Query 009189
Match_columns 540
No_of_seqs 420 out of 1692
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 21:30:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009189.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009189hhsearch_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 2.2E-67 4.7E-72 561.6 26.8 431 53-511 1-436 (444)
2 KOG1814 Predicted E3 ubiquitin 100.0 8.9E-35 1.9E-39 290.6 13.4 210 128-342 182-421 (445)
3 KOG1812 Predicted E3 ubiquitin 100.0 1.8E-34 3.9E-39 300.5 11.2 223 129-377 145-374 (384)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.5E-23 3.2E-28 202.8 8.4 193 127-328 218-438 (446)
5 smart00647 IBR In Between Ring 99.2 2.8E-11 6.1E-16 94.2 6.2 62 204-266 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 3.8E-11 8.3E-16 93.4 1.7 62 204-266 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.8 3.4E-09 7.3E-14 75.2 2.2 41 133-179 1-41 (42)
8 PF13923 zf-C3HC4_2: Zinc fing 98.3 3.5E-07 7.6E-12 63.8 2.8 37 133-179 1-38 (39)
9 PF00097 zf-C3HC4: Zinc finger 98.3 5.5E-07 1.2E-11 63.5 3.7 39 133-179 1-40 (41)
10 PF13639 zf-RING_2: Ring finge 98.3 4.2E-07 9.1E-12 65.2 2.6 40 132-179 2-42 (44)
11 PLN03208 E3 ubiquitin-protein 98.3 7.7E-07 1.7E-11 83.3 4.0 65 127-195 15-87 (193)
12 PF13445 zf-RING_UBOX: RING-ty 98.2 1.2E-06 2.6E-11 62.2 2.8 41 133-178 1-43 (43)
13 KOG0320 Predicted E3 ubiquitin 98.2 1.1E-06 2.4E-11 80.1 2.7 53 128-190 129-181 (187)
14 smart00647 IBR In Between Ring 98.1 4.5E-06 9.8E-11 64.7 4.6 39 289-327 17-60 (64)
15 PF13920 zf-C3HC4_3: Zinc fing 98.0 4.7E-06 1E-10 61.5 3.6 46 130-187 2-48 (50)
16 PF01485 IBR: IBR domain; Int 98.0 2.2E-06 4.7E-11 66.4 1.8 39 289-327 17-60 (64)
17 PF14634 zf-RING_5: zinc-RING 97.9 6.7E-06 1.5E-10 58.9 2.9 42 132-183 1-43 (44)
18 cd00162 RING RING-finger (Real 97.9 9.4E-06 2E-10 57.5 3.6 43 132-185 1-44 (45)
19 smart00504 Ubox Modified RING 97.9 1.7E-05 3.8E-10 61.2 4.1 47 131-189 2-48 (63)
20 KOG0823 Predicted E3 ubiquitin 97.8 9.9E-06 2.1E-10 77.3 2.4 55 128-191 45-99 (230)
21 PHA02926 zinc finger-like prot 97.8 1.5E-05 3.3E-10 75.4 3.4 57 127-187 167-230 (242)
22 KOG0317 Predicted E3 ubiquitin 97.8 1.2E-05 2.7E-10 78.8 2.9 51 129-191 238-288 (293)
23 KOG2164 Predicted E3 ubiquitin 97.7 1.4E-05 3E-10 84.2 2.1 60 130-196 186-245 (513)
24 smart00184 RING Ring finger. E 97.7 3E-05 6.6E-10 52.9 3.2 38 133-179 1-38 (39)
25 TIGR00599 rad18 DNA repair pro 97.7 3E-05 6.6E-10 81.1 3.9 66 127-207 23-89 (397)
26 PHA02929 N1R/p28-like protein; 97.7 3.5E-05 7.6E-10 75.3 3.8 50 128-187 172-227 (238)
27 KOG2177 Predicted E3 ubiquitin 97.6 2.9E-05 6.4E-10 78.6 2.6 45 128-184 11-55 (386)
28 KOG4367 Predicted Zn-finger pr 97.6 0.00051 1.1E-08 70.6 10.8 34 129-164 3-36 (699)
29 KOG0287 Postreplication repair 97.4 7.5E-05 1.6E-09 74.5 1.7 64 129-207 22-86 (442)
30 KOG0978 E3 ubiquitin ligase in 97.1 0.00033 7.2E-09 77.5 3.0 56 128-194 641-696 (698)
31 PF04564 U-box: U-box domain; 97.1 0.00051 1.1E-08 54.9 3.3 51 128-189 2-52 (73)
32 TIGR00570 cdk7 CDK-activating 97.0 0.00053 1.2E-08 69.1 3.1 54 130-192 3-59 (309)
33 COG5540 RING-finger-containing 96.7 0.0013 2.8E-08 65.0 3.2 52 128-188 321-373 (374)
34 PF11789 zf-Nse: Zinc-finger o 96.7 0.0015 3.3E-08 49.5 2.8 47 129-183 10-57 (57)
35 COG5574 PEX10 RING-finger-cont 96.6 0.0013 2.7E-08 64.2 2.9 53 129-191 214-266 (271)
36 PF14835 zf-RING_6: zf-RING of 96.5 0.00038 8.3E-09 53.2 -1.4 44 129-186 6-50 (65)
37 KOG0804 Cytoplasmic Zn-finger 96.4 0.23 5E-06 52.2 17.6 118 54-187 85-222 (493)
38 PF12678 zf-rbx1: RING-H2 zinc 96.3 0.0035 7.5E-08 50.1 3.0 42 130-179 19-71 (73)
39 PF14555 UBA_4: UBA-like domai 96.1 0.015 3.3E-07 41.3 5.3 40 65-104 1-40 (43)
40 KOG1002 Nucleotide excision re 96.1 0.003 6.6E-08 66.6 2.1 56 127-189 533-588 (791)
41 TIGR00570 cdk7 CDK-activating 95.9 1.2 2.7E-05 45.2 19.7 53 223-304 5-57 (309)
42 KOG4628 Predicted E3 ubiquitin 95.9 0.0048 1E-07 63.4 2.5 45 131-184 230-275 (348)
43 COG5432 RAD18 RING-finger-cont 95.8 0.0037 8.1E-08 61.4 1.4 48 129-188 24-71 (391)
44 KOG2879 Predicted E3 ubiquitin 95.6 0.033 7.2E-07 54.7 6.9 53 125-187 234-287 (298)
45 KOG1814 Predicted E3 ubiquitin 95.3 0.065 1.4E-06 55.6 8.2 39 288-326 271-312 (445)
46 PF11793 FANCL_C: FANCL C-term 95.1 0.012 2.5E-07 46.7 1.7 57 130-188 2-67 (70)
47 KOG4159 Predicted E3 ubiquitin 95.0 0.028 6.1E-07 59.2 4.7 48 128-187 82-129 (398)
48 COG5243 HRD1 HRD ubiquitin lig 94.8 0.023 5E-07 57.9 3.4 48 129-186 286-344 (491)
49 KOG0824 Predicted E3 ubiquitin 94.8 0.015 3.3E-07 57.8 1.9 54 128-192 5-58 (324)
50 KOG0006 E3 ubiquitin-protein l 94.4 0.1 2.3E-06 52.1 6.6 95 149-263 341-438 (446)
51 KOG1812 Predicted E3 ubiquitin 94.2 0.034 7.3E-07 58.9 3.1 102 130-264 238-345 (384)
52 COG5152 Uncharacterized conser 94.1 0.017 3.7E-07 53.8 0.6 32 129-162 195-226 (259)
53 KOG0311 Predicted E3 ubiquitin 94.1 0.0081 1.8E-07 60.9 -1.7 50 127-186 40-89 (381)
54 PF14570 zf-RING_4: RING/Ubox 94.1 0.032 6.9E-07 40.4 1.8 44 133-185 1-46 (48)
55 PF10571 UPF0547: Uncharacteri 93.9 0.026 5.6E-07 35.5 0.9 23 291-317 1-24 (26)
56 KOG2660 Locus-specific chromos 93.1 0.03 6.5E-07 56.5 0.3 46 129-186 14-60 (331)
57 KOG1039 Predicted E3 ubiquitin 93.0 0.062 1.3E-06 55.5 2.6 56 127-185 158-219 (344)
58 KOG0802 E3 ubiquitin ligase [P 93.0 0.053 1.1E-06 60.2 2.2 46 129-184 290-338 (543)
59 PF12861 zf-Apc11: Anaphase-pr 92.7 0.12 2.5E-06 42.3 3.1 50 130-186 21-81 (85)
60 KOG1645 RING-finger-containing 92.1 0.1 2.2E-06 54.0 2.8 49 130-186 4-55 (463)
61 PRK00420 hypothetical protein; 92.1 1.2 2.6E-05 38.5 8.8 27 290-324 23-49 (112)
62 KOG4185 Predicted E3 ubiquitin 92.0 0.22 4.8E-06 50.8 5.1 57 130-195 3-65 (296)
63 PF05883 Baculo_RING: Baculovi 91.2 0.089 1.9E-06 46.6 1.0 35 129-163 25-66 (134)
64 PF13240 zinc_ribbon_2: zinc-r 90.3 0.13 2.7E-06 31.4 0.8 21 292-316 1-22 (23)
65 smart00744 RINGv The RING-vari 90.3 0.32 6.9E-06 35.6 3.0 42 132-179 1-47 (49)
66 KOG0826 Predicted E3 ubiquitin 90.0 0.94 2E-05 45.9 7.1 48 129-186 299-347 (357)
67 KOG1428 Inhibitor of type V ad 89.9 0.51 1.1E-05 55.8 5.7 74 129-208 3485-3561(3738)
68 KOG4265 Predicted E3 ubiquitin 89.1 0.45 9.8E-06 48.8 4.1 48 128-187 288-336 (349)
69 KOG4692 Predicted E3 ubiquitin 88.5 0.29 6.3E-06 49.7 2.3 51 126-188 418-468 (489)
70 KOG0828 Predicted E3 ubiquitin 88.1 0.27 5.8E-06 52.1 1.8 53 127-188 568-635 (636)
71 KOG4739 Uncharacterized protei 87.8 0.43 9.2E-06 46.5 2.9 44 131-186 4-47 (233)
72 COG5220 TFB3 Cdk activating ki 87.7 0.17 3.6E-06 48.8 0.1 51 130-187 10-64 (314)
73 KOG1785 Tyrosine kinase negati 87.7 0.24 5.2E-06 51.1 1.1 46 131-184 370-415 (563)
74 KOG1734 Predicted RING-contain 87.3 0.25 5.5E-06 48.5 1.0 52 129-188 223-282 (328)
75 KOG2817 Predicted E3 ubiquitin 87.3 1.8 3.9E-05 45.1 7.2 126 53-190 255-388 (394)
76 KOG1001 Helicase-like transcri 86.8 0.27 5.8E-06 55.7 1.0 47 131-188 455-501 (674)
77 smart00661 RPOL9 RNA polymeras 85.8 0.58 1.3E-05 34.3 2.1 27 291-317 1-30 (52)
78 PF13248 zf-ribbon_3: zinc-rib 85.6 0.4 8.6E-06 30.1 0.9 13 291-303 3-15 (26)
79 KOG4172 Predicted E3 ubiquitin 85.0 0.34 7.4E-06 35.8 0.5 46 131-187 8-54 (62)
80 PF00643 zf-B_box: B-box zinc 84.9 0.47 1E-05 33.2 1.1 33 291-330 4-38 (42)
81 PHA00626 hypothetical protein 84.8 0.65 1.4E-05 34.5 1.9 31 292-322 2-38 (59)
82 KOG1813 Predicted E3 ubiquitin 84.3 0.42 9.2E-06 47.7 0.9 45 130-186 241-285 (313)
83 KOG0823 Predicted E3 ubiquitin 83.8 0.53 1.1E-05 45.5 1.4 33 247-302 64-96 (230)
84 PF00627 UBA: UBA/TS-N domain; 83.6 3.9 8.5E-05 27.7 5.3 34 65-99 3-36 (37)
85 KOG0297 TNF receptor-associate 83.6 0.6 1.3E-05 49.7 1.8 48 127-186 18-66 (391)
86 KOG1815 Predicted E3 ubiquitin 83.5 0.67 1.4E-05 50.2 2.2 38 290-327 158-198 (444)
87 KOG0317 Predicted E3 ubiquitin 82.9 0.21 4.6E-06 49.6 -1.7 34 287-326 236-270 (293)
88 cd00021 BBOX B-Box-type zinc f 82.5 1 2.2E-05 30.6 2.1 32 292-330 2-35 (39)
89 PF14952 zf-tcix: Putative tre 81.6 0.92 2E-05 32.0 1.5 30 284-317 5-37 (44)
90 PF04641 Rtf2: Rtf2 RING-finge 80.3 1.8 3.8E-05 43.4 3.7 58 128-196 111-170 (260)
91 PF09297 zf-NADH-PPase: NADH p 79.9 2.1 4.5E-05 28.2 2.7 28 289-316 2-30 (32)
92 KOG0825 PHD Zn-finger protein 79.7 0.94 2E-05 50.7 1.6 18 150-167 121-138 (1134)
93 PF14447 Prok-RING_4: Prokaryo 79.6 0.55 1.2E-05 35.0 -0.1 46 130-189 7-52 (55)
94 PF10168 Nup88: Nuclear pore c 79.5 37 0.00081 39.1 14.3 52 447-498 601-658 (717)
95 PRK00432 30S ribosomal protein 79.5 0.9 2E-05 33.4 1.0 27 289-317 19-47 (50)
96 PRK14559 putative protein seri 79.2 1.2 2.7E-05 50.2 2.4 23 291-324 28-50 (645)
97 KOG1493 Anaphase-promoting com 79.1 0.56 1.2E-05 37.2 -0.2 49 131-186 21-80 (84)
98 KOG0827 Predicted E3 ubiquitin 78.9 0.87 1.9E-05 47.1 1.0 48 130-184 4-53 (465)
99 PF10367 Vps39_2: Vacuolar sor 78.8 0.85 1.9E-05 38.7 0.8 33 128-160 76-108 (109)
100 PHA03096 p28-like protein; Pro 78.1 1.3 2.9E-05 44.8 2.0 37 131-167 179-221 (284)
101 PF10446 DUF2457: Protein of u 78.0 1.2 2.5E-05 47.2 1.6 11 125-135 189-199 (458)
102 PF09726 Macoilin: Transmembra 77.6 73 0.0016 36.6 15.9 73 399-494 586-658 (697)
103 COG5222 Uncharacterized conser 77.6 1.3 2.8E-05 44.2 1.7 43 131-184 275-318 (427)
104 PF02845 CUE: CUE domain; Int 77.4 8.9 0.00019 26.8 5.6 38 65-102 2-40 (42)
105 KOG4445 Uncharacterized conser 77.2 5.3 0.00012 40.1 5.8 39 129-167 114-153 (368)
106 PF14835 zf-RING_6: zf-RING of 76.6 1.7 3.6E-05 33.6 1.7 21 291-311 8-31 (65)
107 PF13920 zf-C3HC4_3: Zinc fing 76.5 1.7 3.6E-05 31.6 1.7 30 247-302 19-49 (50)
108 PF12773 DZR: Double zinc ribb 76.1 1.7 3.8E-05 31.5 1.7 14 291-304 30-43 (50)
109 KOG3039 Uncharacterized conser 76.1 1.7 3.7E-05 42.3 2.0 52 129-190 220-273 (303)
110 KOG3800 Predicted E3 ubiquitin 75.3 2 4.4E-05 42.9 2.4 47 132-187 2-51 (300)
111 KOG3002 Zn finger protein [Gen 72.6 5.9 0.00013 40.5 5.0 46 128-187 46-91 (299)
112 KOG2034 Vacuolar sorting prote 72.3 2.1 4.6E-05 48.9 1.9 39 128-166 815-853 (911)
113 COG5175 MOT2 Transcriptional r 72.2 2.1 4.5E-05 43.5 1.6 54 129-191 13-68 (480)
114 KOG1832 HIV-1 Vpr-binding prot 71.8 2.1 4.5E-05 48.9 1.6 9 4-12 1405-1413(1516)
115 cd00194 UBA Ubiquitin Associat 70.8 15 0.00032 24.8 5.2 34 67-101 4-37 (38)
116 smart00336 BBOX B-Box-type zin 70.4 4.1 8.8E-05 28.0 2.4 33 291-330 4-38 (42)
117 PRK00398 rpoP DNA-directed RNA 70.3 3.5 7.6E-05 29.5 2.1 28 291-318 4-32 (46)
118 KOG3130 Uncharacterized conser 70.0 3.4 7.4E-05 43.0 2.7 6 135-140 396-401 (514)
119 KOG1952 Transcription factor N 69.9 3.5 7.6E-05 46.9 2.9 50 129-179 190-241 (950)
120 PF09026 CENP-B_dimeris: Centr 69.7 1.5 3.2E-05 36.4 0.0 7 68-74 53-59 (101)
121 cd07666 BAR_SNX7 The Bin/Amphi 68.9 1.3E+02 0.0027 29.9 15.7 101 396-507 138-238 (243)
122 KOG3579 Predicted E3 ubiquitin 68.7 3.7 8E-05 40.8 2.5 54 128-184 266-322 (352)
123 PRK14559 putative protein seri 68.7 3.6 7.7E-05 46.6 2.7 12 291-302 42-53 (645)
124 KOG0320 Predicted E3 ubiquitin 68.6 1.3 2.8E-05 41.2 -0.7 29 247-301 150-178 (187)
125 PF10446 DUF2457: Protein of u 68.3 3 6.4E-05 44.2 1.8 6 156-161 211-216 (458)
126 KOG1701 Focal adhesion adaptor 68.3 3.5 7.5E-05 43.4 2.3 16 292-307 396-411 (468)
127 PRK08665 ribonucleotide-diphos 68.0 2.9 6.2E-05 48.3 1.8 26 291-318 725-751 (752)
128 smart00165 UBA Ubiquitin assoc 67.5 15 0.00032 24.6 4.7 32 68-100 5-36 (37)
129 KOG3970 Predicted E3 ubiquitin 67.5 4.4 9.5E-05 38.9 2.6 54 131-186 51-104 (299)
130 KOG1941 Acetylcholine receptor 67.2 2.3 5E-05 44.0 0.8 48 129-184 364-413 (518)
131 COG4647 AcxC Acetone carboxyla 67.2 15 0.00033 32.2 5.6 59 242-301 69-131 (165)
132 KOG2177 Predicted E3 ubiquitin 66.0 3.3 7.1E-05 41.4 1.6 31 292-329 88-120 (386)
133 PLN03086 PRLI-interacting fact 65.7 10 0.00023 42.0 5.5 57 173-252 406-463 (567)
134 COG1645 Uncharacterized Zn-fin 65.5 3.6 7.9E-05 36.5 1.6 25 290-323 28-52 (131)
135 KOG0943 Predicted ubiquitin-pr 64.6 2.8 6.2E-05 49.1 0.9 17 451-467 2419-2435(3015)
136 COG1998 RPS31 Ribosomal protei 64.5 4.4 9.6E-05 29.4 1.5 25 291-315 20-45 (51)
137 COG5219 Uncharacterized conser 64.5 2.3 5E-05 48.8 0.2 52 128-187 1467-1523(1525)
138 PF08274 PhnA_Zn_Ribbon: PhnA 64.3 5 0.00011 26.2 1.6 26 291-317 3-29 (30)
139 PF04931 DNA_pol_phi: DNA poly 64.3 17 0.00038 42.3 7.3 20 81-100 764-783 (784)
140 PF13719 zinc_ribbon_5: zinc-r 63.8 7.5 0.00016 26.5 2.5 28 222-252 3-35 (37)
141 PF13717 zinc_ribbon_4: zinc-r 63.6 7.5 0.00016 26.4 2.5 28 222-252 3-35 (36)
142 KOG2807 RNA polymerase II tran 63.5 2.3 4.9E-05 43.2 -0.1 20 243-262 345-365 (378)
143 KOG2114 Vacuolar assembly/sort 63.4 6 0.00013 45.1 3.1 41 130-184 840-880 (933)
144 PF09538 FYDLN_acid: Protein o 63.1 4.1 8.9E-05 35.1 1.4 26 291-317 10-36 (108)
145 smart00546 CUE Domain that may 63.1 26 0.00055 24.5 5.3 37 65-101 3-40 (43)
146 PF02150 RNA_POL_M_15KD: RNA p 62.9 5.7 0.00012 26.8 1.8 27 222-251 2-29 (35)
147 TIGR00622 ssl1 transcription f 62.6 6.8 0.00015 33.9 2.6 20 243-262 81-101 (112)
148 PF07191 zinc-ribbons_6: zinc- 62.2 6.3 0.00014 31.0 2.2 32 292-325 3-40 (70)
149 PF06677 Auto_anti-p27: Sjogre 61.7 6.8 0.00015 27.5 2.1 22 291-314 18-41 (41)
150 KOG1991 Nuclear transport rece 61.7 9.5 0.00021 44.3 4.4 9 80-88 977-985 (1010)
151 KOG0943 Predicted ubiquitin-pr 61.7 4.6 9.9E-05 47.6 1.9 17 293-309 2281-2297(3015)
152 KOG3268 Predicted E3 ubiquitin 61.6 8.5 0.00018 35.7 3.2 57 129-187 164-228 (234)
153 KOG3800 Predicted E3 ubiquitin 61.2 1E+02 0.0022 31.1 10.9 31 223-257 2-32 (300)
154 KOG2906 RNA polymerase III sub 60.8 5.4 0.00012 33.3 1.6 29 291-319 2-33 (105)
155 KOG3039 Uncharacterized conser 60.4 6.9 0.00015 38.2 2.6 37 131-169 44-80 (303)
156 PF14803 Nudix_N_2: Nudix N-te 60.3 7.5 0.00016 26.1 2.0 25 291-315 1-30 (34)
157 PF07282 OrfB_Zn_ribbon: Putat 58.8 6.7 0.00015 30.5 1.9 28 289-316 27-55 (69)
158 PLN03208 E3 ubiquitin-protein 58.7 3.3 7.2E-05 39.3 0.1 30 291-325 19-48 (193)
159 KOG4275 Predicted E3 ubiquitin 58.3 4.3 9.4E-05 40.6 0.8 29 130-160 300-329 (350)
160 cd07630 BAR_SNX_like The Bin/A 57.4 1.8E+02 0.0039 27.8 14.2 100 398-507 94-193 (198)
161 PF13834 DUF4193: Domain of un 57.3 3.9 8.5E-05 34.3 0.3 32 127-158 67-98 (99)
162 COG5574 PEX10 RING-finger-cont 55.9 3.3 7.2E-05 40.9 -0.4 30 291-326 216-247 (271)
163 KOG1571 Predicted E3 ubiquitin 55.2 7 0.00015 40.4 1.8 44 128-186 303-346 (355)
164 PHA02926 zinc finger-like prot 55.2 5.9 0.00013 38.3 1.2 35 247-301 196-230 (242)
165 PRK05654 acetyl-CoA carboxylas 55.0 3 6.5E-05 42.5 -0.9 28 290-317 27-56 (292)
166 KOG3161 Predicted E3 ubiquitin 54.6 4.2 9.1E-05 44.8 0.1 36 130-165 11-48 (861)
167 TIGR01384 TFS_arch transcripti 54.4 8 0.00017 32.8 1.8 24 291-316 1-25 (104)
168 TIGR00595 priA primosomal prot 54.1 11 0.00024 41.5 3.3 34 291-324 223-262 (505)
169 KOG2932 E3 ubiquitin ligase in 53.9 4.8 0.0001 40.5 0.4 53 218-306 87-139 (389)
170 COG1198 PriA Primosomal protei 53.1 10 0.00023 43.4 2.9 35 290-324 444-484 (730)
171 PF12906 RINGv: RING-variant d 52.3 9.7 0.00021 27.5 1.7 33 133-165 1-38 (47)
172 TIGR03655 anti_R_Lar restricti 52.2 12 0.00027 27.6 2.2 20 291-310 2-27 (53)
173 PRK12495 hypothetical protein; 51.9 16 0.00036 35.2 3.5 17 290-306 42-58 (226)
174 TIGR02098 MJ0042_CXXC MJ0042 f 51.4 17 0.00037 24.6 2.7 27 223-252 4-35 (38)
175 COG1997 RPL43A Ribosomal prote 50.9 12 0.00026 30.7 2.1 27 291-317 36-63 (89)
176 PF14569 zf-UDP: Zinc-binding 50.6 23 0.00049 28.5 3.5 49 129-186 8-61 (80)
177 TIGR00515 accD acetyl-CoA carb 50.4 4 8.6E-05 41.5 -0.9 29 290-318 26-56 (285)
178 PRK14714 DNA polymerase II lar 50.1 13 0.00027 44.7 2.9 13 456-468 800-812 (1337)
179 PF08938 HBS1_N: HBS1 N-termin 50.0 3.7 8.1E-05 33.2 -0.9 47 55-102 20-69 (79)
180 CHL00174 accD acetyl-CoA carbo 49.4 4.1 8.8E-05 41.5 -1.0 27 291-317 39-67 (296)
181 PRK04023 DNA polymerase II lar 49.2 13 0.00028 43.6 2.8 33 217-259 622-660 (1121)
182 PF02318 FYVE_2: FYVE-type zin 48.6 26 0.00057 30.5 4.2 42 289-331 53-95 (118)
183 PF09889 DUF2116: Uncharacteri 48.6 4.5 9.8E-05 30.8 -0.6 24 291-325 4-28 (59)
184 PF14569 zf-UDP: Zinc-binding 48.3 15 0.00031 29.5 2.2 54 229-307 14-68 (80)
185 PF14445 Prok-RING_2: Prokaryo 47.8 4.2 9.1E-05 29.6 -0.8 34 129-162 6-40 (57)
186 PF06827 zf-FPG_IleRS: Zinc fi 47.0 14 0.00031 23.7 1.7 24 291-314 2-28 (30)
187 PRK14873 primosome assembly pr 46.8 15 0.00033 41.8 3.0 34 291-324 393-431 (665)
188 PF08882 Acetone_carb_G: Aceto 46.7 6.6 0.00014 33.7 0.0 17 243-260 24-40 (112)
189 PF01363 FYVE: FYVE zinc finge 46.3 11 0.00023 29.3 1.2 33 290-324 9-42 (69)
190 PF14369 zf-RING_3: zinc-finge 46.0 19 0.00042 24.3 2.2 28 222-252 3-31 (35)
191 COG5432 RAD18 RING-finger-cont 46.0 11 0.00023 37.8 1.3 32 291-329 26-59 (391)
192 PF15616 TerY-C: TerY-C metal 45.5 13 0.00029 33.0 1.8 23 223-255 79-101 (131)
193 COG0777 AccD Acetyl-CoA carbox 45.1 7.4 0.00016 38.8 0.1 29 290-318 28-58 (294)
194 KOG4739 Uncharacterized protei 45.0 2E+02 0.0043 28.3 9.8 35 291-325 4-47 (233)
195 PF03119 DNA_ligase_ZBD: NAD-d 45.0 20 0.00043 22.9 2.0 20 292-311 1-20 (28)
196 PRK05580 primosome assembly pr 44.6 18 0.0004 41.4 3.2 34 291-324 391-430 (679)
197 PF14446 Prok-RING_1: Prokaryo 44.3 22 0.00048 26.5 2.5 33 129-161 4-38 (54)
198 KOG3130 Uncharacterized conser 43.6 15 0.00032 38.5 2.0 9 39-47 301-309 (514)
199 PF05320 Pox_RNA_Pol_19: Poxvi 43.6 8.7 0.00019 34.8 0.3 32 129-165 125-156 (167)
200 KOG4460 Nuclear pore complex, 43.3 5E+02 0.011 28.8 13.3 18 453-470 630-647 (741)
201 PF03943 TAP_C: TAP C-terminal 43.2 32 0.00069 25.3 3.2 37 66-102 2-38 (51)
202 KOG1940 Zn-finger protein [Gen 43.1 20 0.00043 36.1 2.8 47 128-184 156-204 (276)
203 KOG3053 Uncharacterized conser 42.7 16 0.00035 36.0 2.0 54 129-185 19-80 (293)
204 PF14149 YhfH: YhfH-like prote 42.2 2.2 4.7E-05 29.2 -2.8 25 289-313 12-37 (37)
205 PF03884 DUF329: Domain of unk 41.9 6.9 0.00015 29.6 -0.5 14 290-303 2-15 (57)
206 KOG4362 Transcriptional regula 41.5 6.9 0.00015 44.0 -0.8 50 129-187 20-69 (684)
207 smart00804 TAP_C C-terminal do 41.1 1.1E+02 0.0025 23.5 6.1 40 63-102 11-50 (63)
208 PF08746 zf-RING-like: RING-li 40.9 22 0.00048 25.1 2.0 41 133-179 1-42 (43)
209 PF01599 Ribosomal_S27: Riboso 40.8 18 0.00039 26.2 1.5 25 291-315 19-46 (47)
210 PF02891 zf-MIZ: MIZ/SP-RING z 40.0 22 0.00047 26.0 1.9 46 131-184 3-49 (50)
211 TIGR02300 FYDLN_acid conserved 39.5 17 0.00036 32.1 1.4 25 291-316 10-35 (129)
212 PRK11827 hypothetical protein; 39.4 24 0.00052 27.0 2.1 24 291-314 9-33 (60)
213 PRK14811 formamidopyrimidine-D 39.1 22 0.00047 35.9 2.4 26 290-315 235-263 (269)
214 PRK14892 putative transcriptio 38.7 23 0.00049 30.0 2.1 26 291-316 22-51 (99)
215 COG0266 Nei Formamidopyrimidin 38.0 22 0.00048 35.7 2.2 25 290-314 245-272 (273)
216 COG1594 RPB9 DNA-directed RNA 37.8 25 0.00054 30.5 2.2 27 291-317 3-32 (113)
217 PRK12775 putative trifunctiona 37.4 4.2E+02 0.0092 32.0 13.2 15 290-304 796-810 (1006)
218 PF14471 DUF4428: Domain of un 37.1 28 0.00061 25.6 2.1 30 132-162 1-30 (51)
219 PF05290 Baculo_IE-1: Baculovi 37.1 26 0.00056 31.2 2.2 51 129-187 79-132 (140)
220 PRK09710 lar restriction allev 37.0 32 0.00069 26.6 2.4 14 289-302 5-18 (64)
221 PF06844 DUF1244: Protein of u 36.9 25 0.00054 27.3 1.8 17 153-169 11-27 (68)
222 PF06906 DUF1272: Protein of u 36.8 28 0.00061 26.1 2.0 44 131-186 6-51 (57)
223 PRK01103 formamidopyrimidine/5 36.7 24 0.00052 35.6 2.3 25 290-314 245-272 (274)
224 TIGR00577 fpg formamidopyrimid 36.7 24 0.00052 35.6 2.3 24 291-314 246-272 (272)
225 COG2888 Predicted Zn-ribbon RN 36.6 17 0.00038 27.5 0.9 6 292-297 29-34 (61)
226 PRK14810 formamidopyrimidine-D 36.6 24 0.00053 35.5 2.3 25 290-314 244-271 (272)
227 PF05605 zf-Di19: Drought indu 36.5 30 0.00065 25.5 2.2 46 130-192 2-47 (54)
228 KOG1464 COP9 signalosome, subu 36.0 21 0.00045 35.8 1.7 12 1-12 1-12 (440)
229 PF03615 GCM: GCM motif protei 35.9 37 0.00079 30.1 2.9 22 291-318 83-108 (143)
230 PRK10445 endonuclease VIII; Pr 35.8 26 0.00056 35.2 2.3 25 290-314 235-262 (263)
231 PHA02929 N1R/p28-like protein; 35.6 16 0.00034 36.1 0.8 38 290-327 174-214 (238)
232 PF08792 A2L_zn_ribbon: A2L zi 35.5 32 0.0007 22.9 2.0 12 290-301 3-14 (33)
233 PRK13945 formamidopyrimidine-D 35.4 25 0.00055 35.6 2.2 25 290-314 254-281 (282)
234 PF10122 Mu-like_Com: Mu-like 35.3 16 0.00035 26.8 0.6 25 291-315 5-32 (51)
235 TIGR00993 3a0901s04IAP86 chlor 35.3 42 0.0009 38.2 4.0 42 50-95 411-452 (763)
236 PRK04023 DNA polymerase II lar 35.2 24 0.00052 41.5 2.2 31 288-324 624-660 (1121)
237 PF12861 zf-Apc11: Anaphase-pr 35.0 21 0.00045 29.3 1.2 35 291-328 33-67 (85)
238 PF00098 zf-CCHC: Zinc knuckle 35.0 23 0.0005 20.1 1.1 16 252-267 2-17 (18)
239 PF07800 DUF1644: Protein of u 34.8 47 0.001 30.5 3.6 36 130-167 2-50 (162)
240 PRK14714 DNA polymerase II lar 34.7 21 0.00045 43.0 1.6 31 290-326 667-703 (1337)
241 COG5194 APC11 Component of SCF 34.6 42 0.00091 27.1 2.8 28 149-186 53-80 (88)
242 COG3813 Uncharacterized protei 34.2 26 0.00055 27.6 1.5 43 132-186 7-51 (84)
243 PLN03086 PRLI-interacting fact 34.1 27 0.00059 38.8 2.4 30 288-317 431-463 (567)
244 TIGR00686 phnA alkylphosphonat 34.0 29 0.00062 29.7 1.9 27 291-318 3-30 (109)
245 KOG2164 Predicted E3 ubiquitin 33.8 14 0.00031 39.9 0.1 28 290-324 186-215 (513)
246 COG5175 MOT2 Transcriptional r 33.5 9.5 0.00021 38.9 -1.2 30 223-257 16-45 (480)
247 COG5151 SSL1 RNA polymerase II 33.4 9.4 0.0002 38.5 -1.2 19 243-261 388-407 (421)
248 PF08580 KAR9: Yeast cortical 33.4 4.9E+02 0.011 30.0 12.2 62 449-510 272-337 (683)
249 COG2816 NPY1 NTP pyrophosphohy 33.3 37 0.0008 34.2 2.9 36 281-317 103-139 (279)
250 PF05764 YL1: YL1 nuclear prot 33.2 29 0.00062 34.3 2.2 9 23-31 57-65 (240)
251 PHA02825 LAP/PHD finger-like p 33.2 44 0.00095 30.7 3.1 49 128-187 6-59 (162)
252 PF13453 zf-TFIIB: Transcripti 33.0 27 0.00059 24.2 1.4 29 292-325 1-29 (41)
253 KOG0825 PHD Zn-finger protein 32.8 30 0.00066 39.4 2.4 49 131-189 124-173 (1134)
254 PRK09521 exosome complex RNA-b 31.4 32 0.00069 32.6 2.1 24 292-316 151-175 (189)
255 PF11932 DUF3450: Protein of u 31.1 5.2E+02 0.011 25.4 14.4 15 497-511 149-163 (251)
256 KOG4677 Golgi integral membran 30.8 7.2E+02 0.016 26.9 12.8 56 357-420 167-223 (554)
257 KOG2932 E3 ubiquitin ligase in 30.7 22 0.00048 36.0 0.8 28 290-324 90-120 (389)
258 PF07975 C1_4: TFIIH C1-like d 30.1 34 0.00074 25.3 1.6 16 149-165 26-41 (51)
259 COG5236 Uncharacterized conser 30.0 27 0.00059 35.9 1.3 46 129-184 60-105 (493)
260 COG3809 Uncharacterized protei 29.6 36 0.00078 27.3 1.7 28 291-325 2-31 (88)
261 cd07622 BAR_SNX4 The Bin/Amphi 29.5 5.1E+02 0.011 24.8 16.2 97 397-507 98-194 (201)
262 KOG2906 RNA polymerase III sub 28.8 57 0.0012 27.4 2.8 27 222-251 2-30 (105)
263 COG1096 Predicted RNA-binding 28.7 36 0.00078 32.2 1.8 24 291-316 150-174 (188)
264 PRK06369 nac nascent polypepti 28.7 1.4E+02 0.0029 26.1 5.2 36 65-100 77-112 (115)
265 smart00659 RPOLCX RNA polymera 28.7 42 0.00091 23.9 1.8 10 291-300 20-29 (44)
266 PF06044 DRP: Dam-replacing fa 28.7 41 0.00088 33.1 2.2 35 282-317 24-63 (254)
267 PF03115 Astro_capsid: Astrovi 28.7 19 0.00041 41.6 0.0 6 76-81 721-726 (787)
268 PF06056 Terminase_5: Putative 28.6 78 0.0017 23.9 3.4 32 67-98 15-46 (58)
269 TIGR00373 conserved hypothetic 28.6 76 0.0016 29.2 4.0 33 216-251 104-137 (158)
270 KOG4684 Uncharacterized conser 28.6 66 0.0014 31.0 3.5 15 222-237 139-153 (275)
271 cd07662 BAR_SNX6 The Bin/Amphi 28.1 5.7E+02 0.012 24.9 13.4 57 451-507 155-211 (218)
272 TIGR00264 alpha-NAC-related pr 28.1 1.4E+02 0.003 26.1 5.1 34 65-98 79-112 (116)
273 COG1623 Predicted nucleic-acid 27.9 6.7E+02 0.015 25.7 10.9 31 348-378 151-181 (349)
274 cd00065 FYVE FYVE domain; Zinc 27.6 38 0.00082 24.9 1.5 34 131-164 3-38 (57)
275 PF14353 CpXC: CpXC protein 27.6 16 0.00035 32.1 -0.6 50 175-237 2-51 (128)
276 PF15616 TerY-C: TerY-C metal 27.3 34 0.00075 30.5 1.4 34 291-324 78-114 (131)
277 PF07503 zf-HYPF: HypF finger; 27.0 32 0.0007 23.3 0.9 31 154-186 1-31 (35)
278 TIGR02443 conserved hypothetic 27.0 57 0.0012 24.8 2.3 27 291-317 10-41 (59)
279 PRK13130 H/ACA RNA-protein com 27.0 36 0.00079 25.6 1.3 29 289-330 4-32 (56)
280 KOG0801 Predicted E3 ubiquitin 27.0 23 0.00049 32.5 0.2 27 129-155 176-203 (205)
281 KOG0309 Conserved WD40 repeat- 26.8 44 0.00095 38.0 2.3 37 129-165 1027-1063(1081)
282 PRK10220 hypothetical protein; 26.4 48 0.001 28.4 2.0 26 291-317 4-30 (111)
283 PLN02189 cellulose synthase 26.3 43 0.00093 39.8 2.3 56 229-309 39-95 (1040)
284 KOG2041 WD40 repeat protein [G 26.2 87 0.0019 35.6 4.4 19 200-218 1091-1109(1189)
285 PRK08115 ribonucleotide-diphos 25.7 32 0.0007 40.2 1.2 24 291-316 828-853 (858)
286 PRK13182 racA polar chromosome 25.2 5.7E+02 0.012 24.0 9.8 61 446-507 85-145 (175)
287 PF09526 DUF2387: Probable met 25.0 61 0.0013 25.7 2.3 26 291-316 9-39 (71)
288 PRK02935 hypothetical protein; 24.7 27 0.00058 29.7 0.2 16 291-306 71-89 (110)
289 smart00064 FYVE Protein presen 24.7 57 0.0012 25.0 2.1 36 130-165 10-47 (68)
290 KOG0995 Centromere-associated 24.5 1E+03 0.022 26.6 16.4 43 351-393 269-312 (581)
291 KOG2417 Predicted G-protein co 24.5 7.4E+02 0.016 26.1 10.3 15 400-414 226-240 (462)
292 PTZ00009 heat shock 70 kDa pro 24.5 1E+03 0.022 27.2 12.9 58 455-516 569-626 (653)
293 PRK06266 transcription initiat 24.4 92 0.002 29.3 3.8 33 216-251 112-145 (178)
294 PF15358 TSKS: Testis-specific 24.4 6.4E+02 0.014 26.9 10.0 89 353-470 123-212 (558)
295 PF10083 DUF2321: Uncharacteri 24.1 2.2E+02 0.0047 26.2 5.8 11 291-301 40-50 (158)
296 PF01428 zf-AN1: AN1-like Zinc 24.0 65 0.0014 22.6 2.1 25 228-258 4-29 (43)
297 COG2051 RPS27A Ribosomal prote 23.7 80 0.0017 24.6 2.6 31 222-255 20-51 (67)
298 PLN02638 cellulose synthase A 23.4 47 0.001 39.6 1.9 56 229-309 22-78 (1079)
299 PRK00241 nudC NADH pyrophospha 23.4 53 0.0012 32.8 2.1 30 288-317 97-127 (256)
300 PF14319 Zn_Tnp_IS91: Transpos 23.2 40 0.00087 29.1 1.0 12 247-258 57-68 (111)
301 PF11023 DUF2614: Protein of u 22.9 28 0.00061 30.0 0.0 12 290-301 69-80 (114)
302 COG3024 Uncharacterized protei 22.8 39 0.00085 26.0 0.8 13 290-302 7-19 (65)
303 cd07667 BAR_SNX30 The Bin/Amph 22.6 7.6E+02 0.017 24.4 14.6 97 398-507 137-235 (240)
304 PF14354 Lar_restr_allev: Rest 22.4 66 0.0014 24.1 2.0 12 290-301 3-14 (61)
305 PF03604 DNA_RNApol_7kD: DNA d 22.4 47 0.001 22.0 1.0 10 291-300 18-27 (32)
306 COG4068 Uncharacterized protei 22.4 22 0.00048 26.8 -0.6 12 291-302 9-20 (64)
307 COG4640 Predicted membrane pro 22.2 43 0.00093 35.2 1.2 8 291-298 2-9 (465)
308 PF10272 Tmpp129: Putative tra 22.1 91 0.002 32.8 3.5 38 150-187 311-351 (358)
309 PRK08332 ribonucleotide-diphos 22.0 54 0.0012 41.4 2.2 27 291-319 1705-1738(1740)
310 PF07754 DUF1610: Domain of un 22.0 67 0.0014 19.9 1.5 7 291-297 17-23 (24)
311 PF05715 zf-piccolo: Piccolo Z 21.8 33 0.00072 26.0 0.2 34 291-324 3-39 (61)
312 cd07621 BAR_SNX5_6 The Bin/Amp 21.7 7.6E+02 0.016 24.1 14.3 60 451-510 156-215 (219)
313 KOG2930 SCF ubiquitin ligase, 21.6 83 0.0018 26.7 2.5 23 149-179 80-102 (114)
314 PF05278 PEARLI-4: Arabidopsis 21.3 8.5E+02 0.018 24.5 13.1 52 401-467 167-218 (269)
315 COG5222 Uncharacterized conser 21.3 47 0.001 33.5 1.2 29 291-324 275-304 (427)
316 smart00531 TFIIE Transcription 21.3 1.3E+02 0.0029 27.2 4.1 18 70-87 20-37 (147)
317 PRK12286 rpmF 50S ribosomal pr 21.2 56 0.0012 24.7 1.3 13 289-301 26-38 (57)
318 PF13851 GAS: Growth-arrest sp 21.2 7.3E+02 0.016 23.7 16.2 23 401-423 108-130 (201)
319 KOG2807 RNA polymerase II tran 21.0 61 0.0013 33.2 1.9 35 132-167 332-367 (378)
320 PF09862 DUF2089: Protein of u 20.9 60 0.0013 28.2 1.6 9 293-301 1-9 (113)
321 KOG1512 PHD Zn-finger protein 20.8 73 0.0016 32.0 2.4 64 252-323 281-345 (381)
322 PLN02436 cellulose synthase A 20.7 64 0.0014 38.5 2.3 56 229-309 41-97 (1094)
323 KOG3623 Homeobox transcription 20.5 50 0.0011 37.5 1.3 20 292-311 311-331 (1007)
324 PHA02325 hypothetical protein 20.4 46 0.00099 25.6 0.7 11 289-299 2-12 (72)
325 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.3 63 0.0014 29.7 1.8 26 291-317 35-61 (166)
326 TIGR01206 lysW lysine biosynth 20.3 1.1E+02 0.0025 22.8 2.8 27 223-252 4-32 (54)
327 KOG3970 Predicted E3 ubiquitin 20.1 38 0.00082 32.8 0.2 81 249-343 20-101 (299)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.2e-67 Score=561.63 Aligned_cols=431 Identities=40% Similarity=0.757 Sum_probs=384.1
Q ss_pred eeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhhCHHHHHHHcCCCcccCCCCCCcCCccccc
Q 009189 53 KVITKESLLAAQMEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLVEYGKERLFAKAGLTIVETDDVSSSQVSSSYC 132 (540)
Q Consensus 53 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~~~~ 132 (540)
.|+|.+++...+.++|..|+++|+++..+|++||.+|.|+++++++.|++ +++.++...|+.... ......+
T Consensus 1 ~vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~-------~~~~~~~ 72 (444)
T KOG1815|consen 1 EVLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWP-------KKKGDVQ 72 (444)
T ss_pred CCCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccC-------CCCcccc
Confidence 37899999999999999999999999999999999999999999999994 667777788876443 1235789
Q ss_pred cccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhccCChhHHHHHHHHHHH
Q 009189 133 CNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVRARDSDLADKFDRFMLE 212 (540)
Q Consensus 133 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~~~~ 212 (540)
|.||++.++. .+..+.|||.||..||..|+..+|..|....|+||.++|.+.+....|..+++. ++..++|.+++++
T Consensus 73 c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~--~~~~~ky~~~i~~ 149 (444)
T KOG1815|consen 73 CGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSD--KEDKEKYQRYILR 149 (444)
T ss_pred CCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCC--HHHHHHHHHHHHH
Confidence 9999999865 678889999999999999999999888754599999999999999999999982 2589999999999
Q ss_pred HhhhcCCccccCCCCCCCCCeEEeccCccceeecCCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCC
Q 009189 213 SYIEDNKRVKWCPSVPHCGNAIRIEVDELREVECACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKH 292 (540)
Q Consensus 213 ~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~ 292 (540)
+||+.+..++|||+ |+|+.++.........|.|.||+.|||.|+.+||.|.+|..+..|..+..+++++.+||..|+++
T Consensus 150 syve~~~~lkwCP~-~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~ 228 (444)
T KOG1815|consen 150 SYVEDNVPLKWCPA-PGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKE 228 (444)
T ss_pred HHHhcCCccccCCC-CCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCcc
Confidence 99999999999996 99999998755556679999999999999999999999999999999999999999999999999
Q ss_pred CCCCccceeecCCCCeeEec---cCccccccccccccCCCCccccCCccCCCCccchHHH-HHHHHHHHHHHHHHHHHHH
Q 009189 293 CPKCQKLVEKNGGCNLVSCI---CGQPFCWLCGAATGSDHTWTSIAGHSCGRYKEDREKE-TESAKRSLERYIHYYSRYE 368 (540)
Q Consensus 293 CP~C~~~IeK~~GCnhm~C~---C~~~FCw~C~~~~~~~H~~~~~~g~~C~~~~~~~~~~-~~~~~~~l~ry~~y~~r~~ 368 (540)
||+|..+|||++|||||+|. |++.|||+|++.| .+|+... ++.||+|....... +..++..+.||.|||.||+
T Consensus 229 CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~-~~h~~~~--~~~c~~~~~~~~~~~~~~a~~~l~r~~~~~~~~~ 305 (444)
T KOG1815|consen 229 CPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASL-SDHGSST--GYSCNRYVDGKSKSARSKARRSLKRYTHYYNRWM 305 (444)
T ss_pred CCCcccchhccCCccccccccCCcCCeeceeeeccc-ccccccc--eeeeeeeechhhhhHHHHHHHHHHHHHHHHhhHH
Confidence 99999999999999999994 9999999999888 5675443 79999999877655 7888999999999999999
Q ss_pred hhhhhHHHHHHHHHHHHHH-HHHHHHhcCCCcchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHH
Q 009189 369 AHRDSSKLESKMKETMEDN-IKILEECSTASSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMK 447 (540)
Q Consensus 369 ~h~~s~k~e~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~ 447 (540)
+|..+++++..+...+++. +..+.......+.+++|+.+++.+|.++|++|+|||+|+||+..+ .+
T Consensus 306 ~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~~~-------------~~ 372 (444)
T KOG1815|consen 306 EHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLSEN-------------NK 372 (444)
T ss_pred hhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhccc-------------ch
Confidence 9999999998877666543 334433344568899999999999999999999999999998732 44
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 009189 448 QNLFEDQQQQFEANIEKLSSFLDEKFHLYNEDEIKDLKLRVIALSATTDNLCRNLYECIETDLL 511 (540)
Q Consensus 448 ~~lfe~~q~~le~~~e~L~~~le~~~~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e~~l~ 511 (540)
+++||++|.+++..+|.|+..+++++...+..++.++|+++.+++.++++++.+++..+++||.
T Consensus 373 ~~~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 436 (444)
T KOG1815|consen 373 RNLFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLE 436 (444)
T ss_pred hhhhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccchhhhhHHHHHHHHHHhccc
Confidence 5899999999999999999999998876777889999999999999999999999999999986
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.9e-35 Score=290.61 Aligned_cols=210 Identities=25% Similarity=0.660 Sum_probs=178.2
Q ss_pred ccccccccccccCCC-CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhccCChhHHHHH
Q 009189 128 SSSYCCNICFDDVSL-EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVRARDSDLADKF 206 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 206 (540)
.+.+.|.|||+.... ..+..+||+|.||+.|++.|+...|++|.+..++||+++|+...++..++.++. .+++++|
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 467999999999766 556778999999999999999999999999999999999999999999999999 8899999
Q ss_pred HHHHHHHhhhcCCccccCCCCCCCCCeEEeccCccceeecC-CCceecccccCccCCCCCchhh--------HHHhH---
Q 009189 207 DRFMLESYIEDNKRVKWCPSVPHCGNAIRIEVDELREVECA-CGLQFCFRCSYEAHSPCSCYMW--------DLWSK--- 274 (540)
Q Consensus 207 ~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~--------~~~~~--- 274 (540)
+..++++.++...++++|| .+.|...+. .+++...+.|. |..+||+.|+..||...+|... ..|..
T Consensus 259 e~l~lqk~l~~msdv~yCP-r~~Cq~p~~-~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCP-RACCQLPVK-QDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE 336 (445)
T ss_pred HHHHHHHHHHhhcccccCC-hhhccCccc-cCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence 9999999999999999999 489998873 33445568895 9999999999999999999743 11221
Q ss_pred ----------------HhhhhhHHHHHHHhccCCCCCCccceeecCCCCeeEe-ccCccccccccccccCCCCccccCCc
Q 009189 275 ----------------KCQDESETVNYIAVHTKHCPKCQKLVEKNGGCNLVSC-ICGQPFCWLCGAATGSDHTWTSIAGH 337 (540)
Q Consensus 275 ----------------~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~~~~~~g~ 337 (540)
...++-.+..|+..|.|+||+|+++|||++|||||+| .|++.|||+|.....+..+|.|+.+.
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 1112334568999999999999999999999999999 69999999999987767778887664
Q ss_pred cCCCC
Q 009189 338 SCGRY 342 (540)
Q Consensus 338 ~C~~~ 342 (540)
.+..|
T Consensus 417 ~s~c~ 421 (445)
T KOG1814|consen 417 GSECY 421 (445)
T ss_pred cCccc
Confidence 44333
No 3
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-34 Score=300.46 Aligned_cols=223 Identities=30% Similarity=0.680 Sum_probs=183.2
Q ss_pred cccccccccccCCC-Cceee-cCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhccCChhHHHHH
Q 009189 129 SSYCCNICFDDVSL-EEITT-MDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVRARDSDLADKF 206 (540)
Q Consensus 129 ~~~~C~IC~e~~~~-~~~~~-l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky 206 (540)
...+|+||+...+. ..++. ..|+|.||.+||++|+..+...| ..++||..+|...++.+....+++ +.+.++|
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt---~kl~e~~ 219 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLT---PKLREMW 219 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcC---HHHHHHH
Confidence 46789999955433 34444 58999999999999999985544 489999999999999999999999 7899999
Q ss_pred HHHHHHHhhhcCCccccCCCCCCCCCeEEecc----CccceeecC-CCceecccccCccCCCCCchhhHHHhHHhhhhhH
Q 009189 207 DRFMLESYIEDNKRVKWCPSVPHCGNAIRIEV----DELREVECA-CGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESE 281 (540)
Q Consensus 207 ~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~----~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~ 281 (540)
++++.+.++.....+ +|| .|+|...+.... .......|. |+..||..|+.+||.+.+|..+++|..+...+..
T Consensus 220 e~~~~e~~i~~~~~~-ycp-~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~ 297 (384)
T KOG1812|consen 220 EQRLKEEVIPSLDRV-YCP-YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDI 297 (384)
T ss_pred HHHHHHHhhhhhhcc-cCC-CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHH
Confidence 999999999999888 999 499988776433 223335675 9999999999999999999999999987777788
Q ss_pred HHHHHHhccCCCCCCccceeecCCCCeeEeccCccccccccccccCCCCccccCCccCCCCccchHHHHHHHHHHHHHHH
Q 009189 282 TVNYIAVHTKHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAATGSDHTWTSIAGHSCGRYKEDREKETESAKRSLERYI 361 (540)
Q Consensus 282 ~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~H~~~~~~g~~C~~~~~~~~~~~~~~~~~l~ry~ 361 (540)
+.+++..+|+.||+|+..|++++|||||+||||+.|||.|+++|.. |. ...+.|.++.+. +
T Consensus 298 ~~~~la~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~-~~---~~~~~~~r~~~~---------------~ 358 (384)
T KOG1812|consen 298 TLKYLAKRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKT-HN---GECYECCRYKES---------------T 358 (384)
T ss_pred HHHHHHHhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhh-CC---ccccCccccccc---------------c
Confidence 8899999999999999999999999999999999999999999832 21 012455555543 6
Q ss_pred HHHHHHHhhhhhHHHH
Q 009189 362 HYYSRYEAHRDSSKLE 377 (540)
Q Consensus 362 ~y~~r~~~h~~s~k~e 377 (540)
+++.++.+|.....++
T Consensus 359 ~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 359 HYFEDDENHDKSIQLE 374 (384)
T ss_pred cccccccccccccccc
Confidence 7777777776655443
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.5e-23 Score=202.75 Aligned_cols=193 Identities=26% Similarity=0.613 Sum_probs=144.5
Q ss_pred CccccccccccccCCCCceeecCCC--CcccHHHHHHHHHHhhhcCCc-------ccccccCcccccccchh-HHHHhhc
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCG--HYFCNSCWTEHFIVKINEGQS-------RRITCMEHKCNAICDES-KIRCLVR 196 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~y~~~~i~~g~~-------~~i~CP~~~C~~~~~~~-~i~~ll~ 196 (540)
+....+|..|-+.- +.+..++|. |..|.+|++.|..+.+++.++ ..+.||. +|...+-.+ .--++|.
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 55778999998873 334456888 999999999999999987653 3456664 465544322 2234566
Q ss_pred cCChhHHHHHHHHHHHHhhhcCCccccCCCCCCCCCeEEeccCccceeecC--CCceecccccCccCCCC----------
Q 009189 197 ARDSDLADKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIEVDELREVECA--CGLQFCFRCSYEAHSPC---------- 264 (540)
Q Consensus 197 ~~~~e~~eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~--C~~~fC~~C~~~~H~~~---------- 264 (540)
.+.+.+|+++..+.+|.....+ -|| .|+|+..+..+++ ...++|+ ||..||..|++.+|.+.
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-RPGCGAGLLPEPD-QRKVTCEGGCGFAFCRECKEAYHEGECSAVFEASGT 368 (446)
T ss_pred ---hhHHHHHHHhhhhhheeecCCE-ecC-CCCCCcccccCCC-CCcccCCCCchhHhHHHHHhhhccccceeeeccccc
Confidence 7899999999999999888865 899 5999998877663 4469994 99999999999999762
Q ss_pred -Cchhh--HHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCCeeEe-c--cCccccccccccccCC
Q 009189 265 -SCYMW--DLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCNLVSC-I--CGQPFCWLCGAATGSD 328 (540)
Q Consensus 265 -~C~~~--~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~--C~~~FCw~C~~~~~~~ 328 (540)
+|.-. ..-....+-+..+..-|+..||+||+|+.|.||||||+||.| + ||.+|||.|+-.|.+.
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhh
Confidence 24310 000001111233445578889999999999999999999999 4 9999999999999653
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.20 E-value=2.8e-11 Score=94.21 Aligned_cols=62 Identities=48% Similarity=1.159 Sum_probs=54.9
Q ss_pred HHHHHHHHHHhhhcCCccccCCCCCCCCCeEEec-cCccceeec-CCCceecccccCccCCCCCc
Q 009189 204 DKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIE-VDELREVEC-ACGLQFCFRCSYEAHSPCSC 266 (540)
Q Consensus 204 eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~-~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C 266 (540)
++|++++++++|+.+++++||| .|+|+.++... ......+.| .|++.||+.|+.+||.|.+|
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 4789999999999988999999 59999998876 345567999 59999999999999999987
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=99.08 E-value=3.8e-11 Score=93.44 Aligned_cols=62 Identities=34% Similarity=0.952 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhhcCCccccCCCCCCCCCeEEeccCccc-eeecC-CCceecccccCccCCCCCc
Q 009189 204 DKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIEVDELR-EVECA-CGLQFCFRCSYEAHSPCSC 266 (540)
Q Consensus 204 eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~-~v~C~-C~~~fC~~C~~~~H~~~~C 266 (540)
++|.+++++.+|+.++.++||| .|+|+.++........ .+.|+ |++.||+.|+.+||.|.+|
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 5788999999998888999999 5999999987765444 39997 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=98.77 E-value=3.4e-09 Score=75.19 Aligned_cols=41 Identities=32% Similarity=0.795 Sum_probs=30.4
Q ss_pred cccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 133 CNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 133 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
|+||++.+ .+|++++|||+||..|+..+|...-. ..+.||.
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 89999998 79999999999999999999876322 1378986
No 8
>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=98.33 E-value=3.5e-07 Score=63.83 Aligned_cols=37 Identities=30% Similarity=0.810 Sum_probs=29.2
Q ss_pred cccccccCCCCce-eecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 133 CNICFDDVSLEEI-TTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 133 C~IC~e~~~~~~~-~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
|+||++.+ .++ +.++|||.||.+||..|+... .+||.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 89999987 456 678999999999999998762 47876
No 9
>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=98.32 E-value=5.5e-07 Score=63.46 Aligned_cols=39 Identities=28% Similarity=0.793 Sum_probs=32.3
Q ss_pred cccccccCCCCcee-ecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 133 CNICFDDVSLEEIT-TMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 133 C~IC~e~~~~~~~~-~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
|+||++.+ .++. .++|||.||..||.+++.. . ..++||.
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 89999987 4455 7899999999999999987 2 2468986
No 10
>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=98.30 E-value=4.2e-07 Score=65.19 Aligned_cols=40 Identities=30% Similarity=0.708 Sum_probs=33.0
Q ss_pred ccccccccCC-CCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 132 CCNICFDDVS-LEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 132 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
+|+||++.+. ...++.++|||.||.+|+..|+... .+||.
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 6999999984 4667888999999999999999762 28887
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.25 E-value=7.7e-07 Score=83.30 Aligned_cols=65 Identities=25% Similarity=0.544 Sum_probs=48.0
Q ss_pred CccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhc--------CCcccccccCcccccccchhHHHHhh
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINE--------GQSRRITCMEHKCNAICDESKIRCLV 195 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~--------g~~~~i~CP~~~C~~~~~~~~i~~ll 195 (540)
....++|+||++.+ .+++.++|||.||..|+..|+...-.. ......+||. |+..++...+..+.
T Consensus 15 ~~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy 87 (193)
T PLN03208 15 SGGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY 87 (193)
T ss_pred CCCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence 34679999999987 678889999999999999987642110 0113579999 99988765544443
No 12
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.18 E-value=1.2e-06 Score=62.23 Aligned_cols=41 Identities=29% Similarity=0.678 Sum_probs=22.9
Q ss_pred cccccccCCC--CceeecCCCCcccHHHHHHHHHHhhhcCCccccccc
Q 009189 133 CNICFDDVSL--EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCM 178 (540)
Q Consensus 133 C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP 178 (540)
|+||.+ +.. ..++.|+|||.||.+|+.+.+.... ...++||
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 622 2367889999999999999988532 1358887
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=1.1e-06 Score=80.10 Aligned_cols=53 Identities=28% Similarity=0.684 Sum_probs=42.2
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhH
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESK 190 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~ 190 (540)
...+.||||++.+....+++..|||.||..|++.-+.. + .+||. |+..++...
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~----~----~~CP~--C~kkIt~k~ 181 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN----T----NKCPT--CRKKITHKQ 181 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHh----C----CCCCC--cccccchhh
Confidence 45689999999998777788999999999999976654 2 48999 665665443
No 14
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.08 E-value=4.5e-06 Score=64.65 Aligned_cols=39 Identities=38% Similarity=0.918 Sum_probs=34.9
Q ss_pred ccCCCC--CCccceeecC--CCCeeEe-ccCccccccccccccC
Q 009189 289 HTKHCP--KCQKLVEKNG--GCNLVSC-ICGQPFCWLCGAATGS 327 (540)
Q Consensus 289 ~~k~CP--~C~~~IeK~~--GCnhm~C-~C~~~FCw~C~~~~~~ 327 (540)
+++.|| +|+..|+... |.++|+| .|++.|||.|+.+||.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 468899 9999999864 9999999 7999999999999853
No 15
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.04 E-value=4.7e-06 Score=61.50 Aligned_cols=46 Identities=26% Similarity=0.751 Sum_probs=36.7
Q ss_pred ccccccccccCCCCceeecCCCCc-ccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHY-FCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
...|.||++.. .+++.+||||. ||..|+..++.. ..+||. |+..+.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~--------~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR--------KKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT--------TSBBTT--TTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc--------CCCCCc--CChhhc
Confidence 46799999985 56788899999 999999999882 358998 887664
No 16
>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=98.02 E-value=2.2e-06 Score=66.43 Aligned_cols=39 Identities=41% Similarity=1.139 Sum_probs=29.2
Q ss_pred ccCCCCC--CccceeecCCCCe--eEec-cCccccccccccccC
Q 009189 289 HTKHCPK--CQKLVEKNGGCNL--VSCI-CGQPFCWLCGAATGS 327 (540)
Q Consensus 289 ~~k~CP~--C~~~IeK~~GCnh--m~C~-C~~~FCw~C~~~~~~ 327 (540)
+.+.||+ |...|.+..|+++ |+|. |++.|||.|+++||.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 3589988 9999999999999 9996 999999999999854
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.94 E-value=6.7e-06 Score=58.93 Aligned_cols=42 Identities=36% Similarity=0.911 Sum_probs=33.6
Q ss_pred ccccccccCC-CCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccc
Q 009189 132 CCNICFDDVS-LEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCN 183 (540)
Q Consensus 132 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~ 183 (540)
.|+||++.+. ...++.++|||.||..|+.... + ..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~------~--~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK------G--KSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc------C--CCCCCcC--CC
Confidence 4999999993 3456778999999999999876 1 3579998 65
No 18
>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=97.93 E-value=9.4e-06 Score=57.53 Aligned_cols=43 Identities=35% Similarity=0.869 Sum_probs=33.0
Q ss_pred ccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccc
Q 009189 132 CCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAI 185 (540)
Q Consensus 132 ~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~ 185 (540)
+|+||++.+ ..++.+ +|||.||..|+..|+.. + ..+||. |+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~----~---~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS----G---KNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh----C---cCCCCC--CCCc
Confidence 599999987 344444 69999999999999875 2 367987 7653
No 19
>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=97.85 E-value=1.7e-05 Score=61.20 Aligned_cols=47 Identities=9% Similarity=0.149 Sum_probs=38.9
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchh
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDES 189 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~ 189 (540)
+.|+||.+.+ .+++.++|||.||+.|+..|+.. + ..||. |+..++..
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~----~----~~cP~--~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS----H----GTDPV--TGQPLTHE 48 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH----C----CCCCC--CcCCCChh
Confidence 6799999987 67888999999999999999976 1 37988 77766543
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.81 E-value=9.9e-06 Score=77.31 Aligned_cols=55 Identities=27% Similarity=0.619 Sum_probs=44.5
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHH
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKI 191 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i 191 (540)
...|+|.||++.. .+++...|||.||-.||-+|+....+. -.||. |+..++.+.+
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~v 99 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTV 99 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceE
Confidence 4679999999986 789999999999999999999886432 36788 8877765543
No 21
>PHA02926 zinc finger-like protein; Provisional
Probab=97.79 E-value=1.5e-05 Score=75.45 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=40.6
Q ss_pred CccccccccccccCC-----CCc--eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 127 VSSSYCCNICFDDVS-----LEE--ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~-----~~~--~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.+...+|+||++..- ... .+..+|+|.||..|+..|-..+-..|. .-.||. |+..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~--~rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGA--SDNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCc--CCcCCC--Ccceee
Confidence 356789999999852 111 233489999999999999886533332 357999 887654
No 22
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=1.2e-05 Score=78.85 Aligned_cols=51 Identities=29% Similarity=0.670 Sum_probs=42.9
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKI 191 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i 191 (540)
....|.+|++.. .+|..+||||.||.+|+.+|...+- .||. |+..+.+..+
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 457899999986 6888899999999999999987742 4999 9998887643
No 23
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=1.4e-05 Score=84.21 Aligned_cols=60 Identities=20% Similarity=0.469 Sum_probs=47.5
Q ss_pred ccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhc
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVR 196 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 196 (540)
...|||||+..+ -+..+.|||.||-.||-+||...... .+.+||. |...+.+..+..+..
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 788999999863 35566799999999999999987322 3579999 999888776665554
No 24
>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=97.72 E-value=3e-05 Score=52.89 Aligned_cols=38 Identities=34% Similarity=0.920 Sum_probs=30.8
Q ss_pred cccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 133 CNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 133 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
|+||++.. ..++.++|||.||..|+..|+. .+ ..+||.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~----~~---~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK----SG---NNTCPI 38 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH----hC---cCCCCC
Confidence 78999884 6778889999999999999987 12 357875
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.68 E-value=3e-05 Score=81.14 Aligned_cols=66 Identities=27% Similarity=0.542 Sum_probs=47.4
Q ss_pred CccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHH-HHhhccCChhHHHH
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKI-RCLVRARDSDLADK 205 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i-~~ll~~~~~e~~ek 205 (540)
....+.|+||++.+ .+++.++|||.||..|+..|+... ..||. |+..+....+ .+.+. .++++.
T Consensus 23 Le~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~~--------~~CP~--Cr~~~~~~~Lr~N~~L---~~iVe~ 87 (397)
T TIGR00599 23 LDTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSNQ--------PKCPL--CRAEDQESKLRSNWLV---SEIVES 87 (397)
T ss_pred cccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhCC--------CCCCC--CCCccccccCccchHH---HHHHHH
Confidence 34678999999988 677888999999999999998641 37998 8887754322 22222 345555
Q ss_pred HH
Q 009189 206 FD 207 (540)
Q Consensus 206 y~ 207 (540)
|.
T Consensus 88 ~~ 89 (397)
T TIGR00599 88 FK 89 (397)
T ss_pred HH
Confidence 54
No 26
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.66 E-value=3.5e-05 Score=75.31 Aligned_cols=50 Identities=28% Similarity=0.483 Sum_probs=37.4
Q ss_pred ccccccccccccCCCCc------eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEE------ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
+...+|+||++.+.... .+..+|||.||..|+..|+.. ...||. |+..+.
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 35689999999864322 244589999999999998753 248999 887654
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.61 E-value=2.9e-05 Score=78.56 Aligned_cols=45 Identities=29% Similarity=0.808 Sum_probs=38.1
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
...+.|+||++.+ ..+..++|||+||..|+...+. ..+.||. |+.
T Consensus 11 ~~~~~C~iC~~~~--~~p~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYF--REPVLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP 55 (386)
T ss_pred cccccChhhHHHh--hcCccccccchHhHHHHHHhcC--------CCcCCcc--cCC
Confidence 3678999999998 4557789999999999999998 2489998 773
No 28
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.57 E-value=0.00051 Score=70.61 Aligned_cols=34 Identities=21% Similarity=0.570 Sum_probs=29.4
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFI 164 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~ 164 (540)
+++.|+||..-+ .+|..++|+|..|+.|-...+.
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhcc
Confidence 567899999888 7899999999999999886554
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.36 E-value=7.5e-05 Score=74.46 Aligned_cols=64 Identities=22% Similarity=0.556 Sum_probs=49.1
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHH-hhccCChhHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRC-LVRARDSDLADKFD 207 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~-ll~~~~~e~~eky~ 207 (540)
..+.|.||++-| .-++.+||+|.||.=|++.|+.. ...||. |..++.+..+++ .+. .++++-|.
T Consensus 22 ~lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il---~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRIL---DEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHh--cCceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHH---HHHHHHHH
Confidence 467899999998 45677899999999999999876 358998 999988776653 222 35665554
No 30
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.06 E-value=0.00033 Score=77.50 Aligned_cols=56 Identities=21% Similarity=0.639 Sum_probs=45.8
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHh
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCL 194 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~l 194 (540)
....+||+|..-. .+.+...|||.||..|++..+.+. .=+||. |+..|++.+|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR-------QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh-------cCCCCC--CCCCCCccccccc
Confidence 4678999999543 677788999999999999998874 248998 9999998776654
No 31
>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=97.06 E-value=0.00051 Score=54.91 Aligned_cols=51 Identities=16% Similarity=0.113 Sum_probs=38.0
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchh
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDES 189 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~ 189 (540)
++.|.|+|+.+.+ .+|+.+++||.|++.||..|+.. ....||. |+..++..
T Consensus 2 P~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 2 PDEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp SGGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGG
T ss_pred CcccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcc
Confidence 3579999999997 79999999999999999999876 1358888 66666653
No 32
>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=96.95 E-value=0.00053 Score=69.12 Aligned_cols=54 Identities=26% Similarity=0.547 Sum_probs=37.3
Q ss_pred ccccccccccCC-CCceee--cCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHH
Q 009189 130 SYCCNICFDDVS-LEEITT--MDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIR 192 (540)
Q Consensus 130 ~~~C~IC~e~~~-~~~~~~--l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 192 (540)
...||||..+.- ..++.. .+|||.||.+|+...|.. | +..||. |+.++....++
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~---~~~CP~--C~~~lrk~~fr 59 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G---SGSCPE--CDTPLRKNNFR 59 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C---CCCCCC--CCCccchhhcc
Confidence 357999998632 222211 279999999999998732 3 358997 98887765443
No 33
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.66 E-value=0.0013 Score=64.98 Aligned_cols=52 Identities=17% Similarity=0.477 Sum_probs=42.0
Q ss_pred ccccccccccccCCC-CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 128 SSSYCCNICFDDVSL-EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
....+|.||++.+.. +....+||.|.|...|+.+|+.. ...+||. |+..+++
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP 373 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP 373 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 456899999999754 34566799999999999999864 2468998 9988875
No 34
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.65 E-value=0.0015 Score=49.46 Aligned_cols=47 Identities=23% Similarity=0.416 Sum_probs=30.8
Q ss_pred cccccccccccCCCCceee-cCCCCcccHHHHHHHHHHhhhcCCcccccccCcccc
Q 009189 129 SSYCCNICFDDVSLEEITT-MDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCN 183 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~ 183 (540)
..+.|||.+..+ .+|+. ..|||.|.++.+..|+. . ...++||..+|+
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~----~--~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQ----R--NGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCT----T--TS-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHH----h--cCCCCCCCCCCC
Confidence 468899999987 66765 59999999999999991 1 136899999985
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.0013 Score=64.21 Aligned_cols=53 Identities=30% Similarity=0.655 Sum_probs=41.6
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKI 191 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i 191 (540)
..+.|.||++.. ..+..++|||.||..|+-..|..+ ..-.||. |++.+.+..|
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 367899999985 677888999999999999865542 1336998 9988776655
No 36
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.48 E-value=0.00038 Score=53.17 Aligned_cols=44 Identities=32% Similarity=0.754 Sum_probs=22.2
Q ss_pred cccccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 129 SSYCCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
+...|++|.+.+ .+|+.+ .|.|.||..|++..+. ..||. |..+-
T Consensus 6 ~lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Pa 50 (65)
T PF14835_consen 6 ELLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPA 50 (65)
T ss_dssp HTTS-SSS-S----SS-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-
T ss_pred HhcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC----------CCCCC--cCChH
Confidence 346799999997 677765 8999999999976321 25998 77654
No 37
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=96.40 E-value=0.23 Score=52.16 Aligned_cols=118 Identities=19% Similarity=0.396 Sum_probs=66.7
Q ss_pred eeCHHHHHHHHHHHHHHHHHHhCCCH--HHHHHHHHHcCCChHH--HHHHHHhhCHHHHHHH-----cCC------Cccc
Q 009189 54 VITKESLLAAQMEDLIRVMDLLSLKE--QHARTLLIHYRWDVEK--VLAVLVEYGKERLFAK-----AGL------TIVE 118 (540)
Q Consensus 54 vlt~~~i~~~~~~~i~~v~~~l~i~~--~~a~~LL~~~~W~~~~--l~~~~~~~~~~~~~~~-----~gl------~~~~ 118 (540)
-+|.-||..-+-..+..|+++.-|-. ..-..+|++|+=..+. ..+.|. | +-|.. ..+ ....
T Consensus 85 ~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efN--G--k~Fn~le~e~Chll~V~~ve~~~ 160 (493)
T KOG0804|consen 85 YMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFN--G--KQFNSLEPEVCHLLYVDRVEVTE 160 (493)
T ss_pred cccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcC--C--CcCCCCCccceeEEEEEEEEEEe
Confidence 37888999888888888888775531 2234455566544322 222221 1 11110 000 0001
Q ss_pred CCCCC---CcCCccccccccccccCCCC--ceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 119 TDDVS---SSQVSSSYCCNICFDDVSLE--EITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 119 ~~~~~---~~~~~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
..+.+ .....+.-+||||++-++.+ -+.+..|.|+|--.|+..|+. .+||. |+....
T Consensus 161 s~d~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~~q~ 222 (493)
T KOG0804|consen 161 SEDGASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRYCQS 222 (493)
T ss_pred cccCCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhhhcC
Confidence 11111 11234567999999987532 235668999999999998864 47887 764433
No 38
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.29 E-value=0.0035 Score=50.10 Aligned_cols=42 Identities=26% Similarity=0.460 Sum_probs=29.6
Q ss_pred ccccccccccCCCC-----------ceeecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 130 SYCCNICFDDVSLE-----------EITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 130 ~~~C~IC~e~~~~~-----------~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
...|.||++.+... .+...+|||.|...||..|+... -.||.
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 12334899999999999998552 28987
No 39
>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=96.12 E-value=0.015 Score=41.29 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhhC
Q 009189 65 MEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLVEYG 104 (540)
Q Consensus 65 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~ 104 (540)
++.|...++++|+++..|..+|...+||++..++.|++.+
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 3568899999999999999999999999999999999643
No 40
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.08 E-value=0.003 Score=66.64 Aligned_cols=56 Identities=23% Similarity=0.510 Sum_probs=44.7
Q ss_pred CccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchh
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDES 189 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~ 189 (540)
+.....|.+|-+.- .+.+...|.|.||+-|++.|+.....+. .+.||. |...++.+
T Consensus 533 nk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 533 NKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred ccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 34678999998875 6777889999999999999998765433 389998 88766544
No 41
>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=95.91 E-value=1.2 Score=45.23 Aligned_cols=53 Identities=25% Similarity=0.540 Sum_probs=34.1
Q ss_pred cCCCCCCCCCeEEeccCccceeecCCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceee
Q 009189 223 WCPSVPHCGNAIRIEVDELREVECACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEK 302 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 302 (540)
-|| .|..-....+.....+. +|||.||..|.... | .....+||.|+.++.|
T Consensus 5 ~CP---~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----------~--------------~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCP---RCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----------F--------------VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCC---cCCCCCccCcccccccC-CCCCcccHHHHHHH-----------h--------------cCCCCCCCCCCCccch
Confidence 587 58765444443333455 79999999996321 1 1122589999999886
Q ss_pred cC
Q 009189 303 NG 304 (540)
Q Consensus 303 ~~ 304 (540)
+.
T Consensus 56 ~~ 57 (309)
T TIGR00570 56 NN 57 (309)
T ss_pred hh
Confidence 54
No 42
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.87 E-value=0.0048 Score=63.37 Aligned_cols=45 Identities=22% Similarity=0.589 Sum_probs=36.8
Q ss_pred cccccccccCCCCc-eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 131 YCCNICFDDVSLEE-ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 131 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
++|.||+|++...+ ...|||+|.|...|+..|+... + -.||. |+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r----~~CPv--CK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---R----TFCPV--CKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---C----ccCCC--CCC
Confidence 79999999986554 5667999999999999999874 2 36999 554
No 43
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.82 E-value=0.0037 Score=61.37 Aligned_cols=48 Identities=29% Similarity=0.534 Sum_probs=38.0
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
....|-||-+-+ .-+...+|||.||.=|++.|+..+ ..||. |....-.
T Consensus 24 s~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~q--------p~CP~--Cr~~~~e 71 (391)
T COG5432 24 SMLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGTQ--------PFCPV--CREDPCE 71 (391)
T ss_pred hHHHhhhhhhee--ecceecccccchhHHHHHHHhcCC--------CCCcc--ccccHHh
Confidence 567899998887 456778999999999999998663 57888 7765443
No 44
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.033 Score=54.71 Aligned_cols=53 Identities=23% Similarity=0.508 Sum_probs=39.0
Q ss_pred cCCccccccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 125 SQVSSSYCCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 125 ~~~~~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
+..+...+|++|-+.- ..|..+ +|||.||--|+..-.... ..+.||. |+..+.
T Consensus 234 s~~t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 234 STGTSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred ccccCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 3445678999998752 445555 699999999999866542 2479998 887665
No 45
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.065 Score=55.58 Aligned_cols=39 Identities=33% Similarity=0.710 Sum_probs=35.1
Q ss_pred hccCCCCC--CccceeecCCCCeeEe-ccCcccccccccccc
Q 009189 288 VHTKHCPK--CQKLVEKNGGCNLVSC-ICGQPFCWLCGAATG 326 (540)
Q Consensus 288 ~~~k~CP~--C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~ 326 (540)
++..-||+ |..|+-...|++-..| +|.+.||-+|...||
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H 312 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH 312 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc
Confidence 45689998 9999977889999999 799999999999884
No 46
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.09 E-value=0.012 Score=46.68 Aligned_cols=57 Identities=26% Similarity=0.416 Sum_probs=26.6
Q ss_pred ccccccccccCC-CCc-eee----cCCCCcccHHHHHHHHHHhhhcCCcc-cc--cccCcccccccch
Q 009189 130 SYCCNICFDDVS-LEE-ITT----MDCGHYFCNSCWTEHFIVKINEGQSR-RI--TCMEHKCNAICDE 188 (540)
Q Consensus 130 ~~~C~IC~e~~~-~~~-~~~----l~CgH~fC~~Cl~~y~~~~i~~g~~~-~i--~CP~~~C~~~~~~ 188 (540)
...|+||+..+. ... +.. ..|++.|...||.+|+...-+....+ ++ .||. |...+.-
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 468999998754 222 221 25899999999999998765544322 33 6998 9887653
No 47
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.01 E-value=0.028 Score=59.24 Aligned_cols=48 Identities=23% Similarity=0.597 Sum_probs=37.8
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.+.+.|.||+..+ .+++++||||.||..|+..- +.. .-.||. |+..+.
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r~----ld~----~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDRS----LDQ----ETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHHH----hcc----CCCCcc--cccccc
Confidence 5789999999987 57888899999999997762 221 347887 888776
No 48
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.83 E-value=0.023 Score=57.86 Aligned_cols=48 Identities=25% Similarity=0.576 Sum_probs=37.6
Q ss_pred ccccccccccc-CCCC----------ceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 129 SSYCCNICFDD-VSLE----------EITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 129 ~~~~C~IC~e~-~~~~----------~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
....|.||+|+ +... .|..+||||.+...|++.|++.+ -.||. |+.++
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ 344 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPV 344 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCcc
Confidence 56789999999 3222 24678999999999999999863 38998 88764
No 49
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.79 E-value=0.015 Score=57.76 Aligned_cols=54 Identities=22% Similarity=0.430 Sum_probs=41.3
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHH
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIR 192 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 192 (540)
...-+|.||+.+- .-++.++|+|.||.-|+++-... +. -.|+. |+.+++...+.
T Consensus 5 ~~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----dk---~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 5 TKKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----DK---KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred ccCCcceeeeccC--CcCccccccchhhhhhhcchhhc----CC---CCCce--ecCCCCcchhc
Confidence 3467899999985 56789999999999999975432 22 36998 99988766543
No 50
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.38 E-value=0.1 Score=52.10 Aligned_cols=95 Identities=23% Similarity=0.462 Sum_probs=55.7
Q ss_pred CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhccCChhHHHHHHHHHHHHhhhcCCccccCCCCC
Q 009189 149 DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVRARDSDLADKFDRFMLESYIEDNKRVKWCPSVP 228 (540)
Q Consensus 149 ~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~~~~~~v~~~~~~~~CP~~p 228 (540)
.||-.||+.|+..|-...-..+... . -...|...+++. .....+|...... ......+.||
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~a--s-~t~tc~y~vde~----------~a~~arwd~as~~---TIk~tTkpCP--- 401 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEA--S-GTTTCAYRVDER----------AAEQARWDAASKE---TIKKTTKPCP--- 401 (446)
T ss_pred CchhHhHHHHHhhhccccceeeecc--c-cccceeeecChh----------hhhhhhhhhhhhh---hhhhccCCCC---
Confidence 4999999999999965432221100 0 011244444443 2233445443221 1233557888
Q ss_pred CCCCeEEeccCccceeec--C-CCceecccccCccCCC
Q 009189 229 HCGNAIRIEVDELREVEC--A-CGLQFCFRCSYEAHSP 263 (540)
Q Consensus 229 ~C~~~i~~~~~~~~~v~C--~-C~~~fC~~C~~~~H~~ 263 (540)
.|......++ +...+.| + ||..+||+|+.+|...
T Consensus 402 kChvptErnG-GCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 402 KCHVPTERNG-GCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred CccCccccCC-ceEEeecCCCCCCceeEeccCChhhhh
Confidence 6877665544 3445788 2 9999999999988654
No 51
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.23 E-value=0.034 Score=58.86 Aligned_cols=102 Identities=22% Similarity=0.520 Sum_probs=61.1
Q ss_pred ccccccccccCCC---Ccee---ecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhccCChhHH
Q 009189 130 SYCCNICFDDVSL---EEIT---TMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVRARDSDLA 203 (540)
Q Consensus 130 ~~~C~IC~e~~~~---~~~~---~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~ 203 (540)
...|+.|...... .... -..|+-.||..|-..|-. ++.| +.++++.+.. ..
T Consensus 238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~---------~~sC-----------~eykk~~~~~---~~ 294 (384)
T KOG1812|consen 238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA---------NLSC-----------EEYKKLNPEE---YV 294 (384)
T ss_pred CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC---------CCCH-----------HHHHHhCCcc---cc
Confidence 4457777765321 1121 226888899998665422 2343 3445544311 11
Q ss_pred HHHHHHHHHHhhhcCCccccCCCCCCCCCeEEeccCccceeecCCCceecccccCccCCCC
Q 009189 204 DKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIEVDELREVECACGLQFCFRCSYEAHSPC 264 (540)
Q Consensus 204 eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~ 264 (540)
......++. ...+.|| .|+..|..... ...++|.||+.||+.|+.+|+...
T Consensus 295 ----d~~~~~~la--~~wr~Cp---kC~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 295 ----DDITLKYLA--KRWRQCP---KCKFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred ----cHHHHHHHH--HhcCcCc---ccceeeeecCC-cceEEeeccccchhhcCcchhhCC
Confidence 111222222 4567898 69988865554 667999999999999998886654
No 52
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.14 E-value=0.017 Score=53.82 Aligned_cols=32 Identities=34% Similarity=0.849 Sum_probs=27.4
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEH 162 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y 162 (540)
-+|.|.||-.++ ..|+...|||.||..|...-
T Consensus 195 IPF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 195 IPFLCGICKKDY--ESPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred Cceeehhchhhc--cchhhhhcchhHHHHHHHHH
Confidence 468999999998 66888899999999997643
No 53
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.10 E-value=0.0081 Score=60.90 Aligned_cols=50 Identities=24% Similarity=0.528 Sum_probs=36.2
Q ss_pred CccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
....+.|+||++.+. .-+.+..|+|.||.+||-.-+.. .| -.||. |+..+
T Consensus 40 ~~~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~---gn----~ecpt--cRk~l 89 (381)
T KOG0311|consen 40 FDIQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS---GN----NECPT--CRKKL 89 (381)
T ss_pred hhhhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh---cC----CCCch--HHhhc
Confidence 446899999999974 23455689999999998765443 23 37887 77643
No 54
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.10 E-value=0.032 Score=40.44 Aligned_cols=44 Identities=23% Similarity=0.690 Sum_probs=21.0
Q ss_pred cccccccCCCCc--eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccc
Q 009189 133 CNICFDDVSLEE--ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAI 185 (540)
Q Consensus 133 C~IC~e~~~~~~--~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~ 185 (540)
|++|.+++..++ +.-.+||+.+|+.||..-... .+ =+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~~----g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---EG----GRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S-----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---cC----CCCCC--CCCC
Confidence 789999875443 344579999999999876541 12 37987 8764
No 55
>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=93.92 E-value=0.026 Score=35.50 Aligned_cols=23 Identities=39% Similarity=0.914 Sum_probs=17.3
Q ss_pred CCCCCCccceeecCCCCeeEec-cCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~F 317 (540)
|.||.|+..|-.+. ..|. ||+.|
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 67999998886544 6774 88876
No 56
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=93.07 E-value=0.03 Score=56.53 Aligned_cols=46 Identities=26% Similarity=0.632 Sum_probs=36.2
Q ss_pred cccccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 129 SSYCCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
...+|.+|-.-+ .+..++ .|-|.||++||-.|+... ..||. |...+
T Consensus 14 ~~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~~--------~~CP~--C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEES--------KYCPT--CDIVI 60 (331)
T ss_pred cceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHHh--------ccCCc--cceec
Confidence 578999998776 444444 799999999999999882 48998 66554
No 57
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.03 E-value=0.062 Score=55.54 Aligned_cols=56 Identities=21% Similarity=0.451 Sum_probs=37.4
Q ss_pred CccccccccccccCCCCc-----eee-cCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccc
Q 009189 127 VSSSYCCNICFDDVSLEE-----ITT-MDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAI 185 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~ 185 (540)
.+...+|+||++...... .-. .+|.|.||..|++.|-...- .+....-.||. |+..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q-~~~~~sksCP~--CRv~ 219 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQ-FESKTSKSCPF--CRVP 219 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhc-cccccccCCCc--ccCc
Confidence 356789999999963222 112 36999999999999754321 12223458998 8764
No 58
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.053 Score=60.23 Aligned_cols=46 Identities=30% Similarity=0.706 Sum_probs=36.5
Q ss_pred cccccccccccCCCC---ceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 129 SSYCCNICFDDVSLE---EITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~---~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
....|.||.+.+... .+..++|||.||..|++.|++.+ -.||. |+.
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 367899999997421 15678999999999999999882 37998 554
No 59
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.65 E-value=0.12 Score=42.28 Aligned_cols=50 Identities=18% Similarity=0.357 Sum_probs=33.7
Q ss_pred ccccccccccCCC---------Cc-e-eecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 130 SYCCNICFDDVSL---------EE-I-TTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 130 ~~~C~IC~e~~~~---------~~-~-~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
...|+||...|.. ++ + +.-.|+|.|...||..++.++-. .-.||. |+..+
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 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPW 81 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCee
Confidence 4456666665432 12 2 22369999999999999998521 238999 88765
No 60
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.15 E-value=0.1 Score=54.02 Aligned_cols=49 Identities=27% Similarity=0.693 Sum_probs=37.5
Q ss_pred ccccccccccCCC---CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 130 SYCCNICFDDVSL---EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 130 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
..+||||++.+.. ..++++.|||.|=.+|+++|+. ++ ....||. |...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~-----~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK-----TKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh-----hhhhCcc--cCChh
Confidence 5789999999632 2467889999999999999994 22 3468998 66543
No 61
>PRK00420 hypothetical protein; Validated
Probab=92.13 E-value=1.2 Score=38.53 Aligned_cols=27 Identities=30% Similarity=0.555 Sum_probs=20.7
Q ss_pred cCCCCCCccceeecCCCCeeEeccCcccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAA 324 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~ 324 (540)
...||.|+.|+.+. +-|..||..|+..
T Consensus 23 ~~~CP~Cg~pLf~l--------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL--------KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec--------CCCceECCCCCCe
Confidence 48999999988741 3467788888875
No 62
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.01 E-value=0.22 Score=50.76 Aligned_cols=57 Identities=28% Similarity=0.604 Sum_probs=41.2
Q ss_pred ccccccccccCCCCc----eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccc--cchhHHHHhh
Q 009189 130 SYCCNICFDDVSLEE----ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAI--CDESKIRCLV 195 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~----~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~--~~~~~i~~ll 195 (540)
-..|.||-++++..+ |..+.|||.+|..|....+.. ..+.||. |+.+ ++...++.+-
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l~ 65 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSLQ 65 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhhh
Confidence 357999999987543 455679999999999987654 2477877 8877 5555555443
No 63
>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=91.21 E-value=0.089 Score=46.61 Aligned_cols=35 Identities=26% Similarity=0.640 Sum_probs=28.5
Q ss_pred cccccccccccCCC-CceeecCCC------CcccHHHHHHHH
Q 009189 129 SSYCCNICFDDVSL-EEITTMDCG------HYFCNSCWTEHF 163 (540)
Q Consensus 129 ~~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~Cl~~y~ 163 (540)
...+|.||++.+.. .-.+.++|| |.||.+|++.|-
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 36899999999865 345667887 789999999983
No 64
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.27 E-value=0.13 Score=31.42 Aligned_cols=21 Identities=38% Similarity=1.028 Sum_probs=13.3
Q ss_pred CCCCCccceeecCCCCeeEe-ccCcc
Q 009189 292 HCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
.||+|+..|+.+. .+| .||+.
T Consensus 1 ~Cp~CG~~~~~~~----~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDA----KFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcC----cchhhhCCc
Confidence 4888888887544 455 35543
No 65
>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=90.25 E-value=0.32 Score=35.59 Aligned_cols=42 Identities=21% Similarity=0.415 Sum_probs=31.7
Q ss_pred ccccccccCCCCceeecCCC-----CcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 132 CCNICFDDVSLEEITTMDCG-----HYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 132 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
.|-||++.....++...||. |.+...|+..|+..+- ..+||.
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 48999984444666677885 8899999999998752 247876
No 66
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=90.00 E-value=0.94 Score=45.90 Aligned_cols=48 Identities=21% Similarity=0.433 Sum_probs=34.9
Q ss_pred cccccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 129 SSYCCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
....|+||+... .++..+ --|=.||-.|+-.|+.. .| +||..+|+..+
T Consensus 299 ~~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~---~~-----~CPVT~~p~~v 347 (357)
T KOG0826|consen 299 DREVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVN---YG-----HCPVTGYPASV 347 (357)
T ss_pred ccccChhHHhcc--CCCceEEecceEEeHHHHHHHHHh---cC-----CCCccCCcchH
Confidence 456799999875 334333 45899999999999884 33 68887776543
No 67
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=89.91 E-value=0.51 Score=55.81 Aligned_cols=74 Identities=19% Similarity=0.425 Sum_probs=54.7
Q ss_pred ccccccccccc-CCCCceeecCCCCcccHHHHHHHHHHhhhcCC--cccccccCcccccccchhHHHHhhccCChhHHHH
Q 009189 129 SSYCCNICFDD-VSLEEITTMDCGHYFCNSCWTEHFIVKINEGQ--SRRITCMEHKCNAICDESKIRCLVRARDSDLADK 205 (540)
Q Consensus 129 ~~~~C~IC~e~-~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~--~~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~ek 205 (540)
....|.|||.+ +.......+.|+|.|...|-+..++..-.... +..|.||. |...+....++.|+. .+.+.
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 45679999977 44445578899999999999998887654322 23579999 999998888888876 24444
Q ss_pred HHH
Q 009189 206 FDR 208 (540)
Q Consensus 206 y~~ 208 (540)
|+.
T Consensus 3559 ~ed 3561 (3738)
T KOG1428|consen 3559 YED 3561 (3738)
T ss_pred HHH
Confidence 543
No 68
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.07 E-value=0.45 Score=48.81 Aligned_cols=48 Identities=21% Similarity=0.555 Sum_probs=37.0
Q ss_pred ccccccccccccCCCCceeecCCCCc-ccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHY-FCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.+..+|-||+.+. .+.+.|||.|. .|.+|-+..- - . .=+||. |+..+.
T Consensus 288 ~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr-~--q-----~n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR-Y--Q-----TNNCPI--CRQPIE 336 (349)
T ss_pred cCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH-H--h-----hcCCCc--cccchH
Confidence 3478899999985 67888999997 8999977654 1 1 127999 988764
No 69
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.54 E-value=0.29 Score=49.73 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=36.9
Q ss_pred CCccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 126 QVSSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 126 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
|.++...|+||+-.- -..+..||+|.-|.+|+.+|+-.. -+|-. |+.++..
T Consensus 418 p~sEd~lCpICyA~p--i~Avf~PC~H~SC~~CI~qHlmN~--------k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAGP--INAVFAPCSHRSCYGCITQHLMNC--------KRCFF--CKTTVID 468 (489)
T ss_pred CCcccccCcceeccc--chhhccCCCCchHHHHHHHHHhcC--------CeeeE--ecceeee
Confidence 445778999998652 334556999999999999997542 25666 7776654
No 70
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.11 E-value=0.27 Score=52.13 Aligned_cols=53 Identities=21% Similarity=0.485 Sum_probs=37.9
Q ss_pred CccccccccccccCCCC-----ce----------eecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 127 VSSSYCCNICFDDVSLE-----EI----------TTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~-----~~----------~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
......|.||+.+++.. .+ ...||.|.|...|+.+|+.+ ..+.||. |+.++++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 34567899999986431 11 12389999999999999875 2368998 6665553
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=87.77 E-value=0.43 Score=46.49 Aligned_cols=44 Identities=27% Similarity=0.594 Sum_probs=32.7
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
+.|..|+.--+....+.+.|+|.||..|.+.- .+-.||. |+..+
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~i 47 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSI 47 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccC----------Ccccccc--cccee
Confidence 56998987766555667799999999997632 1228998 88765
No 72
>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=87.74 E-value=0.17 Score=48.79 Aligned_cols=51 Identities=27% Similarity=0.569 Sum_probs=36.9
Q ss_pred ccccccccccC-CCCceeec--C-CCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 130 SYCCNICFDDV-SLEEITTM--D-CGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 130 ~~~C~IC~e~~-~~~~~~~l--~-CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.-.||||-.+. -..++..+ | |-|..|-+|....++. | |-.||-++|+.++.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G---pAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G---PAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C---CCCCCCccHHHHHH
Confidence 34699998773 22334333 4 9999999999988765 3 57899999987543
No 73
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=87.65 E-value=0.24 Score=51.09 Aligned_cols=46 Identities=33% Similarity=0.771 Sum_probs=33.8
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
..|-||-+.- .++..-||||..|..|+..|-.. .+|+ .||.+.|..
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcEI 415 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCEI 415 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhccc--CCCC----CCCceeeEe
Confidence 3599999874 44555599999999999988443 2355 899966653
No 74
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.29 E-value=0.25 Score=48.47 Aligned_cols=52 Identities=27% Similarity=0.613 Sum_probs=39.7
Q ss_pred cccccccccccCCCC--------ceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 129 SSYCCNICFDDVSLE--------EITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
+...|.||-..+..+ +...++|+|.|...|+++|... |. .-.||- |+..++.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK--kqtCPY--CKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK--KQTCPY--CKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC--CCCCch--HHHHhhH
Confidence 456799998876432 4678999999999999999765 22 358998 8877653
No 75
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.28 E-value=1.8 Score=45.13 Aligned_cols=126 Identities=13% Similarity=0.150 Sum_probs=72.2
Q ss_pred eeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHhhCHHHHHHHcCCCcccCCCC-------CCc
Q 009189 53 KVITKESLLAAQMEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLVEYGKERLFAKAGLTIVETDDV-------SSS 125 (540)
Q Consensus 53 ~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~~~~~~~~~~~gl~~~~~~~~-------~~~ 125 (540)
..|++..+......-+..-..+||++......++...+-..=-.+-.+. .++..+...-...+.. ...
T Consensus 255 ~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~v~v~aG~~Alp~Llk~~-----~v~~~~~~~W~~~deLPveIeL~~~~ 329 (394)
T KOG2817|consen 255 EILSPKLWKELTEEFTREYCALLGISVESPLSVLVNAGCIALPQLLKYK-----SVMELKHGEWNTKDELPVEIELGKEY 329 (394)
T ss_pred HHhCHHHHHHHHHHHHHHHHHHcCCCccCcHHHHHHhhHHHHHHHHHHH-----HHHHHhccCccccccCccceeccccc
Confidence 4566777777777778888899999877666665544433222221121 1111111100000000 011
Q ss_pred CCccccccccccccCCC-CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhH
Q 009189 126 QVSSSYCCNICFDDVSL-EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESK 190 (540)
Q Consensus 126 ~~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~ 190 (540)
..-+-|.|||=-+.-.. +.|..|.|||..|++=+.... ++|. ..++||- |+..-....
T Consensus 330 ~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS----~ng~-~sfKCPY--CP~e~~~~~ 388 (394)
T KOG2817|consen 330 HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLS----KNGS-QSFKCPY--CPVEQLASD 388 (394)
T ss_pred cccceeecccchhhccCCCCCeeeeccceecHHHHHHHh----hCCC-eeeeCCC--CCcccCHHh
Confidence 13467999997665433 446788999999998776543 3344 4789998 876554443
No 76
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=86.81 E-value=0.27 Score=55.70 Aligned_cols=47 Identities=32% Similarity=0.740 Sum_probs=36.5
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccch
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDE 188 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~ 188 (540)
+.|.||.+ .+.++..+|||.||.+||..++...-. -.||. |...+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC------CCCcH--HHHHHHH
Confidence 89999999 367888899999999999999876321 26776 7765543
No 77
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=85.77 E-value=0.58 Score=34.30 Aligned_cols=27 Identities=30% Similarity=0.654 Sum_probs=19.6
Q ss_pred CCCCCCccceeecC--CCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEKNG--GCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~--GCnhm~C-~C~~~F 317 (540)
+.||.|+.++.... +-+++.| .||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 47999999887543 3568899 498753
No 78
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.56 E-value=0.4 Score=30.09 Aligned_cols=13 Identities=23% Similarity=0.848 Sum_probs=9.4
Q ss_pred CCCCCCccceeec
Q 009189 291 KHCPKCQKLVEKN 303 (540)
Q Consensus 291 k~CP~C~~~IeK~ 303 (540)
+.||+|+..|...
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 6788888877643
No 79
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.01 E-value=0.34 Score=35.78 Aligned_cols=46 Identities=24% Similarity=0.519 Sum_probs=33.5
Q ss_pred cccccccccCCCCceeecCCCCc-ccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 131 YCCNICFDDVSLEEITTMDCGHY-FCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
-+|.||++.- .+.+.-.|||. .|-+|-.+.+.. .. =.||. |++++.
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~--~~-----g~CPi--CRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA--LH-----GCCPI--CRAPIK 54 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc--cC-----CcCcc--hhhHHH
Confidence 6799999873 34555689997 899998887765 12 26888 877653
No 80
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=84.87 E-value=0.47 Score=33.16 Aligned_cols=33 Identities=24% Similarity=0.706 Sum_probs=26.7
Q ss_pred CCCCCCccc-eeecCCCCeeEe-ccCccccccccccccCCCC
Q 009189 291 KHCPKCQKL-VEKNGGCNLVSC-ICGQPFCWLCGAATGSDHT 330 (540)
Q Consensus 291 k~CP~C~~~-IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~ 330 (540)
..|+.|... +. ++| .|+..+|..|....|.+|.
T Consensus 4 ~~C~~H~~~~~~-------~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp SB-SSTTTSBEE-------EEETTTTEEEEHHHHHTSTTTSE
T ss_pred ccCccCCccceE-------EEecCCCCccCccCCCCCCCCCE
Confidence 689999887 77 999 5999999999987666553
No 81
>PHA00626 hypothetical protein
Probab=84.80 E-value=0.65 Score=34.51 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=22.5
Q ss_pred CCCCCcc-ceeecCCCCe----eEe-ccCcccccccc
Q 009189 292 HCPKCQK-LVEKNGGCNL----VSC-ICGQPFCWLCG 322 (540)
Q Consensus 292 ~CP~C~~-~IeK~~GCnh----m~C-~C~~~FCw~C~ 322 (540)
.||+|+. -|-|++-|+. ..| .||+.|=-.-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhh
Confidence 6999998 5878777655 778 48888754433
No 82
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.25 E-value=0.42 Score=47.68 Aligned_cols=45 Identities=29% Similarity=0.725 Sum_probs=34.5
Q ss_pred ccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
+|-|.||-..+ .+++...|||.||..|....+.. | -+|+. |....
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk----~----~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK----G----EKCYV--CSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc----C----Cccee--ccccc
Confidence 57799999998 67888999999999997765432 2 36776 66543
No 83
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.83 E-value=0.53 Score=45.50 Aligned_cols=33 Identities=33% Similarity=0.867 Sum_probs=22.8
Q ss_pred CCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceee
Q 009189 247 ACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEK 302 (540)
Q Consensus 247 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 302 (540)
.|||.|||-|. .+|.+- ..+.+.||-|+..|..
T Consensus 64 lCGHLFCWpCl------------yqWl~~-----------~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 64 LCGHLFCWPCL------------YQWLQT-----------RPNSKECPVCKAEVSI 96 (230)
T ss_pred ecccceehHHH------------HHHHhh-----------cCCCeeCCcccccccc
Confidence 39999999996 234431 2234789999887763
No 84
>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=83.61 E-value=3.9 Score=27.73 Aligned_cols=34 Identities=21% Similarity=0.337 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHH
Q 009189 65 MEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAV 99 (540)
Q Consensus 65 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~ 99 (540)
.+.|..+.+. |.+...|+.-|+..+||++..++.
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 999999999999999999988764
No 85
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=83.57 E-value=0.6 Score=49.66 Aligned_cols=48 Identities=25% Similarity=0.654 Sum_probs=36.7
Q ss_pred CccccccccccccCCCCceee-cCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 127 VSSSYCCNICFDDVSLEEITT-MDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
......|++|...+ .+++. ..|||.||..|+..+... ...||. |...+
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~ 66 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQEL 66 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc--------CcCCcc--ccccc
Confidence 45678999999987 55666 599999999999988765 247776 54433
No 86
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.50 E-value=0.67 Score=50.22 Aligned_cols=38 Identities=37% Similarity=0.784 Sum_probs=32.2
Q ss_pred cCCCC--CCccceee-cCCCCeeEeccCccccccccccccC
Q 009189 290 TKHCP--KCQKLVEK-NGGCNLVSCICGQPFCWLCGAATGS 327 (540)
Q Consensus 290 ~k~CP--~C~~~IeK-~~GCnhm~C~C~~~FCw~C~~~~~~ 327 (540)
.|-|| .|+..+.- .+.+.-+.|.|++.|||.|+.+||.
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~ 198 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHS 198 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccC
Confidence 46666 69988887 8889999999999999999998753
No 87
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=82.90 E-value=0.21 Score=49.62 Aligned_cols=34 Identities=29% Similarity=0.612 Sum_probs=26.6
Q ss_pred HhccCCCCCCccceeecCCCCeeEe-ccCcccccccccccc
Q 009189 287 AVHTKHCPKCQKLVEKNGGCNLVSC-ICGQPFCWLCGAATG 326 (540)
Q Consensus 287 ~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~ 326 (540)
..++.+|--|-...+ |-+| .|||-|||-|...|-
T Consensus 236 ~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 236 PEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHH
Confidence 345677887777665 5788 499999999999884
No 88
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=82.46 E-value=1 Score=30.60 Aligned_cols=32 Identities=19% Similarity=0.387 Sum_probs=25.8
Q ss_pred CCCCCcc-ceeecCCCCeeEe-ccCccccccccccccCCCC
Q 009189 292 HCPKCQK-LVEKNGGCNLVSC-ICGQPFCWLCGAATGSDHT 330 (540)
Q Consensus 292 ~CP~C~~-~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~ 330 (540)
.||.|+. ++. ++| .|+...|..|....+++|.
T Consensus 2 ~C~~H~~~~~~-------~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 2 LCDEHGEEPLS-------LFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred CCCccCCcceE-------EEeCccChhhhhhcChhhcCCCC
Confidence 5899977 888 999 5999999999875455553
No 89
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=81.62 E-value=0.92 Score=31.97 Aligned_cols=30 Identities=33% Similarity=0.657 Sum_probs=22.4
Q ss_pred HHHHhccCCCCCCccceeecCCCCeeEec---cCccc
Q 009189 284 NYIAVHTKHCPKCQKLVEKNGGCNLVSCI---CGQPF 317 (540)
Q Consensus 284 ~~i~~~~k~CP~C~~~IeK~~GCnhm~C~---C~~~F 317 (540)
.|+....|.||+|+..- |+--+.|+ |++.|
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 35666789999999865 77778884 77655
No 90
>PF04641 Rtf2: Rtf2 RING-finger
Probab=80.28 E-value=1.8 Score=43.44 Aligned_cols=58 Identities=17% Similarity=0.326 Sum_probs=42.4
Q ss_pred ccccccccccccCCCC-ceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHHHhhc
Q 009189 128 SSSYCCNICFDDVSLE-EITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIRCLVR 196 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~~ll~ 196 (540)
...+.|||....+... .++.+ +|||.|+..+++..- .+ -.||. |..+|....|-.|.+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-----~~----~~Cp~--c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-----KS----KKCPV--CGKPFTEEDIIPLNP 170 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-----cc----ccccc--cCCccccCCEEEecC
Confidence 4678999999998542 34444 999999999999871 11 25998 999988665554444
No 91
>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=79.86 E-value=2.1 Score=28.20 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=16.9
Q ss_pred ccCCCCCCccceeecCCCCeeEe-ccCcc
Q 009189 289 HTKHCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 289 ~~k~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
+.+.||+|+.+.....|=-.|.| .|+..
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 34789999999988877677888 48764
No 92
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=79.67 E-value=0.94 Score=50.70 Aligned_cols=18 Identities=11% Similarity=0.001 Sum_probs=10.9
Q ss_pred CCCcccHHHHHHHHHHhh
Q 009189 150 CGHYFCNSCWTEHFIVKI 167 (540)
Q Consensus 150 CgH~fC~~Cl~~y~~~~i 167 (540)
|+|.||..||..+...-+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhHHHHHHHHHhh
Confidence 666666666666655544
No 93
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=79.62 E-value=0.55 Score=34.96 Aligned_cols=46 Identities=24% Similarity=0.505 Sum_probs=31.6
Q ss_pred ccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchh
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDES 189 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~ 189 (540)
...|-.|...- ...+.++|||..|..||-.. .---||. |...+...
T Consensus 7 ~~~~~~~~~~~--~~~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVG--TKGTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEccccc--cccccccccceeeccccChh----------hccCCCC--CCCcccCC
Confidence 45566665543 45667899999999998742 1236998 88877543
No 94
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=79.50 E-value=37 Score=39.12 Aligned_cols=52 Identities=17% Similarity=0.388 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccCChhH------HHHHHHHHHHHHHHHHHH
Q 009189 447 KQNLFEDQQQQFEANIEKLSSFLDEKFHLYNEDE------IKDLKLRVIALSATTDNL 498 (540)
Q Consensus 447 ~~~lfe~~q~~le~~~e~L~~~le~~~~~~~~~~------~~~~r~~~~~l~~~~~~~ 498 (540)
+.+-....|+.|..+++++...+......+...| +..++.++..|..-++..
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~~si~~l 658 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLKASIEQL 658 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777899999999999888875444444432 344444444444444443
No 95
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=79.50 E-value=0.9 Score=33.39 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=19.5
Q ss_pred ccCCCCCCcc-ceeecCCCCeeEe-ccCccc
Q 009189 289 HTKHCPKCQK-LVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 289 ~~k~CP~C~~-~IeK~~GCnhm~C-~C~~~F 317 (540)
..+.||+|+. .+.... +.++| +||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 3479999988 444433 67999 699865
No 96
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.24 E-value=1.2 Score=50.20 Aligned_cols=23 Identities=39% Similarity=0.836 Sum_probs=15.7
Q ss_pred CCCCCCccceeecCCCCeeEeccCcccccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~ 324 (540)
+.||+|+..+.. +..||..||..
T Consensus 28 ~~Cp~CG~~~~~-----------~~~fC~~CG~~ 50 (645)
T PRK14559 28 KPCPQCGTEVPV-----------DEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCCCCc-----------ccccccccCCc
Confidence 568888887663 34577777765
No 97
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=79.07 E-value=0.56 Score=37.15 Aligned_cols=49 Identities=20% Similarity=0.440 Sum_probs=34.3
Q ss_pred cccccccccCCC---------Cceeec--CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 131 YCCNICFDDVSL---------EEITTM--DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 131 ~~C~IC~e~~~~---------~~~~~l--~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
.+|+||.-.|.. ++...+ -|.|.|-.-|+.+++.+.-++| .||. |+..+
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~-----~CPm--cRq~~ 80 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG-----QCPM--CRQTW 80 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc-----cCCc--chhee
Confidence 378888766543 222112 4899999999999998876554 5888 87654
No 98
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.95 E-value=0.87 Score=47.06 Aligned_cols=48 Identities=29% Similarity=0.651 Sum_probs=33.6
Q ss_pred ccccccccccCCCC-ceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 130 SYCCNICFDDVSLE-EITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 130 ~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
.-.|.||-+-+|.. +...+ .|||.|...|+.+|+...-.. -.||. |..
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~i 53 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQI 53 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eee
Confidence 35799996665543 34445 499999999999999874322 26887 653
No 99
>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=78.84 E-value=0.85 Score=38.68 Aligned_cols=33 Identities=24% Similarity=0.532 Sum_probs=26.9
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHH
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWT 160 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~ 160 (540)
.+...|++|...+....++..||||.|...|.+
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 345679999999876666677999999999975
No 100
>PHA03096 p28-like protein; Provisional
Probab=78.06 E-value=1.3 Score=44.75 Aligned_cols=37 Identities=16% Similarity=0.418 Sum_probs=28.5
Q ss_pred cccccccccCCC----Cceee-c-CCCCcccHHHHHHHHHHhh
Q 009189 131 YCCNICFDDVSL----EEITT-M-DCGHYFCNSCWTEHFIVKI 167 (540)
Q Consensus 131 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~Cl~~y~~~~i 167 (540)
..|+||++..-. +..+. + .|.|.||..|++.|..+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~ 221 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL 221 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh
Confidence 789999998532 22233 3 7999999999999988765
No 101
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=77.96 E-value=1.2 Score=47.16 Aligned_cols=11 Identities=18% Similarity=0.468 Sum_probs=6.5
Q ss_pred cCCcccccccc
Q 009189 125 SQVSSSYCCNI 135 (540)
Q Consensus 125 ~~~~~~~~C~I 135 (540)
.|.+..|.|+-
T Consensus 189 LPDSTDFVCGT 199 (458)
T PF10446_consen 189 LPDSTDFVCGT 199 (458)
T ss_pred CCCcccccCCC
Confidence 34556677764
No 102
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=77.60 E-value=73 Score=36.63 Aligned_cols=73 Identities=25% Similarity=0.334 Sum_probs=52.7
Q ss_pred cchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCh
Q 009189 399 SKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSSFLDEKFHLYNE 478 (540)
Q Consensus 399 ~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~~le~~~~~~~~ 478 (540)
..|..-|..||..+.+--..|..|-. .+...|..||..+ ++..+.+|.+...|-+. +
T Consensus 586 ~~~~e~L~~aL~amqdk~~~LE~sLs-----------------aEtriKldLfsaL-g~akrq~ei~~~~~~~~-----d 642 (697)
T PF09726_consen 586 EKDTEVLMSALSAMQDKNQHLENSLS-----------------AETRIKLDLFSAL-GDAKRQLEIAQGQLRKK-----D 642 (697)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhh-----------------HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH-----H
Confidence 34666777788777776666653322 2456788999887 56777888888777754 6
Q ss_pred hHHHHHHHHHHHHHHH
Q 009189 479 DEIKDLKLRVIALSAT 494 (540)
Q Consensus 479 ~~~~~~r~~~~~l~~~ 494 (540)
.+|.++|++|++|..+
T Consensus 643 ~ei~~lk~ki~~~~av 658 (697)
T PF09726_consen 643 KEIEELKAKIAQLLAV 658 (697)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 7799999999888765
No 103
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.59 E-value=1.3 Score=44.15 Aligned_cols=43 Identities=23% Similarity=0.668 Sum_probs=33.0
Q ss_pred cccccccccCCCCceeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 131 YCCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
+.|+.|-..+ .++... .|+|.||.+|+..-+.. ..+.||. |..
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 7899998886 455555 69999999999876544 2479998 654
No 104
>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=77.42 E-value=8.9 Score=26.76 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=32.9
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHHHh
Q 009189 65 MEDLIRVMDLL-SLKEQHARTLLIHYRWDVEKVLAVLVE 102 (540)
Q Consensus 65 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~~~~~~ 102 (540)
.+.|..|.+++ ++++......|..++++++..++.+.+
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 35688999999 799999999999999999999998763
No 105
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=77.19 E-value=5.3 Score=40.11 Aligned_cols=39 Identities=21% Similarity=0.456 Sum_probs=31.0
Q ss_pred cccccccccccCCCCc-eeecCCCCcccHHHHHHHHHHhh
Q 009189 129 SSYCCNICFDDVSLEE-ITTMDCGHYFCNSCWTEHFIVKI 167 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~y~~~~i 167 (540)
....|.||+--|...+ +..++|-|+|..-|+..|+....
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 3567888887776555 56679999999999999998654
No 106
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=76.63 E-value=1.7 Score=33.58 Aligned_cols=21 Identities=29% Similarity=0.907 Sum_probs=9.3
Q ss_pred CCCCCCccceee---cCCCCeeEe
Q 009189 291 KHCPKCQKLVEK---NGGCNLVSC 311 (540)
Q Consensus 291 k~CP~C~~~IeK---~~GCnhm~C 311 (540)
-+|++|...+.. .+||.|++|
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 589999887765 367777776
No 107
>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=76.52 E-value=1.7 Score=31.65 Aligned_cols=30 Identities=37% Similarity=0.895 Sum_probs=21.6
Q ss_pred CCCce-ecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceee
Q 009189 247 ACGLQ-FCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEK 302 (540)
Q Consensus 247 ~C~~~-fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 302 (540)
+|||. ||..|...+ .. ..+.||-|+.+|++
T Consensus 19 pCgH~~~C~~C~~~~------------~~--------------~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 19 PCGHLCFCEECAERL------------LK--------------RKKKCPICRQPIES 49 (50)
T ss_dssp TTCEEEEEHHHHHHH------------HH--------------TTSBBTTTTBB-SE
T ss_pred CCCChHHHHHHhHHh------------cc--------------cCCCCCcCChhhcC
Confidence 79999 999996321 11 33899999999974
No 108
>PF12773 DZR: Double zinc ribbon
Probab=76.10 E-value=1.7 Score=31.53 Aligned_cols=14 Identities=36% Similarity=0.695 Sum_probs=10.5
Q ss_pred CCCCCCccceeecC
Q 009189 291 KHCPKCQKLVEKNG 304 (540)
Q Consensus 291 k~CP~C~~~IeK~~ 304 (540)
+.||+|+..+..+.
T Consensus 30 ~~C~~Cg~~~~~~~ 43 (50)
T PF12773_consen 30 KICPNCGAENPPNA 43 (50)
T ss_pred CCCcCCcCCCcCCc
Confidence 68888888877543
No 109
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.09 E-value=1.7 Score=42.29 Aligned_cols=52 Identities=12% Similarity=0.230 Sum_probs=36.7
Q ss_pred cccccccccccCCCCc-eeec-CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhH
Q 009189 129 SSYCCNICFDDVSLEE-ITTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESK 190 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~ 190 (540)
..+.|+||-+.+...- ...| +|||.||.+|....+.. ...||. |..++.+..
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrd 273 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRD 273 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccc
Confidence 5688999999984322 2333 89999999999988754 235676 666665543
No 110
>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=75.33 E-value=2 Score=42.90 Aligned_cols=47 Identities=34% Similarity=0.764 Sum_probs=32.5
Q ss_pred ccccccccC-CCCceeec--CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 132 CCNICFDDV-SLEEITTM--DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 132 ~C~IC~e~~-~~~~~~~l--~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.||+|-.+. -..+++.+ +|||..|.+|+-..+.. | +-.||. |..++.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g---~~~Cpe--C~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G---PAQCPE--CMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C---CCCCCc--ccchhh
Confidence 489997662 21233333 89999999999887764 2 357984 988664
No 111
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=72.61 E-value=5.9 Score=40.48 Aligned_cols=46 Identities=30% Similarity=0.590 Sum_probs=34.2
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
..-++||||++.+.. .++..+=||..|.+|-.. ..-+||. |+..++
T Consensus 46 ~~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG 91 (299)
T ss_pred hhhccCchhhccCcc-cceecCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence 356899999999742 234445589999999762 2458998 998887
No 112
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.29 E-value=2.1 Score=48.89 Aligned_cols=39 Identities=21% Similarity=0.553 Sum_probs=31.9
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHh
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVK 166 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~ 166 (540)
.+..+|.+|.-.+-....+..+|||.|..+|+..++...
T Consensus 815 ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred cCccchHHhcchhhcCcceeeeccchHHHHHHHHHHHcc
Confidence 356789999998866666677999999999999887653
No 113
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=72.18 E-value=2.1 Score=43.52 Aligned_cols=54 Identities=19% Similarity=0.597 Sum_probs=38.1
Q ss_pred cccccccccccCCC--CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHH
Q 009189 129 SSYCCNICFDDVSL--EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKI 191 (540)
Q Consensus 129 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i 191 (540)
+...|+.|.+.+.. .+++.++||-..|+=||... .+.++ =+||. |+...+++-+
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~ln------grcpa--crr~y~denv 68 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNLN------GRCPA--CRRKYDDENV 68 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhcc------CCChH--hhhhccccce
Confidence 44559999999754 45677799999999999753 33332 37998 8876654433
No 114
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.75 E-value=2.1 Score=48.91 Aligned_cols=9 Identities=22% Similarity=0.357 Sum_probs=4.0
Q ss_pred CCCCCCCCC
Q 009189 4 YRSSDDDYD 12 (540)
Q Consensus 4 ~~~~~~~~~ 12 (540)
++++++||+
T Consensus 1405 dd~DeeeD~ 1413 (1516)
T KOG1832|consen 1405 DDSDEEEDD 1413 (1516)
T ss_pred cccCccccc
Confidence 444444444
No 115
>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=70.80 E-value=15 Score=24.75 Aligned_cols=34 Identities=21% Similarity=0.364 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHH
Q 009189 67 DLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLV 101 (540)
Q Consensus 67 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~ 101 (540)
.|..+.+ +|.+...++..|...+||+++.++.++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4455555 599999999999999999999887654
No 116
>smart00336 BBOX B-Box-type zinc finger.
Probab=70.36 E-value=4.1 Score=28.02 Aligned_cols=33 Identities=30% Similarity=0.651 Sum_probs=26.9
Q ss_pred CCCCCCc-cceeecCCCCeeEe-ccCccccccccccccCCCC
Q 009189 291 KHCPKCQ-KLVEKNGGCNLVSC-ICGQPFCWLCGAATGSDHT 330 (540)
Q Consensus 291 k~CP~C~-~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~ 330 (540)
..|+.|. .++. ++| .|....|..|....+.+|.
T Consensus 4 ~~C~~h~~~~~~-------~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred CcCCCCCCCceE-------EECCCCCcccccccChhhcCCCc
Confidence 5799998 8888 999 5999999999976555553
No 117
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.33 E-value=3.5 Score=29.51 Aligned_cols=28 Identities=29% Similarity=0.581 Sum_probs=18.0
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQPFC 318 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~FC 318 (540)
-.||+|+..++-..+=..++| .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 468888888765443335777 4776554
No 118
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.03 E-value=3.4 Score=42.95 Aligned_cols=6 Identities=50% Similarity=0.911 Sum_probs=3.4
Q ss_pred cccccC
Q 009189 135 ICFDDV 140 (540)
Q Consensus 135 IC~e~~ 140 (540)
||++.-
T Consensus 396 Ic~~ts 401 (514)
T KOG3130|consen 396 ICSDTS 401 (514)
T ss_pred ccccCC
Confidence 666553
No 119
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=69.91 E-value=3.5 Score=46.90 Aligned_cols=50 Identities=22% Similarity=0.397 Sum_probs=38.4
Q ss_pred cccccccccccCCCCce-eec-CCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 129 SSYCCNICFDDVSLEEI-TTM-DCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~-~~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
...+|.||++.+....+ .+. .|-|.|-..||+.|....-..|. ...+||.
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 57899999999865443 343 68899999999999988544444 4568887
No 120
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=69.66 E-value=1.5 Score=36.42 Aligned_cols=7 Identities=14% Similarity=0.069 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 009189 68 LIRVMDL 74 (540)
Q Consensus 68 i~~v~~~ 74 (540)
+..|..-
T Consensus 53 ~~~v~rY 59 (101)
T PF09026_consen 53 FTMVKRY 59 (101)
T ss_dssp HHHHHHH
T ss_pred cchHhhh
Confidence 3334333
No 121
>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=68.94 E-value=1.3e+02 Score=29.93 Aligned_cols=101 Identities=9% Similarity=0.207 Sum_probs=66.0
Q ss_pred CCCcchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 009189 396 TASSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSSFLDEKFHL 475 (540)
Q Consensus 396 ~~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~~le~~~~~ 475 (540)
..+++|+-.+..|++.++..|..+...+.. ..+..+. .+ .-+..++.-...+|..++..+..|..++..
T Consensus 138 ~~~Lkeyv~y~~slK~vlk~R~~~Q~~le~---------k~e~l~k-~~-~dr~~~~~ev~~~e~kve~a~~~~k~e~~R 206 (243)
T cd07666 138 LPVIHEYVLYSETLMGVIKRRDQIQAELDS---------KVEALAN-KK-ADRDLLKEEIEKLEDKVECANNALKADWER 206 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHh-hh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677777888888888888766655440 0000000 01 112344444555667777777777788887
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 476 YNEDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 476 ~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
+...+..++|.-++.....--.++++++..-|
T Consensus 207 f~~~k~~D~k~~~~~yae~~i~~~~~~~~~We 238 (243)
T cd07666 207 WKQNMQTDLRSAFTDMAENNISYYEECLATWE 238 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77788888888888887777777878877776
No 122
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.73 E-value=3.7 Score=40.83 Aligned_cols=54 Identities=24% Similarity=0.593 Sum_probs=40.0
Q ss_pred ccccccccccccCCCCceeecC--CCCcccHHHHHHHHHHhhhcCCcccccccC-ccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMD--CGHYFCNSCWTEHFIVKINEGQSRRITCME-HKCNA 184 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~-~~C~~ 184 (540)
+..+.|.+|-+.+..+.++.+| =.|.||.-|-++.|+.+-..|. +.||. .+|..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sge---vYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGE---VYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCc---eeCCCCCcCcc
Confidence 4568999999998555555443 2699999999999998765554 78887 35654
No 123
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=68.70 E-value=3.6 Score=46.57 Aligned_cols=12 Identities=33% Similarity=0.891 Sum_probs=9.7
Q ss_pred CCCCCCccceee
Q 009189 291 KHCPKCQKLVEK 302 (540)
Q Consensus 291 k~CP~C~~~IeK 302 (540)
+.||+|+.++.+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 889999987763
No 124
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.63 E-value=1.3 Score=41.18 Aligned_cols=29 Identities=34% Similarity=0.913 Sum_probs=21.2
Q ss_pred CCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCcccee
Q 009189 247 ACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVE 301 (540)
Q Consensus 247 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 301 (540)
.|||.||..|.+. ...++..||-|++.|-
T Consensus 150 kCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 150 KCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 5999999999632 1234589999998664
No 125
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=68.30 E-value=3 Score=44.20 Aligned_cols=6 Identities=33% Similarity=0.562 Sum_probs=2.7
Q ss_pred HHHHHH
Q 009189 156 NSCWTE 161 (540)
Q Consensus 156 ~~Cl~~ 161 (540)
.+|+..
T Consensus 211 ~Scle~ 216 (458)
T PF10446_consen 211 ISCLEA 216 (458)
T ss_pred HHHHHH
Confidence 445443
No 126
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=68.28 E-value=3.5 Score=43.38 Aligned_cols=16 Identities=19% Similarity=0.540 Sum_probs=6.9
Q ss_pred CCCCCccceeecCCCC
Q 009189 292 HCPKCQKLVEKNGGCN 307 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCn 307 (540)
+|--|+.+|--..|+.
T Consensus 396 rCs~C~~PI~P~~G~~ 411 (468)
T KOG1701|consen 396 RCSVCGNPILPRDGKD 411 (468)
T ss_pred chhhccCCccCCCCCc
Confidence 3444444444444444
No 127
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=67.96 E-value=2.9 Score=48.33 Aligned_cols=26 Identities=42% Similarity=1.187 Sum_probs=22.9
Q ss_pred CCCCCCccceeecCCCCeeEec-cCcccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPFC 318 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~FC 318 (540)
..||.|+..+...+|| ++|+ ||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC--~~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGC--VVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCC--CcCCCCCCCCC
Confidence 3599999999999999 5995 999876
No 128
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=67.49 E-value=15 Score=24.59 Aligned_cols=32 Identities=16% Similarity=0.244 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHH
Q 009189 68 LIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVL 100 (540)
Q Consensus 68 i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~ 100 (540)
|..+.+. |++...|+..|...+||+++.++-+
T Consensus 5 v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 5 IDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4444443 9999999999999999999887643
No 129
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.46 E-value=4.4 Score=38.95 Aligned_cols=54 Identities=19% Similarity=0.340 Sum_probs=41.2
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
-.|..|-..+...+.+.+-|-|.|.-.|+...-..--.+..-....||. |...+
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 4699999999889999999999999999998754432222223579998 88654
No 130
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=67.19 E-value=2.3 Score=44.05 Aligned_cols=48 Identities=25% Similarity=0.689 Sum_probs=37.2
Q ss_pred cccccccccccCCC--CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 129 SSYCCNICFDDVSL--EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 129 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
.+..|+.|-+.+.. +....+||.|.|...|+..|+.. +| +-.||. |+.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HHH
Confidence 46789999998643 44567899999999999999943 33 358998 773
No 131
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=67.16 E-value=15 Score=32.23 Aligned_cols=59 Identities=17% Similarity=0.317 Sum_probs=32.3
Q ss_pred ceeecCCCceecccccCccCCCCCc---hhhHHHhHHh-hhhhHHHHHHHhccCCCCCCcccee
Q 009189 242 REVECACGLQFCFRCSYEAHSPCSC---YMWDLWSKKC-QDESETVNYIAVHTKHCPKCQKLVE 301 (540)
Q Consensus 242 ~~v~C~C~~~fC~~C~~~~H~~~~C---~~~~~~~~~~-~~~~~~~~~i~~~~k~CP~C~~~Ie 301 (540)
..+.|.||++||.. .+.|...++= ....+..+.. ..+....+|+...--.||.|+.+.+
T Consensus 69 rv~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 69 RVIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred cEEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 35789999999986 4444322110 0111111100 0112234677666678999999887
No 132
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.02 E-value=3.3 Score=41.36 Aligned_cols=31 Identities=23% Similarity=0.406 Sum_probs=21.7
Q ss_pred CCCCCccceeecCCCCeeEe-ccCcccccccc-ccccCCC
Q 009189 292 HCPKCQKLVEKNGGCNLVSC-ICGQPFCWLCG-AATGSDH 329 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~-~~~~~~H 329 (540)
.|+.+... .+++| .|+...|+.|. ..-|..|
T Consensus 88 ~c~~~~~~-------~~~~c~~~~~~~c~~c~~~~~h~~h 120 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCEEDEKLLCVLCRESGEHRGH 120 (386)
T ss_pred hhhhcCCc-------ceEEecccccccCCCCCCcccccCC
Confidence 56666555 45999 69999999998 3333444
No 133
>PLN03086 PRLI-interacting factor K; Provisional
Probab=65.66 E-value=10 Score=42.01 Aligned_cols=57 Identities=25% Similarity=0.564 Sum_probs=31.5
Q ss_pred ccccccCcccccccchhHHHHhhccCChhHHHHHHHHHHHHhhhcCCccccCCCCCCCCCeEEeccCccceeecC-CCce
Q 009189 173 RRITCMEHKCNAICDESKIRCLVRARDSDLADKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIEVDELREVECA-CGLQ 251 (540)
Q Consensus 173 ~~i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 251 (540)
..+.||. |...++...+...+. .-....+.||+ .+|+..+...... .-..|+ |+..
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-------------------YCSRHNVVCPH-DGCGIVLRVEEAK-NHVHCEKCGQA 462 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHh-------------------hCCCcceeCCc-ccccceeeccccc-cCccCCCCCCc
Confidence 3568987 888776554332211 12223457984 5799887644322 124564 6655
Q ss_pred e
Q 009189 252 F 252 (540)
Q Consensus 252 f 252 (540)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 4
No 134
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=65.48 E-value=3.6 Score=36.46 Aligned_cols=25 Identities=44% Similarity=0.978 Sum_probs=19.2
Q ss_pred cCCCCCCccceeecCCCCeeEeccCccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGA 323 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~ 323 (540)
.+.||.|+.|+.+ +-|.-||.+|+.
T Consensus 28 ~~hCp~Cg~PLF~---------KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFR---------KDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCccee---------eCCeEECCCCCc
Confidence 3799999999975 356677777773
No 135
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=64.60 E-value=2.8 Score=49.15 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 009189 451 FEDQQQQFEANIEKLSS 467 (540)
Q Consensus 451 fe~~q~~le~~~e~L~~ 467 (540)
||..|....+..|+|..
T Consensus 2419 FEtKer~Fnka~EK~Rn 2435 (3015)
T KOG0943|consen 2419 FETKERKFNKAMEKLRN 2435 (3015)
T ss_pred cchHHHHHHHHHHHHHh
Confidence 55555555555555543
No 136
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=64.54 E-value=4.4 Score=29.44 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=14.1
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQ 315 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~ 315 (540)
+.||+|+--+.-..-=+...| +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 789999853332111124677 6765
No 137
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.51 E-value=2.3 Score=48.78 Aligned_cols=52 Identities=21% Similarity=0.508 Sum_probs=36.8
Q ss_pred ccccccccccccCCCCc---ee-ec-CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEE---IT-TM-DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~---~~-~l-~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
+.-.+|+||+..+...+ |. ++ .|.|.|...|+-.|+.+. | .-+||. |+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss---~---~s~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS---A---RSNCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc---C---CCCCCc--cccccc
Confidence 34568999998864222 11 12 488999999999999874 2 248998 876554
No 138
>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=64.27 E-value=5 Score=26.17 Aligned_cols=26 Identities=31% Similarity=0.796 Sum_probs=12.2
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
-+||+|+....-.+|. .|.| .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCCcceeccCC-EEeCCcccccC
Confidence 3699998877665555 3778 588875
No 139
>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=64.26 E-value=17 Score=42.34 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=14.1
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 009189 81 HARTLLIHYRWDVEKVLAVL 100 (540)
Q Consensus 81 ~a~~LL~~~~W~~~~l~~~~ 100 (540)
.++..++||+-.+=.|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 57777788877666666654
No 140
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=63.76 E-value=7.5 Score=26.52 Aligned_cols=28 Identities=39% Similarity=0.871 Sum_probs=20.4
Q ss_pred ccCCCCCCCCCeEEeccC----ccceeecC-CCcee
Q 009189 222 KWCPSVPHCGNAIRIEVD----ELREVECA-CGLQF 252 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 252 (540)
..|| +|+....++++ ....|.|+ |++.|
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 69998887652 34578896 98876
No 141
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=63.62 E-value=7.5 Score=26.40 Aligned_cols=28 Identities=36% Similarity=0.810 Sum_probs=19.9
Q ss_pred ccCCCCCCCCCeEEecc----CccceeecC-CCcee
Q 009189 222 KWCPSVPHCGNAIRIEV----DELREVECA-CGLQF 252 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~----~~~~~v~C~-C~~~f 252 (540)
..|| +|+....+++ .....+.|+ |++.|
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 3688 6998887665 334568896 98876
No 142
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=63.49 E-value=2.3 Score=43.16 Aligned_cols=20 Identities=30% Similarity=0.828 Sum_probs=15.8
Q ss_pred eeecC-CCceecccccCccCC
Q 009189 243 EVECA-CGLQFCFRCSYEAHS 262 (540)
Q Consensus 243 ~v~C~-C~~~fC~~C~~~~H~ 262 (540)
...|. |...||..|..-.|.
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred cEEchhccceeeccchHHHHh
Confidence 47894 999999999765553
No 143
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.38 E-value=6 Score=45.14 Aligned_cols=41 Identities=20% Similarity=0.533 Sum_probs=31.1
Q ss_pred ccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
...|..|--++. -.++...|||.|...|+. ++ .-.||. |..
T Consensus 840 ~skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~---~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK---EDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccc-cceeeeecccHHHHHhhc--------cC---cccCCc--cch
Confidence 357999987764 245667999999999998 33 358987 876
No 144
>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=63.08 E-value=4.1 Score=35.08 Aligned_cols=26 Identities=27% Similarity=0.767 Sum_probs=16.6
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
+.||+|++..---.- +-++| +||..|
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 689999986652222 55777 466554
No 145
>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=63.08 E-value=26 Score=24.48 Aligned_cols=37 Identities=24% Similarity=0.317 Sum_probs=33.1
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHHH
Q 009189 65 MEDLIRVMDLL-SLKEQHARTLLIHYRWDVEKVLAVLV 101 (540)
Q Consensus 65 ~~~i~~v~~~l-~i~~~~a~~LL~~~~W~~~~l~~~~~ 101 (540)
.+.+..|.+++ +++...++..|..++++++..++.+.
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 45688899999 79999999999999999999998876
No 146
>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=62.90 E-value=5.7 Score=26.80 Aligned_cols=27 Identities=37% Similarity=1.042 Sum_probs=17.2
Q ss_pred ccCCCCCCCCCeEEeccCccceeecC-CCce
Q 009189 222 KWCPSVPHCGNAIRIEVDELREVECA-CGLQ 251 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 251 (540)
+.|| .|++.+.+..+....+.|. |++.
T Consensus 2 ~FCp---~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP---ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BET---TTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCC---CCCccceEcCCCccCcCCCCCCCc
Confidence 5788 7999988766444334674 7765
No 147
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.56 E-value=6.8 Score=33.86 Aligned_cols=20 Identities=35% Similarity=0.813 Sum_probs=16.2
Q ss_pred eeecC-CCceecccccCccCC
Q 009189 243 EVECA-CGLQFCFRCSYEAHS 262 (540)
Q Consensus 243 ~v~C~-C~~~fC~~C~~~~H~ 262 (540)
...|+ |+..||..|-.-+|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 46795 999999999876665
No 148
>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=62.19 E-value=6.3 Score=31.02 Aligned_cols=32 Identities=41% Similarity=0.934 Sum_probs=20.9
Q ss_pred CCCCCccceeecCCCCeeEe-ccCcc-----ccccccccc
Q 009189 292 HCPKCQKLVEKNGGCNLVSC-ICGQP-----FCWLCGAAT 325 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~~ 325 (540)
.||.|+.+++.++ .+.+| .|+.. +|.-|+.+.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 6999999999888 68999 58764 699998764
No 149
>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=61.75 E-value=6.8 Score=27.53 Aligned_cols=22 Identities=36% Similarity=1.090 Sum_probs=16.2
Q ss_pred CCCCCCccceee-cCCCCeeEe-ccC
Q 009189 291 KHCPKCQKLVEK-NGGCNLVSC-ICG 314 (540)
Q Consensus 291 k~CP~C~~~IeK-~~GCnhm~C-~C~ 314 (540)
..||.|+.|+-+ ..| .++| .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 689999999987 444 4677 353
No 150
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=61.74 E-value=9.5 Score=44.32 Aligned_cols=9 Identities=11% Similarity=0.121 Sum_probs=3.4
Q ss_pred HHHHHHHHH
Q 009189 80 QHARTLLIH 88 (540)
Q Consensus 80 ~~a~~LL~~ 88 (540)
.....|..+
T Consensus 977 ~~yq~l~~~ 985 (1010)
T KOG1991|consen 977 VRYQKLIST 985 (1010)
T ss_pred HHHHHHHhc
Confidence 333344333
No 151
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=61.74 E-value=4.6 Score=47.56 Aligned_cols=17 Identities=29% Similarity=0.509 Sum_probs=8.0
Q ss_pred CCCCccceeecCCCCee
Q 009189 293 CPKCQKLVEKNGGCNLV 309 (540)
Q Consensus 293 CP~C~~~IeK~~GCnhm 309 (540)
=|+|-.-+.-.+.|--|
T Consensus 2281 r~kclfE~rn~g~~Lam 2297 (3015)
T KOG0943|consen 2281 RGKCLFEVRNDGNCLAM 2297 (3015)
T ss_pred CCcceEEEecCCceeec
Confidence 35555544444444443
No 152
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.62 E-value=8.5 Score=35.69 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=38.6
Q ss_pred cccccccccccC-CCCce----eecCCCCcccHHHHHHHHHHhhhcCCcccc---cccCcccccccc
Q 009189 129 SSYCCNICFDDV-SLEEI----TTMDCGHYFCNSCWTEHFIVKINEGQSRRI---TCMEHKCNAICD 187 (540)
Q Consensus 129 ~~~~C~IC~e~~-~~~~~----~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i---~CP~~~C~~~~~ 187 (540)
....|+||+--. ..+-+ -...||..|..-|+..|+..-+...+++.| .||- |..++.
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 345677777541 11111 234799999999999999988777766544 6887 776654
No 153
>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=61.18 E-value=1e+02 Score=31.12 Aligned_cols=31 Identities=26% Similarity=0.663 Sum_probs=18.8
Q ss_pred cCCCCCCCCCeEEeccCccceeecCCCceeccccc
Q 009189 223 WCPSVPHCGNAIRIEVDELREVECACGLQFCFRCS 257 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~ 257 (540)
-|| .|..-....++-...+. +|+|..|..|.
T Consensus 2 ~Cp---~CKt~~Y~np~lk~~in-~C~H~lCEsCv 32 (300)
T KOG3800|consen 2 ACP---KCKTDRYLNPDLKLMIN-ECGHRLCESCV 32 (300)
T ss_pred CCc---ccccceecCccceeeec-cccchHHHHHH
Confidence 366 56665555444333344 78888888874
No 154
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=60.78 E-value=5.4 Score=33.31 Aligned_cols=29 Identities=34% Similarity=0.800 Sum_probs=21.4
Q ss_pred CCCCCCccce--eecCCCCeeEec-cCccccc
Q 009189 291 KHCPKCQKLV--EKNGGCNLVSCI-CGQPFCW 319 (540)
Q Consensus 291 k~CP~C~~~I--eK~~GCnhm~C~-C~~~FCw 319 (540)
..||.|+..+ ++.+-||.+.|+ |.+.|=-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 3699998744 455669999995 9887643
No 155
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.41 E-value=6.9 Score=38.23 Aligned_cols=37 Identities=16% Similarity=0.327 Sum_probs=31.0
Q ss_pred cccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhc
Q 009189 131 YCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINE 169 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~ 169 (540)
..|+.|+... .+|+..+=||.||++||-+||..+-++
T Consensus 44 dcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 44 DCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 3578888876 788888999999999999999877653
No 156
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=60.26 E-value=7.5 Score=26.11 Aligned_cols=25 Identities=32% Similarity=0.838 Sum_probs=11.8
Q ss_pred CCCCCCccceeec----CCCCeeEe-ccCc
Q 009189 291 KHCPKCQKLVEKN----GGCNLVSC-ICGQ 315 (540)
Q Consensus 291 k~CP~C~~~IeK~----~GCnhm~C-~C~~ 315 (540)
|.||.|+.+++.. ++=..+.| .||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4688888888752 44555677 4764
No 157
>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=58.79 E-value=6.7 Score=30.48 Aligned_cols=28 Identities=25% Similarity=0.721 Sum_probs=18.8
Q ss_pred ccCCCCCCccceeecCCCCeeEec-cCcc
Q 009189 289 HTKHCPKCQKLVEKNGGCNLVSCI-CGQP 316 (540)
Q Consensus 289 ~~k~CP~C~~~IeK~~GCnhm~C~-C~~~ 316 (540)
.++.||.|+....++..=..++|. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 368999999999874333456663 5543
No 158
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=58.68 E-value=3.3 Score=39.29 Aligned_cols=30 Identities=33% Similarity=0.794 Sum_probs=22.8
Q ss_pred CCCCCCccceeecCCCCeeEeccCccccccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAAT 325 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~ 325 (540)
-.||-|...+.. . +.=.|||.|||.|...|
T Consensus 19 ~~CpICld~~~d-P----VvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 19 FDCNICLDQVRD-P----VVTLCGHLFCWPCIHKW 48 (193)
T ss_pred cCCccCCCcCCC-c----EEcCCCchhHHHHHHHH
Confidence 579999887642 1 33369999999999887
No 159
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.30 E-value=4.3 Score=40.59 Aligned_cols=29 Identities=31% Similarity=0.851 Sum_probs=23.9
Q ss_pred ccccccccccCCCCceeecCCCCc-ccHHHHH
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHY-FCNSCWT 160 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~ 160 (540)
...|.||++.- .+.+.|+|||. -|..|=+
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhcc
Confidence 56799999974 78899999996 6888844
No 160
>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=57.36 E-value=1.8e+02 Score=27.82 Aligned_cols=100 Identities=9% Similarity=0.198 Sum_probs=62.3
Q ss_pred CcchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Q 009189 398 SSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSSFLDEKFHLYN 477 (540)
Q Consensus 398 ~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~~le~~~~~~~ 477 (540)
++.++..+..|++.++..|.-..-+|--+ ...+ ...+..++..-|..+.+++..-|+++..+..++..+.
T Consensus 94 ~L~~Y~r~i~a~K~~l~~R~~~~~~~~~a---------~k~l-~Kar~~k~~~ae~~~~~a~~~fe~iS~~~k~EL~rF~ 163 (198)
T cd07630 94 TLDLYSRYSESEKDMLFRRTCKLIEFENA---------SKAL-EKAKPQKKEQAEEAKKKAETEFEEISSLAKKELERFH 163 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHH-HHhHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666666666554443333211 0111 1222345567888888899999999999999888877
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 478 EDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 478 ~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
...+.++|.-+..+....-..-+..++.+.
T Consensus 164 ~~Rv~~fk~~l~~~~E~~i~~ak~~~~~~~ 193 (198)
T cd07630 164 RQRVLELQSALVCYAESQIKNAKEAAAVLT 193 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777888887777776555555555554443
No 161
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=57.29 E-value=3.9 Score=34.30 Aligned_cols=32 Identities=19% Similarity=0.549 Sum_probs=25.0
Q ss_pred CccccccccccccCCCCceeecCCCCcccHHH
Q 009189 127 VSSSYCCNICFDDVSLEEITTMDCGHYFCNSC 158 (540)
Q Consensus 127 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 158 (540)
....|+|.-||-....+....-.=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45789999999887655555545689999998
No 162
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.90 E-value=3.3 Score=40.89 Aligned_cols=30 Identities=33% Similarity=0.634 Sum_probs=24.2
Q ss_pred CCCCCCccceeecCCCCeeEec-cCcccccccccc-cc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPFCWLCGAA-TG 326 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~FCw~C~~~-~~ 326 (540)
.+|+-|-...+. -.|+ |||-|||.|+-. |.
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t 247 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWT 247 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHHHHH
Confidence 679999888773 5674 999999999876 64
No 163
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.24 E-value=7 Score=40.38 Aligned_cols=44 Identities=23% Similarity=0.562 Sum_probs=30.4
Q ss_pred ccccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
+....|.||.+.. .+.+.+||||.-| |..-+ . ..+.||. |...+
T Consensus 303 ~~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs--~-------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCS--K-------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCCceEEecCCc--cceeeecCCcEEE--chHHH--h-------hCCCCch--hHHHH
Confidence 3467899999986 5577889999976 54322 1 1246998 87544
No 164
>PHA02926 zinc finger-like protein; Provisional
Probab=55.21 E-value=5.9 Score=38.30 Aligned_cols=35 Identities=26% Similarity=0.642 Sum_probs=23.0
Q ss_pred CCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCcccee
Q 009189 247 ACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVE 301 (540)
Q Consensus 247 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 301 (540)
+|+|.||+.|-..|.... . + ....+.||-|+....
T Consensus 196 ~CnHsFCl~CIr~Wr~~r------------~-~-------~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 196 SCNHIFCITCINIWHRTR------------R-E-------TGASDNCPICRTRFR 230 (242)
T ss_pred CCCchHHHHHHHHHHHhc------------c-c-------cCcCCcCCCCcceee
Confidence 599999999975543311 0 0 012378999998765
No 165
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=54.97 E-value=3 Score=42.48 Aligned_cols=28 Identities=29% Similarity=0.738 Sum_probs=20.9
Q ss_pred cCCCCCCccceee-cCCCCeeEe-ccCccc
Q 009189 290 TKHCPKCQKLVEK-NGGCNLVSC-ICGQPF 317 (540)
Q Consensus 290 ~k~CP~C~~~IeK-~~GCnhm~C-~C~~~F 317 (540)
|.+||+|+..|-+ .-.=|.+.| .|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 4889999987764 334566889 599888
No 166
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.61 E-value=4.2 Score=44.84 Aligned_cols=36 Identities=25% Similarity=0.626 Sum_probs=28.0
Q ss_pred ccccccccccCC--CCceeecCCCCcccHHHHHHHHHH
Q 009189 130 SYCCNICFDDVS--LEEITTMDCGHYFCNSCWTEHFIV 165 (540)
Q Consensus 130 ~~~C~IC~e~~~--~~~~~~l~CgH~fC~~Cl~~y~~~ 165 (540)
-..|+||+..+- .-.++++.|||..|+-|...-...
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 467999987753 245788999999999999876543
No 167
>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=54.40 E-value=8 Score=32.78 Aligned_cols=24 Identities=38% Similarity=0.941 Sum_probs=17.9
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
+.||.|+.++...+ +.+.| .|++.
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCc
Confidence 36999999887654 37888 48775
No 168
>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=54.07 E-value=11 Score=41.49 Aligned_cols=34 Identities=26% Similarity=0.682 Sum_probs=23.9
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc-----cccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP-----FCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 324 (540)
-.||+|..++.--..=|.+.| .||+. .|..|+..
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 478888877763333346889 58876 68888875
No 169
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=53.92 E-value=4.8 Score=40.55 Aligned_cols=53 Identities=30% Similarity=0.674 Sum_probs=36.8
Q ss_pred CCccccCCCCCCCCCeEEeccCccceeecCCCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCc
Q 009189 218 NKRVKWCPSVPHCGNAIRIEVDELREVECACGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQ 297 (540)
Q Consensus 218 ~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~ 297 (540)
++.+-+|- .|+..|.+=+.- + +|.+.||..|... |. .|.||.|.
T Consensus 87 ~p~VHfCd---~Cd~PI~IYGRm---I--PCkHvFCl~CAr~-~~---------------------------dK~Cp~C~ 130 (389)
T KOG2932|consen 87 GPRVHFCD---RCDFPIAIYGRM---I--PCKHVFCLECARS-DS---------------------------DKICPLCD 130 (389)
T ss_pred CcceEeec---ccCCcceeeecc---c--ccchhhhhhhhhc-Cc---------------------------cccCcCcc
Confidence 34566675 798877643321 1 6899999999643 11 18999999
Q ss_pred cceeecCCC
Q 009189 298 KLVEKNGGC 306 (540)
Q Consensus 298 ~~IeK~~GC 306 (540)
-+|+|.+-|
T Consensus 131 d~VqrIeq~ 139 (389)
T KOG2932|consen 131 DRVQRIEQI 139 (389)
T ss_pred cHHHHHHHh
Confidence 999987655
No 170
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.13 E-value=10 Score=43.44 Aligned_cols=35 Identities=26% Similarity=0.730 Sum_probs=28.8
Q ss_pred cCCCCCCccceeecCCCCeeEe-ccCcc-----cccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSC-ICGQP-----FCWLCGAA 324 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 324 (540)
+-.||+|..++.-..+=|.|.| .||++ .|.-||+.
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 3479999988876666689999 59997 89999986
No 171
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=52.28 E-value=9.7 Score=27.46 Aligned_cols=33 Identities=24% Similarity=0.551 Sum_probs=22.9
Q ss_pred cccccccCCCCceeecCCC-----CcccHHHHHHHHHH
Q 009189 133 CNICFDDVSLEEITTMDCG-----HYFCNSCWTEHFIV 165 (540)
Q Consensus 133 C~IC~e~~~~~~~~~l~Cg-----H~fC~~Cl~~y~~~ 165 (540)
|-||++......+...||+ .....+|+..|+..
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 7799998765555556765 25678899999987
No 172
>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=52.17 E-value=12 Score=27.59 Aligned_cols=20 Identities=20% Similarity=0.172 Sum_probs=12.7
Q ss_pred CCCCCCcccee------ecCCCCeeE
Q 009189 291 KHCPKCQKLVE------KNGGCNLVS 310 (540)
Q Consensus 291 k~CP~C~~~Ie------K~~GCnhm~ 310 (540)
|+||.|+-.-+ .+.+..+++
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~ 27 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYF 27 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEE
Confidence 89999986444 234555554
No 173
>PRK12495 hypothetical protein; Provisional
Probab=51.92 E-value=16 Score=35.21 Aligned_cols=17 Identities=24% Similarity=0.671 Sum_probs=14.9
Q ss_pred cCCCCCCccceeecCCC
Q 009189 290 TKHCPKCQKLVEKNGGC 306 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GC 306 (540)
.+.||.|+.||.+..||
T Consensus 42 a~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ 58 (226)
T ss_pred hhhcccccCcccCCCCe
Confidence 57999999999987776
No 174
>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=51.36 E-value=17 Score=24.57 Aligned_cols=27 Identities=30% Similarity=0.801 Sum_probs=18.1
Q ss_pred cCCCCCCCCCeEEeccC----ccceeecC-CCcee
Q 009189 223 WCPSVPHCGNAIRIEVD----ELREVECA-CGLQF 252 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~~----~~~~v~C~-C~~~f 252 (540)
.|| +|+..+.+..+ ....+.|+ |++.|
T Consensus 4 ~CP---~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCP---NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECC---CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 587 69998876642 22357885 88765
No 175
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=50.91 E-value=12 Score=30.72 Aligned_cols=27 Identities=30% Similarity=0.714 Sum_probs=21.0
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
..||.|+++.-|..+=---.| +||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 689999999888776666777 477665
No 176
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=50.60 E-value=23 Score=28.46 Aligned_cols=49 Identities=31% Similarity=0.740 Sum_probs=20.8
Q ss_pred cccccccccccCCC---Cceeec--CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 129 SSYCCNICFDDVSL---EEITTM--DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 129 ~~~~C~IC~e~~~~---~~~~~l--~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
....|.||-+.+.. .++|.. .|+-..|+.|+. ..+++|. -.||+ |+...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE----YErkeg~---q~Cpq--Ckt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE----YERKEGN---QVCPQ--CKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH----HHHHTS----SB-TT--T--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHH----HHhhcCc---ccccc--cCCCc
Confidence 46789999999643 344433 688899999976 3445665 47888 77543
No 177
>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=50.41 E-value=4 Score=41.47 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=19.6
Q ss_pred cCCCCCCccceeec-CCCCeeEe-ccCcccc
Q 009189 290 TKHCPKCQKLVEKN-GGCNLVSC-ICGQPFC 318 (540)
Q Consensus 290 ~k~CP~C~~~IeK~-~GCnhm~C-~C~~~FC 318 (540)
|.+||+|+..|-+. -.=|.+.| .|+++|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 47888888877643 33455788 5888753
No 178
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.06 E-value=13 Score=44.75 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHH
Q 009189 456 QQFEANIEKLSSF 468 (540)
Q Consensus 456 ~~le~~~e~L~~~ 468 (540)
.++--.+|+|.++
T Consensus 800 ~Eigvs~eklreL 812 (1337)
T PRK14714 800 REIGVSVEKLREL 812 (1337)
T ss_pred HHcCCCHHHHHHc
Confidence 3455566777665
No 179
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=49.99 E-value=3.7 Score=33.17 Aligned_cols=47 Identities=30% Similarity=0.449 Sum_probs=35.4
Q ss_pred eCHHHHHHHHHHHHHHHHHHhC--C-CHHHHHHHHHHcCCChHHHHHHHHh
Q 009189 55 ITKESLLAAQMEDLIRVMDLLS--L-KEQHARTLLIHYRWDVEKVLAVLVE 102 (540)
Q Consensus 55 lt~~~i~~~~~~~i~~v~~~l~--i-~~~~a~~LL~~~~W~~~~l~~~~~~ 102 (540)
||+++-.+ +..-+.+|.++|| + +.....-.|++|.|++++.+..+.+
T Consensus 20 Ls~ed~~~-L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 20 LSPEDQAQ-LYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp -TCHHHHH-HCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCHHHHHH-HHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 66666554 6777889999997 4 6667788899999999999998774
No 180
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=49.36 E-value=4.1 Score=41.45 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=12.8
Q ss_pred CCCCCCccceee-cCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEK-NGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK-~~GCnhm~C-~C~~~F 317 (540)
.+||+|+..|-+ .-.=|.+.| .|+++|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 456666555542 222334555 355544
No 181
>PRK04023 DNA polymerase II large subunit; Validated
Probab=49.21 E-value=13 Score=43.59 Aligned_cols=33 Identities=33% Similarity=0.734 Sum_probs=21.3
Q ss_pred cCCccccCCCCCCCCCeEEeccCccceeecC-CCc-----eecccccCc
Q 009189 217 DNKRVKWCPSVPHCGNAIRIEVDELREVECA-CGL-----QFCFRCSYE 259 (540)
Q Consensus 217 ~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~-----~fC~~C~~~ 259 (540)
.....+.|| .|+... ....|+ ||. .||..|+..
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 334556888 588752 236786 884 478888654
No 182
>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=48.64 E-value=26 Score=30.49 Aligned_cols=42 Identities=24% Similarity=0.577 Sum_probs=28.8
Q ss_pred ccCCCCCCccceeecCCCCeeEe-ccCccccccccccccCCCCc
Q 009189 289 HTKHCPKCQKLVEKNGGCNLVSC-ICGQPFCWLCGAATGSDHTW 331 (540)
Q Consensus 289 ~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~~~~~~H~~ 331 (540)
+.+.|..|+.+.-.-.+.. ..| .|++.+|-.|+........|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~~~~~~~W 95 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVYSKKEPIW 95 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEETSSSCCE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCcCCCCCCE
Confidence 4678999999876554444 889 59999999999863333333
No 183
>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=48.60 E-value=4.5 Score=30.78 Aligned_cols=24 Identities=38% Similarity=0.892 Sum_probs=16.9
Q ss_pred CCCCCCccceeecCCCCeeEeccCcccc-ccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCICGQPFC-WLCGAAT 325 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~C~~~FC-w~C~~~~ 325 (540)
|.||.|+.+|.-+ ..|| -.|...|
T Consensus 4 kHC~~CG~~Ip~~-----------~~fCS~~C~~~~ 28 (59)
T PF09889_consen 4 KHCPVCGKPIPPD-----------ESFCSPKCREEY 28 (59)
T ss_pred CcCCcCCCcCCcc-----------hhhhCHHHHHHH
Confidence 7899999999843 4566 3666653
No 184
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=48.34 E-value=15 Score=29.53 Aligned_cols=54 Identities=20% Similarity=0.601 Sum_probs=19.3
Q ss_pred CCCCeEEeccCccceeecC-CCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCC
Q 009189 229 HCGNAIRIEVDELREVECA-CGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCN 307 (540)
Q Consensus 229 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 307 (540)
-|+--|.........|.|. |+...|..|. ++. ++...+.||.|+.+..+..|+-
T Consensus 14 iCGD~VGl~~~Ge~FVAC~eC~fPvCr~Cy----------EYE---------------rkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 14 ICGDDVGLTENGEVFVACHECAFPVCRPCY----------EYE---------------RKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp SS--B--B-SSSSB--S-SSS-----HHHH----------HHH---------------HHTS-SB-TTT--B----TT--
T ss_pred cccCccccCCCCCEEEEEcccCCccchhHH----------HHH---------------hhcCcccccccCCCcccccCCC
Confidence 4766666555555668895 9999998774 221 1223489999999988777664
No 185
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=47.80 E-value=4.2 Score=29.59 Aligned_cols=34 Identities=35% Similarity=1.031 Sum_probs=28.2
Q ss_pred cccccccccccCCCCceeec-CCCCcccHHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTM-DCGHYFCNSCWTEH 162 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y 162 (540)
+.++|..|-+.+|..+.... -||.--|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 47899999999887666554 69999999999864
No 186
>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=47.04 E-value=14 Score=23.68 Aligned_cols=24 Identities=29% Similarity=0.811 Sum_probs=13.2
Q ss_pred CCCCCCccceee--cCCCCeeEe-ccC
Q 009189 291 KHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 291 k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
++||+|+.+|++ .+|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 589999999875 345555666 464
No 187
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.75 E-value=15 Score=41.83 Aligned_cols=34 Identities=24% Similarity=0.619 Sum_probs=22.2
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc----cccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP----FCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~----FCw~C~~~ 324 (540)
-.||+|..++.-..+=+.+.| .||+. .|..|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 468888777764444456888 48763 47777664
No 188
>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=46.67 E-value=6.6 Score=33.67 Aligned_cols=17 Identities=35% Similarity=0.776 Sum_probs=13.4
Q ss_pred eeecCCCceecccccCcc
Q 009189 243 EVECACGLQFCFRCSYEA 260 (540)
Q Consensus 243 ~v~C~C~~~fC~~C~~~~ 260 (540)
.+.|.||+.||.. +..|
T Consensus 24 ~vkc~CGh~f~d~-r~Nw 40 (112)
T PF08882_consen 24 VVKCDCGHEFCDA-RENW 40 (112)
T ss_pred eeeccCCCeecCh-hcCh
Confidence 6899999999986 4333
No 189
>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=46.31 E-value=11 Score=29.31 Aligned_cols=33 Identities=24% Similarity=0.514 Sum_probs=17.9
Q ss_pred cCCCCCCccceeecCCCCeeEec-cCcccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSCI-CGQPFCWLCGAA 324 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C~-C~~~FCw~C~~~ 324 (540)
...|+.|++..- -.-..-.|+ ||.-||-.|...
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-TTT--EEECCCS-E
T ss_pred CCcCcCcCCcCC--CceeeEccCCCCCEECCchhCC
Confidence 479999999873 334457895 999999999875
No 190
>PF14369 zf-RING_3: zinc-finger
Probab=46.00 E-value=19 Score=24.26 Aligned_cols=28 Identities=32% Similarity=0.821 Sum_probs=18.7
Q ss_pred ccCCCCCCCCCeEEeccCccceeecC-CCcee
Q 009189 222 KWCPSVPHCGNAIRIEVDELREVECA-CGLQF 252 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~f 252 (540)
.||- .|...|.+.......+.|+ |+..|
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 6999888754333345686 77654
No 191
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=45.98 E-value=11 Score=37.83 Aligned_cols=32 Identities=28% Similarity=0.764 Sum_probs=25.7
Q ss_pred CCCCCCccceeecCCCCeeEe--ccCccccccccccccCCC
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC--ICGQPFCWLCGAATGSDH 329 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C--~C~~~FCw~C~~~~~~~H 329 (540)
-+|--|.-.|. +-| .|||-||++|-...-..|
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~q 59 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQ 59 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCC
Confidence 47888988888 899 399999999988643444
No 192
>PF15616 TerY-C: TerY-C metal binding domain
Probab=45.47 E-value=13 Score=33.03 Aligned_cols=23 Identities=48% Similarity=1.178 Sum_probs=17.1
Q ss_pred cCCCCCCCCCeEEeccCccceeecCCCceeccc
Q 009189 223 WCPSVPHCGNAIRIEVDELREVECACGLQFCFR 255 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~ 255 (540)
-|| .|++.. ..+.|.||..+|..
T Consensus 79 gCP---~CGn~~-------~fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 79 GCP---HCGNQY-------AFAVCGCGKLFCID 101 (131)
T ss_pred CCC---CCcChh-------cEEEecCCCEEEeC
Confidence 455 788753 24788999999986
No 193
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=45.15 E-value=7.4 Score=38.83 Aligned_cols=29 Identities=28% Similarity=0.697 Sum_probs=21.4
Q ss_pred cCCCCCCccceee-cCCCCeeEe-ccCcccc
Q 009189 290 TKHCPKCQKLVEK-NGGCNLVSC-ICGQPFC 318 (540)
Q Consensus 290 ~k~CP~C~~~IeK-~~GCnhm~C-~C~~~FC 318 (540)
|.+||.|+..+-+ .-+=|...| +|+++|=
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCcccc
Confidence 4789999988864 446667788 5877763
No 194
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=45.00 E-value=2e+02 Score=28.33 Aligned_cols=35 Identities=29% Similarity=0.649 Sum_probs=23.1
Q ss_pred CCCCCCccceee----cCCCCeeEe-c----cCccccccccccc
Q 009189 291 KHCPKCQKLVEK----NGGCNLVSC-I----CGQPFCWLCGAAT 325 (540)
Q Consensus 291 k~CP~C~~~IeK----~~GCnhm~C-~----C~~~FCw~C~~~~ 325 (540)
..|-+|+..--+ -..|.||+| . +...+|.+|....
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~i 47 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSI 47 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCcccccccccee
Confidence 345555443322 357999999 4 5566999998863
No 195
>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=44.95 E-value=20 Score=22.90 Aligned_cols=20 Identities=25% Similarity=0.669 Sum_probs=13.0
Q ss_pred CCCCCccceeecCCCCeeEe
Q 009189 292 HCPKCQKLVEKNGGCNLVSC 311 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C 311 (540)
.||.|+..+.+..|=-.++|
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 49999999998887667777
No 196
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.62 E-value=18 Score=41.40 Aligned_cols=34 Identities=26% Similarity=0.669 Sum_probs=23.4
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc-----cccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP-----FCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~-----FCw~C~~~ 324 (540)
-.||+|..++.-...=|.+.| .||+. .|..|++.
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 478888887763223356888 58876 58888775
No 197
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.29 E-value=22 Score=26.54 Aligned_cols=33 Identities=21% Similarity=0.716 Sum_probs=26.4
Q ss_pred cccccccccccCC-CCceeec-CCCCcccHHHHHH
Q 009189 129 SSYCCNICFDDVS-LEEITTM-DCGHYFCNSCWTE 161 (540)
Q Consensus 129 ~~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~Cl~~ 161 (540)
....|++|-+.+. .++.+.. .||-.|.++||..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3456999999985 4666666 6999999999975
No 198
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.64 E-value=15 Score=38.46 Aligned_cols=9 Identities=22% Similarity=0.261 Sum_probs=3.4
Q ss_pred hcCCCCCCC
Q 009189 39 AVEPEIPPN 47 (540)
Q Consensus 39 ~~~~~~~~~ 47 (540)
.++.-..+.
T Consensus 301 ~v~dN~~p~ 309 (514)
T KOG3130|consen 301 GVGDNSIPT 309 (514)
T ss_pred ccCCCcCcc
Confidence 344433333
No 199
>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=43.61 E-value=8.7 Score=34.79 Aligned_cols=32 Identities=16% Similarity=0.228 Sum_probs=15.1
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIV 165 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~ 165 (540)
+..+|||=-+.- ++..++ .-|=..|++.|+..
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 456677755432 222222 23445566555543
No 200
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.25 E-value=5e+02 Score=28.81 Aligned_cols=18 Identities=17% Similarity=0.329 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009189 453 DQQQQFEANIEKLSSFLD 470 (540)
Q Consensus 453 ~~q~~le~~~e~L~~~le 470 (540)
+.|+.|++...+|.....
T Consensus 630 e~qe~L~~~~~~L~~~~~ 647 (741)
T KOG4460|consen 630 EKQEDLMNRMKKLLHSFH 647 (741)
T ss_pred HhHHHHHHHHHHHHhccc
Confidence 345555555555544443
No 201
>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=43.19 E-value=32 Score=25.29 Aligned_cols=37 Identities=19% Similarity=0.291 Sum_probs=31.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 009189 66 EDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLVE 102 (540)
Q Consensus 66 ~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~ 102 (540)
+-|..++...|++..-+...|...+||-++.+..|.+
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 4578899999999999999999999999999988874
No 202
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=43.12 E-value=20 Score=36.14 Aligned_cols=47 Identities=34% Similarity=0.771 Sum_probs=35.6
Q ss_pred ccccccccccccCCC--CceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 128 SSSYCCNICFDDVSL--EEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
+....||||.+.+.. ..+..++|||..-..|+..+... . ++||. |..
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 356679999988532 34556799999999999988654 2 79998 877
No 203
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.71 E-value=16 Score=35.98 Aligned_cols=54 Identities=20% Similarity=0.516 Sum_probs=38.3
Q ss_pred cccccccccccCCCCceee---cCCC-----CcccHHHHHHHHHHhhhcCCcccccccCcccccc
Q 009189 129 SSYCCNICFDDVSLEEITT---MDCG-----HYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAI 185 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~---l~Cg-----H~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~ 185 (540)
.+-.|=|||..-. ++... -||. |-....|+..|+..+-......++.||+ |...
T Consensus 19 ~eR~CWiCF~Tde-Dn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDE-DNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred cceeEEEEeccCc-ccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 4567999998743 22222 2664 5688999999999876644446899999 8763
No 204
>PF14149 YhfH: YhfH-like protein
Probab=42.24 E-value=2.2 Score=29.15 Aligned_cols=25 Identities=32% Similarity=0.788 Sum_probs=20.1
Q ss_pred ccCCCCCCccceeecCCCCeeEe-cc
Q 009189 289 HTKHCPKCQKLVEKNGGCNLVSC-IC 313 (540)
Q Consensus 289 ~~k~CP~C~~~IeK~~GCnhm~C-~C 313 (540)
..|.||.|+..|+--.-|-.+.| +|
T Consensus 12 p~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 12 PPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 35999999999998777777777 45
No 205
>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=41.88 E-value=6.9 Score=29.57 Aligned_cols=14 Identities=50% Similarity=0.814 Sum_probs=7.8
Q ss_pred cCCCCCCccceeec
Q 009189 290 TKHCPKCQKLVEKN 303 (540)
Q Consensus 290 ~k~CP~C~~~IeK~ 303 (540)
+..||.|+++++-.
T Consensus 2 ~v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 2 TVKCPICGKPVEWS 15 (57)
T ss_dssp EEE-TTT--EEE-S
T ss_pred cccCCCCCCeeccc
Confidence 36899999999853
No 206
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=41.45 E-value=6.9 Score=44.00 Aligned_cols=50 Identities=26% Similarity=0.585 Sum_probs=38.0
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
...+|+||+..+ .+++.+.|.|.||..||..-+...-. ...||. |+..+.
T Consensus 20 k~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~e 69 (684)
T KOG4362|consen 20 KILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIE 69 (684)
T ss_pred hhccCCceeEEe--eccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhh
Confidence 467899999987 45678899999999999987665421 467887 765444
No 207
>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=41.09 E-value=1.1e+02 Score=23.52 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHHHh
Q 009189 63 AQMEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVLVE 102 (540)
Q Consensus 63 ~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~~~ 102 (540)
.+.+-|..++...|++..-+...|...+||-+..+..|.+
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4677788999999999999999999999999998887763
No 208
>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=40.90 E-value=22 Score=25.10 Aligned_cols=41 Identities=20% Similarity=0.509 Sum_probs=19.5
Q ss_pred cccccccCCCCce-eecCCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 133 CNICFDDVSLEEI-TTMDCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 133 C~IC~e~~~~~~~-~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
|.+|-+.+..... ....|+=.+...|+..||...- ..+||.
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 6677776532211 1124888899999999987642 127886
No 209
>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=40.85 E-value=18 Score=26.19 Aligned_cols=25 Identities=32% Similarity=0.611 Sum_probs=16.4
Q ss_pred CCCC--CCccceeecCCCCeeEe-ccCc
Q 009189 291 KHCP--KCQKLVEKNGGCNLVSC-ICGQ 315 (540)
Q Consensus 291 k~CP--~C~~~IeK~~GCnhm~C-~C~~ 315 (540)
+.|| .|+.-+.-..--+..+| +|+.
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCcccCCceEeeecCCCccCCCccc
Confidence 7899 99986654444467888 7874
No 210
>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=39.98 E-value=22 Score=26.05 Aligned_cols=46 Identities=17% Similarity=0.405 Sum_probs=23.6
Q ss_pred cccccccccCCCCcee-ecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 131 YCCNICFDDVSLEEIT-TMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~-~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
+.|+|-+..+ .-|+ ...|.|.-|.+ +..|+....+.+. .+||. |+.
T Consensus 3 L~CPls~~~i--~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~---W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRI--RIPVRGKNCKHLQCFD-LESFLESNQRTPK---WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB---SSEEEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEE--EeCccCCcCcccceEC-HHHHHHHhhccCC---eECcC--CcC
Confidence 5688888776 3344 45899998755 6777777665544 79998 754
No 211
>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=39.51 E-value=17 Score=32.11 Aligned_cols=25 Identities=12% Similarity=0.206 Sum_probs=15.7
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
+.||+|++..---.- +-++| +||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCc
Confidence 689999986642111 44777 46655
No 212
>PRK11827 hypothetical protein; Provisional
Probab=39.39 E-value=24 Score=26.97 Aligned_cols=24 Identities=21% Similarity=0.315 Sum_probs=16.9
Q ss_pred CCCCCCccceeecCCCCeeEec-cC
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CG 314 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~ 314 (540)
-.||.|+.+++-..+=+.+.|+ |+
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~ 33 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDN 33 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccC
Confidence 5799999998865544556663 54
No 213
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.05 E-value=22 Score=35.87 Aligned_cols=26 Identities=35% Similarity=0.798 Sum_probs=18.2
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccCc
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICGQ 315 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~~ 315 (540)
-++||.|+.+|++ .+|=.-.+| .|+.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 3799999999986 456555555 3543
No 214
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=38.74 E-value=23 Score=30.02 Aligned_cols=26 Identities=27% Similarity=0.778 Sum_probs=15.3
Q ss_pred CCCCCCccce---eecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQKLV---EKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~~I---eK~~GCnhm~C-~C~~~ 316 (540)
-.||+|+... ....|=-|..| .||+.
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 5799998422 22335556777 46654
No 215
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=38.02 E-value=22 Score=35.74 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=20.4
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccC
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
-++|+.|+.+|+| -+|=+-.+| .|+
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4799999999997 478777888 476
No 216
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=37.78 E-value=25 Score=30.53 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=18.4
Q ss_pred CCCCCCccceee--cCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEK--NGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK--~~GCnhm~C-~C~~~F 317 (540)
+.||+|+.++.- .++=+-+.| +||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 789999987764 112226888 488765
No 217
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=37.44 E-value=4.2e+02 Score=32.03 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=12.0
Q ss_pred cCCCCCCccceeecC
Q 009189 290 TKHCPKCQKLVEKNG 304 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~ 304 (540)
.-.||+|++|+|-..
T Consensus 796 ~~~~~~~~~~~~~~~ 810 (1006)
T PRK12775 796 VATCPKCHRPLEGDE 810 (1006)
T ss_pred CccCcccCCCCCCCc
Confidence 468999999998543
No 218
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=37.13 E-value=28 Score=25.61 Aligned_cols=30 Identities=27% Similarity=0.647 Sum_probs=23.6
Q ss_pred ccccccccCCCCceeecCCCCcccHHHHHHH
Q 009189 132 CCNICFDDVSLEEITTMDCGHYFCNSCWTEH 162 (540)
Q Consensus 132 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y 162 (540)
.|+||-..+..-..+.+.=| ..|.+|++..
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 49999998765555667777 8999999875
No 219
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=37.10 E-value=26 Score=31.20 Aligned_cols=51 Identities=27% Similarity=0.548 Sum_probs=37.8
Q ss_pred cccccccccccCCCCceeec---CCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 129 SSYCCNICFDDVSLEEITTM---DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l---~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.-.+|.||-+.-. ++-+.- -||=..|.-|....|...- ....||. |+..+-
T Consensus 79 ~lYeCnIC~etS~-ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 79 KLYECNICKETSA-EERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFK 132 (140)
T ss_pred CceeccCcccccc-hhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--cccccc
Confidence 5689999998853 222222 3999999999999998853 3468998 887653
No 220
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=36.96 E-value=32 Score=26.60 Aligned_cols=14 Identities=29% Similarity=0.517 Sum_probs=10.5
Q ss_pred ccCCCCCCccceee
Q 009189 289 HTKHCPKCQKLVEK 302 (540)
Q Consensus 289 ~~k~CP~C~~~IeK 302 (540)
+.|+||.|+..+..
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 35999999876553
No 221
>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=36.90 E-value=25 Score=27.28 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=12.1
Q ss_pred cccHHHHHHHHHHhhhc
Q 009189 153 YFCNSCWTEHFIVKINE 169 (540)
Q Consensus 153 ~fC~~Cl~~y~~~~i~~ 169 (540)
-||++||..|+...-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999876643
No 222
>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=36.76 E-value=28 Score=26.12 Aligned_cols=44 Identities=20% Similarity=0.471 Sum_probs=30.5
Q ss_pred cccccccccCCCCceeecCCC--CcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 131 YCCNICFDDVSLEEITTMDCG--HYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
-.|..|-.+++.+..-..-|. ..||.+|-...+. -.||. |+..+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGel 51 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN----------GVCPN--CGGEL 51 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc----------CcCcC--CCCcc
Confidence 358888888876654444455 4799999887652 26887 77654
No 223
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=36.73 E-value=24 Score=35.57 Aligned_cols=25 Identities=32% Similarity=0.783 Sum_probs=18.5
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccC
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
-++||.|+.+|+| .+|=.-.+| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 3689999999986 466556666 465
No 224
>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=36.69 E-value=24 Score=35.55 Aligned_cols=24 Identities=33% Similarity=0.761 Sum_probs=17.9
Q ss_pred CCCCCCccceee--cCCCCeeEe-ccC
Q 009189 291 KHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 291 k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
++||.|+.+|+| .+|=+-.+| .|+
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 699999999996 466555666 463
No 225
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=36.63 E-value=17 Score=27.53 Aligned_cols=6 Identities=50% Similarity=1.625 Sum_probs=3.8
Q ss_pred CCCCCc
Q 009189 292 HCPKCQ 297 (540)
Q Consensus 292 ~CP~C~ 297 (540)
.||+|+
T Consensus 29 ~CPnCG 34 (61)
T COG2888 29 PCPNCG 34 (61)
T ss_pred eCCCCC
Confidence 566666
No 226
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.56 E-value=24 Score=35.53 Aligned_cols=25 Identities=20% Similarity=0.579 Sum_probs=18.7
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccC
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
.++||+|+.+|++ .+|=.-.+| .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 4799999999986 466555666 465
No 227
>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=36.55 E-value=30 Score=25.51 Aligned_cols=46 Identities=24% Similarity=0.460 Sum_probs=24.6
Q ss_pred ccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchhHHH
Q 009189 130 SYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDESKIR 192 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~~i~ 192 (540)
.+.||.|...++. .. |..++...=... ...+.||. |...+...++.
T Consensus 2 ~f~CP~C~~~~~~---~~-----------L~~H~~~~H~~~-~~~v~CPi--C~~~~~~~l~~ 47 (54)
T PF05605_consen 2 SFTCPYCGKGFSE---SS-----------LVEHCEDEHRSE-SKNVVCPI--CSSRVTDNLIR 47 (54)
T ss_pred CcCCCCCCCccCH---HH-----------HHHHHHhHCcCC-CCCccCCC--chhhhhhHHHH
Confidence 5889999885421 11 233333322111 13689998 87655543333
No 228
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=36.00 E-value=21 Score=35.83 Aligned_cols=12 Identities=25% Similarity=0.196 Sum_probs=8.4
Q ss_pred CCCCCCCCCCCC
Q 009189 1 MGEYRSSDDDYD 12 (540)
Q Consensus 1 ~~~~~~~~~~~~ 12 (540)
|+|.|.+|+|||
T Consensus 1 m~D~~MdddEDY 12 (440)
T KOG1464|consen 1 MSDDFMDDDEDY 12 (440)
T ss_pred CCccccccchhc
Confidence 777666666666
No 229
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=35.94 E-value=37 Score=30.14 Aligned_cols=22 Identities=45% Similarity=1.170 Sum_probs=11.9
Q ss_pred CCCCC--CccceeecCCCCeeEec--cCcccc
Q 009189 291 KHCPK--CQKLVEKNGGCNLVSCI--CGQPFC 318 (540)
Q Consensus 291 k~CP~--C~~~IeK~~GCnhm~C~--C~~~FC 318 (540)
|.||+ |.-+++ ++-|+ ||+-.=
T Consensus 83 k~Cpn~~C~g~L~------~~pCrGh~GYPVT 108 (143)
T PF03615_consen 83 KPCPNRNCKGRLE------LIPCRGHCGYPVT 108 (143)
T ss_dssp SB-SS--S--BEE------EE---TBTTB--E
T ss_pred CCCCccccCCcee------EEeccCcCCCcee
Confidence 99999 999998 68995 887543
No 230
>PRK10445 endonuclease VIII; Provisional
Probab=35.76 E-value=26 Score=35.17 Aligned_cols=25 Identities=24% Similarity=0.599 Sum_probs=18.9
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccC
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
-++||.|+.+|++ .+|=.-.+| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 3799999999986 467666666 465
No 231
>PHA02929 N1R/p28-like protein; Provisional
Probab=35.64 E-value=16 Score=36.10 Aligned_cols=38 Identities=24% Similarity=0.425 Sum_probs=25.7
Q ss_pred cCCCCCCccceeecCCCCe---eEeccCccccccccccccC
Q 009189 290 TKHCPKCQKLVEKNGGCNL---VSCICGQPFCWLCGAATGS 327 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnh---m~C~C~~~FCw~C~~~~~~ 327 (540)
...||-|...+.....-+. +.-.|+|.||..|...|..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 4689999988764432211 3335888888888888754
No 232
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=35.53 E-value=32 Score=22.90 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=8.9
Q ss_pred cCCCCCCcccee
Q 009189 290 TKHCPKCQKLVE 301 (540)
Q Consensus 290 ~k~CP~C~~~Ie 301 (540)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 378999987655
No 233
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.44 E-value=25 Score=35.60 Aligned_cols=25 Identities=32% Similarity=0.639 Sum_probs=19.3
Q ss_pred cCCCCCCccceee--cCCCCeeEe-ccC
Q 009189 290 TKHCPKCQKLVEK--NGGCNLVSC-ICG 314 (540)
Q Consensus 290 ~k~CP~C~~~IeK--~~GCnhm~C-~C~ 314 (540)
-++||.|+.+|.| .+|=+-.+| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 3799999999986 467666777 465
No 234
>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=35.35 E-value=16 Score=26.85 Aligned_cols=25 Identities=32% Similarity=0.744 Sum_probs=13.6
Q ss_pred CCCCCCccceeecCCC--CeeEe-ccCc
Q 009189 291 KHCPKCQKLVEKNGGC--NLVSC-ICGQ 315 (540)
Q Consensus 291 k~CP~C~~~IeK~~GC--nhm~C-~C~~ 315 (540)
-+|++|++.+-+.++= -.|.| ||+.
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 4677777766653222 24566 5554
No 235
>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=35.35 E-value=42 Score=38.24 Aligned_cols=42 Identities=21% Similarity=0.248 Sum_probs=25.7
Q ss_pred CCceeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHH
Q 009189 50 PSSKVITKESLLAAQMEDLIRVMDLLSLKEQHARTLLIHYRWDVEK 95 (540)
Q Consensus 50 ~~~~vlt~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~ 95 (540)
+.++.|++.++....++.-..-.+.+ +.-..||++-+|..+.
T Consensus 411 ppf~~l~ksq~~kl~k~q~k~y~de~----dyr~kl~~kkq~ke~~ 452 (763)
T TIGR00993 411 PPFKPLTKAQMAKLSKEQRKAYLEEY----DYRVKLLQKKQWREEL 452 (763)
T ss_pred CCCccccHHHHHHHhHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 45688999888777666433222222 3345778888887554
No 236
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.20 E-value=24 Score=41.49 Aligned_cols=31 Identities=32% Similarity=0.811 Sum_probs=23.9
Q ss_pred hccCCCCCCccceeecCCCCeeEe-ccCc-----ccccccccc
Q 009189 288 VHTKHCPKCQKLVEKNGGCNLVSC-ICGQ-----PFCWLCGAA 324 (540)
Q Consensus 288 ~~~k~CP~C~~~IeK~~GCnhm~C-~C~~-----~FCw~C~~~ 324 (540)
...+.||.|+... ....| .||. .||..|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCc
Confidence 3468999999885 34789 4986 499999775
No 237
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=35.02 E-value=21 Score=29.34 Aligned_cols=35 Identities=29% Similarity=0.482 Sum_probs=28.2
Q ss_pred CCCCCCccceeecCCCCeeEeccCccccccccccccCC
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAATGSD 328 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~ 328 (540)
.-||.|+.| ...|--+.+.|++.|=..|...|...
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHcc
Confidence 468888887 45777788889999999999998543
No 238
>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=34.99 E-value=23 Score=20.09 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=13.1
Q ss_pred ecccccCccCCCCCch
Q 009189 252 FCFRCSYEAHSPCSCY 267 (540)
Q Consensus 252 fC~~C~~~~H~~~~C~ 267 (540)
.|++|++.-|....|.
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 5899999999876664
No 239
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=34.79 E-value=47 Score=30.50 Aligned_cols=36 Identities=19% Similarity=0.542 Sum_probs=23.6
Q ss_pred ccccccccccCCCCceeecCC-------CCccc------HHHHHHHHHHhh
Q 009189 130 SYCCNICFDDVSLEEITTMDC-------GHYFC------NSCWTEHFIVKI 167 (540)
Q Consensus 130 ~~~C~IC~e~~~~~~~~~l~C-------gH~fC------~~Cl~~y~~~~i 167 (540)
..+||||++-- .+.+.|-| .-+.| .+||.+|-....
T Consensus 2 d~~CpICme~P--HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEHP--HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccCC--CceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 46899999863 45566544 33334 578888876544
No 240
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.70 E-value=21 Score=42.98 Aligned_cols=31 Identities=32% Similarity=0.754 Sum_probs=23.4
Q ss_pred cCCCCCCccceeecCCCCeeEe-ccCccc-----ccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSC-ICGQPF-----CWLCGAATG 326 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C-~C~~~F-----Cw~C~~~~~ 326 (540)
..+||+|+..+.. -+| .||... |-.|+....
T Consensus 667 ~rkCPkCG~~t~~------~fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTETYE------NRCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCcccc------ccCcccCCcCCCceeCccCCCccC
Confidence 3789999997653 289 499774 999988653
No 241
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=34.58 E-value=42 Score=27.09 Aligned_cols=28 Identities=25% Similarity=0.447 Sum_probs=22.0
Q ss_pred CCCCcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 149 DCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 149 ~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
-|.|.|-.-|+.+++.++ | .||. ++.++
T Consensus 53 ~CnHaFH~HCI~rWL~Tk---~-----~CPl--d~q~w 80 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTK---G-----VCPL--DRQTW 80 (88)
T ss_pred ecchHHHHHHHHHHHhhC---C-----CCCC--CCcee
Confidence 599999999999999882 2 5887 55443
No 242
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.21 E-value=26 Score=27.64 Aligned_cols=43 Identities=23% Similarity=0.595 Sum_probs=29.3
Q ss_pred ccccccccCCCCceeecCCC--CcccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 132 CCNICFDDVSLEEITTMDCG--HYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 132 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
.|..|-.+++....-.+-|. |.||.+|-..-+. | .||. |+..+
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-----g-----~CPn--CGGel 51 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLH-----G-----LCPN--CGGEL 51 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-----C-----cCCC--CCchh
Confidence 47778888876555445554 8999999875432 2 5887 77644
No 243
>PLN03086 PRLI-interacting factor K; Provisional
Probab=34.10 E-value=27 Score=38.81 Aligned_cols=30 Identities=37% Similarity=0.795 Sum_probs=24.7
Q ss_pred hccCCCCC--CccceeecCCCCeeEe-ccCccc
Q 009189 288 VHTKHCPK--CQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 288 ~~~k~CP~--C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
.+...||+ |+..+.+...=+|..| .|+..|
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 34578995 9999999999999999 588776
No 244
>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=33.97 E-value=29 Score=29.74 Aligned_cols=27 Identities=26% Similarity=0.596 Sum_probs=16.3
Q ss_pred CCCCCCccceeecCCCCeeEec-cCcccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPFC 318 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~FC 318 (540)
-.||+|+.-.-=..|= .+.|. |+++|=
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCC-eeECcccccccc
Confidence 4799998755444443 36663 666543
No 245
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.84 E-value=14 Score=39.93 Aligned_cols=28 Identities=32% Similarity=0.713 Sum_probs=17.9
Q ss_pred cCCCCCCccceeecCCCCeeEec--cCcccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSCI--CGQPFCWLCGAA 324 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C~--C~~~FCw~C~~~ 324 (540)
-..||-|-.+-. .-++ |||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 378999977554 3331 666677776543
No 246
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=33.45 E-value=9.5 Score=38.91 Aligned_cols=30 Identities=33% Similarity=0.874 Sum_probs=20.8
Q ss_pred cCCCCCCCCCeEEeccCccceeecCCCceeccccc
Q 009189 223 WCPSVPHCGNAIRIEVDELREVECACGLQFCFRCS 257 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~~~~~~v~C~C~~~fC~~C~ 257 (540)
+|| -|-..+.+.+.. .+.|+||+..|.-|-
T Consensus 16 ~cp---lcie~mditdkn--f~pc~cgy~ic~fc~ 45 (480)
T COG5175 16 YCP---LCIEPMDITDKN--FFPCPCGYQICQFCY 45 (480)
T ss_pred cCc---ccccccccccCC--cccCCcccHHHHHHH
Confidence 598 576555544433 378999999888774
No 247
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.42 E-value=9.4 Score=38.52 Aligned_cols=19 Identities=32% Similarity=0.849 Sum_probs=14.8
Q ss_pred eeecC-CCceecccccCccC
Q 009189 243 EVECA-CGLQFCFRCSYEAH 261 (540)
Q Consensus 243 ~v~C~-C~~~fC~~C~~~~H 261 (540)
...|. |...||..|..-.|
T Consensus 388 rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred ceechhhhhhhhhhhHHHHH
Confidence 46795 99999999975544
No 248
>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=33.38 E-value=4.9e+02 Score=29.97 Aligned_cols=62 Identities=11% Similarity=0.124 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccc----CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009189 449 NLFEDQQQQFEANIEKLSSFLDEKFHL----YNEDEIKDLKLRVIALSATTDNLCRNLYECIETDL 510 (540)
Q Consensus 449 ~lfe~~q~~le~~~e~L~~~le~~~~~----~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e~~l 510 (540)
.+|.++-.++...++.|...+.+.-.. +....-..+-.++...+..+.+++..++++++..+
T Consensus 272 ~vFr~l~~q~~~m~esver~~~kl~~~~~~~~~~~~~~~l~~~i~s~~~k~~~~~~~I~ka~~~sI 337 (683)
T PF08580_consen 272 IVFRNLGRQAQKMCESVERSLSKLQEAIDSGIHLDNPSKLSKQIESKEKKKSHYFPAIYKARVLSI 337 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccccccchHHHHHHHHHHHHHHhccHHHHHHHHHHHh
Confidence 356666666666666666555432111 00011123445555556555566655555554443
No 249
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.34 E-value=37 Score=34.23 Aligned_cols=36 Identities=19% Similarity=0.517 Sum_probs=25.6
Q ss_pred HHHHHHHhccCCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 281 ETVNYIAVHTKHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 281 ~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
+-..|...+ |.||+|+.+.+-..|=-.+.| .||+.+
T Consensus 103 ~l~~w~~~~-RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 103 QLLEWYRSH-RFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHHHhhC-cCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 344564444 899999998887777777788 477654
No 250
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=33.21 E-value=29 Score=34.34 Aligned_cols=9 Identities=33% Similarity=0.782 Sum_probs=4.7
Q ss_pred CCCcCCCcc
Q 009189 23 EVDFVDDDE 31 (540)
Q Consensus 23 ~~~~~~~~~ 31 (540)
|.||+++++
T Consensus 57 Dsdf~~se~ 65 (240)
T PF05764_consen 57 DSDFDDSED 65 (240)
T ss_pred ccccCcccc
Confidence 555655543
No 251
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=33.16 E-value=44 Score=30.73 Aligned_cols=49 Identities=24% Similarity=0.490 Sum_probs=34.0
Q ss_pred ccccccccccccCCCCceeecCCC--C---cccHHHHHHHHHHhhhcCCcccccccCcccccccc
Q 009189 128 SSSYCCNICFDDVSLEEITTMDCG--H---YFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICD 187 (540)
Q Consensus 128 ~~~~~C~IC~e~~~~~~~~~l~Cg--H---~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~ 187 (540)
.....|-||++.-. .. .-||. . ....+|+..|+..+ | ..+|+. |...+.
T Consensus 6 ~~~~~CRIC~~~~~-~~--~~PC~CkGs~k~VH~sCL~rWi~~s---~---~~~Cei--C~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEYD-VV--TNYCNCKNENKIVHKECLEEWINTS---K---NKSCKI--CNGPYN 59 (162)
T ss_pred CCCCeeEecCCCCC-Cc--cCCcccCCCchHHHHHHHHHHHhcC---C---CCcccc--cCCeEE
Confidence 34678999998853 22 23554 3 45899999999863 2 468998 887654
No 252
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.97 E-value=27 Score=24.21 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=17.6
Q ss_pred CCCCCccceeecCCCCeeEeccCccccccccccc
Q 009189 292 HCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAAT 325 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~ 325 (540)
.||+|+..++...- ..+.- ..|-.|++.|
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 59999998775332 11222 3356778776
No 253
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=32.77 E-value=30 Score=39.36 Aligned_cols=49 Identities=20% Similarity=0.352 Sum_probs=32.6
Q ss_pred cccccccccCCCCc-eeecCCCCcccHHHHHHHHHHhhhcCCcccccccCcccccccchh
Q 009189 131 YCCNICFDDVSLEE-ITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNAICDES 189 (540)
Q Consensus 131 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~~~~ 189 (540)
-.|++|+..+.... .....|+|.||..|+..|-... =.||. |...|..-
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~~v 173 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFGEV 173 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhhhee
Confidence 45778876653211 2234899999999999885442 27887 77766543
No 254
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=31.45 E-value=32 Score=32.60 Aligned_cols=24 Identities=33% Similarity=0.798 Sum_probs=19.5
Q ss_pred CCCCCccceeecCCCCeeEe-ccCcc
Q 009189 292 HCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 292 ~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
.||+|+.++.+ .+.|+|.| .|++.
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCPNCGNI 175 (189)
T ss_pred EccccCCceEE-CCCCEEECCCCCCE
Confidence 69999999987 44599999 58864
No 255
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=31.06 E-value=5.2e+02 Score=25.41 Aligned_cols=15 Identities=13% Similarity=0.268 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHhhhh
Q 009189 497 NLCRNLYECIETDLL 511 (540)
Q Consensus 497 ~~~~~~~~~~e~~l~ 511 (540)
..++.++++++-+.-
T Consensus 149 ek~r~vlea~~~E~~ 163 (251)
T PF11932_consen 149 EKFRRVLEAYQIEME 163 (251)
T ss_pred HHHHHHHHHHHHHHH
Confidence 346777777765553
No 256
>KOG4677 consensus Golgi integral membrane protein [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=30.83 E-value=7.2e+02 Score=26.93 Aligned_cols=56 Identities=18% Similarity=0.291 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHH-HHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHhh
Q 009189 357 LERYIHYYSRYEAHRDSSKLESK-MKETMEDNIKILEECSTASSKDFVWLFNGVDRLFRSRRVLA 420 (540)
Q Consensus 357 l~ry~~y~~r~~~h~~s~k~e~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~l~~~r~~L~ 420 (540)
++.|..|.++|..-....+.+-+ .++.++.++..++. ++.+....+.|..++..++
T Consensus 167 ~~q~~d~~e~~~~kdSQlkvrlqe~~~ll~~Rve~le~--------~Sal~~lq~~L~la~~~~~ 223 (554)
T KOG4677|consen 167 GEQYRDYSEDWSPKDSQLKVRLQEVRRLLKGRVESLER--------FSALRSLQDKLQLAEEAVS 223 (554)
T ss_pred hhhHhhHhhhcccchhhHHHHHHHHHHHHHhhhHHHHH--------HHHHHHHHHHHHHHHHHHH
Confidence 44678888888877665555432 44455555555543 2345555666666665554
No 257
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.68 E-value=22 Score=36.02 Aligned_cols=28 Identities=21% Similarity=0.691 Sum_probs=23.0
Q ss_pred cCCCCCCccceeecCCCCeeEec---cCcccccccccc
Q 009189 290 TKHCPKCQKLVEKNGGCNLVSCI---CGQPFCWLCGAA 324 (540)
Q Consensus 290 ~k~CP~C~~~IeK~~GCnhm~C~---C~~~FCw~C~~~ 324 (540)
...|-+|..+|- ++=| |++-||+.|-..
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 467999999998 6664 888999988764
No 258
>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=30.08 E-value=34 Score=25.25 Aligned_cols=16 Identities=25% Similarity=0.677 Sum_probs=8.6
Q ss_pred CCCCcccHHHHHHHHHH
Q 009189 149 DCGHYFCNSCWTEHFIV 165 (540)
Q Consensus 149 ~CgH~fC~~Cl~~y~~~ 165 (540)
.|++.||.+| .-|+..
T Consensus 26 ~C~~~FC~dC-D~fiHE 41 (51)
T PF07975_consen 26 KCKNHFCIDC-DVFIHE 41 (51)
T ss_dssp TTT--B-HHH-HHTTTT
T ss_pred CCCCccccCc-Chhhhc
Confidence 6899999999 334333
No 259
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.99 E-value=27 Score=35.88 Aligned_cols=46 Identities=22% Similarity=0.554 Sum_probs=31.3
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHHhhhcCCcccccccCccccc
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIVKINEGQSRRITCMEHKCNA 184 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~ 184 (540)
+...|.||-..+ +-...+||+|..|.-|--..- ++-. .-.||. |+.
T Consensus 60 en~~C~ICA~~~--TYs~~~PC~H~~CH~Ca~RlR--ALY~----~K~C~~--CrT 105 (493)
T COG5236 60 ENMNCQICAGST--TYSARYPCGHQICHACAVRLR--ALYM----QKGCPL--CRT 105 (493)
T ss_pred ccceeEEecCCc--eEEEeccCCchHHHHHHHHHH--HHHh----ccCCCc--ccc
Confidence 467899998876 344557999999999965532 2211 236887 765
No 260
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.63 E-value=36 Score=27.32 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=21.4
Q ss_pred CCCCCCccceeecCCCCeeEeccC--ccccccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCICG--QPFCWLCGAAT 325 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~C~--~~FCw~C~~~~ 325 (540)
..||.|++.+. |.=+=+ ...|..|++.|
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEe
Confidence 57999999887 665533 45689999988
No 261
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. 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. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=29.46 E-value=5.1e+02 Score=24.78 Aligned_cols=97 Identities=11% Similarity=0.227 Sum_probs=53.9
Q ss_pred CCcchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Q 009189 397 ASSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSSFLDEKFHLY 476 (540)
Q Consensus 397 ~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~~le~~~~~~ 476 (540)
.+++++.....+++.+++.|....+.|. ++.+.-..+.+.++..-+......+...+.+.+++..+
T Consensus 98 e~LkEy~~ya~slk~vlk~r~~~q~~~e--------------~~~~~L~~k~~~l~~~ve~a~~~~e~f~~~~~~E~~rF 163 (201)
T cd07622 98 DQLKEYLFFADSLRAVCKKHELLQYDLE--------------KAEDALANKKQQGEEAVKEAKDELNEFVKKALEDVERF 163 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467777788888888887777775554 11111112222222222222222333333444555555
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 477 NEDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 477 ~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
...+..++|.-+.+++..=-.++++++..-+
T Consensus 164 ~~~K~~dlk~~l~~~A~~qi~~~~~~~~~W~ 194 (201)
T cd07622 164 KKQKVRDLKEILISYAKLQIKLAKKGLQTWT 194 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566677787777777776677777766554
No 262
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=28.78 E-value=57 Score=27.43 Aligned_cols=27 Identities=33% Similarity=0.858 Sum_probs=17.0
Q ss_pred ccCCCCCCCCCeEEeccCcc-ceeecC-CCce
Q 009189 222 KWCPSVPHCGNAIRIEVDEL-REVECA-CGLQ 251 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~~~~-~~v~C~-C~~~ 251 (540)
..|| .|++.+.++.... ..+.|. |++.
T Consensus 2 ~FCP---~Cgn~Live~g~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP---TCGNMLIVESGESCNRFSCRTCPYV 30 (105)
T ss_pred cccC---CCCCEEEEecCCeEeeEEcCCCCce
Confidence 3688 6999988776443 345553 5544
No 263
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=28.71 E-value=36 Score=32.15 Aligned_cols=24 Identities=29% Similarity=0.850 Sum_probs=17.6
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~ 316 (540)
-.|++|+.++++ .=+.|+| +||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 369999999888 3366788 57754
No 264
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=28.71 E-value=1.4e+02 Score=26.11 Aligned_cols=36 Identities=25% Similarity=0.263 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHH
Q 009189 65 MEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLAVL 100 (540)
Q Consensus 65 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~~~ 100 (540)
.++|.-|++..|++...|+..|...+||.-..+-.+
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 567889999999999999999999999976655443
No 265
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.68 E-value=42 Score=23.90 Aligned_cols=10 Identities=20% Similarity=0.667 Sum_probs=5.0
Q ss_pred CCCCCCccce
Q 009189 291 KHCPKCQKLV 300 (540)
Q Consensus 291 k~CP~C~~~I 300 (540)
-+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 3555555444
No 266
>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=28.66 E-value=41 Score=33.13 Aligned_cols=35 Identities=26% Similarity=0.615 Sum_probs=0.0
Q ss_pred HHHHHHhccCCCCCCccc-eee---cCCCCeeEe-ccCccc
Q 009189 282 TVNYIAVHTKHCPKCQKL-VEK---NGGCNLVSC-ICGQPF 317 (540)
Q Consensus 282 ~~~~i~~~~k~CP~C~~~-IeK---~~GCnhm~C-~C~~~F 317 (540)
+..|+..|. .||+|+.. +.+ |.-=--.+| .|+.+|
T Consensus 24 tE~Wv~~n~-yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 24 TEDWVAENM-YCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp HHHHHHHH----TTT--SS-EE--------EEE-TTT--EE
T ss_pred HHHHHHHCC-cCCCCCChhHhhccCCCccceeECCCCchHH
No 267
>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=28.65 E-value=19 Score=41.62 Aligned_cols=6 Identities=17% Similarity=0.473 Sum_probs=0.0
Q ss_pred CCCHHH
Q 009189 76 SLKEQH 81 (540)
Q Consensus 76 ~i~~~~ 81 (540)
|++.+.
T Consensus 721 Gi~eer 726 (787)
T PF03115_consen 721 GIPEER 726 (787)
T ss_dssp ------
T ss_pred CCCHHH
Confidence 444443
No 268
>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=28.62 E-value=78 Score=23.92 Aligned_cols=32 Identities=13% Similarity=0.285 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHH
Q 009189 67 DLIRVMDLLSLKEQHARTLLIHYRWDVEKVLA 98 (540)
Q Consensus 67 ~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~ 98 (540)
.+.+|++.||++......-...++|+...-++
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~~ 46 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLPIE 46 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCchh
Confidence 47899999999999999999999999654443
No 269
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=28.58 E-value=76 Score=29.21 Aligned_cols=33 Identities=21% Similarity=0.387 Sum_probs=20.2
Q ss_pred hcCCccccCCCCCCCCCeEEeccCccceeecC-CCce
Q 009189 216 EDNKRVKWCPSVPHCGNAIRIEVDELREVECA-CGLQ 251 (540)
Q Consensus 216 ~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 251 (540)
+.++.+..|| .|+.-+.....-...+.|| ||..
T Consensus 104 e~~~~~Y~Cp---~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICP---NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECC---CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 3455677898 4876555544333457776 7765
No 270
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=28.56 E-value=66 Score=30.95 Aligned_cols=15 Identities=33% Similarity=0.886 Sum_probs=12.1
Q ss_pred ccCCCCCCCCCeEEec
Q 009189 222 KWCPSVPHCGNAIRIE 237 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~ 237 (540)
+.|| .|+|..+|...
T Consensus 139 IACP-RpnCkRiInL~ 153 (275)
T KOG4684|consen 139 IACP-RPNCKRIINLD 153 (275)
T ss_pred eccC-CCCcceeeecC
Confidence 4799 59999988754
No 271
>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=28.12 E-value=5.7e+02 Score=24.92 Aligned_cols=57 Identities=12% Similarity=0.178 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 451 FEDQQQQFEANIEKLSSFLDEKFHLYNEDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 451 fe~~q~~le~~~e~L~~~le~~~~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
-|..|.+.+..-|++|+.+..++..+....+..+|.-++.+..+--.+-+.-+..+.
T Consensus 155 aE~~~~~a~~~Fe~IS~~aK~El~rF~~~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~~ 211 (218)
T cd07662 155 AETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQLLQ 211 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888888999999999999888877777888888888877766666666555554
No 272
>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=28.06 E-value=1.4e+02 Score=26.08 Aligned_cols=34 Identities=21% Similarity=0.260 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHH
Q 009189 65 MEDLIRVMDLLSLKEQHARTLLIHYRWDVEKVLA 98 (540)
Q Consensus 65 ~~~i~~v~~~l~i~~~~a~~LL~~~~W~~~~l~~ 98 (540)
.++|.-|++..|++...|+..|...+||.-..+-
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 5678899999999999999999999999765543
No 273
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=27.94 E-value=6.7e+02 Score=25.65 Aligned_cols=31 Identities=23% Similarity=0.296 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhHHHHH
Q 009189 348 KETESAKRSLERYIHYYSRYEAHRDSSKLES 378 (540)
Q Consensus 348 ~~~~~~~~~l~ry~~y~~r~~~h~~s~k~e~ 378 (540)
.+..++-..|++|.+-++|-.+....+.++.
T Consensus 151 ~ranQAi~TLEkYk~~Ld~~~~~L~~lEled 181 (349)
T COG1623 151 SRANQAIQTLEKYKTVLDRVLNQLNLLELED 181 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhHHHhh
Confidence 5677888899999999998777766666553
No 274
>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=27.59 E-value=38 Score=24.94 Aligned_cols=34 Identities=24% Similarity=0.583 Sum_probs=23.2
Q ss_pred cccccccccCCCCce--eecCCCCcccHHHHHHHHH
Q 009189 131 YCCNICFDDVSLEEI--TTMDCGHYFCNSCWTEHFI 164 (540)
Q Consensus 131 ~~C~IC~e~~~~~~~--~~l~CgH~fC~~Cl~~y~~ 164 (540)
..|.+|-..|..... .--.||+.||.+|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 358888777643211 1127999999999987644
No 275
>PF14353 CpXC: CpXC protein
Probab=27.56 E-value=16 Score=32.14 Aligned_cols=50 Identities=26% Similarity=0.494 Sum_probs=29.1
Q ss_pred ccccCcccccccchhHHHHhhccCChhHHHHHHHHHHHHhhhcCCccccCCCCCCCCCeEEec
Q 009189 175 ITCMEHKCNAICDESKIRCLVRARDSDLADKFDRFMLESYIEDNKRVKWCPSVPHCGNAIRIE 237 (540)
Q Consensus 175 i~CP~~~C~~~~~~~~i~~ll~~~~~e~~eky~~~~~~~~v~~~~~~~~CP~~p~C~~~i~~~ 237 (540)
|+||. |+..+.-.....+-...+|++.++.. ...-....|| .||..+.+.
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~il--------~g~l~~~~CP---~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEKIL--------DGSLFSFTCP---SCGHKFRLE 51 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHHHH--------cCCcCEEECC---CCCCceecC
Confidence 78998 88877655444443333455555322 2333445788 688876543
No 276
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.34 E-value=34 Score=30.47 Aligned_cols=34 Identities=32% Similarity=0.760 Sum_probs=20.9
Q ss_pred CCCCCCcccee-ecCCCCeeEec--cCcccccccccc
Q 009189 291 KHCPKCQKLVE-KNGGCNLVSCI--CGQPFCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~Ie-K~~GCnhm~C~--C~~~FCw~C~~~ 324 (540)
--||.|+...- -.-+|.+++|. =+...|..|+..
T Consensus 78 PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred CCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCe
Confidence 67999998743 23356666662 445556666654
No 277
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=27.04 E-value=32 Score=23.26 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=15.7
Q ss_pred ccHHHHHHHHHHhhhcCCcccccccCccccccc
Q 009189 154 FCNSCWTEHFIVKINEGQSRRITCMEHKCNAIC 186 (540)
Q Consensus 154 fC~~Cl~~y~~~~i~~g~~~~i~CP~~~C~~~~ 186 (540)
.|.+|+++|....-.-=....+.|+. |+-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCE
Confidence 48999999865432111224789988 76543
No 278
>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=27.01 E-value=57 Score=24.84 Aligned_cols=27 Identities=33% Similarity=0.700 Sum_probs=18.5
Q ss_pred CCCCCCccc----eeecCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKL----VEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~----IeK~~GCnhm~C-~C~~~F 317 (540)
-.||+|+.+ +-+..|=.++-| .||+.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 369999863 334556678889 588753
No 279
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.01 E-value=36 Score=25.63 Aligned_cols=29 Identities=34% Similarity=0.799 Sum_probs=20.8
Q ss_pred ccCCCCCCccceeecCCCCeeEeccCccccccccccccCCCC
Q 009189 289 HTKHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAATGSDHT 330 (540)
Q Consensus 289 ~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~H~ 330 (540)
..+.||+|+..--| ..|-.||++....|+
T Consensus 4 ~mr~C~~CgvYTLk-------------~~CP~CG~~t~~~~P 32 (56)
T PRK13130 4 KIRKCPKCGVYTLK-------------EICPVCGGKTKNPHP 32 (56)
T ss_pred cceECCCCCCEEcc-------------ccCcCCCCCCCCCCC
Confidence 45889999886653 457788888766664
No 280
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.00 E-value=23 Score=32.48 Aligned_cols=27 Identities=22% Similarity=0.567 Sum_probs=19.5
Q ss_pred cccccccccccCCCCc-eeecCCCCccc
Q 009189 129 SSYCCNICFDDVSLEE-ITTMDCGHYFC 155 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~-~~~l~CgH~fC 155 (540)
..-+|.||++++...+ +..|||-..|.
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEee
Confidence 5678999999986544 56788876553
No 281
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=26.84 E-value=44 Score=38.00 Aligned_cols=37 Identities=30% Similarity=0.455 Sum_probs=28.8
Q ss_pred cccccccccccCCCCceeecCCCCcccHHHHHHHHHH
Q 009189 129 SSYCCNICFDDVSLEEITTMDCGHYFCNSCWTEHFIV 165 (540)
Q Consensus 129 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~y~~~ 165 (540)
..+.|.||.-.+...-.+-..|||.-..+|...||..
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc
Confidence 3466888876665555556689999999999999986
No 282
>PRK10220 hypothetical protein; Provisional
Probab=26.37 E-value=48 Score=28.42 Aligned_cols=26 Identities=27% Similarity=0.749 Sum_probs=15.1
Q ss_pred CCCCCCccceeecCCCCeeEec-cCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~F 317 (540)
-.||+|..-.-=..|= .+.|. |+++|
T Consensus 4 P~CP~C~seytY~d~~-~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECCcccCcC
Confidence 5799998755433332 35563 55554
No 283
>PLN02189 cellulose synthase
Probab=26.31 E-value=43 Score=39.76 Aligned_cols=56 Identities=30% Similarity=0.673 Sum_probs=37.8
Q ss_pred CCCCeEEeccCccceeecC-CCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCC
Q 009189 229 HCGNAIRIEVDELREVECA-CGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCN 307 (540)
Q Consensus 229 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 307 (540)
-|+--+.....+..-|.|. |+...|..|-+ +.. +...+.||.|+.+..+-.|++
T Consensus 39 iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye----------yer---------------~eg~q~CpqCkt~Y~r~kgs~ 93 (1040)
T PLN02189 39 ICGDEIGLTVDGDLFVACNECGFPVCRPCYE----------YER---------------REGTQNCPQCKTRYKRLKGSP 93 (1040)
T ss_pred ccccccCcCCCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCchhhccCCC
Confidence 5777666555555669996 99999998862 100 112378999998888666665
Q ss_pred ee
Q 009189 308 LV 309 (540)
Q Consensus 308 hm 309 (540)
.+
T Consensus 94 ~v 95 (1040)
T PLN02189 94 RV 95 (1040)
T ss_pred Cc
Confidence 54
No 284
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=26.19 E-value=87 Score=35.62 Aligned_cols=19 Identities=0% Similarity=0.263 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHHHhhhcC
Q 009189 200 SDLADKFDRFMLESYIEDN 218 (540)
Q Consensus 200 ~e~~eky~~~~~~~~v~~~ 218 (540)
....++|+.+.++.+.+..
T Consensus 1091 ~a~kq~ye~La~~iFsk~~ 1109 (1189)
T KOG2041|consen 1091 DAEKQEYENLAFRIFSKNP 1109 (1189)
T ss_pred HHHHHHHHHHHHHHhccCC
Confidence 5678889988888765433
No 285
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=25.70 E-value=32 Score=40.17 Aligned_cols=24 Identities=50% Similarity=1.284 Sum_probs=19.1
Q ss_pred CCCCCCcc-ceeecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQK-LVEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~-~IeK~~GCnhm~C-~C~~~ 316 (540)
-.||-|+. .|+..|||| +| .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 47999975 788999996 78 47654
No 286
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=25.24 E-value=5.7e+02 Score=23.95 Aligned_cols=61 Identities=13% Similarity=0.138 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 446 MKQNLFEDQQQQFEANIEKLSSFLDEKFHLYNEDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 446 ~~~~lfe~~q~~le~~~e~L~~~le~~~~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
...++++.+...++..+++|...++..-...-.-.+..-|+++.++..-...+-..+-+ +|
T Consensus 85 ~R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr~e~ee~~~~l~~le~~~~~-~e 145 (175)
T PRK13182 85 VDFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEEMLERLQKLEARLKK-LE 145 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhHHHHHHHHHHHHHHHHHHHH-HH
Confidence 34678888888888888888888775422111122455677777776665555555544 44
No 287
>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=25.01 E-value=61 Score=25.69 Aligned_cols=26 Identities=38% Similarity=0.951 Sum_probs=18.2
Q ss_pred CCCCCCccc----eeecCCCCeeEe-ccCcc
Q 009189 291 KHCPKCQKL----VEKNGGCNLVSC-ICGQP 316 (540)
Q Consensus 291 k~CP~C~~~----IeK~~GCnhm~C-~C~~~ 316 (540)
-.||+|+.. +-+..|=.++.| .|||.
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 234566778899 58875
No 288
>PRK02935 hypothetical protein; Provisional
Probab=24.68 E-value=27 Score=29.73 Aligned_cols=16 Identities=31% Similarity=0.899 Sum_probs=11.1
Q ss_pred CCCCCCcccee---ecCCC
Q 009189 291 KHCPKCQKLVE---KNGGC 306 (540)
Q Consensus 291 k~CP~C~~~Ie---K~~GC 306 (540)
-.||+|+++.. |.+.|
T Consensus 71 V~CP~C~K~TKmLGrvD~C 89 (110)
T PRK02935 71 VICPSCEKPTKMLGRVDAC 89 (110)
T ss_pred eECCCCCchhhhccceeec
Confidence 47999998764 44444
No 289
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=24.53 E-value=1e+03 Score=26.63 Aligned_cols=43 Identities=12% Similarity=0.322 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhHHHH-HHHHHHHHHHHHHHHH
Q 009189 351 ESAKRSLERYIHYYSRYEAHRDSSKLE-SKMKETMEDNIKILEE 393 (540)
Q Consensus 351 ~~~~~~l~ry~~y~~r~~~h~~s~k~e-~~~~~~~~~~~~~~~~ 393 (540)
...+..+.+|..|...+..+...+... ..++..++++..+++.
T Consensus 269 ~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Eie~kEeE~e~ 312 (581)
T KOG0995|consen 269 ARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEIEEKEEEIEK 312 (581)
T ss_pred HHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334556677888888777776555433 2355566666555543
No 291
>KOG2417 consensus Predicted G-protein coupled receptor [Signal transduction mechanisms]
Probab=24.52 E-value=7.4e+02 Score=26.06 Aligned_cols=15 Identities=7% Similarity=-0.144 Sum_probs=8.8
Q ss_pred chhhhHHHHHHHHHH
Q 009189 400 KDFVWLFNGVDRLFR 414 (540)
Q Consensus 400 ~~~~~l~~a~~~l~~ 414 (540)
++-+|++.-+..+.+
T Consensus 226 k~pSff~r~w~~~~~ 240 (462)
T KOG2417|consen 226 KEPSFFRRFWGMFSS 240 (462)
T ss_pred cCCcHHHHHHHHHHH
Confidence 345666666666544
No 292
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=24.49 E-value=1e+03 Score=27.20 Aligned_cols=58 Identities=10% Similarity=0.292 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccc
Q 009189 455 QQQFEANIEKLSSFLDEKFHLYNEDEIKDLKLRVIALSATTDNLCRNLYECIETDLLGSLKH 516 (540)
Q Consensus 455 q~~le~~~e~L~~~le~~~~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~ 516 (540)
...+...++++..-|+.. ......+++.++.+|..+.+.....++..-..|+++....
T Consensus 569 ~~~l~~~l~~~~~wL~~~----~~~~~~~~~~kl~eL~~~~~pi~~r~~~~~~~~~~~~~~~ 626 (653)
T PTZ00009 569 KATIEKAIDEALEWLEKN----QLAEKEEFEHKQKEVESVCNPIMTKMYQAAGGGMPGGMPG 626 (653)
T ss_pred HHHHHHHHHHHHHHHhcC----CchhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCC
Confidence 344555555555555521 1234667888888998888888777765544455443333
No 293
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.45 E-value=92 Score=29.32 Aligned_cols=33 Identities=24% Similarity=0.587 Sum_probs=19.0
Q ss_pred hcCCccccCCCCCCCCCeEEeccCccceeecC-CCce
Q 009189 216 EDNKRVKWCPSVPHCGNAIRIEVDELREVECA-CGLQ 251 (540)
Q Consensus 216 ~~~~~~~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~ 251 (540)
+.++.+..|| .|+.-+.....-...+.|+ ||..
T Consensus 112 e~~~~~Y~Cp---~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 112 EENNMFFFCP---NCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred ccCCCEEECC---CCCcEEeHHHHhhcCCcCCCCCCC
Confidence 3455677898 4887665544333346664 5544
No 294
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=24.38 E-value=6.4e+02 Score=26.91 Aligned_cols=89 Identities=24% Similarity=0.264 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHH-HHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHhhhhcceeeeccc
Q 009189 353 AKRSLERYIHYYSRYEAHRDSSKLESK-MKETMEDNIKILEECSTASSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFD 431 (540)
Q Consensus 353 ~~~~l~ry~~y~~r~~~h~~s~k~e~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~ 431 (540)
+|.++-....--.|++.|.+.++-+-. +.+.++.+-++.++ |..-..+|.++=+++..|
T Consensus 123 AKDSItSlKekt~~vnQHVq~LQseCsvlsEnLErrrQEaeE-----------LEgyCsqLk~nCrkVt~S--------- 182 (558)
T PF15358_consen 123 AKDSITSLKEKTSRVNQHVQTLQSECSVLSENLERRRQEAEE-----------LEGYCSQLKENCRKVTRS--------- 182 (558)
T ss_pred cccchhhHHHhhHHHHHHHHHHHHHhHHHHHHHHhhhhHHHH-----------HHHHHHHHHHHHHHHhhh---------
Confidence 344444444455678888888888754 55555555554444 566666665543333222
Q ss_pred CcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 432 GDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSSFLD 470 (540)
Q Consensus 432 ~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~~le 470 (540)
.+..+.+.+.++.+-.-||..+--|...|.
T Consensus 183 ---------VedaEiKtnvLkqnS~~LEekLr~lq~qLq 212 (558)
T PF15358_consen 183 ---------VEDAEIKTNVLKQNSALLEEKLRYLQQQLQ 212 (558)
T ss_pred ---------HHHHHHHhcccccchHHHHHHHHHHHHHhc
Confidence 223345667777776666666655555544
No 295
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.08 E-value=2.2e+02 Score=26.20 Aligned_cols=11 Identities=27% Similarity=0.993 Sum_probs=9.8
Q ss_pred CCCCCCcccee
Q 009189 291 KHCPKCQKLVE 301 (540)
Q Consensus 291 k~CP~C~~~Ie 301 (540)
..||+|+.+|.
T Consensus 40 ~~Cp~C~~~Ir 50 (158)
T PF10083_consen 40 TSCPNCSTPIR 50 (158)
T ss_pred HHCcCCCCCCC
Confidence 68999999997
No 296
>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=23.96 E-value=65 Score=22.58 Aligned_cols=25 Identities=28% Similarity=0.768 Sum_probs=13.7
Q ss_pred CCCCCeEEeccCccceeecC-CCceecccccC
Q 009189 228 PHCGNAIRIEVDELREVECA-CGLQFCFRCSY 258 (540)
Q Consensus 228 p~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~ 258 (540)
++|+.... ..+.|. |+..||..++.
T Consensus 4 ~~C~~~~~------~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 4 PGCKKKDF------LPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp TTT--BCT------SHEE-TTTS-EE-TTTHS
T ss_pred CcCcCccC------CCeECCCCCcccCccccC
Confidence 56765432 348897 99999999763
No 297
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=23.65 E-value=80 Score=24.60 Aligned_cols=31 Identities=29% Similarity=0.590 Sum_probs=22.2
Q ss_pred ccCCCCCCCCCeEEeccCccceeecC-CCceeccc
Q 009189 222 KWCPSVPHCGNAIRIEVDELREVECA-CGLQFCFR 255 (540)
Q Consensus 222 ~~CP~~p~C~~~i~~~~~~~~~v~C~-C~~~fC~~ 255 (540)
..|| +|++.-.+=+.....|.|. ||...+.-
T Consensus 20 VkCp---dC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 20 VKCP---DCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EECC---CCCCEEEEeccCceEEEecccccEEEec
Confidence 4688 7998765555556678995 99887654
No 298
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.44 E-value=47 Score=39.63 Aligned_cols=56 Identities=23% Similarity=0.620 Sum_probs=36.7
Q ss_pred CCCCeEEeccCccceeecC-CCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCC
Q 009189 229 HCGNAIRIEVDELREVECA-CGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCN 307 (540)
Q Consensus 229 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 307 (540)
-||--|....++..-|.|. |+...|..|-+ +.+ +...+-||.|+.+..+-.||.
T Consensus 22 ICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE----------YEr---------------~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 22 ICGDNVGKTVDGEPFVACDVCAFPVCRPCYE----------YER---------------KDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred ecccccCcCCCCCEEEEeccCCCccccchhh----------hhh---------------hcCCccCCccCCchhhhcCCC
Confidence 4666666555555669996 99999998862 110 112378888888877655655
Q ss_pred ee
Q 009189 308 LV 309 (540)
Q Consensus 308 hm 309 (540)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 44
No 299
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.39 E-value=53 Score=32.78 Aligned_cols=30 Identities=13% Similarity=0.381 Sum_probs=22.0
Q ss_pred hccCCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 288 VHTKHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 288 ~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
.+.+.||.|+.++....|=..+.| .|+...
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCEE
Confidence 346899999999876555567888 588543
No 300
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.17 E-value=40 Score=29.09 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=9.9
Q ss_pred CCCceecccccC
Q 009189 247 ACGLQFCFRCSY 258 (540)
Q Consensus 247 ~C~~~fC~~C~~ 258 (540)
+|+..+|..|+.
T Consensus 57 SCk~R~CP~C~~ 68 (111)
T PF14319_consen 57 SCKNRHCPSCQA 68 (111)
T ss_pred cccCcCCCCCCC
Confidence 688999999874
No 301
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.92 E-value=28 Score=29.97 Aligned_cols=12 Identities=33% Similarity=0.886 Sum_probs=8.7
Q ss_pred cCCCCCCcccee
Q 009189 290 TKHCPKCQKLVE 301 (540)
Q Consensus 290 ~k~CP~C~~~Ie 301 (540)
.-.||+|+++..
T Consensus 69 ~V~CP~C~K~TK 80 (114)
T PF11023_consen 69 QVECPNCGKQTK 80 (114)
T ss_pred eeECCCCCChHh
Confidence 357999988653
No 302
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.82 E-value=39 Score=26.05 Aligned_cols=13 Identities=46% Similarity=0.726 Sum_probs=11.3
Q ss_pred cCCCCCCccceee
Q 009189 290 TKHCPKCQKLVEK 302 (540)
Q Consensus 290 ~k~CP~C~~~IeK 302 (540)
+.+||.|++++..
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5799999999984
No 303
>cd07667 BAR_SNX30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 30. 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 SNX30 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=22.58 E-value=7.6e+02 Score=24.44 Aligned_cols=97 Identities=7% Similarity=0.209 Sum_probs=52.3
Q ss_pred CcchhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 009189 398 SSKDFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGE--REMKQNLFEDQQQQFEANIEKLSSFLDEKFHL 475 (540)
Q Consensus 398 ~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~--~~~~~~lfe~~q~~le~~~e~L~~~le~~~~~ 475 (540)
.++++....+|++.+++.|-....-|- ..++.. +..++.-++...+.++..+|...+.+.+++..
T Consensus 137 ~Lke~~~Y~~slk~vlK~RdqkQ~d~E-------------~l~E~l~~rre~~~kLe~~ie~~~~~ve~f~~~~~~E~~~ 203 (240)
T cd07667 137 VLREYILYSESMKNVLKKRDQVQAEYE-------------AKLEAVALRKEERPKVPTDVEKCQDRVECFNADLKADMER 203 (240)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777788888888888877775554 111111 01111222222222223333333333344444
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 476 YNEDEIKDLKLRVIALSATTDNLCRNLYECIE 507 (540)
Q Consensus 476 ~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e 507 (540)
+...+-.++|..+..++..-=.++.+++..-|
T Consensus 204 Fe~~K~~e~k~~l~~~Ad~~i~fy~~~~~~We 235 (240)
T cd07667 204 WQNNKRQDFRQLLMGMADKNIQYYEKCLTAWE 235 (240)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445567777777777766677777776666
No 304
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.39 E-value=66 Score=24.11 Aligned_cols=12 Identities=33% Similarity=0.589 Sum_probs=8.9
Q ss_pred cCCCCCCcccee
Q 009189 290 TKHCPKCQKLVE 301 (540)
Q Consensus 290 ~k~CP~C~~~Ie 301 (540)
.|+||-|+....
T Consensus 3 LkPCPFCG~~~~ 14 (61)
T PF14354_consen 3 LKPCPFCGSADV 14 (61)
T ss_pred CcCCCCCCCcce
Confidence 489999985443
No 305
>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=22.39 E-value=47 Score=21.98 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=4.9
Q ss_pred CCCCCCccce
Q 009189 291 KHCPKCQKLV 300 (540)
Q Consensus 291 k~CP~C~~~I 300 (540)
-+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 3566665544
No 306
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.35 E-value=22 Score=26.81 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=9.1
Q ss_pred CCCCCCccceee
Q 009189 291 KHCPKCQKLVEK 302 (540)
Q Consensus 291 k~CP~C~~~IeK 302 (540)
+.||-|+++|.-
T Consensus 9 ~HC~VCg~aIp~ 20 (64)
T COG4068 9 RHCVVCGKAIPP 20 (64)
T ss_pred ccccccCCcCCC
Confidence 678888888873
No 307
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.22 E-value=43 Score=35.19 Aligned_cols=8 Identities=63% Similarity=1.497 Sum_probs=6.1
Q ss_pred CCCCCCcc
Q 009189 291 KHCPKCQK 298 (540)
Q Consensus 291 k~CP~C~~ 298 (540)
+.||+|+.
T Consensus 2 ~fC~kcG~ 9 (465)
T COG4640 2 KFCPKCGS 9 (465)
T ss_pred Cccccccc
Confidence 67888884
No 308
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=22.10 E-value=91 Score=32.76 Aligned_cols=38 Identities=18% Similarity=0.391 Sum_probs=23.3
Q ss_pred CCCcccHHHHHHHHHHhhhcCC---cccccccCcccccccc
Q 009189 150 CGHYFCNSCWTEHFIVKINEGQ---SRRITCMEHKCNAICD 187 (540)
Q Consensus 150 CgH~fC~~Cl~~y~~~~i~~g~---~~~i~CP~~~C~~~~~ 187 (540)
|.-..|.+|+.+++.++-.+.. ...=+||-|.|++.|-
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 4456799999999987643321 1122444444998763
No 309
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.03 E-value=54 Score=41.37 Aligned_cols=27 Identities=33% Similarity=0.989 Sum_probs=22.8
Q ss_pred CCCCCCccc------eeecCCCCeeEe-ccCccccc
Q 009189 291 KHCPKCQKL------VEKNGGCNLVSC-ICGQPFCW 319 (540)
Q Consensus 291 k~CP~C~~~------IeK~~GCnhm~C-~C~~~FCw 319 (540)
..||.|+.. +...+|| .+| .||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc--~~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGC--ATCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCc--eeCCCCCCcccc
Confidence 349999998 7889999 699 59998774
No 310
>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=22.02 E-value=67 Score=19.86 Aligned_cols=7 Identities=43% Similarity=1.236 Sum_probs=4.4
Q ss_pred CCCCCCc
Q 009189 291 KHCPKCQ 297 (540)
Q Consensus 291 k~CP~C~ 297 (540)
-.||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 3677765
No 311
>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=21.76 E-value=33 Score=26.01 Aligned_cols=34 Identities=29% Similarity=0.725 Sum_probs=26.0
Q ss_pred CCCCCCccceee--cCCCCeeEe-ccCcccccccccc
Q 009189 291 KHCPKCQKLVEK--NGGCNLVSC-ICGQPFCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK--~~GCnhm~C-~C~~~FCw~C~~~ 324 (540)
..||-|+...-- .+-=|+=+| .|+...|-+||=.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 579999886621 244588999 4999999999854
No 312
>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=21.70 E-value=7.6e+02 Score=24.08 Aligned_cols=60 Identities=12% Similarity=0.168 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009189 451 FEDQQQQFEANIEKLSSFLDEKFHLYNEDEIKDLKLRVIALSATTDNLCRNLYECIETDL 510 (540)
Q Consensus 451 fe~~q~~le~~~e~L~~~le~~~~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~~~~e~~l 510 (540)
-|..|.+.+..-|.++..+..++..+....+.++|.-++.++..--.+-+..+..+.+-+
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 555778888999999999999998888888999999999998887777777777776443
No 313
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=21.58 E-value=83 Score=26.74 Aligned_cols=23 Identities=22% Similarity=0.466 Sum_probs=20.0
Q ss_pred CCCCcccHHHHHHHHHHhhhcCCcccccccC
Q 009189 149 DCGHYFCNSCWTEHFIVKINEGQSRRITCME 179 (540)
Q Consensus 149 ~CgH~fC~~Cl~~y~~~~i~~g~~~~i~CP~ 179 (540)
.|.|.|..-|+..++.+. -.||.
T Consensus 80 ~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc--------CcCCC
Confidence 699999999999999873 37887
No 314
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=21.30 E-value=8.5e+02 Score=24.54 Aligned_cols=52 Identities=19% Similarity=0.378 Sum_probs=30.7
Q ss_pred hhhhHHHHHHHHHHHHHHhhhhcceeeecccCcchhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 009189 401 DFVWLFNGVDRLFRSRRVLAYSYPFAYYMFDGDLFADEMTKGEREMKQNLFEDQQQQFEANIEKLSS 467 (540)
Q Consensus 401 ~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~~~~~~~~~~~lfe~~q~~le~~~e~L~~ 467 (540)
++.||+..+..+.+.+....- -++...+++.....++....+++...|+|.+
T Consensus 167 kV~WLR~~L~Ei~Ea~e~~~~---------------~~~~e~eke~~~r~l~~~~~ELe~~~EeL~~ 218 (269)
T PF05278_consen 167 KVDWLRSKLEEILEAKEIYDQ---------------HETREEEKEEKDRKLELKKEELEELEEELKQ 218 (269)
T ss_pred chHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 788999999999888665430 0122233334444555556666665555543
No 315
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.27 E-value=47 Score=33.47 Aligned_cols=29 Identities=34% Similarity=0.801 Sum_probs=20.5
Q ss_pred CCCCCCccceeecCCCCeeEec-cCcccccccccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSCI-CGQPFCWLCGAA 324 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C~-C~~~FCw~C~~~ 324 (540)
-.||-|+.++. |-|.=. |++.||--|.+.
T Consensus 275 LkCplc~~Llr-----np~kT~cC~~~fc~eci~~ 304 (427)
T COG5222 275 LKCPLCHCLLR-----NPMKTPCCGHTFCDECIGT 304 (427)
T ss_pred ccCcchhhhhh-----CcccCccccchHHHHHHhh
Confidence 57999998776 112222 888899889874
No 316
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.26 E-value=1.3e+02 Score=27.16 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=13.4
Q ss_pred HHHHHhCCCHHHHHHHHH
Q 009189 70 RVMDLLSLKEQHARTLLI 87 (540)
Q Consensus 70 ~v~~~l~i~~~~a~~LL~ 87 (540)
.+++.||++....+.+|.
T Consensus 20 dLa~~l~i~~n~vRkiL~ 37 (147)
T smart00531 20 DLAELLGIKQKQLRKILY 37 (147)
T ss_pred HHHHHhCCCHHHHHHHHH
Confidence 566778888888777764
No 317
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.19 E-value=56 Score=24.68 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=10.4
Q ss_pred ccCCCCCCcccee
Q 009189 289 HTKHCPKCQKLVE 301 (540)
Q Consensus 289 ~~k~CP~C~~~Ie 301 (540)
+.-.||.|+.+..
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 3467999999887
No 318
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=21.18 E-value=7.3e+02 Score=23.70 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=11.0
Q ss_pred hhhhHHHHHHHHHHHHHHhhhhc
Q 009189 401 DFVWLFNGVDRLFRSRRVLAYSY 423 (540)
Q Consensus 401 ~~~~l~~a~~~l~~~r~~L~~sy 423 (540)
+...|..-+..+.+-|..|.-.+
T Consensus 108 e~evL~qr~~kle~ErdeL~~kf 130 (201)
T PF13851_consen 108 EHEVLEQRFEKLEQERDELYRKF 130 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344555555555555554333
No 319
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.02 E-value=61 Score=33.24 Aligned_cols=35 Identities=17% Similarity=0.443 Sum_probs=22.6
Q ss_pred ccccccccCCCCceeec-CCCCcccHHHHHHHHHHhh
Q 009189 132 CCNICFDDVSLEEITTM-DCGHYFCNSCWTEHFIVKI 167 (540)
Q Consensus 132 ~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~y~~~~i 167 (540)
.|-.|.+.......+.. .|.+.||.+| ..++...+
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldC-Dv~iHesL 367 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDC-DVFIHESL 367 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccc-hHHHHhhh
Confidence 38888766544445555 6888888888 34444443
No 320
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.90 E-value=60 Score=28.21 Aligned_cols=9 Identities=33% Similarity=0.885 Sum_probs=6.7
Q ss_pred CCCCcccee
Q 009189 293 CPKCQKLVE 301 (540)
Q Consensus 293 CP~C~~~Ie 301 (540)
||.|+..+.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 788877665
No 321
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.78 E-value=73 Score=31.99 Aligned_cols=64 Identities=19% Similarity=0.368 Sum_probs=40.7
Q ss_pred ecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCCeeEe-ccCccccccccc
Q 009189 252 FCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCNLVSC-ICGQPFCWLCGA 323 (540)
Q Consensus 252 fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C-~C~~~FCw~C~~ 323 (540)
-|..|...+|.-+ -.. .........+..|--...+.|.-|+.|..... ||+| +|...|=-.|.+
T Consensus 281 ~C~~C~~~~HP~C--i~M---~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E---~~FCD~CDRG~HT~CVG 345 (381)
T KOG1512|consen 281 VCKPCATRPHPYC--VAM---IPELVGQYKTYFWKCSSCELCRICLGPVIESE---HLFCDVCDRGPHTLCVG 345 (381)
T ss_pred eecccccCCCCcc--hhc---CHHHHhHHhhcchhhcccHhhhccCCcccchh---eeccccccCCCCccccc
Confidence 3556666667642 211 11233445677787777788888988876554 7999 788777777754
No 322
>PLN02436 cellulose synthase A
Probab=20.71 E-value=64 Score=38.47 Aligned_cols=56 Identities=27% Similarity=0.597 Sum_probs=35.9
Q ss_pred CCCCeEEeccCccceeecC-CCceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCC
Q 009189 229 HCGNAIRIEVDELREVECA-CGLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCN 307 (540)
Q Consensus 229 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 307 (540)
-|+--|....++..-|.|. |+...|..|-+- .. +...+.||.|+.+..+-.|++
T Consensus 41 ICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey----------er---------------~eg~~~Cpqckt~Y~r~kgs~ 95 (1094)
T PLN02436 41 ICGDEIELTVDGEPFVACNECAFPVCRPCYEY----------ER---------------REGNQACPQCKTRYKRIKGSP 95 (1094)
T ss_pred ccccccCcCCCCCEEEeeccCCCccccchhhh----------hh---------------hcCCccCcccCCchhhccCCC
Confidence 4666555444555569996 999999988621 00 112378888888877655655
Q ss_pred ee
Q 009189 308 LV 309 (540)
Q Consensus 308 hm 309 (540)
.+
T Consensus 96 ~~ 97 (1094)
T PLN02436 96 RV 97 (1094)
T ss_pred Cc
Confidence 44
No 323
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=20.53 E-value=50 Score=37.46 Aligned_cols=20 Identities=30% Similarity=0.768 Sum_probs=13.8
Q ss_pred CCCCCccceeecCC-CCeeEe
Q 009189 292 HCPKCQKLVEKNGG-CNLVSC 311 (540)
Q Consensus 292 ~CP~C~~~IeK~~G-Cnhm~C 311 (540)
-||+|++..-..|. =.||+=
T Consensus 311 eCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 311 ECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred CCcccccccccCCcccccccc
Confidence 58888888876553 346665
No 324
>PHA02325 hypothetical protein
Probab=20.45 E-value=46 Score=25.61 Aligned_cols=11 Identities=55% Similarity=1.032 Sum_probs=7.2
Q ss_pred ccCCCCCCccc
Q 009189 289 HTKHCPKCQKL 299 (540)
Q Consensus 289 ~~k~CP~C~~~ 299 (540)
++|.||+|+..
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 35778877653
No 325
>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=20.34 E-value=63 Score=29.68 Aligned_cols=26 Identities=31% Similarity=0.790 Sum_probs=18.1
Q ss_pred CCCCCCccceeecCCCCeeEe-ccCccc
Q 009189 291 KHCPKCQKLVEKNGGCNLVSC-ICGQPF 317 (540)
Q Consensus 291 k~CP~C~~~IeK~~GCnhm~C-~C~~~F 317 (540)
..||.|++.+..++. ..+.| +|+..+
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcccEeCCC-CcEECCCCCCcC
Confidence 689999998887653 34777 466553
No 326
>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=20.33 E-value=1.1e+02 Score=22.79 Aligned_cols=27 Identities=37% Similarity=0.829 Sum_probs=19.1
Q ss_pred cCCCCCCCCCeEEecc-CccceeecC-CCcee
Q 009189 223 WCPSVPHCGNAIRIEV-DELREVECA-CGLQF 252 (540)
Q Consensus 223 ~CP~~p~C~~~i~~~~-~~~~~v~C~-C~~~f 252 (540)
-|| .|+.-|.++. .....+.|+ ||..+
T Consensus 4 ~CP---~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP---DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC---CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 587 6999888755 223457886 88775
No 327
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.06 E-value=38 Score=32.78 Aligned_cols=81 Identities=19% Similarity=0.474 Sum_probs=47.9
Q ss_pred CceecccccCccCCCCCchhhHHHhHHhhhhhHHHHHHHhccCCCCCCccceeecCCCCeeEeccCccccccccccccCC
Q 009189 249 GLQFCFRCSYEAHSPCSCYMWDLWSKKCQDESETVNYIAVHTKHCPKCQKLVEKNGGCNLVSCICGQPFCWLCGAATGSD 328 (540)
Q Consensus 249 ~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~C~~~FCw~C~~~~~~~ 328 (540)
....|..|....|..+--..+-+|..... -.-.|.-|+.+++. |.|-.+ .|-+-|=|.|+..|...
T Consensus 20 RVNVCEhClV~nHpkCiVQSYLqWL~DsD-----------Y~pNC~LC~t~La~-gdt~RL--vCyhlfHW~ClneraA~ 85 (299)
T KOG3970|consen 20 RVNVCEHCLVANHPKCIVQSYLQWLQDSD-----------YNPNCRLCNTPLAS-GDTTRL--VCYHLFHWKCLNERAAN 85 (299)
T ss_pred hhhHHHHHHhccCchhhHHHHHHHHhhcC-----------CCCCCceeCCcccc-Ccceee--hhhhhHHHHHhhHHHhh
Confidence 34456777777787655445555543211 12468889999873 222211 28889999999887432
Q ss_pred CCcc-ccCCccCCCCc
Q 009189 329 HTWT-SIAGHSCGRYK 343 (540)
Q Consensus 329 H~~~-~~~g~~C~~~~ 343 (540)
-+-. ...||.|+.-.
T Consensus 86 lPanTAPaGyqCP~Cs 101 (299)
T KOG3970|consen 86 LPANTAPAGYQCPCCS 101 (299)
T ss_pred CCCcCCCCcccCCCCC
Confidence 2111 13678877544
Done!