEEEEccCCCccccchhh----------ee---------------cccCCccCcccCCccccccCCC
Confidence 5877777666666779997 99999998852 10 1234578888888877665654
Q ss_pred c
Q 043224 300 M 300 (516)
Q Consensus 300 h 300 (516)
.
T Consensus 96 r 96 (1085)
T PLN02400 96 R 96 (1085)
T ss_pred C
Confidence 3
No 281
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.89 E-value=26 Score=40.52 Aligned_cols=76 Identities=24% Similarity=0.339 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-Hhhcc---ccHHHHHHHHHH-----------HHHHHHHHHHHHHHHH--------HHH
Q 043224 428 FFEDQQQQFETNIERLSLILE-ENFEK---YSEHQLKDFRMR-----------VITQSVTADYLCRNLY--------EWI 484 (516)
Q Consensus 428 lFe~~Q~~le~~~E~Ls~~le-~~~~~---~~~~~~~~~r~~-----------~~~~t~~~~~~~~~l~--------~~~ 484 (516)
|=.+.=.++--.+|+|.++=- .++.. ..++++.++|.+ +...+++|+..+.++| +..
T Consensus 776 lTHfrP~EIgvsvEkLrELGY~~Di~G~pL~~~dQivELk~QDIils~~aaeyllkva~FIDdLLek~Ygle~fYnv~~~ 855 (900)
T PF03833_consen 776 LTHFRPREIGVSVEKLRELGYTHDIYGKPLESDDQIVELKVQDIILSEDAAEYLLKVAKFIDDLLEKYYGLEPFYNVEKR 855 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccHHhcCCCHHHHHHhCccccccCCccCCccceeEeehhcEecchhHHHHHHHHHHHHHHHHHHHhCCCcccCCCCh
Confidence 344555566777777766521 22110 112334444433 3345555666555542 223
Q ss_pred HhhhhhhhcccccccCCCCCchh
Q 043224 485 ETDLLGSLKHSVHKIAPFNSAAV 507 (516)
Q Consensus 485 e~~l~~~~~~~~~~~~~~~~~~~ 507 (516)
| +|.|-|. ..+||-.|.|+
T Consensus 856 e-DLIGhLV---iGLAPHTSaGv 874 (900)
T PF03833_consen 856 E-DLIGHLV---IGLAPHTSAGV 874 (900)
T ss_dssp -----------------------
T ss_pred h-hhhceee---ecccCccccce
Confidence 3 6766544 55677766665
No 282
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=23.89 E-value=61 Score=32.11 Aligned_cols=56 Identities=18% Similarity=0.277 Sum_probs=32.1
Q ss_pred HHhhCCCChHHHHHHHHHHHHH-hhhcCC-CcccCCCCCCCCceEeecC-----CCcceeecc-CCc
Q 043224 184 RCLVSARDSNIADKFERFLLES-YIDDNR-RVKWCPSVPHCGNAIQVEA-----DELCEVECA-CGF 242 (516)
Q Consensus 184 ~~ll~~~~~e~~~~y~~~~~~~-~v~~~~-~~~~CP~~p~C~~~i~~~~-----~~~~~v~C~-Cg~ 242 (516)
..|..+-+|+++..|++..... -+-.-+ .-.-|- +|...+.... .....|+|| ||.
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~---GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG---GCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc---CCeeeecHHHHHHHhcCCCCccCCccch
Confidence 3444444689999999877654 111111 123475 7888877432 233457776 764
No 283
>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=23.73 E-value=53 Score=20.55 Aligned_cols=8 Identities=50% Similarity=1.406 Sum_probs=4.9
Q ss_pred cccCCCCC
Q 043224 282 TKPCPKCC 289 (516)
Q Consensus 282 tK~CPkC~ 289 (516)
.=.||+|+
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34677775
No 284
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=23.45 E-value=6.2e+02 Score=23.77 Aligned_cols=60 Identities=17% Similarity=0.144 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 425 KQNFFEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLYEWIE 485 (516)
Q Consensus 425 ~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e 485 (516)
...+++.++..++..++.|...++..-...-.-.+..-|++|.++..-+.+.-..+-+ +|
T Consensus 86 R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr~e~ee~~~~l~~le~~~~~-~e 145 (175)
T PRK13182 86 DFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEEMLERLQKLEARLKK-LE 145 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhHHHHHHHHHHHHHHHHHHHH-HH
Confidence 4578888889999988888888876543333334667788998887776665555544 44
No 285
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.26 E-value=53 Score=29.41 Aligned_cols=23 Identities=43% Similarity=1.133 Sum_probs=15.4
Q ss_pred ccCCCCCCCCceEeecCCCcceeecc-CCc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECA-CGF 242 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~ 242 (516)
..|| -||..+...++ .|.|| ||+
T Consensus 29 ~hCp---~Cg~PLF~KdG---~v~CPvC~~ 52 (131)
T COG1645 29 KHCP---KCGTPLFRKDG---EVFCPVCGY 52 (131)
T ss_pred hhCc---ccCCcceeeCC---eEECCCCCc
Confidence 4798 69998887443 36665 554
No 286
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=23.00 E-value=61 Score=26.44 Aligned_cols=17 Identities=24% Similarity=0.593 Sum_probs=16.2
Q ss_pred CCCCcccHHHHHHHHHh
Q 043224 141 DCGHCFCNNCWTEHFIV 157 (516)
Q Consensus 141 ~CgH~fC~~C~~~yl~~ 157 (516)
-|.|.|...|+.++|.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 69999999999999998
No 287
>PRK11426 hypothetical protein; Provisional
Probab=22.99 E-value=1.3e+02 Score=26.97 Aligned_cols=46 Identities=20% Similarity=0.206 Sum_probs=36.5
Q ss_pred ccccCHHHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHhCCChHHHHHHH
Q 043224 43 SMVIPKESLLAAQMG-DLLRVMDLLSLKEKHARTLLIHYRWDVEKVFAVL 91 (516)
Q Consensus 43 ~~vlt~~~i~~~~~~-~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~e~~ 91 (516)
-.-+++++|...+-. .|++++.-+|+++++|...|..+ .-.+++++
T Consensus 58 N~pIs~~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA~~---LP~~VDkl 104 (132)
T PRK11426 58 NQSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQ---LPKIIDAL 104 (132)
T ss_pred CCCCCHHHHHHHhChHHHHHHHHHHCcCHHHHHHHHHHH---hHHHHhcc
Confidence 477999999999975 59999999999999998888754 34444443
No 288
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.98 E-value=41 Score=35.47 Aligned_cols=23 Identities=48% Similarity=1.058 Sum_probs=13.9
Q ss_pred ccCCCCCccceecCCCCceee-cccccc
Q 043224 283 KPCPKCCKPIEKNGGCNMVRC-KCGITF 309 (516)
Q Consensus 283 K~CPkC~~~IEKn~GCnhMtC-~C~~~F 309 (516)
+.||+|+. ++++| .|.| +||+.|
T Consensus 2 ~fC~kcG~--qk~Ed--~~qC~qCG~~~ 25 (465)
T COG4640 2 KFCPKCGS--QKAED--DVQCTQCGHKF 25 (465)
T ss_pred Cccccccc--ccccc--cccccccCCcC
Confidence 57888885 34443 2447 577554
No 289
>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=22.96 E-value=59 Score=24.67 Aligned_cols=43 Identities=23% Similarity=0.572 Sum_probs=30.0
Q ss_pred cccccccccCCCCeeecCCC--CcccHHHHHHHHHhhhhcCCccccccccccccccc
Q 043224 124 CCNICCDDVSPQEVTTMDCG--HCFCNNCWTEHFIVKINDGQSRRIKCMALKCNVVC 178 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~~i 178 (516)
.|..|-.+++.+..-..-|. ..||.+|....+.. .||. |+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~----------~CPN--CgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG----------VCPN--CGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC----------cCcC--CCCcc
Confidence 58888888887664455555 36999998876632 5886 77543
No 290
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=22.86 E-value=69 Score=34.19 Aligned_cols=25 Identities=24% Similarity=0.740 Sum_probs=14.6
Q ss_pred cccCCCCCccce-e--cCCC----Cceee-ccc
Q 043224 282 TKPCPKCCKPIE-K--NGGC----NMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IE-K--n~GC----nhMtC-~C~ 306 (516)
.=.|--|+..+. + ..|| ||+.| .|+
T Consensus 427 CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch 459 (468)
T KOG1701|consen 427 CYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCH 459 (468)
T ss_pred ceehhhcCccccccCCCCcceeccCceeechhh
Confidence 345666776654 2 4566 56777 464
No 291
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=22.78 E-value=1.9e+02 Score=25.05 Aligned_cols=23 Identities=30% Similarity=0.621 Sum_probs=15.7
Q ss_pred cCCcccccccccccCCCCCchhHHHHhHHhH
Q 043224 239 ACGFQFCFSCSSVAHSPCSCLMWELWSKKFE 269 (516)
Q Consensus 239 ~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~ 269 (516)
+|++.+|..|+. ....+|..+..
T Consensus 57 SCk~R~CP~C~~--------~~~~~W~~~~~ 79 (111)
T PF14319_consen 57 SCKNRHCPSCQA--------KATEQWIEKQR 79 (111)
T ss_pred cccCcCCCCCCC--------hHHHHHHHHHH
Confidence 699999999973 34456665543
No 292
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.57 E-value=32 Score=31.80 Aligned_cols=29 Identities=17% Similarity=0.413 Sum_probs=20.8
Q ss_pred CCCcccccccccccCCCCe-eecCCCCccc
Q 043224 119 CSSTFCCNICCDDVSPQEV-TTMDCGHCFC 147 (516)
Q Consensus 119 ~~~~~~C~IC~e~~~~~~~-~~l~CgH~fC 147 (516)
.....+|.||+|++...+. ..|+|-..|.
T Consensus 174 ~ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred cccCCcEEEEhhhccCCCceeccceEEEee
Confidence 3457899999999877554 4578865543
No 293
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.45 E-value=48 Score=25.24 Aligned_cols=24 Identities=29% Similarity=0.736 Sum_probs=17.0
Q ss_pred hcCcccCCCCCccceecCCCCceee-cccc
Q 043224 279 SSHTKPCPKCCKPIEKNGGCNMVRC-KCGI 307 (516)
Q Consensus 279 ~~ntK~CPkC~~~IEKn~GCnhMtC-~C~~ 307 (516)
..+.-.||+|+.++.. |-.| .||+
T Consensus 24 ~~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC-----eEECCCCCc
Confidence 3466789999998875 5566 5653
No 294
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.39 E-value=50 Score=29.62 Aligned_cols=24 Identities=46% Similarity=1.121 Sum_probs=17.5
Q ss_pred ccCCCCCCCCceEeecCCCcceeeccCCcccccc
Q 043224 214 KWCPSVPHCGNAIQVEADELCEVECACGFQFCFS 247 (516)
Q Consensus 214 ~~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~ 247 (516)
--|| .|++..- -+.|.||..||+.
T Consensus 78 PgCP---~CGn~~~-------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 78 PGCP---HCGNQYA-------FAVCGCGKLFCID 101 (131)
T ss_pred CCCC---CCcChhc-------EEEecCCCEEEeC
Confidence 3466 7887643 3789999999983
No 295
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.29 E-value=62 Score=32.24 Aligned_cols=54 Identities=17% Similarity=0.431 Sum_probs=38.1
Q ss_pred CcccccccccccCCCCee--ecCCC-----CcccHHHHHHHHHhhhhcCCccccccccccccc
Q 043224 121 STFCCNICCDDVSPQEVT--TMDCG-----HCFCNNCWTEHFIVKINDGQSRRIKCMALKCNV 176 (516)
Q Consensus 121 ~~~~C~IC~e~~~~~~~~--~l~Cg-----H~fC~~C~~~yl~~~I~~g~~~~i~CP~~~C~~ 176 (516)
.+-.|=|||.+-..+... .-+|. |-....|+..|+.++-..+...++.||+ |..
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqT 79 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQT 79 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcc
Confidence 356799999985433222 12453 5588999999999987644456899998 886
No 296
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=22.24 E-value=3.2e+02 Score=26.71 Aligned_cols=47 Identities=15% Similarity=0.220 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 428 FFEDQQQQFETNIERLSLILEENFEKYSEHQLKDFRMRVITQSVTADYLCRNLY 481 (516)
Q Consensus 428 lFe~~Q~~le~~~E~Ls~~le~~~~~~~~~~~~~~r~~~~~~t~~~~~~~~~l~ 481 (516)
++|.. ..++.++|.+..++|.+.. ....|..++.|-..+..|.++|=
T Consensus 177 ayek~-ek~eealeDyKki~E~dPs------~~ear~~i~rl~~~i~ernEkmK 223 (271)
T KOG4234|consen 177 AYEKM-EKYEEALEDYKKILESDPS------RREAREAIARLPPKINERNEKMK 223 (271)
T ss_pred HHHhh-hhHHHHHHHHHHHHHhCcc------hHHHHHHHHhcCHHHHHHHHHHH
Confidence 44444 5688999999999997543 33678888888888888888873
No 297
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.20 E-value=54 Score=33.77 Aligned_cols=36 Identities=17% Similarity=0.496 Sum_probs=25.8
Q ss_pred cccccccccCCCCeeec-CCCCcccHHHHHHHHHhhhh
Q 043224 124 CCNICCDDVSPQEVTTM-DCGHCFCNNCWTEHFIVKIN 160 (516)
Q Consensus 124 ~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yl~~~I~ 160 (516)
.|-.|.++......+.. .|.+.||.+| ..|+...+.
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldC-Dv~iHesLh 368 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDC-DVFIHESLH 368 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccc-hHHHHhhhh
Confidence 49999777655555665 8999999999 455665543
No 298
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=21.98 E-value=6.7e+02 Score=23.61 Aligned_cols=104 Identities=15% Similarity=0.118 Sum_probs=57.1
Q ss_pred HHHHHHhhccCCCCchhhHHHHHHHHHHHHHHHHhhhhhhhhcccccchhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 364 QDKIKILGEKDTSSKDFGWIKDGLNKLFRARRILSFSYPFAFYMFADDLLKNEMTREERKIKQNFFEDQQQQFETNIERL 443 (516)
Q Consensus 364 ~~k~~~~~~~~~~~~~~~fl~~a~~~l~~~R~~L~~sY~~~yyl~~~~~~~~~~~~~~~~~~~~lFe~~Q~~le~~~E~L 443 (516)
++++..+++......+.+-.....+...-+|+++. ++.. .|++-..-+.+|.++.-.+..-+|+.
T Consensus 81 ~~~i~~i~~~~~~i~~~~~~~~~~~~~~~~~~I~~-------~v~~--------~P~~l~~a~~Fl~~yLp~~~~l~~kY 145 (199)
T PF10112_consen 81 KEKIRRIEKAIKRIRDLEMIEKVSRIEKIARRIFK-------YVEK--------DPERLTQARKFLYYYLPTAVKLLEKY 145 (199)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH-------HHHH--------CHHhHHHHHHHHHHHhhHHHHHHHHH
Confidence 34444444432233444445555556666666654 2221 25555566778888888888888887
Q ss_pred HHHHHHhhccccH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 444 SLILEENFEKYSE-HQLKDFRMRVITQSVTADYLCRNLYE 482 (516)
Q Consensus 444 s~~le~~~~~~~~-~~~~~~r~~~~~~t~~~~~~~~~l~~ 482 (516)
.++-+.+...-.. ....+.+.-+..+....+....+|++
T Consensus 146 ~~l~~~~~~~~~~~~~l~e~~~~L~~l~~~f~~~~~~l~~ 185 (199)
T PF10112_consen 146 AELESQPVKSEEIKQSLEEIEETLDTLNQAFEKDLDKLLE 185 (199)
T ss_pred HHHHhccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777766543211 12344555555555555555555443
No 299
>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=21.90 E-value=48 Score=22.74 Aligned_cols=30 Identities=30% Similarity=0.901 Sum_probs=19.6
Q ss_pred HHhcCcccCCCCCcccee-cCCCCceee-ccccc
Q 043224 277 WISSHTKPCPKCCKPIEK-NGGCNMVRC-KCGIT 308 (516)
Q Consensus 277 wi~~ntK~CPkC~~~IEK-n~GCnhMtC-~C~~~ 308 (516)
|+....-+||.|+...-. +.| ...| +||+.
T Consensus 3 ~~~~~~~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred ccccCCCcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 444445679999876443 455 5777 67764
No 300
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.74 E-value=43 Score=26.07 Aligned_cols=14 Identities=50% Similarity=1.032 Sum_probs=12.2
Q ss_pred CcccCCCCCcccee
Q 043224 281 HTKPCPKCCKPIEK 294 (516)
Q Consensus 281 ntK~CPkC~~~IEK 294 (516)
.+.+||.|+++++.
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 46899999999986
No 301
>PRK00420 hypothetical protein; Validated
Probab=21.59 E-value=2e+02 Score=25.16 Aligned_cols=19 Identities=32% Similarity=0.167 Sum_probs=13.6
Q ss_pred hhhHHHHHHHHHHHHHHHH
Q 043224 379 DFGWIKDGLNKLFRARRIL 397 (516)
Q Consensus 379 ~~~fl~~a~~~l~~~R~~L 397 (516)
.++=|..++.+|.+.|+.+
T Consensus 93 ri~Ei~~~l~~l~ki~~~~ 111 (112)
T PRK00420 93 RITEIIRYLEVLERIRKIK 111 (112)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3445777888888887764
No 302
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=21.49 E-value=1.6e+03 Score=27.78 Aligned_cols=132 Identities=20% Similarity=0.158 Sum_probs=74.8
Q ss_pred HHHHHhhhHHHHHHHHHHHHHHHHHHHhhccCCCCchhhHHHHHHHHHHHHHHHHhhhhhhhhcccccchhhhhhcHHHH
Q 043224 343 HKLYKAHTESFRLEYEMKEDIQDKIKILGEKDTSSKDFGWIKDGLNKLFRARRILSFSYPFAFYMFADDLLKNEMTREER 422 (516)
Q Consensus 343 ~~r~~~h~~s~k~e~~l~~~~~~k~~~~~~~~~~~~~~~fl~~a~~~l~~~R~~L~~sY~~~yyl~~~~~~~~~~~~~~~ 422 (516)
|..|.+-.+.+.+. .. .+..+.+.|++++....--+-+.++-+.|-+-|.+|.-.-|-+ +.-
T Consensus 1166 F~~WD~il~~L~~r--t~-rl~~~A~~l~~tGv~gay~s~f~~me~kl~~ir~il~~~svs~---------------~~i 1227 (1758)
T KOG0994|consen 1166 FQTWDAILQELALR--TH-RLINRAKELKQTGVLGAYASRFLDMEEKLEEIRAILSAPSVSA---------------EDI 1227 (1758)
T ss_pred HHHHHHHHHHHHHH--HH-HHHHHHHHhhhccCchhhHhHHHHHHHHHHHHHHHhcCCCccH---------------HHH
Confidence 56666544333322 21 2334455566665543222234455667777788886443322 212
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 043224 423 KIKQNFFEDQQQQFETNIERLSLILEENFEKY------SEHQLKDFRMRVITQSVTADYLCRNLYEWIETDLLGSLK 493 (516)
Q Consensus 423 ~~~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~------~~~~~~~~r~~~~~~t~~~~~~~~~l~~~~e~~l~~~~~ 493 (516)
+.-...|+-+.++|...+|.|+..=++ +..+ ...++..+..++..|+..++...+++..-=+.+++|.+.
T Consensus 1228 ~~l~~~~~~lr~~l~~~~e~L~~~E~~-Lsdi~~~~~~a~~~LesLq~~~~~l~~~~keL~e~~~~ik~sdi~GA~~ 1303 (1758)
T KOG0994|consen 1228 AQLASATESLRRQLQALTEDLPQEEET-LSDITNSLPLAGKDLESLQREFNGLLTTYKELREQLEKIKESDILGAFN 1303 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhh-hhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCchhHHH
Confidence 233457888888888888888775433 3222 223455566667777777777777776666666666554
No 303
>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=21.49 E-value=63 Score=23.80 Aligned_cols=35 Identities=20% Similarity=0.553 Sum_probs=24.1
Q ss_pred ccccccccccCCCC--eeecCCCCcccHHHHHHHHHh
Q 043224 123 FCCNICCDDVSPQE--VTTMDCGHCFCNNCWTEHFIV 157 (516)
Q Consensus 123 ~~C~IC~e~~~~~~--~~~l~CgH~fC~~C~~~yl~~ 157 (516)
..|.+|-..+.... ..--.||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 35888887765421 112379999999999877554
No 304
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.41 E-value=1e+02 Score=29.03 Aligned_cols=31 Identities=23% Similarity=0.607 Sum_probs=17.9
Q ss_pred cCCCcccCCCCCCCCceEeecCCCcceeecc-CCc
Q 043224 209 DNRRVKWCPSVPHCGNAIQVEADELCEVECA-CGF 242 (516)
Q Consensus 209 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-Cg~ 242 (516)
.++.+-.|| .|+.-+.....-...+.|| ||.
T Consensus 113 ~~~~~Y~Cp---~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 113 ENNMFFFCP---NCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred cCCCEEECC---CCCcEEeHHHHhhcCCcCCCCCC
Confidence 344566799 5887666554322346665 554
No 305
>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=21.29 E-value=67 Score=32.58 Aligned_cols=53 Identities=28% Similarity=0.649 Sum_probs=36.0
Q ss_pred cCCCCCCCCceEeecCCCcceeeccCCcccccccccccCCCCCchhHHHHhHHhHHHHHHHHHHhcCcccCCCCCcccee
Q 043224 215 WCPSVPHCGNAIQVEADELCEVECACGFQFCFSCSSVAHSPCSCLMWELWSKKFEVESLSLNWISSHTKPCPKCCKPIEK 294 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~~~~~wi~~ntK~CPkC~~~IEK 294 (516)
-|| .|..-....++-...|. +|+|..|-.|-- .....+.-.||.|.++.-|
T Consensus 2 ~Cp---~CKt~~Y~np~lk~~in-~C~H~lCEsCvd-------------------------~iF~~g~~~CpeC~~iLRk 52 (300)
T KOG3800|consen 2 ACP---KCKTDRYLNPDLKLMIN-ECGHRLCESCVD-------------------------RIFSLGPAQCPECMVILRK 52 (300)
T ss_pred CCc---ccccceecCccceeeec-cccchHHHHHHH-------------------------HHHhcCCCCCCcccchhhh
Confidence 377 68777776654333444 799999998840 1123466799999998888
Q ss_pred cC
Q 043224 295 NG 296 (516)
Q Consensus 295 n~ 296 (516)
++
T Consensus 53 ~n 54 (300)
T KOG3800|consen 53 NN 54 (300)
T ss_pred cc
Confidence 75
No 306
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.18 E-value=8.2e+02 Score=24.30 Aligned_cols=98 Identities=10% Similarity=0.211 Sum_probs=62.4
Q ss_pred CchhhHHHHHHHHHHHHHHHHhhhhhhhhcccccchhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccH
Q 043224 377 SKDFGWIKDGLNKLFRARRILSFSYPFAFYMFADDLLKNEMTREERKIKQNFFEDQQQQFETNIERLSLILEENFEKYSE 456 (516)
Q Consensus 377 ~~~~~fl~~a~~~l~~~R~~L~~sY~~~yyl~~~~~~~~~~~~~~~~~~~~lFe~~Q~~le~~~E~Ls~~le~~~~~~~~ 456 (516)
.+|+-.+..|++.++.-|-.+..+|-..= ...+- ....+.-.+.--+.||..+|..+..+..++..+..
T Consensus 141 Lkeyv~y~~slK~vlk~R~~~Q~~le~k~---------e~l~k--~~~dr~~~~~ev~~~e~kve~a~~~~k~e~~Rf~~ 209 (243)
T cd07666 141 IHEYVLYSETLMGVIKRRDQIQAELDSKV---------EALAN--KKADRDLLKEEIEKLEDKVECANNALKADWERWKQ 209 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHh--hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666677888888888876665554210 00000 01112233334455777777777777777777777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 457 HQLKDFRMRVITQSVTADYLCRNLYEWIE 485 (516)
Q Consensus 457 ~~~~~~r~~~~~~t~~~~~~~~~l~~~~e 485 (516)
.+..++|.-++.....-=.+++.++..-|
T Consensus 210 ~k~~D~k~~~~~yae~~i~~~~~~~~~We 238 (243)
T cd07666 210 NMQTDLRSAFTDMAENNISYYEECLATWE 238 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77888888888877777777777777666
No 307
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.10 E-value=56 Score=22.31 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=10.9
Q ss_pred cccCCCCCccceec
Q 043224 282 TKPCPKCCKPIEKN 295 (516)
Q Consensus 282 tK~CPkC~~~IEKn 295 (516)
...||.|+..++|.
T Consensus 26 ~~~CP~Cg~~~~r~ 39 (41)
T smart00834 26 LATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCcceec
Confidence 46899999987763
No 308
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.00 E-value=74 Score=36.73 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=7.9
Q ss_pred cccCCCCCcccee
Q 043224 282 TKPCPKCCKPIEK 294 (516)
Q Consensus 282 tK~CPkC~~~IEK 294 (516)
...||+|+..--+
T Consensus 475 p~~Cp~Cgs~~L~ 487 (730)
T COG1198 475 PQSCPECGSEHLR 487 (730)
T ss_pred CCCCCCCCCCeeE
Confidence 3577777766333
No 309
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.86 E-value=40 Score=25.85 Aligned_cols=34 Identities=21% Similarity=0.506 Sum_probs=26.2
Q ss_pred ccCCCCCcccee--cCCCCceee-ccccccccccccc
Q 043224 283 KPCPKCCKPIEK--NGGCNMVRC-KCGITFNWISGLE 316 (516)
Q Consensus 283 K~CPkC~~~IEK--n~GCnhMtC-~C~~~FCw~C~~~ 316 (516)
+.||-|++..-- .+-=|+=+| .|+..-|-+||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 579999887621 234589999 7999999999853
No 310
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=20.76 E-value=2.1e+02 Score=23.63 Aligned_cols=27 Identities=30% Similarity=0.164 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043224 459 LKDFRMRVITQSVTADYLCRNLYEWIE 485 (516)
Q Consensus 459 ~~~~r~~~~~~t~~~~~~~~~l~~~~e 485 (516)
+...|.++.+....+....+...+..+
T Consensus 40 ~~~a~~~~~~~~~~~~~~~~~~~~~~~ 66 (94)
T PF05957_consen 40 LDDARDRAEDAADQAREQAREAAEQTE 66 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555554444444444444444
No 311
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.68 E-value=33 Score=34.87 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=18.7
Q ss_pred cccCCCCCccceecCCCCceee----ccccccccccccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC----KCGITFNWISGLE 316 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC----~C~~~FCw~C~~~ 316 (516)
++.||-|.- .|.| -|+|.|||+|.+-
T Consensus 7 ~~eC~IC~n---------t~n~Pv~l~C~HkFCyiCiKG 36 (324)
T KOG0824|consen 7 KKECLICYN---------TGNCPVNLYCFHKFCYICIKG 36 (324)
T ss_pred CCcceeeec---------cCCcCccccccchhhhhhhcc
Confidence 567777653 2344 3999999999876
No 312
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.63 E-value=61 Score=29.81 Aligned_cols=24 Identities=38% Similarity=0.949 Sum_probs=16.5
Q ss_pred cccCCCCCccceecCCCCceee-ccc
Q 043224 282 TKPCPKCCKPIEKNGGCNMVRC-KCG 306 (516)
Q Consensus 282 tK~CPkC~~~IEKn~GCnhMtC-~C~ 306 (516)
...||+|++.+..++. ....| +|+
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~ 58 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCN 58 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCC
Confidence 4689999999987764 33445 444
No 313
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=20.52 E-value=33 Score=39.70 Aligned_cols=7 Identities=29% Similarity=0.496 Sum_probs=0.0
Q ss_pred CCCHHHH
Q 043224 67 SLKEKHA 73 (516)
Q Consensus 67 ~i~~~~a 73 (516)
|++.+.|
T Consensus 721 Gi~eerA 727 (787)
T PF03115_consen 721 GIPEERA 727 (787)
T ss_dssp -------
T ss_pred CCCHHHH
Confidence 5555543
No 314
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=20.41 E-value=52 Score=35.41 Aligned_cols=32 Identities=25% Similarity=0.635 Sum_probs=17.5
Q ss_pred cCCCCCCCCceEeecCCCcceeeccCCcccccccc
Q 043224 215 WCPSVPHCGNAIQVEADELCEVECACGFQFCFSCS 249 (516)
Q Consensus 215 ~CP~~p~C~~~i~~~~~~~~~v~C~Cg~~fC~~C~ 249 (516)
.|-| ..|...+.+++- .+. .|.-...||..|.
T Consensus 99 rCrN-~aC~s~LP~ddc-~C~-iC~~~~gFC~~C~ 130 (446)
T PF07227_consen 99 RCRN-LACRSQLPVDDC-DCK-ICCSEPGFCRRCM 130 (446)
T ss_pred hcCC-HHhhccCCcccc-Ccc-hhcCCCCccccCC
Confidence 4764 678776654431 111 2334567777774
Done!