Query 016213
Match_columns 393
No_of_seqs 170 out of 658
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 04:50:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0826 Predicted E3 ubiquitin 100.0 3.5E-88 7.7E-93 645.5 21.4 350 1-392 4-356 (357)
2 PF04757 Pex2_Pex12: Pex2 / Pe 100.0 2.4E-39 5.2E-44 304.9 23.3 228 20-304 1-229 (229)
3 KOG0317 Predicted E3 ubiquitin 99.5 1E-13 2.2E-18 132.5 13.6 55 335-390 238-292 (293)
4 smart00504 Ubox Modified RING 99.4 6.6E-13 1.4E-17 100.3 4.9 53 337-390 2-54 (63)
5 KOG0320 Predicted E3 ubiquitin 99.3 2.3E-12 5E-17 115.4 4.7 57 335-391 130-187 (187)
6 PLN03208 E3 ubiquitin-protein 99.3 2.5E-12 5.5E-17 117.7 5.0 56 335-391 17-88 (193)
7 KOG0823 Predicted E3 ubiquitin 99.2 5.3E-12 1.1E-16 117.6 4.0 58 333-391 44-104 (230)
8 PF13923 zf-C3HC4_2: Zinc fing 99.2 1.5E-11 3.2E-16 84.8 2.9 39 339-377 1-39 (39)
9 KOG2879 Predicted E3 ubiquitin 99.1 1.2E-09 2.7E-14 103.9 14.8 233 49-382 50-287 (298)
10 PF04564 U-box: U-box domain; 99.1 6.7E-11 1.4E-15 92.8 3.2 54 335-389 3-57 (73)
11 PF15227 zf-C3HC4_4: zinc fing 98.9 5.3E-10 1.1E-14 78.5 2.6 38 339-377 1-42 (42)
12 PF13639 zf-RING_2: Ring finge 98.9 6E-10 1.3E-14 78.6 1.8 41 337-378 1-44 (44)
13 PF13920 zf-C3HC4_3: Zinc fing 98.9 1.4E-09 2.9E-14 79.0 3.1 46 336-382 2-48 (50)
14 TIGR00599 rad18 DNA repair pro 98.9 1.8E-09 3.8E-14 109.6 5.0 54 334-388 24-77 (397)
15 KOG2164 Predicted E3 ubiquitin 98.9 1.2E-09 2.6E-14 111.8 3.6 55 336-391 186-245 (513)
16 PHA02929 N1R/p28-like protein; 98.8 2.5E-09 5.4E-14 101.7 4.2 48 335-382 173-227 (238)
17 KOG0978 E3 ubiquitin ligase in 98.8 1.6E-09 3.5E-14 115.5 2.2 56 335-391 642-698 (698)
18 cd00162 RING RING-finger (Real 98.8 5.5E-09 1.2E-13 72.2 3.7 43 338-380 1-44 (45)
19 PF00097 zf-C3HC4: Zinc finger 98.7 9.7E-09 2.1E-13 71.1 3.1 38 339-377 1-41 (41)
20 smart00184 RING Ring finger. E 98.7 1.5E-08 3.2E-13 67.6 3.5 38 339-377 1-39 (39)
21 KOG3039 Uncharacterized conser 98.6 2.6E-08 5.6E-13 93.5 3.6 56 335-390 220-278 (303)
22 COG5574 PEX10 RING-finger-cont 98.6 2.4E-08 5.2E-13 94.9 2.4 51 335-386 214-266 (271)
23 PHA02926 zinc finger-like prot 98.5 6.5E-08 1.4E-12 90.0 3.6 48 335-382 169-230 (242)
24 PF13445 zf-RING_UBOX: RING-ty 98.5 5.6E-08 1.2E-12 68.5 2.4 35 339-375 1-43 (43)
25 PF14835 zf-RING_6: zf-RING of 98.5 4.1E-08 8.9E-13 74.3 0.9 50 336-387 7-56 (65)
26 PF11789 zf-Nse: Zinc-finger o 98.4 1.7E-07 3.7E-12 70.0 2.3 44 335-378 10-55 (57)
27 TIGR00570 cdk7 CDK-activating 98.4 3.2E-07 6.9E-12 90.0 4.5 53 335-387 2-59 (309)
28 PF14634 zf-RING_5: zinc-RING 98.3 3.8E-07 8.3E-12 64.4 3.2 42 338-379 1-44 (44)
29 PF12678 zf-rbx1: RING-H2 zinc 98.3 4E-07 8.8E-12 71.4 3.4 43 336-378 19-73 (73)
30 COG5432 RAD18 RING-finger-cont 98.3 2.5E-07 5.4E-12 88.8 2.1 46 335-381 24-69 (391)
31 PF04641 Rtf2: Rtf2 RING-finge 98.1 3.5E-06 7.6E-11 81.6 4.7 57 335-392 112-171 (260)
32 KOG4172 Predicted E3 ubiquitin 98.0 8E-07 1.7E-11 64.9 -0.6 53 336-391 7-61 (62)
33 KOG0287 Postreplication repair 98.0 1.4E-06 3E-11 85.4 0.2 54 334-388 21-74 (442)
34 KOG0824 Predicted E3 ubiquitin 98.0 3E-06 6.5E-11 82.0 1.9 47 336-383 7-54 (324)
35 COG5243 HRD1 HRD ubiquitin lig 97.9 6.4E-06 1.4E-10 81.7 3.0 47 334-381 285-344 (491)
36 KOG2660 Locus-specific chromos 97.9 4.3E-06 9.3E-11 82.0 1.3 48 335-382 14-61 (331)
37 KOG0802 E3 ubiquitin ligase [P 97.9 5.5E-06 1.2E-10 88.2 2.0 46 335-381 290-340 (543)
38 KOG2177 Predicted E3 ubiquitin 97.8 6.5E-06 1.4E-10 78.0 1.6 43 335-378 12-54 (386)
39 KOG0297 TNF receptor-associate 97.8 1E-05 2.3E-10 82.7 2.4 54 334-387 19-72 (391)
40 PF12861 zf-Apc11: Anaphase-pr 97.7 2.8E-05 6E-10 62.5 3.6 48 336-383 32-83 (85)
41 KOG0311 Predicted E3 ubiquitin 97.4 1.3E-05 2.9E-10 79.2 -2.4 48 335-382 42-90 (381)
42 KOG1813 Predicted E3 ubiquitin 97.4 5.1E-05 1.1E-09 73.5 1.2 44 337-381 242-285 (313)
43 COG5222 Uncharacterized conser 97.4 9E-05 2E-09 71.8 2.6 45 336-380 274-319 (427)
44 KOG1002 Nucleotide excision re 97.4 7.2E-05 1.6E-09 77.2 2.0 49 335-384 535-588 (791)
45 COG5540 RING-finger-containing 97.4 7.7E-05 1.7E-09 72.4 1.9 45 336-381 323-371 (374)
46 KOG4628 Predicted E3 ubiquitin 97.3 0.0002 4.3E-09 71.6 4.1 44 337-381 230-277 (348)
47 COG5152 Uncharacterized conser 97.3 0.00012 2.6E-09 67.2 1.7 45 336-381 196-240 (259)
48 KOG4692 Predicted E3 ubiquitin 97.1 0.00028 6.1E-09 69.9 2.8 48 334-382 420-467 (489)
49 KOG4265 Predicted E3 ubiquitin 97.0 0.00039 8.5E-09 69.2 2.5 47 335-382 289-336 (349)
50 KOG0828 Predicted E3 ubiquitin 96.9 0.00056 1.2E-08 70.4 2.5 50 333-382 568-634 (636)
51 KOG1645 RING-finger-containing 96.8 0.00043 9.3E-09 69.8 0.7 57 334-390 2-64 (463)
52 KOG1734 Predicted RING-contain 96.7 0.0024 5.2E-08 61.4 5.2 51 335-386 223-285 (328)
53 COG5175 MOT2 Transcriptional r 96.6 0.0012 2.5E-08 65.2 2.8 51 335-387 13-69 (480)
54 COG5194 APC11 Component of SCF 96.5 0.0023 4.9E-08 50.6 3.2 47 336-382 31-81 (88)
55 KOG4159 Predicted E3 ubiquitin 96.4 0.0015 3.3E-08 66.8 2.3 47 334-381 82-128 (398)
56 PF14570 zf-RING_4: RING/Ubox 96.4 0.0024 5.2E-08 46.0 2.4 41 339-380 1-46 (48)
57 KOG1039 Predicted E3 ubiquitin 96.3 0.0021 4.6E-08 64.5 2.5 48 335-382 160-221 (344)
58 KOG0827 Predicted E3 ubiquitin 96.1 0.0029 6.2E-08 63.6 1.8 52 336-387 4-61 (465)
59 PF11793 FANCL_C: FANCL C-term 95.9 0.0022 4.8E-08 49.9 0.3 49 336-384 2-68 (70)
60 PF14447 Prok-RING_4: Prokaryo 95.8 0.0042 9.2E-08 45.8 1.2 48 336-386 7-54 (55)
61 KOG3039 Uncharacterized conser 95.8 0.0067 1.4E-07 57.7 2.7 34 335-369 42-75 (303)
62 KOG1001 Helicase-like transcri 95.7 0.0025 5.3E-08 69.5 -0.4 48 337-386 455-504 (674)
63 KOG1571 Predicted E3 ubiquitin 95.4 0.0055 1.2E-07 61.2 1.0 43 336-382 305-347 (355)
64 KOG0883 Cyclophilin type, U bo 95.3 0.011 2.4E-07 59.5 2.6 54 336-390 40-93 (518)
65 KOG2817 Predicted E3 ubiquitin 95.3 0.046 9.9E-07 55.4 6.9 97 278-390 287-393 (394)
66 KOG4275 Predicted E3 ubiquitin 95.0 0.0028 6.2E-08 61.5 -2.4 41 336-381 300-341 (350)
67 KOG0825 PHD Zn-finger protein 94.9 0.005 1.1E-07 66.6 -1.3 46 335-380 122-169 (1134)
68 KOG1493 Anaphase-promoting com 94.8 0.014 3.1E-07 45.9 1.3 48 336-383 31-82 (84)
69 KOG1785 Tyrosine kinase negati 94.8 0.012 2.7E-07 59.3 1.3 46 336-382 369-416 (563)
70 KOG0804 Cytoplasmic Zn-finger 94.7 0.016 3.4E-07 59.5 1.8 43 338-382 177-222 (493)
71 KOG2930 SCF ubiquitin ligase, 94.5 0.023 5E-07 47.2 2.0 46 336-381 46-107 (114)
72 smart00744 RINGv The RING-vari 94.4 0.047 1E-06 39.4 3.3 40 338-378 1-49 (49)
73 KOG2932 E3 ubiquitin ligase in 94.4 0.017 3.6E-07 56.7 1.2 42 337-381 91-133 (389)
74 PF10367 Vps39_2: Vacuolar sor 94.1 0.027 5.8E-07 46.4 1.7 30 336-365 78-108 (109)
75 KOG3113 Uncharacterized conser 93.3 0.084 1.8E-06 50.6 3.6 57 334-392 109-168 (293)
76 KOG3579 Predicted E3 ubiquitin 93.2 0.067 1.4E-06 52.0 2.9 40 333-372 265-307 (352)
77 KOG2979 Protein involved in DN 93.1 0.047 1E-06 52.4 1.7 45 336-380 176-222 (262)
78 KOG3002 Zn finger protein [Gen 93.0 0.067 1.4E-06 53.0 2.7 44 335-382 47-91 (299)
79 PF04216 FdhE: Protein involve 92.8 0.021 4.6E-07 56.1 -1.1 46 335-380 171-220 (290)
80 PF02891 zf-MIZ: MIZ/SP-RING z 92.7 0.12 2.5E-06 37.6 2.9 43 337-380 3-50 (50)
81 COG5219 Uncharacterized conser 92.4 0.041 8.8E-07 61.0 0.3 47 336-382 1469-1523(1525)
82 PF10571 UPF0547: Uncharacteri 92.0 0.087 1.9E-06 33.1 1.3 22 338-359 2-24 (26)
83 COG5236 Uncharacterized conser 90.3 0.18 3.8E-06 50.4 2.2 45 335-380 60-106 (493)
84 KOG0298 DEAD box-containing he 90.1 0.056 1.2E-06 61.7 -1.5 43 336-378 1153-1195(1394)
85 TIGR01562 FdhE formate dehydro 89.3 0.13 2.8E-06 51.1 0.5 46 335-380 183-233 (305)
86 PRK04023 DNA polymerase II lar 88.5 0.34 7.4E-06 54.6 3.1 55 332-389 622-681 (1121)
87 KOG1814 Predicted E3 ubiquitin 88.3 0.31 6.7E-06 49.8 2.3 46 335-380 183-238 (445)
88 KOG4367 Predicted Zn-finger pr 88.0 0.29 6.2E-06 50.3 1.9 35 335-370 3-37 (699)
89 PLN02189 cellulose synthase 87.8 0.36 7.9E-06 54.7 2.7 46 335-381 33-86 (1040)
90 PF05883 Baculo_RING: Baculovi 87.5 0.3 6.4E-06 42.7 1.5 43 336-378 26-76 (134)
91 KOG4185 Predicted E3 ubiquitin 87.3 0.34 7.3E-06 47.5 1.9 43 338-381 5-54 (296)
92 PRK03564 formate dehydrogenase 86.9 0.28 6.2E-06 48.8 1.2 46 335-380 186-235 (309)
93 PF10235 Cript: Microtubule-as 86.7 0.42 9.2E-06 39.0 1.9 36 336-381 44-79 (90)
94 PLN02436 cellulose synthase A 86.4 0.48 1E-05 53.9 2.7 46 335-381 35-88 (1094)
95 KOG1941 Acetylcholine receptor 86.4 0.28 6.1E-06 49.8 0.8 42 336-378 365-412 (518)
96 PF05290 Baculo_IE-1: Baculovi 86.1 0.63 1.4E-05 40.6 2.7 46 337-382 81-132 (140)
97 PHA03096 p28-like protein; Pro 86.0 0.42 9E-06 47.1 1.8 45 337-381 179-233 (284)
98 PF07191 zinc-ribbons_6: zinc- 84.7 0.12 2.7E-06 40.1 -2.0 40 337-382 2-41 (70)
99 KOG1812 Predicted E3 ubiquitin 82.6 0.55 1.2E-05 48.2 1.0 41 336-377 306-351 (384)
100 PLN02638 cellulose synthase A 81.1 1.1 2.4E-05 51.2 2.8 45 335-380 16-68 (1079)
101 KOG1812 Predicted E3 ubiquitin 81.0 0.62 1.3E-05 47.9 0.7 51 336-387 146-208 (384)
102 KOG3268 Predicted E3 ubiquitin 80.7 1.5 3.1E-05 40.2 2.9 48 336-384 165-230 (234)
103 KOG2034 Vacuolar sorting prote 80.5 0.8 1.7E-05 50.9 1.4 34 336-369 817-851 (911)
104 PF03854 zf-P11: P-11 zinc fin 79.9 0.97 2.1E-05 32.5 1.2 43 338-382 4-46 (50)
105 PF08746 zf-RING-like: RING-li 79.8 2 4.3E-05 30.2 2.7 39 339-377 1-43 (43)
106 cd00350 rubredoxin_like Rubred 79.6 0.94 2E-05 29.8 1.0 11 370-380 16-26 (33)
107 COG5109 Uncharacterized conser 79.1 1.2 2.6E-05 44.2 1.9 54 335-390 335-395 (396)
108 KOG0825 PHD Zn-finger protein 79.0 1.3 2.7E-05 48.8 2.3 44 335-378 95-150 (1134)
109 KOG3970 Predicted E3 ubiquitin 78.3 1.7 3.7E-05 41.2 2.7 44 338-381 52-104 (299)
110 PRK05978 hypothetical protein; 78.3 1.4 3E-05 39.3 2.0 33 336-384 33-65 (148)
111 PF14446 Prok-RING_1: Prokaryo 78.1 2.7 5.9E-05 31.1 3.1 43 335-381 4-51 (54)
112 KOG3800 Predicted E3 ubiquitin 77.6 1.5 3.2E-05 43.1 2.1 36 352-387 20-56 (300)
113 PLN02195 cellulose synthase A 77.6 2 4.4E-05 48.7 3.4 47 335-382 5-59 (977)
114 PLN02915 cellulose synthase A 76.9 1.8 3.8E-05 49.4 2.7 46 335-381 14-67 (1044)
115 COG5627 MMS21 DNA repair prote 76.4 1.4 3E-05 42.0 1.5 49 336-384 189-241 (275)
116 PF14569 zf-UDP: Zinc-binding 75.8 3.3 7.1E-05 32.9 3.2 47 335-381 8-61 (80)
117 PRK14714 DNA polymerase II lar 75.4 1.4 3E-05 51.0 1.5 48 337-385 668-723 (1337)
118 COG1592 Rubrerythrin [Energy p 74.5 1.9 4.1E-05 39.2 1.8 13 336-348 134-146 (166)
119 PLN02400 cellulose synthase 74.3 1.8 3.9E-05 49.6 1.9 45 335-380 35-87 (1085)
120 PF09538 FYDLN_acid: Protein o 72.6 2.3 4.9E-05 36.0 1.7 28 335-362 8-39 (108)
121 TIGR02300 FYDLN_acid conserved 71.6 2.4 5.1E-05 36.8 1.6 27 335-361 8-38 (129)
122 KOG1815 Predicted E3 ubiquitin 71.5 6.8 0.00015 40.9 5.4 47 335-381 69-123 (444)
123 KOG0269 WD40 repeat-containing 71.1 3.5 7.6E-05 45.3 3.1 50 336-385 779-831 (839)
124 PF12773 DZR: Double zinc ribb 71.1 1.6 3.4E-05 31.1 0.4 16 332-347 8-23 (50)
125 KOG0309 Conserved WD40 repeat- 70.9 2.5 5.5E-05 46.4 2.0 47 336-382 1028-1076(1081)
126 KOG4739 Uncharacterized protei 70.8 2.1 4.5E-05 40.9 1.2 38 337-374 4-43 (233)
127 PHA02862 5L protein; Provision 70.8 3.4 7.4E-05 36.6 2.5 47 336-382 2-53 (156)
128 PF04423 Rad50_zn_hook: Rad50 70.8 0.86 1.9E-05 33.3 -1.1 13 372-384 21-33 (54)
129 KOG2169 Zn-finger transcriptio 70.7 2.6 5.6E-05 46.1 2.1 51 336-387 306-361 (636)
130 PF09986 DUF2225: Uncharacteri 70.7 2.6 5.7E-05 39.7 1.9 56 334-389 3-66 (214)
131 COG0068 HypF Hydrogenase matur 69.9 1.8 4E-05 47.3 0.8 49 333-381 98-183 (750)
132 cd00729 rubredoxin_SM Rubredox 69.7 2.5 5.4E-05 28.1 1.1 10 372-381 19-28 (34)
133 PF06750 DiS_P_DiS: Bacterial 69.7 5.8 0.00013 32.4 3.5 38 336-383 33-70 (92)
134 KOG1940 Zn-finger protein [Gen 69.1 3 6.4E-05 41.0 1.9 44 336-380 158-205 (276)
135 KOG2042 Ubiquitin fusion degra 68.2 4.4 9.5E-05 45.9 3.2 54 335-388 869-922 (943)
136 KOG4718 Non-SMC (structural ma 68.1 2.2 4.9E-05 40.0 0.8 44 335-378 180-223 (235)
137 COG5183 SSM4 Protein involved 68.0 4 8.8E-05 45.2 2.8 54 333-386 9-70 (1175)
138 KOG2114 Vacuolar assembly/sort 67.9 2.8 6.1E-05 46.6 1.6 41 336-379 840-880 (933)
139 PF09889 DUF2116: Uncharacteri 67.6 2.9 6.3E-05 31.5 1.2 16 369-384 1-16 (59)
140 PF03833 PolC_DP2: DNA polymer 66.8 1.9 4E-05 48.1 0.0 44 336-382 655-703 (900)
141 KOG2068 MOT2 transcription fac 66.5 7.1 0.00015 39.1 4.0 44 337-381 250-297 (327)
142 TIGR00622 ssl1 transcription f 65.7 9 0.0002 32.6 3.9 43 336-378 55-110 (112)
143 COG1645 Uncharacterized Zn-fin 64.0 2.4 5.1E-05 37.1 0.1 24 336-364 28-51 (131)
144 PF10497 zf-4CXXC_R1: Zinc-fin 63.9 8.5 0.00018 32.3 3.5 45 335-379 6-69 (105)
145 PF07975 C1_4: TFIIH C1-like d 63.9 5 0.00011 29.4 1.8 28 350-378 22-50 (51)
146 KOG4445 Uncharacterized conser 63.5 2.2 4.7E-05 42.2 -0.2 47 336-383 115-187 (368)
147 KOG1356 Putative transcription 62.2 2.5 5.4E-05 46.9 -0.1 46 336-381 229-281 (889)
148 PHA02825 LAP/PHD finger-like p 60.9 8.8 0.00019 34.6 3.1 47 335-383 7-60 (162)
149 COG5220 TFB3 Cdk activating ki 60.4 4.1 8.8E-05 39.1 1.0 45 336-380 10-62 (314)
150 smart00647 IBR In Between Ring 60.3 1.9 4E-05 31.8 -1.0 18 350-367 41-58 (64)
151 PF05605 zf-Di19: Drought indu 59.9 4.5 9.7E-05 29.4 1.0 39 336-382 2-42 (54)
152 KOG1815 Predicted E3 ubiquitin 59.4 4.6 9.9E-05 42.2 1.3 20 347-367 177-196 (444)
153 PRK00420 hypothetical protein; 57.7 4.3 9.4E-05 34.5 0.6 12 336-347 23-34 (112)
154 PF04641 Rtf2: Rtf2 RING-finge 57.4 15 0.00032 35.6 4.4 54 336-389 34-91 (260)
155 COG3357 Predicted transcriptio 57.1 3.8 8.3E-05 33.5 0.2 28 348-379 57-84 (97)
156 smart00064 FYVE Protein presen 56.8 5 0.00011 30.3 0.8 35 336-370 10-47 (68)
157 PF12312 NeA_P2: Nepovirus sub 56.7 9.5 0.00021 35.6 2.7 32 291-322 172-209 (258)
158 PF04710 Pellino: Pellino; In 56.4 3.7 8E-05 42.1 0.0 55 336-390 328-410 (416)
159 KOG2041 WD40 repeat protein [G 55.7 12 0.00027 41.2 3.7 49 328-382 1123-1185(1189)
160 KOG4362 Transcriptional regula 55.7 3.3 7E-05 45.3 -0.5 44 336-380 21-67 (684)
161 KOG0883 Cyclophilin type, U bo 54.8 9.3 0.0002 39.2 2.5 57 335-391 100-161 (518)
162 PF14205 Cys_rich_KTR: Cystein 54.1 4.9 0.00011 29.7 0.3 26 337-363 5-34 (55)
163 KOG1729 FYVE finger containing 54.0 7.1 0.00015 38.6 1.6 47 335-381 167-224 (288)
164 PF01363 FYVE: FYVE zinc finge 53.9 4.2 9.1E-05 30.8 -0.0 34 335-368 8-44 (69)
165 PF15616 TerY-C: TerY-C metal 52.9 5.6 0.00012 34.8 0.5 40 338-384 79-118 (131)
166 PLN02248 cellulose synthase-li 52.2 10 0.00022 43.9 2.5 35 350-385 146-180 (1135)
167 PTZ00303 phosphatidylinositol 52.1 8.7 0.00019 42.6 2.0 32 337-368 461-500 (1374)
168 KOG1100 Predicted E3 ubiquitin 51.9 6.4 0.00014 37.0 0.8 41 338-382 160-200 (207)
169 PF13240 zinc_ribbon_2: zinc-r 51.3 2.6 5.7E-05 25.6 -1.2 11 339-349 2-12 (23)
170 PF02148 zf-UBP: Zn-finger in 51.2 8.5 0.00018 28.9 1.3 34 339-372 1-38 (63)
171 COG3058 FdhE Uncharacterized p 51.2 14 0.00031 36.2 3.1 47 335-381 184-235 (308)
172 PF12906 RINGv: RING-variant d 51.0 6.3 0.00014 28.0 0.5 32 346-377 14-47 (47)
173 cd00065 FYVE FYVE domain; Zinc 50.9 12 0.00026 27.0 2.1 34 337-370 3-39 (57)
174 smart00132 LIM Zinc-binding do 50.8 11 0.00023 24.4 1.6 36 338-381 1-37 (39)
175 PF06906 DUF1272: Protein of u 50.6 20 0.00044 26.7 3.1 40 338-380 7-50 (57)
176 KOG0824 Predicted E3 ubiquitin 50.3 5.3 0.00011 39.5 -0.0 47 335-381 104-150 (324)
177 PF12660 zf-TFIIIC: Putative z 50.0 9.7 0.00021 31.5 1.5 43 337-381 15-65 (99)
178 TIGR00143 hypF [NiFe] hydrogen 49.3 5.1 0.00011 44.5 -0.3 51 332-382 64-151 (711)
179 PRK14559 putative protein seri 48.8 6.3 0.00014 43.2 0.3 41 333-382 12-52 (645)
180 KOG1952 Transcription factor N 47.8 10 0.00023 42.3 1.8 45 334-378 189-243 (950)
181 COG3813 Uncharacterized protei 47.1 15 0.00033 28.8 2.1 39 339-380 8-50 (84)
182 PRK07218 replication factor A; 46.8 13 0.00028 38.8 2.2 22 337-381 298-319 (423)
183 PF10272 Tmpp129: Putative tra 46.5 29 0.00063 35.4 4.6 52 335-386 270-355 (358)
184 PF09723 Zn-ribbon_8: Zinc rib 46.0 6.3 0.00014 27.3 -0.1 10 370-379 25-34 (42)
185 KOG3842 Adaptor protein Pellin 45.1 19 0.0004 36.1 2.8 54 336-389 341-422 (429)
186 PRK08270 anaerobic ribonucleos 44.9 13 0.00028 41.0 1.9 19 369-389 637-655 (656)
187 PF07800 DUF1644: Protein of u 44.7 12 0.00027 33.7 1.4 34 336-369 2-47 (162)
188 cd00730 rubredoxin Rubredoxin; 44.3 11 0.00023 27.5 0.8 13 368-380 31-43 (50)
189 PF13248 zf-ribbon_3: zinc-rib 43.7 4.5 9.8E-05 25.1 -1.0 9 337-345 3-11 (26)
190 COG1773 Rubredoxin [Energy pro 43.1 12 0.00026 27.8 0.9 15 365-379 30-44 (55)
191 PRK06386 replication factor A; 42.8 15 0.00033 37.4 2.0 12 337-348 237-248 (358)
192 TIGR01031 rpmF_bact ribosomal 42.1 15 0.00032 27.2 1.3 22 336-357 26-47 (55)
193 KOG3161 Predicted E3 ubiquitin 42.1 8.2 0.00018 41.9 -0.1 37 336-375 11-51 (861)
194 KOG3476 Microtubule-associated 41.3 2.4 5.3E-05 34.2 -3.2 35 337-381 55-89 (100)
195 KOG1609 Protein involved in mR 41.1 22 0.00048 34.6 2.8 49 333-381 75-133 (323)
196 smart00734 ZnF_Rad18 Rad18-lik 40.9 9.2 0.0002 23.8 0.0 10 373-382 3-12 (26)
197 PRK12496 hypothetical protein; 40.8 6.6 0.00014 35.5 -0.9 12 372-383 144-155 (164)
198 KOG1814 Predicted E3 ubiquitin 40.3 14 0.0003 38.1 1.2 34 335-368 367-405 (445)
199 KOG2113 Predicted RNA binding 40.3 24 0.00052 35.3 2.8 50 336-390 343-393 (394)
200 PRK12495 hypothetical protein; 40.0 11 0.00024 35.8 0.4 24 336-364 42-65 (226)
201 PRK12286 rpmF 50S ribosomal pr 39.9 18 0.00039 27.0 1.5 23 335-357 26-48 (57)
202 COG4068 Uncharacterized protei 39.7 16 0.00035 27.5 1.1 16 369-384 6-21 (64)
203 PHA00626 hypothetical protein 39.7 23 0.0005 26.4 2.0 7 338-344 2-8 (59)
204 COG5113 UFD2 Ubiquitin fusion 39.1 27 0.00058 38.2 3.1 53 335-387 853-905 (929)
205 PRK06393 rpoE DNA-directed RNA 38.9 15 0.00032 28.2 0.9 34 356-391 4-40 (64)
206 PF00412 LIM: LIM domain; Int 38.6 26 0.00056 25.0 2.2 32 335-366 25-56 (58)
207 PRK07217 replication factor A; 38.2 23 0.0005 35.4 2.4 28 337-387 189-218 (311)
208 KOG3726 Uncharacterized conser 36.5 19 0.0004 39.5 1.5 42 337-381 655-699 (717)
209 PF08271 TF_Zn_Ribbon: TFIIB z 35.5 24 0.00051 24.4 1.4 8 338-345 2-9 (43)
210 PF01783 Ribosomal_L32p: Ribos 35.2 21 0.00045 26.4 1.2 23 335-357 25-47 (56)
211 PF01485 IBR: IBR domain; Int 34.9 12 0.00025 27.4 -0.2 31 337-367 19-58 (64)
212 smart00834 CxxC_CXXC_SSSS Puta 34.8 19 0.00041 24.1 0.8 31 335-379 4-34 (41)
213 smart00661 RPOL9 RNA polymeras 34.7 26 0.00057 24.7 1.6 9 338-346 2-10 (52)
214 smart00154 ZnF_AN1 AN1-like Zi 34.6 28 0.0006 23.8 1.6 23 339-361 1-24 (39)
215 KOG4642 Chaperone-dependent E3 34.2 21 0.00045 34.7 1.3 55 332-388 208-263 (284)
216 PHA02768 hypothetical protein; 34.1 28 0.00062 25.8 1.7 42 336-389 5-50 (55)
217 KOG0006 E3 ubiquitin-protein l 33.6 26 0.00057 35.0 1.9 14 355-368 342-355 (446)
218 TIGR02827 RNR_anaer_Bdell anae 33.4 25 0.00055 38.2 1.9 18 372-390 547-564 (586)
219 PF14471 DUF4428: Domain of un 32.7 38 0.00083 24.6 2.2 28 338-367 1-30 (51)
220 TIGR00375 conserved hypothetic 32.7 11 0.00023 38.8 -1.0 15 369-384 257-271 (374)
221 COG1439 Predicted nucleic acid 32.0 12 0.00026 34.3 -0.6 12 370-381 152-163 (177)
222 PF14803 Nudix_N_2: Nudix N-te 31.7 16 0.00035 24.4 0.1 21 338-358 2-31 (34)
223 PF01428 zf-AN1: AN1-like Zinc 31.4 26 0.00057 24.3 1.1 34 339-375 1-36 (43)
224 PF08394 Arc_trans_TRASH: Arch 30.8 50 0.0011 22.6 2.3 32 339-370 1-36 (37)
225 KOG1428 Inhibitor of type V ad 30.8 16 0.00034 43.5 -0.2 47 336-382 3486-3544(3738)
226 PF07578 LAB_N: Lipid A Biosyn 30.5 43 0.00094 26.3 2.3 19 288-306 5-24 (72)
227 PRK11827 hypothetical protein; 30.5 32 0.00069 26.0 1.5 12 336-347 8-19 (60)
228 PF07282 OrfB_Zn_ribbon: Putat 30.1 36 0.00078 25.6 1.8 14 335-348 27-40 (69)
229 PF06827 zf-FPG_IleRS: Zinc fi 30.0 14 0.0003 23.4 -0.4 27 337-364 2-28 (30)
230 PF00301 Rubredoxin: Rubredoxi 29.7 19 0.00041 25.8 0.2 13 368-380 31-43 (47)
231 PRK00398 rpoP DNA-directed RNA 29.3 17 0.00037 25.4 -0.1 11 372-382 22-32 (46)
232 COG1198 PriA Primosomal protei 28.8 22 0.00049 39.6 0.6 44 336-380 435-484 (730)
233 PRK06266 transcription initiat 28.4 49 0.0011 30.3 2.7 32 335-382 116-147 (178)
234 KOG2272 Focal adhesion protein 28.1 25 0.00054 34.1 0.7 38 335-378 162-199 (332)
235 PF06677 Auto_anti-p27: Sjogre 27.9 19 0.00041 25.1 -0.1 24 336-363 17-40 (41)
236 PLN02720 complex II 27.9 29 0.00063 30.3 1.0 9 294-302 129-137 (140)
237 KOG2462 C2H2-type Zn-finger pr 27.2 59 0.0013 31.9 3.1 10 336-345 130-139 (279)
238 PF02318 FYVE_2: FYVE-type zin 27.0 35 0.00075 28.9 1.4 43 336-379 54-102 (118)
239 PRK08351 DNA-directed RNA poly 26.9 32 0.0007 26.1 1.0 20 360-381 6-25 (61)
240 PRK08271 anaerobic ribonucleos 26.3 21 0.00045 39.1 -0.2 31 350-389 567-597 (623)
241 PF10164 DUF2367: Uncharacteri 26.2 85 0.0018 26.1 3.4 43 336-379 49-96 (98)
242 PF04088 Peroxin-13_N: Peroxin 26.1 83 0.0018 28.4 3.6 26 106-131 131-156 (158)
243 KOG2066 Vacuolar assembly/sort 26.0 23 0.00049 39.5 0.0 41 336-378 784-831 (846)
244 KOG0396 Uncharacterized conser 25.4 37 0.00081 34.7 1.4 54 337-391 331-388 (389)
245 PRK14714 DNA polymerase II lar 25.2 32 0.00069 40.4 1.0 30 336-365 679-717 (1337)
246 COG3647 Predicted membrane pro 25.0 2.8E+02 0.0061 25.4 6.7 16 288-303 142-157 (205)
247 KOG1701 Focal adhesion adaptor 24.6 42 0.00092 34.9 1.7 51 337-389 361-416 (468)
248 PF01258 zf-dskA_traR: Prokary 24.3 29 0.00063 23.0 0.3 30 337-366 4-33 (36)
249 PF14353 CpXC: CpXC protein 24.3 36 0.00078 29.0 1.0 43 337-383 2-50 (128)
250 PF05573 NosL: NosL; InterPro 24.0 41 0.00089 29.7 1.3 36 336-371 25-69 (149)
251 KOG3740 Uncharacterized conser 23.7 66 0.0014 35.1 2.9 42 336-378 462-508 (706)
252 COG2093 DNA-directed RNA polym 23.6 26 0.00056 26.7 -0.1 24 355-380 2-27 (64)
253 COG1655 Uncharacterized protei 23.6 8.7 0.00019 36.7 -3.2 53 335-387 18-78 (267)
254 PRK01343 zinc-binding protein; 23.3 74 0.0016 23.9 2.3 35 336-376 9-48 (57)
255 PRK07726 DNA topoisomerase III 23.3 47 0.001 36.6 1.9 41 336-379 610-657 (658)
256 smart00290 ZnF_UBP Ubiquitin C 23.2 51 0.0011 23.0 1.4 25 338-363 1-25 (50)
257 COG1997 RPL43A Ribosomal prote 23.1 53 0.0011 26.8 1.6 12 335-346 34-45 (89)
258 smart00531 TFIIE Transcription 22.6 46 0.00099 29.3 1.3 37 335-382 98-134 (147)
259 smart00746 TRASH metallochaper 21.8 94 0.002 18.6 2.4 31 339-369 1-37 (39)
260 COG0333 RpmF Ribosomal protein 21.7 56 0.0012 24.5 1.4 22 336-357 27-48 (57)
261 KOG1842 FYVE finger-containing 21.7 30 0.00065 36.2 -0.1 69 284-365 139-212 (505)
262 COG3686 Predicted membrane pro 21.4 3.9E+02 0.0085 23.1 6.5 46 185-231 48-113 (125)
263 PF14354 Lar_restr_allev: Rest 21.2 37 0.0008 24.9 0.4 27 338-364 5-36 (61)
264 PRK09710 lar restriction allev 21.2 33 0.00072 26.3 0.1 27 338-364 8-34 (64)
265 CHL00174 accD acetyl-CoA carbo 21.2 41 0.00088 33.5 0.8 25 336-360 38-68 (296)
266 PRK01110 rpmF 50S ribosomal pr 21.1 48 0.001 25.0 1.0 21 336-357 27-47 (60)
267 PF08273 Prim_Zn_Ribbon: Zinc- 21.0 37 0.00081 23.5 0.3 26 338-363 5-32 (40)
268 KOG2675 Adenylate cyclase-asso 20.8 70 0.0015 33.5 2.3 13 279-291 199-211 (480)
269 KOG4217 Nuclear receptors of t 20.8 73 0.0016 33.7 2.5 41 335-380 268-320 (605)
270 TIGR00398 metG methionyl-tRNA 20.6 60 0.0013 34.5 1.9 43 336-383 136-178 (530)
271 PF10013 DUF2256: Uncharacteri 20.5 55 0.0012 23.0 1.0 9 337-345 9-17 (42)
272 TIGR00515 accD acetyl-CoA carb 20.3 37 0.0008 33.5 0.2 24 336-359 26-55 (285)
273 PRK08579 anaerobic ribonucleos 20.2 17 0.00037 39.8 -2.3 25 356-380 567-591 (625)
274 PRK14873 primosome assembly pr 20.1 33 0.0007 38.0 -0.2 43 336-380 383-431 (665)
275 PRK14892 putative transcriptio 20.1 48 0.001 27.6 0.9 11 335-345 20-30 (99)
276 PF07627 PSCyt3: Protein of un 20.1 61 0.0013 27.0 1.5 13 336-349 69-81 (101)
No 1
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.5e-88 Score=645.48 Aligned_cols=350 Identities=38% Similarity=0.654 Sum_probs=302.9
Q ss_pred CccccCCCCCCCceeeeehhhhchHhhHHHHHHHHHHHHhhCC-ccccccCCcHHHHHHHHHHHHhhccccCCCchhccc
Q 016213 1 MLFQVGGQGTRPTFFEMAAAQQLPASLRAAVTYSVGVLALRRP-FLHKVLDYEDEFFALLMLILETHSLRNTDASFSESL 79 (393)
Q Consensus 1 ~~~~~~~d~~~PS~FEliaqe~L~~lL~pAlryil~~la~r~P-~l~~l~n~~DE~yall~llvE~~~L~~~~aSF~E~F 79 (393)
|..++|+.+.+||||||+|||+|+++|+||++|+++|+|.|.| +++++++||||+|.+|++++|+|||+++||||+|+|
T Consensus 4 ~~~~~~~e~~~PsiFEi~Asq~L~t~lrpAL~~ll~~~A~~~~~~~~~l~r~fdE~f~~l~liLq~hyLr~~~sSF~E~f 83 (357)
T KOG0826|consen 4 GRNGVGLEPLQPSIFEIMASQELDTLLRPALQYLLKYFALRPPRYLLRLLRYFDEWFQALDLILQWHYLRTYNSSFIESF 83 (357)
T ss_pred cccccCcCCCCCcHhhhHhhhhHHHhhHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHhh
Confidence 5678899999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred cCceeeccccccccccccccCCCCCcCCCCCchhHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCcc
Q 016213 80 YGLRRRSVRIRAKKDDTRLKSSDGIHHSGLEKRQRVLSVVFMVVLPYFKSKLHSVYNKEREARLQASLWGPTDERFDDVD 159 (393)
Q Consensus 80 YGLkR~~~~~~~~~~~~~~~~~~~~~~~~Lt~~q~~~sLl~lV~~PYlk~KLd~~~~~~~~~~~~~~l~~~~~~~~~~~~ 159 (393)
|||||...++.-. +.+.++.+|+++|+++|++++|++||+++|||++|++++++.... .
T Consensus 84 YgLqr~ss~drl~--------se~~~~~~l~krQr~~s~~~lv~lPYv~~KL~~i~~k~~e~~~~~----S--------- 142 (357)
T KOG0826|consen 84 YGLQRISSRDRLT--------SEWPQGLGLNKRQRIVSFLFLVILPYVEAKLDEIYEKLRENNEFS----S--------- 142 (357)
T ss_pred hhhhhhhcccccc--------ccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc----C---------
Confidence 9999998775421 346678899999999999999999999999999999965432110 0
Q ss_pred cCCCCCCCCcCCCCCCcchhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHhcceEeecCcc
Q 016213 160 YFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLHASCEGLSFTYQLLYLLDATGFYSVGLHALGIHVCRATGQ 239 (393)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~k~~f~~~YP~i~~~~e~~~l~~~l~YL~g~t~y~sP~l~llgi~l~R~~~~ 239 (393)
. +.-+++.+++|..+||+|++++|+++++.++.|+.+++..||||+|+.|+.++.++++
T Consensus 143 ---------------~------e~~~~~~~~aF~~~~p~i~~a~els~lvq~l~yIlkrs~~hSPll~lsgv~L~~lt~~ 201 (357)
T KOG0826|consen 143 ---------------D------ETENKRPKRAFLRIYPFIKMALELSKLVQQLRYILKRSSHHSPLLYLSGVQLGTLTPE 201 (357)
T ss_pred ---------------c------hhhhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHhhcccccccHH
Confidence 0 1226788999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhhh--hhhhhHHhhhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCCCCCCCCC
Q 016213 240 ELMDNSSRIS--KIRSRERERLLGPLWLKKLQGALLSCAYTMLDYAQTGLIAAVFFFKMMEWWYQSAEERMSAPTVYPPP 317 (393)
Q Consensus 240 d~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~iF~lkfLeWWyss~~~r~~~~~~lp~P 317 (393)
|+.+.+.... ....+..+..+..++...+++.++++...+.++++++|+++||+|||+||||++|+++..+.+..|++
T Consensus 202 dl~a~~~gp~e~~~~~q~~r~t~~e~i~l~~qgaL~~~~~~v~~~~stgl~~~vFflqfldWWyssd~~~~~k~~l~~p~ 281 (357)
T KOG0826|consen 202 DLQALEHGPAELSMMDQPARKTVSEKIFLLMQGALKKAVRGVAFSLSTGLSVGVFFLQFLDWWYSSDNQRKIKSTLDPPI 281 (357)
T ss_pred HHHHhhccccccchhhhhhhhhhhhhHHHHHHhHHHHHHhhHHHHHHhhHHHHHHHHHHHHHHhcchHHHhhccCCCCCC
Confidence 9977433221 22222333333445667788999999999999999999999999999999999998877665554555
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCccC
Q 016213 318 PPPPPPKVAREGIPLPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 392 (393)
Q Consensus 318 pPP~~~~~~~~~~~~p~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy~~ 392 (393)
||||......++...|.++..||+|++.++||||+.+|||||||+||.+||.++|+||||+.|+.++||+|+|.+
T Consensus 282 PpPPh~~~~se~e~l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~~ 356 (357)
T KOG0826|consen 282 PPPPHKQYNSESELLPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFNK 356 (357)
T ss_pred CcCChhhcccccccCCCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHhcC
Confidence 555444555677778889999999999999999999999999999999999999999999999999999999975
No 2
>PF04757 Pex2_Pex12: Pex2 / Pex12 amino terminal region; InterPro: IPR006845 This region is the N-terminal part of a number of peroxisomal biogenesis proteins, including Pex2, Pex10 and Pex12, which contain two predicted transmembrane segments. The majority of these proteins have a C-terminal ring finger domain IPR001841 from INTERPRO.; GO: 0007031 peroxisome organization, 0005778 peroxisomal membrane
Probab=100.00 E-value=2.4e-39 Score=304.89 Aligned_cols=228 Identities=31% Similarity=0.491 Sum_probs=183.2
Q ss_pred hhhchHhhHHHHHHHHHHHHhhCC-ccccccCCcHHHHHHHHHHHHhhccccCCCchhccccCceeeccccccccccccc
Q 016213 20 AQQLPASLRAAVTYSVGVLALRRP-FLHKVLDYEDEFFALLMLILETHSLRNTDASFSESLYGLRRRSVRIRAKKDDTRL 98 (393)
Q Consensus 20 qe~L~~lL~pAlryil~~la~r~P-~l~~l~n~~DE~yall~llvE~~~L~~~~aSF~E~FYGLkR~~~~~~~~~~~~~~ 98 (393)
+|+|+++|+|+++||+.++++ | ..+++.+|+||+++++++++|.|+++++|+||+|+||||+|++....+.
T Consensus 1 d~~l~~~L~~~l~~i~~~l~~--~~~~~~~~~~~~Ei~~ll~~l~~~~tl~~~~~T~gE~~~~L~r~~~~~~~~------ 72 (229)
T PF04757_consen 1 DEELESLLKPALSYILQYLAQ--PRGPRRLLRYFDEIFLLLKLLYESLTLLRGNQTFGEEFYGLKRVNSRSSSR------ 72 (229)
T ss_pred ChHHHHHHHHHHHHHHHHHhc--cccchHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHhhCeEEeecccccc------
Confidence 689999999999999999999 7 9999999999999999999999999999999999999999998543211
Q ss_pred cCCCCCcCCCCCchhHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCcccCCCCCCCCcCCCCCCcch
Q 016213 99 KSSDGIHHSGLEKRQRVLSVVFMVVLPYFKSKLHSVYNKEREARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAET 178 (393)
Q Consensus 99 ~~~~~~~~~~Lt~~q~~~sLl~lV~~PYlk~KLd~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 (393)
.+..+|++|++.+++++|++||+++|+++++++. ........ ....+.
T Consensus 73 ------~~~~ls~~~r~~~l~~~vl~PYl~~Kl~~~~~~~----------~~~~~~~~----------------~~~~~~ 120 (229)
T PF04757_consen 73 ------ERRPLSRRQRLLSLLLLVLGPYLKEKLDSLLERL----------SERSAESI----------------SSRSAR 120 (229)
T ss_pred ------ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh----------cccccccc----------------cchhhh
Confidence 1457999999999999999999999999999983 22111100 000111
Q ss_pred hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHhcceEeecCcccccccchhhhhhhhhHHhh
Q 016213 179 SVRTSLTKKIQKIIFACYPWLHASCEGLSFTYQLLYLLDATGFYSVGLHALGIHVCRATGQELMDNSSRISKIRSRERER 258 (393)
Q Consensus 179 ~~~~~l~~~~k~~f~~~YP~i~~~~e~~~l~~~l~YL~g~t~y~sP~l~llgi~l~R~~~~d~~~~~~~~~~~~~~~~~~ 258 (393)
..+.+++..+++.|+++||++++++++++++++++||+++++|+||++|++||+++|.++.|..+...- +.+.+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fl~~g~~y~s~~~rllgi~~~~~~~~~~~~~~~~------~~l~~ 194 (229)
T PF04757_consen 121 ARRARLKSKLKRRFVKLYPYLNALYELLNLLHLLLFLLGGTPYYSPSKRLLGIRYVRLSPSDLQRNPSY------EFLGR 194 (229)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHhCcEEEECCccchhhhccH------HHHHH
Confidence 223367888999999999999999999999999999999999999999999999999988777542000 01111
Q ss_pred hcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 016213 259 LLGPLWLKKLQGALLSCAYTMLDYAQTGLIAAVFFFKMMEWWYQSA 304 (393)
Q Consensus 259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~iF~lkfLeWWyss~ 304 (393)
. -.+..+...+...+..+++.++|+|||+|||| +|
T Consensus 195 ~----------l~~~~~~~~~~~~~~~l~~~~~~~~~~~eww~-~~ 229 (229)
T PF04757_consen 195 Q----------LLWQLLSEFLLFLLPLLLPRSLFFLKFLEWWY-SD 229 (229)
T ss_pred H----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CC
Confidence 1 01123445666777899999999999999999 75
No 3
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.53 E-value=1e-13 Score=132.49 Aligned_cols=55 Identities=29% Similarity=0.698 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy 390 (393)
...+|.||++.+.||++++ |||+|||.||..|..+...||+|+.+....+++-++
T Consensus 238 a~~kC~LCLe~~~~pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi~Lr 292 (293)
T KOG0317|consen 238 ATRKCSLCLENRSNPSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKVICLR 292 (293)
T ss_pred CCCceEEEecCCCCCCcCc-CcchHHHHHHHHHHccccCCCcccccCCCcceeeec
Confidence 3578999999999999987 999999999999999999999999999999988665
No 4
>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=99.36 E-value=6.6e-13 Score=100.31 Aligned_cols=53 Identities=25% Similarity=0.361 Sum_probs=49.3
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCc
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy 390 (393)
..||||++.++||++++ |||+||..||.+|+++++.||+|+.+++.+++++..
T Consensus 2 ~~Cpi~~~~~~~Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~ 54 (63)
T smart00504 2 FLCPISLEVMKDPVILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNL 54 (63)
T ss_pred cCCcCCCCcCCCCEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCH
Confidence 47999999999999886 999999999999999999999999999999998764
No 5
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.29 E-value=2.3e-12 Score=115.40 Aligned_cols=57 Identities=28% Similarity=0.592 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCCCCce-eccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCcc
Q 016213 335 DRTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~-~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy~ 391 (393)
....||||+.....-. +.+.||||||..||.+.++...+||+|+++++..++.|||.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~L 187 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFHRIYL 187 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhheeccC
Confidence 3589999999877754 42449999999999999999999999999999999999994
No 6
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.29 E-value=2.5e-12 Score=117.66 Aligned_cols=56 Identities=23% Similarity=0.608 Sum_probs=50.5
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc----------------CCCCCCCCCCCCcCCeeeCcc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ----------------YKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~----------------~~~CPv~~~~~~~~~l~riy~ 391 (393)
+...||||++..++|++++ |||+||+.||.+|+.. ..+||+|+.+++.++|++||.
T Consensus 17 ~~~~CpICld~~~dPVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiyg 88 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYG 88 (193)
T ss_pred CccCCccCCCcCCCcEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeec
Confidence 3578999999999999986 9999999999999852 358999999999999999996
No 7
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.23 E-value=5.3e-12 Score=117.60 Aligned_cols=58 Identities=22% Similarity=0.657 Sum_probs=52.7
Q ss_pred CCCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC---CCCCCCCCCCCcCCeeeCcc
Q 016213 333 PPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 333 p~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~~~~~l~riy~ 391 (393)
+.....|-||++.-++|+|+- |||.|||+||++|+..+ +.||||+-.++.+.|+.||.
T Consensus 44 ~~~~FdCNICLd~akdPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCCEEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence 345789999999999999986 99999999999999854 57899999999999999996
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=99.17 E-value=1.5e-11 Score=84.78 Aligned_cols=39 Identities=44% Similarity=1.005 Sum_probs=34.1
Q ss_pred CCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCC
Q 016213 339 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVT 377 (393)
Q Consensus 339 CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~ 377 (393)
||||++.++||+++..|||+||+.||.+|++++.+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 899999999996555699999999999999999999997
No 9
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.13 E-value=1.2e-09 Score=103.88 Aligned_cols=233 Identities=16% Similarity=0.190 Sum_probs=143.9
Q ss_pred cCCcHHHHHHHHHHHHhhccccCCCchhccccCceeeccccccccccccccCCCCCcCCCCCchhHHHHHHHHHhHHhHH
Q 016213 49 LDYEDEFFALLMLILETHSLRNTDASFSESLYGLRRRSVRIRAKKDDTRLKSSDGIHHSGLEKRQRVLSVVFMVVLPYFK 128 (393)
Q Consensus 49 ~n~~DE~yall~llvE~~~L~~~~aSF~E~FYGLkR~~~~~~~~~~~~~~~~~~~~~~~~Lt~~q~~~sLl~lV~~PYlk 128 (393)
.....|.-++|+..|.+.....-++|+.-..-|+++........ +....-+.+.-..-+|.-|+.
T Consensus 50 ~r~epe~~~vl~~~iw~~si~~~~~T~Gqall~v~y~~ek~~~~---------------r~~l~g~IW~~v~sig~~~~~ 114 (298)
T KOG2879|consen 50 LRVEPELDAVLDSAIWFFSIYSVDDTVGQALLNVAYIFEKLPVL---------------RVVLEGKIWTHVFSIGGSWLE 114 (298)
T ss_pred hhhcHHHhHHHHHHHHheeccCCCCcccchhhhHHhhhccCceE---------------EEeecceEEEEeccccCCchh
Confidence 67889999999999999999999999999999999987553111 111121444455667888888
Q ss_pred HHHH-HHHHHHHHHHHhhhccCCCCCCCCCcccCCCCCCCCcCCCCCCcchhhhhhhHHHHHHHHHHHhhHHHHHHHHHH
Q 016213 129 SKLH-SVYNKEREARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLHASCEGLS 207 (393)
Q Consensus 129 ~KLd-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~k~~f~~~YP~i~~~~e~~~ 207 (393)
++++ ++... ++... ..+++ ..-=++...+.+.+
T Consensus 115 ~r~qm~l~r~----------~~~~~----------------------------~~~~~--------~~v~~ve~i~~~~~ 148 (298)
T KOG2879|consen 115 ERNQMDLFRA----------GWVNL----------------------------TPKLI--------TSVFMVEGILKALG 148 (298)
T ss_pred hhhHHHHHHh----------hhhhH----------------------------HHHHH--------HHHHHHHHHHHHHH
Confidence 8866 11111 11100 00111 11124444555556
Q ss_pred HHHHHHHHhCCCCCCCHHHHHhcceEeecCcccccccchhhhhhhhhHHhhhcChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 016213 208 FTYQLLYLLDATGFYSVGLHALGIHVCRATGQELMDNSSRISKIRSRERERLLGPLWLKKLQGALLSCAYTMLDYAQTGL 287 (393)
Q Consensus 208 l~~~l~YL~g~t~y~sP~l~llgi~l~R~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 287 (393)
+.+.+.||.- +++++.+.+++|+......+..... +.- + .-.+..++. .+.+.+...+
T Consensus 149 ~~n~l~fL~~-gr~~tlie~il~~~si~~~~~~~R~----ig~------e----Y~NReLlW~-------~F~e~ll~~l 206 (298)
T KOG2879|consen 149 MLNLLSFLYR-GRMYTLIEAILGLGSILHFPYFNRS----IGY------E----YQNRELLWN-------AFREVLLLTL 206 (298)
T ss_pred HHHHHHHHHh-hhhhHHHHHHhccchhhhcccccch----hhh------H----HHHHHHHHH-------HHHHHHHHHH
Confidence 7777788776 8999999999999988655433321 000 0 001112222 2233444455
Q ss_pred HHHHHHH-H-HHHHHhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeccCccccccHHHHH
Q 016213 288 IAAVFFF-K-MMEWWYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANPSVVTVSGFVFCYACIF 365 (393)
Q Consensus 288 p~~iF~l-k-fLeWWyss~~~r~~~~~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~ 365 (393)
|..-|-. | .|--|... +. +-|+. ..+.+ .+...||+|++..++|.+...|||+|||-||.
T Consensus 207 p~I~~~k~r~~l~sw~~~----------l~-~ap~~---sss~~----t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ 268 (298)
T KOG2879|consen 207 PFINFRKLRRVLKSWKLD----------LD-RAPKF---SSSTG----TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIA 268 (298)
T ss_pred HHHHHHHHHHHHHhhccc----------cc-CCCCc---ccccc----cCCceeeccCCCCCCCeeeccccceeehhhhh
Confidence 5554432 1 24444432 11 11211 11222 35779999999999998877799999999999
Q ss_pred HHhhcC--CCCCCCCCCCC
Q 016213 366 KYVSQY--KRCPVTLMPAT 382 (393)
Q Consensus 366 ~~~~~~--~~CPv~~~~~~ 382 (393)
.-+.-. ..||-|+.++-
T Consensus 269 ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 269 TSRLWDASFTCPLCGENVE 287 (298)
T ss_pred hhhcchhhcccCccCCCCc
Confidence 888755 79999998764
No 10
>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=99.08 E-value=6.7e-11 Score=92.77 Aligned_cols=54 Identities=20% Similarity=0.389 Sum_probs=44.9
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc-CCCCCCCCCCCCcCCeeeC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRRL 389 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~~~~~l~ri 389 (393)
+...||||++.++||++++ |||+||..||.+|+++ ++.||+|+.+++.++|+.-
T Consensus 3 ~~f~CpIt~~lM~dPVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn 57 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN 57 (73)
T ss_dssp GGGB-TTTSSB-SSEEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred cccCCcCcCcHhhCceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence 5789999999999999997 9999999999999999 7899999999999888753
No 11
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.93 E-value=5.3e-10 Score=78.45 Aligned_cols=38 Identities=26% Similarity=0.719 Sum_probs=31.1
Q ss_pred CCCCCCCCCCceeccCccccccHHHHHHHhhcC----CCCCCC
Q 016213 339 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY----KRCPVT 377 (393)
Q Consensus 339 CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~----~~CPv~ 377 (393)
||||++.++||+.++ |||+||..||.+|.++. -.||+|
T Consensus 1 CpiC~~~~~~Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999999999998 99999999999999875 269987
No 12
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.89 E-value=6e-10 Score=78.61 Aligned_cols=41 Identities=27% Similarity=0.673 Sum_probs=34.3
Q ss_pred CCCCCCCCCCCC---ceeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 337 TICPLCSQKRAN---PSVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 337 ~~CpiC~~~~~n---p~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
+.||||++.+.+ ...++ |||+||+.||.+|+++++.||+|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence 369999999843 34566 999999999999999999999995
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.87 E-value=1.4e-09 Score=78.95 Aligned_cols=46 Identities=24% Similarity=0.708 Sum_probs=40.5
Q ss_pred CCCCCCCCCCCCCceeccCcccc-ccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~v-fCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
...|+||++...++.+.+ |||+ ||+.|+.+|++..++||+|+.+++
T Consensus 2 ~~~C~iC~~~~~~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 357999999999988886 9999 999999999999999999998864
No 14
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.87 E-value=1.8e-09 Score=109.56 Aligned_cols=54 Identities=20% Similarity=0.502 Sum_probs=48.0
Q ss_pred CCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeee
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 388 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~r 388 (393)
.+...|+||.+.+.+|++++ |||.||..||..|+...+.||+|+.++...+|++
T Consensus 24 e~~l~C~IC~d~~~~Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRS 77 (397)
T ss_pred ccccCCCcCchhhhCccCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccccCcc
Confidence 35789999999999999876 9999999999999999899999999887666654
No 15
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.86 E-value=1.2e-09 Score=111.83 Aligned_cols=55 Identities=25% Similarity=0.638 Sum_probs=50.2
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhh-----cCCCCCCCCCCCCcCCeeeCcc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS-----QYKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~-----~~~~CPv~~~~~~~~~l~riy~ 391 (393)
...||||+.+..-|..+. |||+||.+||.+|+. +.++||+|+..++..||..|+.
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeee
Confidence 678999999999999887 999999999999986 4589999999999999998875
No 16
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.83 E-value=2.5e-09 Score=101.73 Aligned_cols=48 Identities=25% Similarity=0.600 Sum_probs=40.8
Q ss_pred CCCCCCCCCCCCCCc-------eeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np-------~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
+...||||++.+.++ .+++.|||+||..||.+|++.++.||+|+.+..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 356899999987764 245569999999999999999999999998754
No 17
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=1.6e-09 Score=115.46 Aligned_cols=56 Identities=18% Similarity=0.529 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc-CCCCCCCCCCCCcCCeeeCcc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~~~~~l~riy~ 391 (393)
..-+||+|...+.|.+++. ||||||+.||...++. +.+||.|+.+.+.+|+++||.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hceeCCCccCchhhHHHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 3578999998888888876 9999999999999985 579999999999999999984
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=98.78 E-value=5.5e-09 Score=72.23 Aligned_cols=43 Identities=35% Similarity=0.846 Sum_probs=38.8
Q ss_pred CCCCCCCCCCCceeccCccccccHHHHHHHhhc-CCCCCCCCCC
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMP 380 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~ 380 (393)
.|+||++.+.++..+..|||.||..|+.+|++. +.+||+|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 499999999888877779999999999999998 7889999865
No 19
>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=98.71 E-value=9.7e-09 Score=71.09 Aligned_cols=38 Identities=29% Similarity=0.899 Sum_probs=34.4
Q ss_pred CCCCCCCCCCce-eccCccccccHHHHHHHhh--cCCCCCCC
Q 016213 339 CPLCSQKRANPS-VVTVSGFVFCYACIFKYVS--QYKRCPVT 377 (393)
Q Consensus 339 CpiC~~~~~np~-~~~~~G~vfCy~Ci~~~~~--~~~~CPv~ 377 (393)
||||.+...+|. +++ |||.||+.|+.+|++ +..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLP-CGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999999999 555 999999999999999 55789987
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.69 E-value=1.5e-08 Score=67.63 Aligned_cols=38 Identities=34% Similarity=0.977 Sum_probs=34.9
Q ss_pred CCCCCCCCCCceeccCccccccHHHHHHHhh-cCCCCCCC
Q 016213 339 CPLCSQKRANPSVVTVSGFVFCYACIFKYVS-QYKRCPVT 377 (393)
Q Consensus 339 CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~-~~~~CPv~ 377 (393)
|+||++..+++.+++ |||+||+.|+.+|++ ...+||+|
T Consensus 1 C~iC~~~~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence 899999988888887 999999999999998 66789987
No 21
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.60 E-value=2.6e-08 Score=93.54 Aligned_cols=56 Identities=30% Similarity=0.409 Sum_probs=51.9
Q ss_pred CCCCCCCCCCCCCCc---eeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCc
Q 016213 335 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 335 ~~~~CpiC~~~~~np---~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy 390 (393)
.+++||+|+..++|. +++.+||||+|+.|.-++++..+.||||+.|++..|||.+=
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence 578999999999996 47889999999999999999999999999999999999763
No 22
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.57 E-value=2.4e-08 Score=94.87 Aligned_cols=51 Identities=22% Similarity=0.583 Sum_probs=45.0
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHH-HhhcC-CCCCCCCCCCCcCCe
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFK-YVSQY-KRCPVTLMPATVEQI 386 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~-~~~~~-~~CPv~~~~~~~~~l 386 (393)
...+|+||++...+|+.++ ||||||+.||.. |-.+. ..||+|+..+-.+++
T Consensus 214 ~d~kC~lC~e~~~~ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 4678999999999999987 999999999999 87776 569999998877665
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.51 E-value=6.5e-08 Score=90.03 Aligned_cols=48 Identities=17% Similarity=0.475 Sum_probs=39.0
Q ss_pred CCCCCCCCCCCCCCc--------eeccCccccccHHHHHHHhhcC------CCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANP--------SVVTVSGFVFCYACIFKYVSQY------KRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np--------~~~~~~G~vfCy~Ci~~~~~~~------~~CPv~~~~~~ 382 (393)
....|+||++.+.++ -+++.|||+||..||.+|.+.. ..||+|+.+.+
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 468899999986442 4677799999999999999853 35999998764
No 24
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=5.6e-08 Score=68.49 Aligned_cols=35 Identities=37% Similarity=0.983 Sum_probs=22.6
Q ss_pred CCCCCCCCCC----ceeccCccccccHHHHHHHhhcC----CCCC
Q 016213 339 CPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQY----KRCP 375 (393)
Q Consensus 339 CpiC~~~~~n----p~~~~~~G~vfCy~Ci~~~~~~~----~~CP 375 (393)
||||.+ ..+ |.+++ |||+||..|+.+..++. -+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 999999 777 89998 99999999999999854 2677
No 25
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.47 E-value=4.1e-08 Score=74.31 Aligned_cols=50 Identities=26% Similarity=0.615 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCee
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 387 (393)
...|++|.+.+++|+.+..|.|+||..||-+.+.. .||||+.|+.++|++
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS--
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHH
Confidence 35799999999999877779999999999887664 599999999988875
No 26
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.38 E-value=1.7e-07 Score=70.05 Aligned_cols=44 Identities=30% Similarity=0.524 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc--CCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTL 378 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~ 378 (393)
...+|||++++++||+....|||+|....|.+|+.+ ..+||+.|
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv~G 55 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPVAG 55 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC
T ss_pred eccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCCCC
Confidence 367999999999999998789999999999999944 46899965
No 27
>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=98.37 E-value=3.2e-07 Score=90.01 Aligned_cols=53 Identities=30% Similarity=0.596 Sum_probs=42.4
Q ss_pred CCCCCCCCCCC-CCCce---eccCccccccHHHHHHHh-hcCCCCCCCCCCCCcCCee
Q 016213 335 DRTICPLCSQK-RANPS---VVTVSGFVFCYACIFKYV-SQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 335 ~~~~CpiC~~~-~~np~---~~~~~G~vfCy~Ci~~~~-~~~~~CPv~~~~~~~~~l~ 387 (393)
+...||+|+.. ..||. ++..|||.||-.|+...+ ...+.||+|+.++..++++
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr 59 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR 59 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence 34689999995 56674 444699999999999965 4557999999998877765
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.34 E-value=3.8e-07 Score=64.40 Aligned_cols=42 Identities=26% Similarity=0.641 Sum_probs=34.0
Q ss_pred CCCCCCCCC--CCceeccCccccccHHHHHHHhhcCCCCCCCCC
Q 016213 338 ICPLCSQKR--ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 379 (393)
Q Consensus 338 ~CpiC~~~~--~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 379 (393)
.|++|.+.. ..+..+..|||+||..|+.+.......||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999988 233334459999999999999977789999984
No 29
>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=98.33 E-value=4e-07 Score=71.41 Aligned_cols=43 Identities=26% Similarity=0.679 Sum_probs=35.1
Q ss_pred CCCCCCCCCCCCCc------------eeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRANP------------SVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~np------------~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
.+.|+||++++.++ .+...|||.|...||.+|++.+..||+|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 34599999999333 34556999999999999999999999996
No 30
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.30 E-value=2.5e-07 Score=88.84 Aligned_cols=46 Identities=26% Similarity=0.536 Sum_probs=42.7
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
....|-||...+.-|+.++ |||.||+=||.+|+.++.-||+|+.+-
T Consensus 24 s~lrC~IC~~~i~ip~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 24 SMLRCRICDCRISIPCETT-CGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred hHHHhhhhhheeecceecc-cccchhHHHHHHHhcCCCCCccccccH
Confidence 4678999999999999987 999999999999999999999999764
No 31
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.07 E-value=3.5e-06 Score=81.60 Aligned_cols=57 Identities=28% Similarity=0.414 Sum_probs=48.7
Q ss_pred CCCCCCCCCCCCCCc---eeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCccC
Q 016213 335 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 392 (393)
Q Consensus 335 ~~~~CpiC~~~~~np---~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy~~ 392 (393)
....|||++..+.+- +++.+||||||+.|+.+. ...+.||+|+.+.+.+|||.|-.+
T Consensus 112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDIIPLNPP 171 (260)
T ss_pred ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCEEEecCC
Confidence 578999999999552 567779999999999888 356789999999999999998754
No 32
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=8e-07 Score=64.93 Aligned_cols=53 Identities=21% Similarity=0.613 Sum_probs=44.0
Q ss_pred CCCCCCCCCCCCCceeccCcccc-ccHHHHHHHhh-cCCCCCCCCCCCCcCCeeeCcc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVS-QYKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~v-fCy~Ci~~~~~-~~~~CPv~~~~~~~~~l~riy~ 391 (393)
+..|.||.+...|.++-. |||+ .||.|..+-.+ .++.||+|+.|+ +|++|-|.
T Consensus 7 ~dECTICye~pvdsVlYt-CGHMCmCy~Cg~rl~~~~~g~CPiCRapi--~dvIkTY~ 61 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYT-CGHMCMCYACGLRLKKALHGCCPICRAPI--KDVIKTYR 61 (62)
T ss_pred ccceeeeccCcchHHHHH-cchHHhHHHHHHHHHHccCCcCcchhhHH--HHHHHhhc
Confidence 478999999999988775 9997 69999998887 689999999764 56666653
No 33
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.00 E-value=1.4e-06 Score=85.41 Aligned_cols=54 Identities=26% Similarity=0.544 Sum_probs=49.7
Q ss_pred CCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeee
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 388 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~r 388 (393)
++...|-||.+.+.-|.+++ |||.||-=||-.|+..+..||.|..+.+..+|+.
T Consensus 21 D~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~ 74 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRN 74 (442)
T ss_pred HHHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhccCCCCCceecccchhhhhh
Confidence 35678999999999999998 9999999999999999999999999998888774
No 34
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=3e-06 Score=82.04 Aligned_cols=47 Identities=26% Similarity=0.527 Sum_probs=42.1
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCC-CCCCCCCCCc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~-CPv~~~~~~~ 383 (393)
...|+||.....-|+.+. |+|+|||-||..-.+..++ |+||+.|++.
T Consensus 7 ~~eC~IC~nt~n~Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred CCcceeeeccCCcCcccc-ccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 457999999999998887 9999999999998888876 9999999863
No 35
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=6.4e-06 Score=81.69 Aligned_cols=47 Identities=17% Similarity=0.596 Sum_probs=40.7
Q ss_pred CCCCCCCCCCCCCCCc-------------eeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 334 PDRTICPLCSQKRANP-------------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np-------------~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
.+.+.|.||++.+..| -=++ |||++-..|+..|++.++.||+|+.|+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence 3578999999984433 4576 999999999999999999999999995
No 36
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.88 E-value=4.3e-06 Score=81.98 Aligned_cols=48 Identities=27% Similarity=0.583 Sum_probs=43.3
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
....|++|.+.+.|+|.+.-|=|-||..||++|+++.+.||+|+.-+.
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 367999999999999876679999999999999999999999986653
No 37
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=5.5e-06 Score=88.20 Aligned_cols=46 Identities=17% Similarity=0.548 Sum_probs=42.4
Q ss_pred CCCCCCCCCCCCCC-----ceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..+.|+||.+.+.+ |..++ |||+||-.|+.+|+++.+.||+|+...
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence 36889999999999 78887 999999999999999999999999844
No 38
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=6.5e-06 Score=77.98 Aligned_cols=43 Identities=28% Similarity=0.674 Sum_probs=39.3
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
+...||||++..++|.+++ |||.||..|+..+....-.||+|+
T Consensus 12 ~~~~C~iC~~~~~~p~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLP-CGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCcccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence 5678999999999998887 999999999999998556999999
No 39
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.79 E-value=1e-05 Score=82.73 Aligned_cols=54 Identities=26% Similarity=0.617 Sum_probs=47.5
Q ss_pred CCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCee
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 387 (393)
+....||+|+.++.+|.-.++|||.||..|+..|+..+..||+|..+++.++.+
T Consensus 19 ~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 456899999999999987545999999999999999999999999888766554
No 40
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.74 E-value=2.8e-05 Score=62.50 Aligned_cols=48 Identities=27% Similarity=0.533 Sum_probs=38.9
Q ss_pred CCCCCCCCCCCCC-ceeccCccccccHHHHHHHhhc---CCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p~~~~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~~~~ 383 (393)
.+.||.|.-+-.+ |.|.-.|||.|-..||.+|++. ++.||+|+++-..
T Consensus 32 dg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 32 DGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred ccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 3567888877655 6676679999999999999986 4899999987544
No 41
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=1.3e-05 Score=79.16 Aligned_cols=48 Identities=23% Similarity=0.542 Sum_probs=42.4
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc-CCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~~ 382 (393)
...+||||+.-+++....+.|+|-||..||...++. ++.||-|++.+.
T Consensus 42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 367899999999999888889999999999999875 579999998763
No 42
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=5.1e-05 Score=73.48 Aligned_cols=44 Identities=25% Similarity=0.495 Sum_probs=41.5
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..|-||++...+|+|.. |||-||-.|...-++...+|+||++.+
T Consensus 242 f~c~icr~~f~~pVvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTK-CGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred ccccccccccccchhhc-CCceeehhhhccccccCCcceeccccc
Confidence 57999999999999987 999999999999999999999999875
No 43
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.39 E-value=9e-05 Score=71.79 Aligned_cols=45 Identities=29% Similarity=0.531 Sum_probs=39.9
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhc-CCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~ 380 (393)
+..||+|+.-++||+-+++|||.||..||...|-+ ..+||+|...
T Consensus 274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 47899999999999988889999999999988765 5899999863
No 44
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.39 E-value=7.2e-05 Score=77.24 Aligned_cols=49 Identities=24% Similarity=0.543 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc-----CCCCCCCCCCCCcC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-----YKRCPVTLMPATVE 384 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~-----~~~CPv~~~~~~~~ 384 (393)
....|-+|.++-+++.+.+ |.|+||.-||.+|+.. +-.||+|..+++++
T Consensus 535 ~~~~C~lc~d~aed~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 535 GEVECGLCHDPAEDYIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred CceeecccCChhhhhHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 3568999999999999987 9999999999999974 35899999998765
No 45
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=7.7e-05 Score=72.45 Aligned_cols=45 Identities=24% Similarity=0.569 Sum_probs=37.7
Q ss_pred CCCCCCCCCC-CCCc--eeccCccccccHHHHHHHhhcC-CCCCCCCCCC
Q 016213 336 RTICPLCSQK-RANP--SVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~-~~np--~~~~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~ 381 (393)
.-.|.||+.. +++. .|++ |-|+|--+|+-+|+..+ ++||||+.++
T Consensus 323 GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred CceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCC
Confidence 4579999996 5554 4666 99999999999999965 8999999875
No 46
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.32 E-value=0.0002 Score=71.65 Aligned_cols=44 Identities=20% Similarity=0.527 Sum_probs=37.5
Q ss_pred CCCCCCCCCCCC-c--eeccCccccccHHHHHHHhhcCCC-CCCCCCCC
Q 016213 337 TICPLCSQKRAN-P--SVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~n-p--~~~~~~G~vfCy~Ci~~~~~~~~~-CPv~~~~~ 381 (393)
..|.||++..+. . .+|+ |+|.|--.||..|+.++++ ||||+...
T Consensus 230 ~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcC
Confidence 599999997544 3 4687 9999999999999999976 99999754
No 47
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.26 E-value=0.00012 Score=67.17 Aligned_cols=45 Identities=22% Similarity=0.546 Sum_probs=41.3
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
...|-||.+....|+|.. |||.||-.|+..-.+.-..|=||++.+
T Consensus 196 PF~C~iCKkdy~spvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYESPVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccchhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence 468999999999999987 999999999999998889999999764
No 48
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00028 Score=69.85 Aligned_cols=48 Identities=23% Similarity=0.547 Sum_probs=42.5
Q ss_pred CCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
.+.+.||||.-...|++..+ |||--||.||.+++.+.++|=-|+..+.
T Consensus 420 sEd~lCpICyA~pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence 35789999999999988876 9999999999999999999999985543
No 49
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00039 Score=69.16 Aligned_cols=47 Identities=19% Similarity=0.494 Sum_probs=41.9
Q ss_pred CCCCCCCCCCCCCCceeccCcccc-ccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~v-fCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
+...|-||+...+|-+|++ |=|. .|-.|+....-++++|||||+++.
T Consensus 289 ~gkeCVIClse~rdt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICLSESRDTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCCeeEEEecCCcceEEec-chhhehhHhHHHHHHHhhcCCCccccchH
Confidence 3678999999999999998 9886 599999988888999999998864
No 50
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.00056 Score=70.38 Aligned_cols=50 Identities=22% Similarity=0.538 Sum_probs=39.3
Q ss_pred CCCCCCCCCCCCCCC-----Cce-----------eccCccccccHHHHHHHhhcCC-CCCCCCCCCC
Q 016213 333 PPDRTICPLCSQKRA-----NPS-----------VVTVSGFVFCYACIFKYVSQYK-RCPVTLMPAT 382 (393)
Q Consensus 333 p~~~~~CpiC~~~~~-----np~-----------~~~~~G~vfCy~Ci~~~~~~~~-~CPv~~~~~~ 382 (393)
-.+...|+||++++. +++ ++++|.|+|--.|+.+|++.-+ .||||+.|+-
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 345788999999753 222 2346999999999999999765 9999998863
No 51
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.76 E-value=0.00043 Score=69.79 Aligned_cols=57 Identities=30% Similarity=0.522 Sum_probs=47.5
Q ss_pred CCCCCCCCCCCCCCCc----eeccCccccccHHHHHHHhhcC--CCCCCCCCCCCcCCeeeCc
Q 016213 334 PDRTICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np----~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~~~l~riy 390 (393)
++..+||||.+.++-| .+...|||.|=-.||-+|+-+. ++||.|.-+.+..+|+.+|
T Consensus 2 d~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~ 64 (463)
T KOG1645|consen 2 DCGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEY 64 (463)
T ss_pred CccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHH
Confidence 3578999999998887 3445599999999999999542 6899999888888888776
No 52
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.70 E-value=0.0024 Score=61.38 Aligned_cols=51 Identities=18% Similarity=0.447 Sum_probs=40.6
Q ss_pred CCCCCCCCCCCCCCc----------eeccCccccccHHHHHHHhh--cCCCCCCCCCCCCcCCe
Q 016213 335 DRTICPLCSQKRANP----------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQI 386 (393)
Q Consensus 335 ~~~~CpiC~~~~~np----------~~~~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~~~~l 386 (393)
+.+.|.+|++.+... --++ |+|||---||.-|.- +.+.||-|+++++.+.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rm 285 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRM 285 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhhh
Confidence 467899999976543 2466 999999999999975 56789999998876543
No 53
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.65 E-value=0.0012 Score=65.24 Aligned_cols=51 Identities=25% Similarity=0.565 Sum_probs=38.7
Q ss_pred CCCCCCCCCCCC--CCc--eeccCccccccHHHHHHHhhc--CCCCCCCCCCCCcCCee
Q 016213 335 DRTICPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPATVEQIR 387 (393)
Q Consensus 335 ~~~~CpiC~~~~--~np--~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~~~~l~ 387 (393)
+.+.||+|++++ +|- --|+ |||-.|.=|-. .+++ +|+||.|+..-+.++++
T Consensus 13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~-~irq~lngrcpacrr~y~denv~ 69 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYN-NIRQNLNGRCPACRRKYDDENVR 69 (480)
T ss_pred ccccCcccccccccccCCcccCC-cccHHHHHHHH-HHHhhccCCChHhhhhcccccee
Confidence 356699999985 443 3577 99998888865 4554 59999999888877765
No 54
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=96.54 E-value=0.0023 Score=50.65 Aligned_cols=47 Identities=23% Similarity=0.497 Sum_probs=37.2
Q ss_pred CCCCCCCCCCCCC----ceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~n----p~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
.+.||-|.-..++ |.+--+|.|.|-.-||++||...+.||+++++-.
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence 4567777663322 4566779999999999999999999999998753
No 55
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.45 E-value=0.0015 Score=66.77 Aligned_cols=47 Identities=26% Similarity=0.539 Sum_probs=43.0
Q ss_pred CCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
.+...|-||...+.+|++++ |||-||..||.+-+.+...||.|+.+.
T Consensus 82 ~sef~c~vc~~~l~~pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l 128 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTP-CGHSFCLECLDRSLDQETECPLCRDEL 128 (398)
T ss_pred cchhhhhhhHhhcCCCcccc-ccccccHHHHHHHhccCCCCccccccc
Confidence 36789999999999999996 999999999999999999999998664
No 56
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.40 E-value=0.0024 Score=46.00 Aligned_cols=41 Identities=29% Similarity=0.710 Sum_probs=23.3
Q ss_pred CCCCCCCC--CCc--eeccCccccccHHHHHHHhh-cCCCCCCCCCC
Q 016213 339 CPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVS-QYKRCPVTLMP 380 (393)
Q Consensus 339 CpiC~~~~--~np--~~~~~~G~vfCy~Ci~~~~~-~~~~CPv~~~~ 380 (393)
||+|.+++ ++- .-++ |||-.|..|-++-++ ++++||-|+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 89999987 221 2465 999999999999997 58999999976
No 57
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0021 Score=64.53 Aligned_cols=48 Identities=25% Similarity=0.647 Sum_probs=40.7
Q ss_pred CCCCCCCCCCCCCCce-------eccCccccccHHHHHHHh--hc-----CCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPS-------VVTVSGFVFCYACIFKYV--SQ-----YKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~-------~~~~~G~vfCy~Ci~~~~--~~-----~~~CPv~~~~~~ 382 (393)
+...|-||++.+.... +++.|-|.||-.||.+|- .+ ...||.|+.+.+
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 5678999999988876 566799999999999999 45 478999997754
No 58
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.06 E-value=0.0029 Score=63.60 Aligned_cols=52 Identities=17% Similarity=0.517 Sum_probs=38.3
Q ss_pred CCCCCCCCCCCCCc---eeccCccccccHHHHHHHhhcC---CCCCCCCCCCCcCCee
Q 016213 336 RTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIR 387 (393)
Q Consensus 336 ~~~CpiC~~~~~np---~~~~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~~~~~l~ 387 (393)
...|.||-+-.-|- ..+.+|||+|--.|+.+|.+.. ..||+|+..+...++.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~ 61 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA 61 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence 45799996644332 4566799999999999999964 5799999555444443
No 59
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.94 E-value=0.0022 Score=49.87 Aligned_cols=49 Identities=22% Similarity=0.525 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCC-C---c-eecc--CccccccHHHHHHHhhc-----------CCCCCCCCCCCCcC
Q 016213 336 RTICPLCSQKRA-N---P-SVVT--VSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 384 (393)
Q Consensus 336 ~~~CpiC~~~~~-n---p-~~~~--~~G~vfCy~Ci~~~~~~-----------~~~CPv~~~~~~~~ 384 (393)
...|+||...+. + | .+++ .||.+|-..|+.+|+.. .|+||.|+.+++.+
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 357999999865 3 3 3554 69999999999999973 25799999987653
No 60
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=95.77 E-value=0.0042 Score=45.83 Aligned_cols=48 Identities=21% Similarity=0.523 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCe
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 386 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l 386 (393)
...|-.|+..-+..++++ |||+-|..|-- ++..+-||+|+.|...++.
T Consensus 7 ~~~~~~~~~~~~~~~~~p-CgH~I~~~~f~--~~rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 7 EQPCVFCGFVGTKGTVLP-CGHLICDNCFP--GERYNGCPFCGTPFEFDDP 54 (55)
T ss_pred ceeEEEcccccccccccc-ccceeeccccC--hhhccCCCCCCCcccCCCC
Confidence 456889999988999987 99999999964 4566899999999877653
No 61
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.75 E-value=0.0067 Score=57.71 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=31.1
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhh
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS 369 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~ 369 (393)
+-.-|.+|+++..||++++ .||+||..||.+|+-
T Consensus 42 ~FdcCsLtLqPc~dPvit~-~GylfdrEaILe~il 75 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDPVITP-DGYLFDREAILEYIL 75 (303)
T ss_pred CcceeeeecccccCCccCC-CCeeeeHHHHHHHHH
Confidence 3567999999999999997 999999999999984
No 62
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=95.69 E-value=0.0025 Score=69.53 Aligned_cols=48 Identities=21% Similarity=0.483 Sum_probs=37.8
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcC--CCCCCCCCCCCcCCe
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQI 386 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~~~l 386 (393)
..|++|.+ ...+.++ .|||+||+.|+.+.++.. ..||+|+.....+++
T Consensus 455 ~~c~ic~~-~~~~~it-~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFIT-RCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc-cccceee-cccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 79999999 4445555 599999999999999854 579999876554443
No 63
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.0055 Score=61.19 Aligned_cols=43 Identities=23% Similarity=0.548 Sum_probs=33.4
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
...|-||.....|..-++ |||+.| |+...-.- ..||||+..+.
T Consensus 305 p~lcVVcl~e~~~~~fvp-cGh~cc--ct~cs~~l-~~CPvCR~rI~ 347 (355)
T KOG1571|consen 305 PDLCVVCLDEPKSAVFVP-CGHVCC--CTLCSKHL-PQCPVCRQRIR 347 (355)
T ss_pred CCceEEecCCccceeeec-CCcEEE--chHHHhhC-CCCchhHHHHH
Confidence 457999999999977787 999999 77654332 44999997653
No 64
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.011 Score=59.54 Aligned_cols=54 Identities=19% Similarity=0.249 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy 390 (393)
-+.|.+.+.+..+|+.+. .|-||-+.-|+.||+++|+=|++|++++-++||++-
T Consensus 40 ~~hC~lt~~Pfe~PvC~~-dg~vFd~~~Ivp~lkk~g~nP~tG~kl~~~dLIkL~ 93 (518)
T KOG0883|consen 40 FNHCSLTMLPFEDPVCTV-DGTVFDLTAIVPWLKKHGTNPITGQKLDGKDLIKLK 93 (518)
T ss_pred hhhceeccccccCccccc-CCcEEeeehhhHHHHHcCCCCCCCCccccccceeee
Confidence 468999999999998875 999999999999999999999999999999999874
No 65
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.27 E-value=0.046 Score=55.43 Aligned_cols=97 Identities=16% Similarity=0.323 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH----HhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCc-e
Q 016213 278 TMLDYAQTGLIAAVFFFKMMEW----WYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQK--RANP-S 350 (393)
Q Consensus 278 ~~~~~~~~~lp~~iF~lkfLeW----Wyss~~~r~~~~~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~--~~np-~ 350 (393)
.+...+.++||..+=..-+++= |++.|+ ||+|---+ .+. -.-+-.+|||=++. =.|| .
T Consensus 287 v~v~aG~~Alp~Llk~~~v~~~~~~~W~~~de--------LPveIeL~------~~~-~fHSvF~CPVlKeqtsdeNPPm 351 (394)
T KOG2817|consen 287 VLVNAGCIALPQLLKYKSVMELKHGEWNTKDE--------LPVEIELG------KEY-HFHSVFICPVLKEQTSDENPPM 351 (394)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHhccCcccccc--------Cccceecc------ccc-cccceeecccchhhccCCCCCe
Confidence 3445566777777766666666 665433 44332111 000 02246899998875 4565 5
Q ss_pred eccCccccccHHHHHHHhhcCC---CCCCCCCCCCcCCeeeCc
Q 016213 351 VVTVSGFVFCYACIFKYVSQYK---RCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 351 ~~~~~G~vfCy~Ci~~~~~~~~---~CPv~~~~~~~~~l~riy 390 (393)
.+. ||||-|.+-+.+-.++.. +||=|-.....++-+|||
T Consensus 352 ~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~ 393 (394)
T KOG2817|consen 352 MLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLY 393 (394)
T ss_pred eee-ccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhccccc
Confidence 676 999999999988776654 799998888888888887
No 66
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.02 E-value=0.0028 Score=61.49 Aligned_cols=41 Identities=22% Similarity=0.569 Sum_probs=34.9
Q ss_pred CCCCCCCCCCCCCceeccCccc-cccHHHHHHHhhcCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~-vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
...|.||++..+|-..++ ||| |-|+.|-..- +.||||++.+
T Consensus 300 ~~LC~ICmDaP~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLE-CGHMVTCTKCGKRM----NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEee-cCcEEeehhhcccc----ccCchHHHHH
Confidence 578999999999999998 999 5799998632 4999999764
No 67
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.86 E-value=0.005 Score=66.56 Aligned_cols=46 Identities=20% Similarity=0.413 Sum_probs=37.8
Q ss_pred CCCCCCCCCCCCCCcee--ccCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSV--VTVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~--~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
....||+|.....+--+ =.+|||.||-.|+..|-+-.+.||+|+..
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~E 169 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGE 169 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhh
Confidence 35789999988776522 22599999999999999999999999865
No 68
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=94.78 E-value=0.014 Score=45.86 Aligned_cols=48 Identities=23% Similarity=0.454 Sum_probs=39.4
Q ss_pred CCCCCCCCCCCCC-ceeccCccccccHHHHHHHhhc---CCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p~~~~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~~~~ 383 (393)
.+.||-|.-+-.| |-|+--|-|.|-.-||.+|+.. ++.||+|++.-..
T Consensus 31 dg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 31 DGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 5678888888766 7777789999999999999974 4799999976543
No 69
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.77 E-value=0.012 Score=59.32 Aligned_cols=46 Identities=15% Similarity=0.568 Sum_probs=38.9
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC--CCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 382 (393)
-..|.||-+.=+|--+-+ |||..|-.|+..|-... +.||.|+..++
T Consensus 369 FeLCKICaendKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 369 FELCKICAENDKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHHHhhccCCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 467999999888877755 99999999999998654 68999997764
No 70
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=94.71 E-value=0.016 Score=59.46 Aligned_cols=43 Identities=21% Similarity=0.613 Sum_probs=35.8
Q ss_pred CCCCCCCCCCCce---eccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 338 ICPLCSQKRANPS---VVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 338 ~CpiC~~~~~np~---~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
+||+|++.+..-+ +...|-|.|--+|+.+| .+..||||+.-.+
T Consensus 177 TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 177 TCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS 222 (493)
T ss_pred CcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence 7999999987765 55569999999999988 4679999996444
No 71
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=94.48 E-value=0.023 Score=47.15 Aligned_cols=46 Identities=17% Similarity=0.439 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCce----------------eccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPS----------------VVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~~~np~----------------~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
-+.|.||+..|-|++ +=-+|.|.|-+-||.+||++.+.||.|.++=
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 357888887654332 2346899999999999999999999998763
No 72
>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=94.42 E-value=0.047 Score=39.44 Aligned_cols=40 Identities=18% Similarity=0.536 Sum_probs=29.8
Q ss_pred CCCCCCC--CCCCceeccCcc-----ccccHHHHHHHhhcCC--CCCCCC
Q 016213 338 ICPLCSQ--KRANPSVVTVSG-----FVFCYACIFKYVSQYK--RCPVTL 378 (393)
Q Consensus 338 ~CpiC~~--~~~np~~~~~~G-----~vfCy~Ci~~~~~~~~--~CPv~~ 378 (393)
.|-||.. .-.++.+.+ |. +.+-..|+.+|+.+.+ .||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4889986 344555544 53 8889999999997654 899995
No 73
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=94.40 E-value=0.017 Score=56.73 Aligned_cols=42 Identities=24% Similarity=0.441 Sum_probs=33.9
Q ss_pred CCCCCCCCCCCCc-eeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np-~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
.-|--|..+|.-= .+++ |-|||||+|+. ....+-||.|..++
T Consensus 91 HfCd~Cd~PI~IYGRmIP-CkHvFCl~CAr--~~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIP-CKHVFCLECAR--SDSDKICPLCDDRV 133 (389)
T ss_pred EeecccCCcceeeecccc-cchhhhhhhhh--cCccccCcCcccHH
Confidence 4588899988764 5787 99999999996 34468999998765
No 74
>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=94.10 E-value=0.027 Score=46.36 Aligned_cols=30 Identities=37% Similarity=0.677 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCCCce-eccCccccccHHHHH
Q 016213 336 RTICPLCSQKRANPS-VVTVSGFVFCYACIF 365 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-~~~~~G~vfCy~Ci~ 365 (393)
...|++|++.+.|.+ +.-+|||||.+.|+.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 557999999999874 344599999999974
No 75
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.27 E-value=0.084 Score=50.56 Aligned_cols=57 Identities=18% Similarity=0.232 Sum_probs=45.9
Q ss_pred CCCCCCCCCCCCCCCc---eeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCccC
Q 016213 334 PDRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 392 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np---~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy~~ 392 (393)
....+|||-+-++..- +++-.|||||-++-+.+.= ...|++|+.+...+|+|-|-.+
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvlNg~ 168 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVLNGT 168 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEeeCCC
Confidence 3478999999988775 5677799999997765432 5689999999999999987653
No 76
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.20 E-value=0.067 Score=52.01 Aligned_cols=40 Identities=23% Similarity=0.589 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCCCCCCcee---ccCccccccHHHHHHHhhcCC
Q 016213 333 PPDRTICPLCSQKRANPSV---VTVSGFVFCYACIFKYVSQYK 372 (393)
Q Consensus 333 p~~~~~CpiC~~~~~np~~---~~~~G~vfCy~Ci~~~~~~~~ 372 (393)
+.....|.+|.+.+.|-.. -++.+|-||++|--+.|+.++
T Consensus 265 ~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred CCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhc
Confidence 3345789999999999742 235699999999999999754
No 77
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=93.10 E-value=0.047 Score=52.39 Aligned_cols=45 Identities=22% Similarity=0.366 Sum_probs=40.9
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC--CCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~ 380 (393)
+..||+-.++|.||.+-.-|||||-..-|..++... -+|||-|.+
T Consensus 176 s~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLGCE 222 (262)
T ss_pred cccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeecccccCC
Confidence 689999999999999988899999999999999874 589998765
No 78
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.03 E-value=0.067 Score=53.00 Aligned_cols=44 Identities=25% Similarity=0.611 Sum_probs=38.6
Q ss_pred CCCCCCCCCCCCCCcee-ccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSV-VTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~-~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
+-..||+|...+.-|.. +. .||.-|-.|-. +..++||.|+.+++
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~-nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCD-NGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecC-CCcEehhhhhh---hhcccCCccccccc
Confidence 45789999999999986 55 89999999986 56789999999987
No 79
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=92.83 E-value=0.021 Score=56.14 Aligned_cols=46 Identities=20% Similarity=0.456 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCCCceeccCc--c--ccccHHHHHHHhhcCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVS--G--FVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~--G--~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
..+.||+|+....-..+...- | |.+|.-|-++|--...+||.|+..
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 357999999987766665532 4 789999999999889999999854
No 80
>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=92.68 E-value=0.12 Score=37.59 Aligned_cols=43 Identities=21% Similarity=0.420 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhc---C--CCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ---Y--KRCPVTLMP 380 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~---~--~~CPv~~~~ 380 (393)
..||+..+.++.|+=...|-|+-|++= ..|++. . -+||+|++|
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence 479999999999986666999988754 245542 2 369999875
No 81
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.40 E-value=0.041 Score=60.98 Aligned_cols=47 Identities=21% Similarity=0.465 Sum_probs=37.3
Q ss_pred CCCCCCCCCCCC-----Cce-eccCccccccHHHHHHHhhcC--CCCCCCCCCCC
Q 016213 336 RTICPLCSQKRA-----NPS-VVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~-----np~-~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 382 (393)
...|+||...+. =|. -|+||-|-|--.|+++|.+.. .+||+|+...+
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 468999987643 343 467899999999999999864 68999996544
No 82
>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=91.97 E-value=0.087 Score=33.10 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCc-eeccCccccc
Q 016213 338 ICPLCSQKRANP-SVVTVSGFVF 359 (393)
Q Consensus 338 ~CpiC~~~~~np-~~~~~~G~vf 359 (393)
.||-|.+.+... ..++.|||+|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 699999987554 4677788887
No 83
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.26 E-value=0.18 Score=50.41 Aligned_cols=45 Identities=20% Similarity=0.496 Sum_probs=39.1
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHh--hcCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYV--SQYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~--~~~~~CPv~~~~ 380 (393)
+...|-||-+.++--++++ |||-.|--|.++-- -..+.||+|+..
T Consensus 60 en~~C~ICA~~~TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 60 ENMNCQICAGSTTYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccceeEEecCCceEEEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence 5689999999999999997 99999999998654 467899999854
No 84
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=90.13 E-value=0.056 Score=61.73 Aligned_cols=43 Identities=21% Similarity=0.474 Sum_probs=39.0
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
...|++|++.+.|-..+..|||-+|-.|..-|+..+.+||+|.
T Consensus 1153 ~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~k 1195 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICK 1195 (1394)
T ss_pred ccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchh
Confidence 5689999999998765556999999999999999999999997
No 85
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=89.29 E-value=0.13 Score=51.12 Aligned_cols=46 Identities=22% Similarity=0.512 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCCCceecc---Ccc--ccccHHHHHHHhhcCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVT---VSG--FVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~---~~G--~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
..+.||+|+....-..+.. .-| |..|--|-++|=-...+||.|+..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 4679999999875444422 134 899999999999999999999974
No 86
>PRK04023 DNA polymerase II large subunit; Validated
Probab=88.54 E-value=0.34 Score=54.56 Aligned_cols=55 Identities=18% Similarity=0.300 Sum_probs=39.1
Q ss_pred CCCCCCCCCCCCCCCCCceeccCccc-----cccHHHHHHHhhcCCCCCCCCCCCCcCCeeeC
Q 016213 332 LPPDRTICPLCSQKRANPSVVTVSGF-----VFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 389 (393)
Q Consensus 332 ~p~~~~~CpiC~~~~~np~~~~~~G~-----vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 389 (393)
++.....||-|+... .-..|+.||. .||..|-.. .....||-|+..++...-++|
T Consensus 622 VEVg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~--~~~y~CPKCG~El~~~s~~~i 681 (1121)
T PRK04023 622 VEIGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE--VEEDECEKCGREPTPYSKRKI 681 (1121)
T ss_pred ecccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc--CCCCcCCCCCCCCCccceEEe
Confidence 455678999999985 3456777995 599999433 334679999988765544443
No 87
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.26 E-value=0.31 Score=49.81 Aligned_cols=46 Identities=20% Similarity=0.420 Sum_probs=33.9
Q ss_pred CCCCCCCCCCCCCC--ceeccCccccccHHHHHHHhhc--------CCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN--PSVVTVSGFVFCYACIFKYVSQ--------YKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~n--p~~~~~~G~vfCy~Ci~~~~~~--------~~~CPv~~~~ 380 (393)
.-..|-||...-.- -.+..+|+||||..|..+|..- .-+||-++-+
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 35789999987544 2344459999999999999862 3489876543
No 88
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=87.96 E-value=0.29 Score=50.29 Aligned_cols=35 Identities=23% Similarity=0.593 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ 370 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~ 370 (393)
+..+||||+.-.++|.+++ |||-.|..|+..-+.+
T Consensus 3 eelkc~vc~~f~~epiil~-c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPIILP-CSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhccCceEee-cccHHHHHHHHhhccc
Confidence 3568999999999999997 9999999999987754
No 89
>PLN02189 cellulose synthase
Probab=87.76 E-value=0.36 Score=54.72 Aligned_cols=46 Identities=22% Similarity=0.562 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc--CCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~ 381 (393)
...+|.||++.+-- + ++|..||+--|.+|- +|-++ ++.||-|+.+-
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRY 86 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 35689999998542 2 678889999999998 67655 46899998653
No 90
>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=87.51 E-value=0.3 Score=42.73 Aligned_cols=43 Identities=23% Similarity=0.488 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCC--ceeccCcc------ccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRAN--PSVVTVSG------FVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~n--p~~~~~~G------~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
...|.||.+.|.+ -+|.-+|| ++||-.|+.+|-+++++-|-=+
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR 76 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNR 76 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence 5689999999988 34322366 7999999999987777777543
No 91
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.26 E-value=0.34 Score=47.52 Aligned_cols=43 Identities=23% Similarity=0.579 Sum_probs=35.0
Q ss_pred CCCCCCCC------CCCceeccCccccccHHHHHHHhhcC-CCCCCCCCCC
Q 016213 338 ICPLCSQK------RANPSVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPA 381 (393)
Q Consensus 338 ~CpiC~~~------~~np~~~~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~ 381 (393)
.|-||... ...|.++. |||.+|..|+...+... ..||-|+.+.
T Consensus 5 ~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 5 ECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred ceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence 58888775 34578987 99999999999877765 5799999884
No 92
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=86.89 E-value=0.28 Score=48.78 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=35.5
Q ss_pred CCCCCCCCCCCCCCcee-c-cCcc--ccccHHHHHHHhhcCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSV-V-TVSG--FVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~-~-~~~G--~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
..+.||+|+....-..+ . ..-| |..|--|-++|=-...+||.|+..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 46799999998654433 1 1234 778999999999999999999964
No 93
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=86.74 E-value=0.42 Score=39.01 Aligned_cols=36 Identities=19% Similarity=0.570 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
...|-+|...+.. =|+-||-.|++ +.|.|.+||+.+
T Consensus 44 ~~~C~~CK~~v~q------~g~~YCq~CAY----kkGiCamCGKki 79 (90)
T PF10235_consen 44 SSKCKICKTKVHQ------PGAKYCQTCAY----KKGICAMCGKKI 79 (90)
T ss_pred Ccccccccccccc------CCCccChhhhc----ccCcccccCCee
Confidence 5689999876542 48999999998 679999999987
No 94
>PLN02436 cellulose synthase A
Probab=86.39 E-value=0.48 Score=53.91 Aligned_cols=46 Identities=20% Similarity=0.528 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc--CCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~ 381 (393)
...+|-||++.+-- + ++|..||+--|.+|- +|-++ ++.||-|+.+-
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRY 88 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 35689999998522 2 678899999999998 67665 46899998653
No 95
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=86.37 E-value=0.28 Score=49.77 Aligned_cols=42 Identities=19% Similarity=0.538 Sum_probs=35.6
Q ss_pred CCCCCCCCCC--CCCc--eeccCccccccHHHHHHHhhcC--CCCCCCC
Q 016213 336 RTICPLCSQK--RANP--SVVTVSGFVFCYACIFKYVSQY--KRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~--~~np--~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~ 378 (393)
...|-.|++. ++|. -+++ |.|+|--+|++++++++ ..||-|+
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr 412 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR 412 (518)
T ss_pred hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence 4679999996 4554 4787 99999999999999987 5799998
No 96
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=86.06 E-value=0.63 Score=40.60 Aligned_cols=46 Identities=26% Similarity=0.650 Sum_probs=35.0
Q ss_pred CCCCCCCCCCCCceecc---CccccccHHHHH---HHhhcCCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVT---VSGFVFCYACIF---KYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~---~~G~vfCy~Ci~---~~~~~~~~CPv~~~~~~ 382 (393)
..|-||.+.-.+..-+. .|||--|+-|-. ++-.-+..||||+..-+
T Consensus 81 YeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFK 132 (140)
T PF05290_consen 81 YECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFK 132 (140)
T ss_pred eeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccc
Confidence 57999999888775443 499999999854 44456789999986543
No 97
>PHA03096 p28-like protein; Provisional
Probab=85.97 E-value=0.42 Score=47.11 Aligned_cols=45 Identities=16% Similarity=0.312 Sum_probs=34.2
Q ss_pred CCCCCCCCCCCCc-------eeccCccccccHHHHHHHhhcC---CCCCCCCCCC
Q 016213 337 TICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np-------~~~~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~ 381 (393)
.+|-||++.+..- .+++-|-|+||-.||..|..+. ..||.|+..-
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~ 233 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLN 233 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchh
Confidence 6899999976542 4677899999999999999753 4566665543
No 98
>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=84.75 E-value=0.12 Score=40.13 Aligned_cols=40 Identities=30% Similarity=0.558 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
..||.|.+++. ...|+..|-.|-.+|. ....||-|+.++.
T Consensus 2 ~~CP~C~~~L~-----~~~~~~~C~~C~~~~~-~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELE-----WQGGHYHCEACQKDYK-KEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEE-----EETTEEEETTT--EEE-EEEE-TTT-SB-E
T ss_pred CcCCCCCCccE-----EeCCEEECccccccce-ecccCCCcccHHH
Confidence 47999998732 3358999999998654 5589999999874
No 99
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.64 E-value=0.55 Score=48.24 Aligned_cols=41 Identities=24% Similarity=0.502 Sum_probs=33.4
Q ss_pred CCCCCCCCCCCC-----CceeccCccccccHHHHHHHhhcCCCCCCC
Q 016213 336 RTICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVSQYKRCPVT 377 (393)
Q Consensus 336 ~~~CpiC~~~~~-----np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~ 377 (393)
-..||.|+..+. |...+. |||-|||.|-.+|...++.|.-|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence 567999998754 456787 99999999999999888777544
No 100
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=81.10 E-value=1.1 Score=51.17 Aligned_cols=45 Identities=22% Similarity=0.653 Sum_probs=35.0
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc--CCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~ 380 (393)
+..+|-||++.+-- + ++|..||+--|.+|- +|=++ ++.||-|+.+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCc
Confidence 35689999997432 2 678899999999998 56554 4689999854
No 101
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.97 E-value=0.62 Score=47.86 Aligned_cols=51 Identities=27% Similarity=0.526 Sum_probs=34.3
Q ss_pred CCCCCCCCC-CCCCc---eeccCccccccHHHHHHHhhcC------CCCC--CCCCCCCcCCee
Q 016213 336 RTICPLCSQ-KRANP---SVVTVSGFVFCYACIFKYVSQY------KRCP--VTLMPATVEQIR 387 (393)
Q Consensus 336 ~~~CpiC~~-~~~np---~~~~~~G~vfCy~Ci~~~~~~~------~~CP--v~~~~~~~~~l~ 387 (393)
...|.||.. .+.+. .+.. |||-||..|..+|++.. .+|| .|...++.++..
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~ 208 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCR 208 (384)
T ss_pred cccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHh
Confidence 457999994 33331 3555 99999999999999832 4776 355555554443
No 102
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.67 E-value=1.5 Score=40.23 Aligned_cols=48 Identities=17% Similarity=0.485 Sum_probs=37.0
Q ss_pred CCCCCCCCCC-----CCCcee--ccCccccccHHHHHHHhhc-----------CCCCCCCCCCCCcC
Q 016213 336 RTICPLCSQK-----RANPSV--VTVSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 384 (393)
Q Consensus 336 ~~~CpiC~~~-----~~np~~--~~~~G~vfCy~Ci~~~~~~-----------~~~CPv~~~~~~~~ 384 (393)
.+.|-||.-. +.|-+. ++ ||.-|-.-|+++|++. .|.||-|..|++++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~q-CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQ-CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hhcccceeeeecCCccccccccccc-cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 4678888653 444432 45 9999999999999973 47999999998764
No 103
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.50 E-value=0.8 Score=50.93 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCCC-ceeccCccccccHHHHHHHhh
Q 016213 336 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVS 369 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p~~~~~~G~vfCy~Ci~~~~~ 369 (393)
...|-+|+.++-. |-++-+|||.|-..|+.+.+.
T Consensus 817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence 5789999999666 656566999999999999884
No 104
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=79.90 E-value=0.97 Score=32.50 Aligned_cols=43 Identities=23% Similarity=0.557 Sum_probs=26.6
Q ss_pred CCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
.|--|=-.-++ .+..+-|--|..|+..-+....+||+|++++-
T Consensus 4 nCKsCWf~~k~--Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 4 NCKSCWFANKG--LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ---SS-S--SS--EEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cChhhhhcCCC--eeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 35555544444 44457899999999999999999999998763
No 105
>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=79.83 E-value=2 Score=30.15 Aligned_cols=39 Identities=18% Similarity=0.432 Sum_probs=24.6
Q ss_pred CCCCCCCCCCceecc--CccccccHHHHHHHhhcCC--CCCCC
Q 016213 339 CPLCSQKRANPSVVT--VSGFVFCYACIFKYVSQYK--RCPVT 377 (393)
Q Consensus 339 CpiC~~~~~np~~~~--~~G~vfCy~Ci~~~~~~~~--~CPv~ 377 (393)
|-+|.+.++--..++ .|+--+-..|+..|++... +||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 678888888777666 4888899999999998765 79987
No 106
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=79.65 E-value=0.94 Score=29.84 Aligned_cols=11 Identities=36% Similarity=0.477 Sum_probs=8.6
Q ss_pred cCCCCCCCCCC
Q 016213 370 QYKRCPVTLMP 380 (393)
Q Consensus 370 ~~~~CPv~~~~ 380 (393)
..-+||+|+.+
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 55799999865
No 107
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.08 E-value=1.2 Score=44.22 Aligned_cols=54 Identities=26% Similarity=0.422 Sum_probs=41.0
Q ss_pred CCCCCCCCCCC--CCCc-eeccCccccccHHHHHHHhhcCC----CCCCCCCCCCcCCeeeCc
Q 016213 335 DRTICPLCSQK--RANP-SVVTVSGFVFCYACIFKYVSQYK----RCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 335 ~~~~CpiC~~~--~~np-~~~~~~G~vfCy~Ci~~~~~~~~----~CPv~~~~~~~~~l~riy 390 (393)
.-.+||+-.+. -.|| .++. ||||--..-+. -+.++| +||-|-.-...++++|+|
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~-~LS~nG~~~FKCPYCP~~~~~~~~~rvr 395 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLE-CGHVISKEALS-VLSQNGVLSFKCPYCPEMSKYENILRVR 395 (396)
T ss_pred ceeeccccHhhhcccCCCeeee-ccceeeHHHHH-HHhhcCcEEeeCCCCCcchhhhhhhccc
Confidence 35789997774 4555 6676 99999987765 455555 899998777788888886
No 108
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=78.99 E-value=1.3 Score=48.81 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCCCc------eeccCccccccHHHHHHHhhc------CCCCCCCC
Q 016213 335 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQ------YKRCPVTL 378 (393)
Q Consensus 335 ~~~~CpiC~~~~~np------~~~~~~G~vfCy~Ci~~~~~~------~~~CPv~~ 378 (393)
+...|++|.....+| +.+..|||-||+-||..|..+ +-.|+.|.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~ 150 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCE 150 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHH
Confidence 467788888777773 445579999999999999964 34567774
No 109
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.35 E-value=1.7 Score=41.16 Aligned_cols=44 Identities=20% Similarity=0.410 Sum_probs=35.1
Q ss_pred CCCCCCCCCCCc-eeccCccccccHHHHHHHhhc--------CCCCCCCCCCC
Q 016213 338 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQ--------YKRCPVTLMPA 381 (393)
Q Consensus 338 ~CpiC~~~~~np-~~~~~~G~vfCy~Ci~~~~~~--------~~~CPv~~~~~ 381 (393)
.|.+|..++..- ++--+|-|+|-|+|.-+|-.+ -..||.|..++
T Consensus 52 NC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 52 NCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 599999987663 443359999999999999864 24899999875
No 110
>PRK05978 hypothetical protein; Provisional
Probab=78.34 E-value=1.4 Score=39.34 Aligned_cols=33 Identities=24% Similarity=0.515 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 384 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~ 384 (393)
...||-|++ |++| ..|++-+.+||+|+.+.+.+
T Consensus 33 ~grCP~CG~-----------G~LF-----~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGE-----------GKLF-----RAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCC-----------Cccc-----ccccccCCCccccCCccccC
Confidence 678999987 3444 27888999999999887643
No 111
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=78.07 E-value=2.7 Score=31.08 Aligned_cols=43 Identities=19% Similarity=0.309 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCCC--Cc-eeccCccccccHHHHHHHhhcCCCCCC--CCCCC
Q 016213 335 DRTICPLCSQKRA--NP-SVVTVSGFVFCYACIFKYVSQYKRCPV--TLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~--np-~~~~~~G~vfCy~Ci~~~~~~~~~CPv--~~~~~ 381 (393)
...+|++|+++++ +. ++++.||-++-..|-. ..+.|=. |+.+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~----~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE----KAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh----hCCceEeccCCCCc
Confidence 3568999999994 44 6899999999998864 5677766 55443
No 112
>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=77.64 E-value=1.5 Score=43.07 Aligned_cols=36 Identities=19% Similarity=0.485 Sum_probs=29.2
Q ss_pred ccCccccccHHHHHHHhh-cCCCCCCCCCCCCcCCee
Q 016213 352 VTVSGFVFCYACIFKYVS-QYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 352 ~~~~G~vfCy~Ci~~~~~-~~~~CPv~~~~~~~~~l~ 387 (393)
+.+|||-.|-.|...-.. +.+-||.|+..+-.++++
T Consensus 20 in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr 56 (300)
T KOG3800|consen 20 INECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR 56 (300)
T ss_pred eccccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence 346999999999988765 458999999988766655
No 113
>PLN02195 cellulose synthase A
Probab=77.55 E-value=2 Score=48.65 Aligned_cols=47 Identities=21% Similarity=0.482 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCC-----Cc-eeccCccccccHHHHHHHhhc--CCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRA-----NP-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~-----np-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~ 382 (393)
...+|-||++.+- +| ++|..||+--|.+|- +|=++ ++.||-|+.+-+
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCCCccccchh-hhhhhcCCccCCccCCccc
Confidence 3458999999643 23 678889999999998 66554 468999997654
No 114
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=76.93 E-value=1.8 Score=49.44 Aligned_cols=46 Identities=26% Similarity=0.609 Sum_probs=35.6
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc--CCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~ 381 (393)
+..+|-||++.+-- | ++|..||+--|.+|- +|=++ ++.||-|+.+-
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~~~g~~~cp~c~t~y 67 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYERSEGNQCCPQCNTRY 67 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCch
Confidence 46789999997432 2 678899999999998 66554 46899998653
No 115
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=76.42 E-value=1.4 Score=42.00 Aligned_cols=49 Identities=16% Similarity=0.205 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhc--CCCCCC--CCCCCCcC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPV--TLMPATVE 384 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~--~~~CPv--~~~~~~~~ 384 (393)
.+.|||..++..-|.+.+.|.|+|-.+-|.+++.. ...||+ |......+
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~~~Csq~~~~~ 241 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPRLICSQKEVVD 241 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecchhhcchheecc
Confidence 68999999999999988889999999999999984 467884 54444333
No 116
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=75.78 E-value=3.3 Score=32.89 Aligned_cols=47 Identities=17% Similarity=0.359 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc-CCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~ 381 (393)
+..+|-||++.+-- + +++..||+-.|.+|----.++ ++.||-|+.+-
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 46789999997432 2 567789999999998544443 57899998654
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.41 E-value=1.4 Score=50.98 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=34.7
Q ss_pred CCCCCCCCCCCCceeccCcccc-----ccHHHHHHHhhc---CCCCCCCCCCCCcCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQ---YKRCPVTLMPATVEQ 385 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~v-----fCy~Ci~~~~~~---~~~CPv~~~~~~~~~ 385 (393)
..||-|+..... ..|+.||.. .|-.|-.+.-.. ...||-|+.++....
T Consensus 668 rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~ 723 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQ 723 (1337)
T ss_pred EECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccc
Confidence 689999997543 478889966 499998764433 248999998875443
No 118
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.50 E-value=1.9 Score=39.21 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=8.6
Q ss_pred CCCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRAN 348 (393)
Q Consensus 336 ~~~CpiC~~~~~n 348 (393)
-.+||+|+-...+
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 3578888765544
No 119
>PLN02400 cellulose synthase
Probab=74.34 E-value=1.8 Score=49.57 Aligned_cols=45 Identities=20% Similarity=0.525 Sum_probs=34.9
Q ss_pred CCCCCCCCCCCCCC-----c-eeccCccccccHHHHHHHhhc--CCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~n-----p-~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~ 380 (393)
+..+|-||++.+-- | ++|..||+--|.+|- +|=++ ++.||-|+.+
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq~CPQCkTr 87 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQCCPQCKTR 87 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCccCcccCCc
Confidence 35689999997432 2 678889999999998 66554 4689999854
No 120
>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=72.57 E-value=2.3 Score=35.98 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCC----CCceeccCccccccHH
Q 016213 335 DRTICPLCSQKR----ANPSVVTVSGFVFCYA 362 (393)
Q Consensus 335 ~~~~CpiC~~~~----~np~~~~~~G~vfCy~ 362 (393)
.+.+||-|+..+ ++|.||+.||.+|=-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 367899999973 5799999999988554
No 121
>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=71.65 E-value=2.4 Score=36.82 Aligned_cols=27 Identities=30% Similarity=0.445 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCC----CCceeccCccccccH
Q 016213 335 DRTICPLCSQKR----ANPSVVTVSGFVFCY 361 (393)
Q Consensus 335 ~~~~CpiC~~~~----~np~~~~~~G~vfCy 361 (393)
.+.+||-|++.+ ++|.+|+-||.+|=-
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 367899999974 679999999998744
No 122
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.51 E-value=6.8 Score=40.93 Aligned_cols=47 Identities=23% Similarity=0.519 Sum_probs=34.9
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC--------CCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--------KRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~--------~~CPv~~~~~ 381 (393)
....|.||.....+.++...|||.||-.|...|+.+. -+||..+-+.
T Consensus 69 ~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a 123 (444)
T KOG1815|consen 69 GDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPA 123 (444)
T ss_pred ccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccc
Confidence 3568999999888744433499999999999999742 2577665544
No 123
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=71.12 E-value=3.5 Score=45.32 Aligned_cols=50 Identities=10% Similarity=0.094 Sum_probs=42.4
Q ss_pred CCCCCCCCCCCCCce-eccCccccccHHHHHHHhhcCCCCCC--CCCCCCcCC
Q 016213 336 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPV--TLMPATVEQ 385 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-~~~~~G~vfCy~Ci~~~~~~~~~CPv--~~~~~~~~~ 385 (393)
...|.+|.-+++--. -+++|||..--.|+.+|..++..||- |+.++.-..
T Consensus 779 ~~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~~~ 831 (839)
T KOG0269|consen 779 SAKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHYSS 831 (839)
T ss_pred hcCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCccccCCccccccc
Confidence 468999999998875 48899999999999999999999975 887765433
No 124
>PF12773 DZR: Double zinc ribbon
Probab=71.06 E-value=1.6 Score=31.08 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCCCCC
Q 016213 332 LPPDRTICPLCSQKRA 347 (393)
Q Consensus 332 ~p~~~~~CpiC~~~~~ 347 (393)
++.+...||-|+..+.
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 3445677888887777
No 125
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=70.88 E-value=2.5 Score=46.40 Aligned_cols=47 Identities=17% Similarity=0.321 Sum_probs=37.0
Q ss_pred CCCCCCCCCCCCCce-eccCccccccHHHHHHHhhcCCCCC-CCCCCCC
Q 016213 336 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCP-VTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-~~~~~G~vfCy~Ci~~~~~~~~~CP-v~~~~~~ 382 (393)
...|.+|.-.++--+ +|-+||||.--.|..+|.+..-.|| -||-.+-
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~CpsGCGC~C~ 1076 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPSGCGCHCL 1076 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCCCCCcCch
Confidence 345788777766654 6778999999999999999988998 5665543
No 126
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=70.82 E-value=2.1 Score=40.94 Aligned_cols=38 Identities=24% Similarity=0.516 Sum_probs=25.6
Q ss_pred CCCCCCCCCC-CCceeccCccccccHHHHHHHhhcC-CCC
Q 016213 337 TICPLCSQKR-ANPSVVTVSGFVFCYACIFKYVSQY-KRC 374 (393)
Q Consensus 337 ~~CpiC~~~~-~np~~~~~~G~vfCy~Ci~~~~~~~-~~C 374 (393)
..|-.|.... .+|--++-|+||||-+|...-.... ..|
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lC 43 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLC 43 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCccccccc
Confidence 3577777633 5565566699999999986555432 445
No 127
>PHA02862 5L protein; Provisional
Probab=70.82 E-value=3.4 Score=36.65 Aligned_cols=47 Identities=19% Similarity=0.305 Sum_probs=33.4
Q ss_pred CCCCCCCCCC---CCCceeccCccccccHHHHHHHhhcC--CCCCCCCCCCC
Q 016213 336 RTICPLCSQK---RANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~---~~np~~~~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 382 (393)
+.+|=||.+. ..+|+-++-+--.--..|+.+|+... ..||.|+.+-.
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 3579999886 34566554344455679999999754 58999997753
No 128
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=70.80 E-value=0.86 Score=33.32 Aligned_cols=13 Identities=31% Similarity=0.491 Sum_probs=7.0
Q ss_pred CCCCCCCCCCCcC
Q 016213 372 KRCPVTLMPATVE 384 (393)
Q Consensus 372 ~~CPv~~~~~~~~ 384 (393)
++||||+.+++.+
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 4999999988754
No 129
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=70.75 E-value=2.6 Score=46.15 Aligned_cols=51 Identities=24% Similarity=0.449 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC-----CCCCCCCCCCCcCCee
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY-----KRCPVTLMPATVEQIR 387 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~-----~~CPv~~~~~~~~~l~ 387 (393)
+..||||+..++-|+-.-.|.|.=|.+=.. |+..+ -+||||.+....++|+
T Consensus 306 SL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~-~lq~n~~~pTW~CPVC~~~~~~e~l~ 361 (636)
T KOG2169|consen 306 SLNCPLSKMRMSLPARGHTCKHLQCFDALS-YLQMNEQKPTWRCPVCQKAAPFEGLI 361 (636)
T ss_pred EecCCcccceeecCCcccccccceecchhh-hHHhccCCCeeeCccCCccccccchh
Confidence 678999999999998555699999998664 66533 2899999998887765
No 130
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.69 E-value=2.6 Score=39.72 Aligned_cols=56 Identities=21% Similarity=0.342 Sum_probs=34.6
Q ss_pred CCCCCCCCCCCCCCCceeccCcccc------ccHH--HHHHHhhcCCCCCCCCCCCCcCCeeeC
Q 016213 334 PDRTICPLCSQKRANPSVVTVSGFV------FCYA--CIFKYVSQYKRCPVTLMPATVEQIRRL 389 (393)
Q Consensus 334 ~~~~~CpiC~~~~~np~~~~~~G~v------fCy~--Ci~~~~~~~~~CPv~~~~~~~~~l~ri 389 (393)
.....||+|++..+...|.+..+.+ ||.. =+..++=.-..||.||.....++.-+|
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l 66 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKL 66 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccC
Confidence 3567899999999999886533333 3320 000000123489999998877765543
No 131
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=69.88 E-value=1.8 Score=47.27 Aligned_cols=49 Identities=29% Similarity=0.450 Sum_probs=37.8
Q ss_pred CCCCCCCCCCCCCCCCc---------eeccCccc--------------------cccHHHHHHHhh--------cCCCCC
Q 016213 333 PPDRTICPLCSQKRANP---------SVVTVSGF--------------------VFCYACIFKYVS--------QYKRCP 375 (393)
Q Consensus 333 p~~~~~CpiC~~~~~np---------~~~~~~G~--------------------vfCy~Ci~~~~~--------~~~~CP 375 (393)
|+|-.+|+-|++.+.|| +.|+-||- ..|-.|-.+|-. +...||
T Consensus 98 ~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aCp 177 (750)
T COG0068 98 PPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIACP 177 (750)
T ss_pred CCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccCc
Confidence 44777899999988887 45667884 459999998875 345899
Q ss_pred CCCCCC
Q 016213 376 VTLMPA 381 (393)
Q Consensus 376 v~~~~~ 381 (393)
.||-.+
T Consensus 178 ~CGP~~ 183 (750)
T COG0068 178 KCGPHL 183 (750)
T ss_pred ccCCCe
Confidence 999654
No 132
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=69.70 E-value=2.5 Score=28.14 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 016213 372 KRCPVTLMPA 381 (393)
Q Consensus 372 ~~CPv~~~~~ 381 (393)
..||+|+.+.
T Consensus 19 ~~CP~Cg~~~ 28 (34)
T cd00729 19 EKCPICGAPK 28 (34)
T ss_pred CcCcCCCCch
Confidence 5899998753
No 133
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=69.70 E-value=5.8 Score=32.44 Aligned_cols=38 Identities=24% Similarity=0.460 Sum_probs=32.6
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~ 383 (393)
...|+-|++++.=--.++ |..|+-..|+|.-|+.+...
T Consensus 33 rS~C~~C~~~L~~~~lIP----------i~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP----------ILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccch----------HHHHHHhCCCCcccCCCCCh
Confidence 357999999988777777 77899999999999998764
No 134
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=69.07 E-value=3 Score=40.96 Aligned_cols=44 Identities=20% Similarity=0.527 Sum_probs=37.1
Q ss_pred CCCCCCCCCCCC----CceeccCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 336 RTICPLCSQKRA----NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~----np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
...||||.+.+. +|.+++ |||..=++|.-.+..++-.||+|.++
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~~ 205 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSKP 205 (276)
T ss_pred cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccch
Confidence 445999998644 456787 99999999999999999999999983
No 135
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=68.16 E-value=4.4 Score=45.90 Aligned_cols=54 Identities=20% Similarity=0.181 Sum_probs=50.1
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeee
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 388 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~r 388 (393)
|...=|+-...+.||++++.+|++.|+.=|..++-....-|.||.|++.+++..
T Consensus 869 def~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~v~p 922 (943)
T KOG2042|consen 869 DEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDMVSP 922 (943)
T ss_pred hhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhhcCC
Confidence 677789999999999999999999999999999999999999999999888753
No 136
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=68.10 E-value=2.2 Score=40.05 Aligned_cols=44 Identities=18% Similarity=0.338 Sum_probs=37.4
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
.-..|-+|+.-...-.-|..||--+--+|+..|+.+...||-|+
T Consensus 180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 34689999997666655666998899999999999999999997
No 137
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=68.03 E-value=4 Score=45.22 Aligned_cols=54 Identities=20% Similarity=0.537 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCC--CCCce--eccCcccc--ccHHHHHHHhhcC--CCCCCCCCCCCcCCe
Q 016213 333 PPDRTICPLCSQK--RANPS--VVTVSGFV--FCYACIFKYVSQY--KRCPVTLMPATVEQI 386 (393)
Q Consensus 333 p~~~~~CpiC~~~--~~np~--~~~~~G~v--fCy~Ci~~~~~~~--~~CPv~~~~~~~~~l 386 (393)
..|...|-||+.. ..||- -|.++|-+ .-..|+.+|++-. .+|-+|+.+...+++
T Consensus 9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 3467899999874 33342 23334533 3458999999854 689999998765543
No 138
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.92 E-value=2.8 Score=46.62 Aligned_cols=41 Identities=22% Similarity=0.468 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 379 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 379 (393)
..+|..|...+.-|+|--.|||.|--.|.- ++..+||-|.-
T Consensus 840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLP 880 (933)
T ss_pred eeeecccCCccccceeeeecccHHHHHhhc---cCcccCCccch
Confidence 358999999999999866699999999997 56789999985
No 139
>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=67.57 E-value=2.9 Score=31.50 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=12.1
Q ss_pred hcCCCCCCCCCCCCcC
Q 016213 369 SQYKRCPVTLMPATVE 384 (393)
Q Consensus 369 ~~~~~CPv~~~~~~~~ 384 (393)
+.|+.||+||.|+..+
T Consensus 1 e~HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPPD 16 (59)
T ss_pred CCCCcCCcCCCcCCcc
Confidence 3578899998887654
No 140
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=66.77 E-value=1.9 Score=48.12 Aligned_cols=44 Identities=23% Similarity=0.425 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCceeccCcccc-----ccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~v-----fCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
...||-|+..-. -..|+.||-. +|..|-.+.-. ..||-|+.+.+
T Consensus 655 ~r~Cp~Cg~~t~-~~~Cp~CG~~T~~~~~Cp~C~~~~~~--~~C~~C~~~~~ 703 (900)
T PF03833_consen 655 RRRCPKCGKETF-YNRCPECGSHTEPVYVCPDCGIEVEE--DECPKCGRETT 703 (900)
T ss_dssp ----------------------------------------------------
T ss_pred cccCcccCCcch-hhcCcccCCccccceeccccccccCc--cccccccccCc
Confidence 578999998732 2345558866 89999986654 49999998764
No 141
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=66.52 E-value=7.1 Score=39.09 Aligned_cols=44 Identities=25% Similarity=0.572 Sum_probs=36.0
Q ss_pred CCCCCCCCCC--CC-cee-ccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKR--AN-PSV-VTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~--~n-p~~-~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..||+|..+. ++ ..+ ++ ||+--|..|...-...+++||.|+++.
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~-~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCP-CGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCccccccccccccc-ccccchhhhhhcccccCCCCCccCCcc
Confidence 5799999975 22 233 44 999999999999999999999999764
No 142
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.74 E-value=9 Score=32.60 Aligned_cols=43 Identities=26% Similarity=0.481 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCce-------------eccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRANPS-------------VVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-------------~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
+..|=-|...+..+. .++.|+.+||.+|=.=.-+.-+.||-|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 346888888776542 2778999999999865555558899986
No 143
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.04 E-value=2.4 Score=37.05 Aligned_cols=24 Identities=33% Similarity=0.703 Sum_probs=17.6
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHH
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACI 364 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci 364 (393)
...||.|+.++.. . .|-|||--|-
T Consensus 28 ~~hCp~Cg~PLF~----K-dG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFR----K-DGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCccee----e-CCeEECCCCC
Confidence 4689999998776 4 7888864443
No 144
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=63.95 E-value=8.5 Score=32.29 Aligned_cols=45 Identities=20% Similarity=0.417 Sum_probs=31.3
Q ss_pred CCCCCCCCCCCCCCc-eec------cCc---cccccHHHHHHHhhc---------CCCCCCCCC
Q 016213 335 DRTICPLCSQKRANP-SVV------TVS---GFVFCYACIFKYVSQ---------YKRCPVTLM 379 (393)
Q Consensus 335 ~~~~CpiC~~~~~np-~~~------~~~---G~vfCy~Ci~~~~~~---------~~~CPv~~~ 379 (393)
....|--|.+.-.+. +.+ +.| .-.||+.|+.....+ +-.||.|+-
T Consensus 6 ~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 6 NGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 356788888865554 344 445 777999998877643 357999864
No 145
>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=63.94 E-value=5 Score=29.36 Aligned_cols=28 Identities=18% Similarity=0.417 Sum_probs=16.2
Q ss_pred eeccCccccccHHHHHHHhhcC-CCCCCCC
Q 016213 350 SVVTVSGFVFCYACIFKYVSQY-KRCPVTL 378 (393)
Q Consensus 350 ~~~~~~G~vfCy~Ci~~~~~~~-~~CPv~~ 378 (393)
-.++.|+.+||.+|=. |+-+. +.||-|.
T Consensus 22 y~C~~C~~~FC~dCD~-fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDV-FIHETLHNCPGCE 50 (51)
T ss_dssp E--TTTT--B-HHHHH-TTTTTS-SSSTT-
T ss_pred EECCCCCCccccCcCh-hhhccccCCcCCC
Confidence 3567799999999975 66554 8899884
No 146
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=63.48 E-value=2.2 Score=42.18 Aligned_cols=47 Identities=23% Similarity=0.532 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCC-c--eeccCccccccHHHHHHHhh-----------------------cCCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRAN-P--SVVTVSGFVFCYACIFKYVS-----------------------QYKRCPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p--~~~~~~G~vfCy~Ci~~~~~-----------------------~~~~CPv~~~~~~~ 383 (393)
.+.|.||+--+.+ | +++. |-|-|-..|.-+||. ..-.||||+.++..
T Consensus 115 ~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 4579999988776 4 4554 999999999999983 12369999988753
No 147
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=62.17 E-value=2.5 Score=46.95 Aligned_cols=46 Identities=22% Similarity=0.523 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCC-ceeccCccccccHHHHHHHh----hc--CCCCCCCCCCC
Q 016213 336 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYV----SQ--YKRCPVTLMPA 381 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p~~~~~~G~vfCy~Ci~~~~----~~--~~~CPv~~~~~ 381 (393)
..+|-.|.+.+.| -=+|+.||+.+|.+|+..|- ++ -.+|+.|...+
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~~~~C 281 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWYPRLSKEEVAEKCEFSWLKC 281 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhccccchHhHhhhhhhHHHHhc
Confidence 5689999999998 55899999999999999993 22 24677665444
No 148
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=60.87 E-value=8.8 Score=34.64 Aligned_cols=47 Identities=15% Similarity=0.355 Sum_probs=32.3
Q ss_pred CCCCCCCCCCCC---CCceeccCcc--ccccHHHHHHHhhcC--CCCCCCCCCCCc
Q 016213 335 DRTICPLCSQKR---ANPSVVTVSG--FVFCYACIFKYVSQY--KRCPVTLMPATV 383 (393)
Q Consensus 335 ~~~~CpiC~~~~---~np~~~~~~G--~vfCy~Ci~~~~~~~--~~CPv~~~~~~~ 383 (393)
....|-||.+.- .+|+-+ .| -.---.|+.+|+... .+|++|+.+-..
T Consensus 7 ~~~~CRIC~~~~~~~~~PC~C--kGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYDVVTNYCNC--KNENKIVHKECLEEWINTSKNKSCKICNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCCCccCCccc--CCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence 356899998863 455544 34 122468999999865 689999977543
No 149
>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=60.42 E-value=4.1 Score=39.10 Aligned_cols=45 Identities=22% Similarity=0.479 Sum_probs=34.0
Q ss_pred CCCCCCCCCC-CCCce----eccCccccccHHHHHHHhhc-CCCCC--CCCCC
Q 016213 336 RTICPLCSQK-RANPS----VVTVSGFVFCYACIFKYVSQ-YKRCP--VTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~-~~np~----~~~~~G~vfCy~Ci~~~~~~-~~~CP--v~~~~ 380 (393)
...||+|... --||- |-+.|-|-.|-.|..+-... .-.|| -|++-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 3589999986 45773 33449999999999987764 46899 78643
No 150
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=60.31 E-value=1.9 Score=31.80 Aligned_cols=18 Identities=28% Similarity=0.853 Sum_probs=14.1
Q ss_pred eeccCccccccHHHHHHH
Q 016213 350 SVVTVSGFVFCYACIFKY 367 (393)
Q Consensus 350 ~~~~~~G~vfCy~Ci~~~ 367 (393)
+.++.||+.||+.|-..|
T Consensus 41 v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 41 VTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eECCCCCCeECCCCCCcC
Confidence 456459999999997766
No 151
>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=59.90 E-value=4.5 Score=29.43 Aligned_cols=39 Identities=26% Similarity=0.441 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhc--CCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~ 382 (393)
...||.|++........ .-|..+...+ ...||+|....+
T Consensus 2 ~f~CP~C~~~~~~~~L~--------~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLV--------EHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCccCHHHHH--------HHHHhHCcCCCCCccCCCchhhhh
Confidence 57899999943333322 2344444432 357999987543
No 152
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.37 E-value=4.6 Score=42.23 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=14.7
Q ss_pred CCceeccCccccccHHHHHHH
Q 016213 347 ANPSVVTVSGFVFCYACIFKY 367 (393)
Q Consensus 347 ~np~~~~~~G~vfCy~Ci~~~ 367 (393)
..++.+. |||.||+.|...|
T Consensus 177 ~~~v~C~-~g~~FC~~C~~~~ 196 (444)
T KOG1815|consen 177 SVEVDCG-CGHEFCFACGEES 196 (444)
T ss_pred ccceeCC-CCchhHhhccccc
Confidence 3346676 9999999996554
No 153
>PRK00420 hypothetical protein; Validated
Probab=57.66 E-value=4.3 Score=34.53 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRA 347 (393)
Q Consensus 336 ~~~CpiC~~~~~ 347 (393)
...||.|+.++.
T Consensus 23 ~~~CP~Cg~pLf 34 (112)
T PRK00420 23 SKHCPVCGLPLF 34 (112)
T ss_pred cCCCCCCCCcce
Confidence 367999997764
No 154
>PF04641 Rtf2: Rtf2 RING-finger
Probab=57.38 E-value=15 Score=35.58 Aligned_cols=54 Identities=22% Similarity=0.377 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCC---CCCCCCCC-CcCCeeeC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR---CPVTLMPA-TVEQIRRL 389 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~---CPv~~~~~-~~~~l~ri 389 (393)
-..|+|-++++..|+|+-.-|++|-..=|.+||...+. =|.....+ ++.||+.|
T Consensus 34 w~~CaLS~~pL~~PiV~d~~G~LynKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l 91 (260)
T PF04641_consen 34 WTHCALSQQPLEDPIVSDRLGRLYNKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVEL 91 (260)
T ss_pred cCcccCcCCccCCCeeeCCCCeeEcHHHHHHHHHhcCcCCCCccccccccCccceeeE
Confidence 57899999999999976569999999999999987642 23333233 45666654
No 155
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=57.12 E-value=3.8 Score=33.47 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=16.6
Q ss_pred CceeccCccccccHHHHHHHhhcCCCCCCCCC
Q 016213 348 NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 379 (393)
Q Consensus 348 np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 379 (393)
.|+.|..|||+|=- +-++.-.+||.|..
T Consensus 57 ~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc----cccCCcccCCcchh
Confidence 34445557777654 23445568888863
No 156
>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 PF12312 NeA_P2: Nepovirus subgroup A polyprotein ; InterPro: IPR021081 Proteins in this entry are typically between 259 and 1110 amino acids in length. They are found in association with PF03688 from PFAM, PF03689 from PFAM and PF03391 from PFAM. This entry includes RNA2 polyprotein (Protein 2A) which is implicated in RNA2 replication.
Probab=56.72 E-value=9.5 Score=35.63 Aligned_cols=32 Identities=44% Similarity=1.184 Sum_probs=15.5
Q ss_pred HHHHHHHHH--HhcccccccC----CCCCCCCCCCCCC
Q 016213 291 VFFFKMMEW--WYQSAEERMS----APTVYPPPPPPPP 322 (393)
Q Consensus 291 iF~lkfLeW--Wyss~~~r~~----~~~~lp~PpPP~~ 322 (393)
.-++|---| ||....+|+. ++..||+|||||+
T Consensus 172 fa~lkhttwrkWYDTSDeR~l~~hpGgp~lpppPPpP~ 209 (258)
T PF12312_consen 172 FAMLKHTTWRKWYDTSDERLLRAHPGGPCLPPPPPPPP 209 (258)
T ss_pred HHHHhhhHHHhhcccchHHHhhcCCCCCcccCCCCCCc
Confidence 344555555 6654433432 2445655555543
No 158
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=56.40 E-value=3.7 Score=42.07 Aligned_cols=55 Identities=24% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCCCCCCCCC--------------CC---ce-eccCccccccHHHHHHHhhc---------CCCCCCCCCCCCc-CCee
Q 016213 336 RTICPLCSQKR--------------AN---PS-VVTVSGFVFCYACIFKYVSQ---------YKRCPVTLMPATV-EQIR 387 (393)
Q Consensus 336 ~~~CpiC~~~~--------------~n---p~-~~~~~G~vfCy~Ci~~~~~~---------~~~CPv~~~~~~~-~~l~ 387 (393)
...||+|+++- .| |+ +-.+||||.--+.+.-|-+- +..||.|..+++- ...+
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~v 407 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYV 407 (416)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCCCCce
Confidence 67899998641 12 32 34459999999998888752 3589999999874 4566
Q ss_pred eCc
Q 016213 388 RLF 390 (393)
Q Consensus 388 riy 390 (393)
|++
T Consensus 408 rLi 410 (416)
T PF04710_consen 408 RLI 410 (416)
T ss_dssp ---
T ss_pred EEE
Confidence 654
No 159
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=55.73 E-value=12 Score=41.20 Aligned_cols=49 Identities=22% Similarity=0.524 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCCCCCC----------CCCCceeccCccccccHHHHHHH----hhcCCCCCCCCCCCC
Q 016213 328 EGIPLPPDRTICPLCSQ----------KRANPSVVTVSGFVFCYACIFKY----VSQYKRCPVTLMPAT 382 (393)
Q Consensus 328 ~~~~~p~~~~~CpiC~~----------~~~np~~~~~~G~vfCy~Ci~~~----~~~~~~CPv~~~~~~ 382 (393)
.|.++++..-.||-|.. +|+++. +-.|-.|-+.. +..++.||.|..+..
T Consensus 1123 cg~~i~~~~~~c~ec~~kfP~CiasG~pIt~~~------fWlC~~CkH~a~~~EIs~y~~CPLCHs~~~ 1185 (1189)
T KOG2041|consen 1123 CGAKIDPYDLQCSECQTKFPVCIASGRPITDNI------FWLCPRCKHRAHQHEISKYNCCPLCHSMES 1185 (1189)
T ss_pred cCCcCCccCCCChhhcCcCceeeccCCccccce------EEEccccccccccccccccccCccccChhh
Confidence 45556666777877754 344443 12344444433 445689999987643
No 160
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=55.69 E-value=3.3 Score=45.33 Aligned_cols=44 Identities=23% Similarity=0.523 Sum_probs=35.8
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhc---CCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~ 380 (393)
...||||...+..|+.+. |-|.||.-|+..-+.. ...||||+.-
T Consensus 21 ~lEc~ic~~~~~~p~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~ 67 (684)
T KOG4362|consen 21 ILECPICLEHVKEPSLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSD 67 (684)
T ss_pred hccCCceeEEeeccchhh-hhHHHHhhhhhceeeccCccccchhhhhh
Confidence 457999999999997776 9999999998765543 4689999843
No 161
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=54.78 E-value=9.3 Score=39.15 Aligned_cols=57 Identities=18% Similarity=0.150 Sum_probs=43.4
Q ss_pred CCCCCCCCCCCCCCc---eeccCccccccHHHHHHHhh--cCCCCCCCCCCCCcCCeeeCcc
Q 016213 335 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 335 ~~~~CpiC~~~~~np---~~~~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~~~~l~riy~ 391 (393)
....||+-.++.++- +++.++|.||||.-|.+.=- +|-+--++-.|.+-+|||-|=.
T Consensus 100 geyhcPvlfk~FT~~sHIvAv~TTGNvy~~eai~~LNiK~knwkdLltdepFtR~DiItiQd 161 (518)
T KOG0883|consen 100 GEYHCPVLFKVFTRFSHIVAVRTTGNVYSWEAIEELNIKTKNWKDLLTDEPFTRADIITIQD 161 (518)
T ss_pred CcccCceeeeeecccceEEEEEecCceeeHHHHHHhCcchhhHHHhhccCCcchhceeeecC
Confidence 578999999998886 35667999999998876532 2346677888888888887644
No 162
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=54.12 E-value=4.9 Score=29.73 Aligned_cols=26 Identities=27% Similarity=0.797 Sum_probs=15.9
Q ss_pred CCCCCCCCC----CCCceeccCccccccHHH
Q 016213 337 TICPLCSQK----RANPSVVTVSGFVFCYAC 363 (393)
Q Consensus 337 ~~CpiC~~~----~~np~~~~~~G~vfCy~C 363 (393)
..||+|+.. +...|++. -=-+||-.|
T Consensus 5 i~CP~CgnKTR~kir~DT~Lk-NfPlyCpKC 34 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLK-NFPLYCPKC 34 (55)
T ss_pred EECCCCCCccceeeecCceec-cccccCCCC
Confidence 369999954 55667776 434444333
No 163
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=54.04 E-value=7.1 Score=38.59 Aligned_cols=47 Identities=15% Similarity=0.365 Sum_probs=31.9
Q ss_pred CCCCCCCCCCCCCCc----eeccCccccccHHHHHH-Hhhc----C--CCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANP----SVVTVSGFVFCYACIFK-YVSQ----Y--KRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~np----~~~~~~G~vfCy~Ci~~-~~~~----~--~~CPv~~~~~ 381 (393)
+...|.+|.....+. .=+.-||++||.+|=.. ++-. . ..|+.|...+
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el 224 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEEL 224 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHH
Confidence 578999999953332 12556999999999876 3322 1 3688886543
No 164
>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=53.85 E-value=4.2 Score=30.80 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=18.1
Q ss_pred CCCCCCCCCCCC---CCceeccCccccccHHHHHHHh
Q 016213 335 DRTICPLCSQKR---ANPSVVTVSGFVFCYACIFKYV 368 (393)
Q Consensus 335 ~~~~CpiC~~~~---~np~~~~~~G~vfCy~Ci~~~~ 368 (393)
+...|.+|.+.+ ..---+..||.+||..|....+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 456899999985 2234677899999999986544
No 165
>PF15616 TerY-C: TerY-C metal binding domain
Probab=52.87 E-value=5.6 Score=34.80 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcC
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 384 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~ 384 (393)
-||-|+...- =+++. ||.+||+.= ++...||-|++.....
T Consensus 79 gCP~CGn~~~-fa~C~-CGkl~Ci~g-----~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 79 GCPHCGNQYA-FAVCG-CGKLFCIDG-----EGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCCCcChhc-EEEec-CCCEEEeCC-----CCCEECCCCCCeeeec
Confidence 5999997543 25666 999999832 3356899999876543
No 166
>PLN02248 cellulose synthase-like protein
Probab=52.20 E-value=10 Score=43.85 Aligned_cols=35 Identities=26% Similarity=0.435 Sum_probs=30.3
Q ss_pred eeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCC
Q 016213 350 SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQ 385 (393)
Q Consensus 350 ~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~ 385 (393)
.-|. ||+--|.+|-.+.++..+.||-|+.+-+..|
T Consensus 146 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (1135)
T PLN02248 146 LPCE-CGFKICRDCYIDAVKSGGICPGCKEPYKVTD 180 (1135)
T ss_pred Cccc-ccchhHHhHhhhhhhcCCCCCCCcccccccc
Confidence 3476 9999999999999999999999998875443
No 167
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=52.10 E-value=8.7 Score=42.64 Aligned_cols=32 Identities=25% Similarity=0.548 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCC--------ceeccCccccccHHHHHHHh
Q 016213 337 TICPLCSQKRAN--------PSVVTVSGFVFCYACIFKYV 368 (393)
Q Consensus 337 ~~CpiC~~~~~n--------p~~~~~~G~vfCy~Ci~~~~ 368 (393)
..|..|.+.... .-=|..||.|||-.|-.+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 579999998742 33377899999999997654
No 168
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.93 E-value=6.4 Score=37.03 Aligned_cols=41 Identities=22% Similarity=0.547 Sum_probs=31.2
Q ss_pred CCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
.|-.|++.-..-.++++--|+.|-.|--. -..||+|+.+.+
T Consensus 160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 160 SCRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred cceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 39999988777667774455789999853 356999998764
No 169
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.31 E-value=2.6 Score=25.55 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.0
Q ss_pred CCCCCCCCCCc
Q 016213 339 CPLCSQKRANP 349 (393)
Q Consensus 339 CpiC~~~~~np 349 (393)
||-|+..+.+-
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 67777666554
No 170
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=51.24 E-value=8.5 Score=28.91 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=23.2
Q ss_pred CCCCCCCCCCceeccCccccccHH----HHHHHhhcCC
Q 016213 339 CPLCSQKRANPSVVTVSGFVFCYA----CIFKYVSQYK 372 (393)
Q Consensus 339 CpiC~~~~~np~~~~~~G~vfCy~----Ci~~~~~~~~ 372 (393)
|-.|.....+.-++-+||+++|.+ .+.++.++.+
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~ 38 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKETG 38 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHHT
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhcccC
Confidence 667776645555655699999997 8888877543
No 171
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=51.17 E-value=14 Score=36.21 Aligned_cols=47 Identities=19% Similarity=0.472 Sum_probs=35.8
Q ss_pred CCCCCCCCCCCCCCceecc---Ccc--ccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVT---VSG--FVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~---~~G--~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
....||+|+....--.|.- ..| |.-|-=|..+|-.-.-+|--|+..-
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~ 235 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSK 235 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccC
Confidence 4678999999877666542 112 6779999999998888999998643
No 172
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=51.01 E-value=6.3 Score=28.04 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=17.9
Q ss_pred CCCceeccCccccccHHHHHHHhhc--CCCCCCC
Q 016213 346 RANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVT 377 (393)
Q Consensus 346 ~~np~~~~~~G~vfCy~Ci~~~~~~--~~~CPv~ 377 (393)
+.+|.-++-+-...-..|+.+|+.. +.+|++|
T Consensus 14 li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 14 LISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred eecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 4445444322234456899999985 4689987
No 173
>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=50.93 E-value=12 Score=26.97 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCC---ceeccCccccccHHHHHHHhhc
Q 016213 337 TICPLCSQKRAN---PSVVTVSGFVFCYACIFKYVSQ 370 (393)
Q Consensus 337 ~~CpiC~~~~~n---p~~~~~~G~vfCy~Ci~~~~~~ 370 (393)
..|.+|.+.+.- ..-+..||++||..|....+..
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 468999885332 2345569999999999877653
No 174
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=50.76 E-value=11 Score=24.44 Aligned_cols=36 Identities=22% Similarity=0.429 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCc-eeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 338 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 338 ~CpiC~~~~~np-~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
.|..|.+.|.+. .++..-|..|...|. +|..|+.++
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf--------~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECF--------KCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCC--------CCcccCCcC
Confidence 488899988875 343435566555443 567777655
No 175
>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=50.61 E-value=20 Score=26.72 Aligned_cols=40 Identities=18% Similarity=0.364 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCc----eeccCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 338 ICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 338 ~CpiC~~~~~np----~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
.|--|.+.+... -|++ =--.||-+|....+ ++.||-||=.
T Consensus 7 nCE~C~~dLp~~s~~A~ICS-fECTFC~~C~e~~l--~~~CPNCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICS-FECTFCADCAETML--NGVCPNCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEe-EeCcccHHHHHHHh--cCcCcCCCCc
Confidence 477777765433 2443 45579999998877 7899999843
No 176
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.25 E-value=5.3 Score=39.54 Aligned_cols=47 Identities=26% Similarity=0.468 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
+.++|-+|.+.++-|+-..-|+|-|||-|--.|-+-.+.||.|+...
T Consensus 104 ~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 104 DHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred CccceeeeeeeEEecccccCceeeeeecCCchhhhhhhccchhhcCc
Confidence 57899999999999998887899999999999998888888876443
No 177
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=50.01 E-value=9.7 Score=31.53 Aligned_cols=43 Identities=23% Similarity=0.576 Sum_probs=15.4
Q ss_pred CCCCCCCCCC--CCc--eeccCccccccHHHHHHHhh----cCCCCCCCCCCC
Q 016213 337 TICPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVS----QYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~--~np--~~~~~~G~vfCy~Ci~~~~~----~~~~CPv~~~~~ 381 (393)
..|++|.+.+ .|+ +.+. .||+|= +|...++. +...|++|+...
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~-~GH~w~-RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCE-NGHVWP-RCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-T-TS-EEE-B-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECC-CCCEEe-eeeeeeeeeccCCeeEcCCCCCEE
Confidence 6899999976 454 4565 999974 47777764 226899998653
No 178
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=49.27 E-value=5.1 Score=44.46 Aligned_cols=51 Identities=24% Similarity=0.459 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCCCCCc---------eeccCcc--------------------ccccHHHHHHHhhc--------CCCC
Q 016213 332 LPPDRTICPLCSQKRANP---------SVVTVSG--------------------FVFCYACIFKYVSQ--------YKRC 374 (393)
Q Consensus 332 ~p~~~~~CpiC~~~~~np---------~~~~~~G--------------------~vfCy~Ci~~~~~~--------~~~C 374 (393)
+|+|..+|+-|.+.+.|| +-|+-|| +..|-.|..+|-.. -..|
T Consensus 64 ippD~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~rr~h~~~~~C 143 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIAC 143 (711)
T ss_pred cCCchhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccccCCCCCccC
Confidence 455777788888777776 2344466 45699999999652 2489
Q ss_pred CCCCCCCC
Q 016213 375 PVTLMPAT 382 (393)
Q Consensus 375 Pv~~~~~~ 382 (393)
|.||-++.
T Consensus 144 ~~Cgp~l~ 151 (711)
T TIGR00143 144 PRCGPQLN 151 (711)
T ss_pred CCCCcEEE
Confidence 99997764
No 179
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=48.82 E-value=6.3 Score=43.25 Aligned_cols=41 Identities=17% Similarity=0.376 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 333 PPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 333 p~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
|.+...|+-|+..+.. . .|-.|-..--.+.+-||-||.++.
T Consensus 12 ~~~akFC~~CG~~l~~-~--------~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 12 PNNNRFCQKCGTSLTH-K--------PCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCCccccccCCCCCC-C--------cCCCCCCCCCcccccccccCCccc
Confidence 4444556666665532 1 233443333344567888887653
No 180
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=47.79 E-value=10 Score=42.31 Aligned_cols=45 Identities=24% Similarity=0.498 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCCCC--ce-eccCccccccHHHHHHHhhc-------CCCCCCCC
Q 016213 334 PDRTICPLCSQKRAN--PS-VVTVSGFVFCYACIFKYVSQ-------YKRCPVTL 378 (393)
Q Consensus 334 ~~~~~CpiC~~~~~n--p~-~~~~~G~vfCy~Ci~~~~~~-------~~~CPv~~ 378 (393)
.+...|-||.+.|.- |+ .+.+|-|||-+.||.+|-+. .-+||-|.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCccc
Confidence 357899999997654 44 46779999999999999963 13899998
No 181
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.08 E-value=15 Score=28.81 Aligned_cols=39 Identities=21% Similarity=0.441 Sum_probs=26.3
Q ss_pred CCCCCCCC----CCceeccCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 339 CPLCSQKR----ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 339 CpiC~~~~----~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
|--|.+.+ .++.|++ =-+.||-.|+..-+ ++.||.||-.
T Consensus 8 CECCDrDLpp~s~dA~ICt-fEcTFCadCae~~l--~g~CPnCGGe 50 (84)
T COG3813 8 CECCDRDLPPDSTDARICT-FECTFCADCAENRL--HGLCPNCGGE 50 (84)
T ss_pred CcccCCCCCCCCCceeEEE-EeeehhHhHHHHhh--cCcCCCCCch
Confidence 44454432 2344554 78899999997554 6899999843
No 182
>PRK07218 replication factor A; Provisional
Probab=46.81 E-value=13 Score=38.77 Aligned_cols=22 Identities=18% Similarity=0.403 Sum_probs=17.2
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..||.|.+.+++ +.||.|+..-
T Consensus 298 ~rCP~C~r~v~~-----------------------~~C~~hG~ve 319 (423)
T PRK07218 298 ERCPECGRVIQK-----------------------GQCRSHGAVE 319 (423)
T ss_pred ecCcCccccccC-----------------------CcCCCCCCcC
Confidence 579999998844 6899998653
No 183
>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=46.52 E-value=29 Score=35.43 Aligned_cols=52 Identities=19% Similarity=0.400 Sum_probs=33.0
Q ss_pred CCCCCCCCCCCCCCceeccCc----------------cc-----cccHHHHHHHhh-------------cCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVS----------------GF-----VFCYACIFKYVS-------------QYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~----------------G~-----vfCy~Ci~~~~~-------------~~~~CPv~~~~ 380 (393)
+...|--|++...|=.+.+.| +- +-|-.|+=+|.. +...||.|+.+
T Consensus 270 e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~ 349 (358)
T PF10272_consen 270 ELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAK 349 (358)
T ss_pred ccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccc
Confidence 345677777765554444334 22 337799988884 34479999988
Q ss_pred CCcCCe
Q 016213 381 ATVEQI 386 (393)
Q Consensus 381 ~~~~~l 386 (393)
-=+-|+
T Consensus 350 FCilDV 355 (358)
T PF10272_consen 350 FCILDV 355 (358)
T ss_pred ceeeee
Confidence 655544
No 184
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=46.02 E-value=6.3 Score=27.32 Aligned_cols=10 Identities=20% Similarity=0.205 Sum_probs=7.3
Q ss_pred cCCCCCCCCC
Q 016213 370 QYKRCPVTLM 379 (393)
Q Consensus 370 ~~~~CPv~~~ 379 (393)
..-.||.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 3468999985
No 185
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=45.06 E-value=19 Score=36.05 Aligned_cols=54 Identities=17% Similarity=0.352 Sum_probs=36.6
Q ss_pred CCCCCCCCCCC--------------CC---ce-eccCccccccHHHHHHHhhc---------CCCCCCCCCCCC-cCCee
Q 016213 336 RTICPLCSQKR--------------AN---PS-VVTVSGFVFCYACIFKYVSQ---------YKRCPVTLMPAT-VEQIR 387 (393)
Q Consensus 336 ~~~CpiC~~~~--------------~n---p~-~~~~~G~vfCy~Ci~~~~~~---------~~~CPv~~~~~~-~~~l~ 387 (393)
...||+|+..- .| |+ +-.+||||.-.+-..-|-.- |-.||.|...+. ....+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~~i 420 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQGYI 420 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCCceE
Confidence 67899998641 12 11 33469999888877777652 458999998875 44555
Q ss_pred eC
Q 016213 388 RL 389 (393)
Q Consensus 388 ri 389 (393)
|+
T Consensus 421 kl 422 (429)
T KOG3842|consen 421 KL 422 (429)
T ss_pred EE
Confidence 54
No 186
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=44.89 E-value=13 Score=41.02 Aligned_cols=19 Identities=21% Similarity=0.275 Sum_probs=12.7
Q ss_pred hcCCCCCCCCCCCCcCCeeeC
Q 016213 369 SQYKRCPVTLMPATVEQIRRL 389 (393)
Q Consensus 369 ~~~~~CPv~~~~~~~~~l~ri 389 (393)
..+..||.||.+ ++-..||
T Consensus 637 g~~~~CP~CG~~--~~v~sRi 655 (656)
T PRK08270 637 GEHEFCPKCGEE--TEVYSRV 655 (656)
T ss_pred CCCCCCcCCcCc--cceEEee
Confidence 345799999976 4444444
No 187
>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=44.68 E-value=12 Score=33.69 Aligned_cols=34 Identities=21% Similarity=0.521 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCCCceeccCcc-ccccH-----------HHHHHHhh
Q 016213 336 RTICPLCSQKRANPSVVTVSG-FVFCY-----------ACIFKYVS 369 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G-~vfCy-----------~Ci~~~~~ 369 (393)
...||||++..-|++.|..+- .--|. -|+.+|-+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 457999999999998765333 34452 57777764
No 188
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=44.29 E-value=11 Score=27.46 Aligned_cols=13 Identities=23% Similarity=0.261 Sum_probs=9.4
Q ss_pred hhcCCCCCCCCCC
Q 016213 368 VSQYKRCPVTLMP 380 (393)
Q Consensus 368 ~~~~~~CPv~~~~ 380 (393)
|..+-+||+|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (50)
T cd00730 31 LPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCc
Confidence 5556689999854
No 189
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.71 E-value=4.5 Score=25.09 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=5.8
Q ss_pred CCCCCCCCC
Q 016213 337 TICPLCSQK 345 (393)
Q Consensus 337 ~~CpiC~~~ 345 (393)
..||-|+..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 357777764
No 190
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.05 E-value=12 Score=27.83 Aligned_cols=15 Identities=20% Similarity=0.315 Sum_probs=10.8
Q ss_pred HHHhhcCCCCCCCCC
Q 016213 365 FKYVSQYKRCPVTLM 379 (393)
Q Consensus 365 ~~~~~~~~~CPv~~~ 379 (393)
++-|..+-.||+|+.
T Consensus 30 fedlPd~w~CP~Cg~ 44 (55)
T COG1773 30 FEDLPDDWVCPECGV 44 (55)
T ss_pred hhhCCCccCCCCCCC
Confidence 455666778999985
No 191
>PRK06386 replication factor A; Reviewed
Probab=42.75 E-value=15 Score=37.40 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCC
Q 016213 337 TICPLCSQKRAN 348 (393)
Q Consensus 337 ~~CpiC~~~~~n 348 (393)
..||.|.+.+++
T Consensus 237 ~rCP~C~R~l~~ 248 (358)
T PRK06386 237 TKCSVCNKIIED 248 (358)
T ss_pred ecCcCCCeEccC
Confidence 579999998875
No 192
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=42.08 E-value=15 Score=27.21 Aligned_cols=22 Identities=23% Similarity=0.620 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCceeccCccc
Q 016213 336 RTICPLCSQKRANPSVVTVSGF 357 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~ 357 (393)
-..||.|++....-.|++.||+
T Consensus 26 l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred ceECCCCCCcccCeeECCccCe
Confidence 4579999998887788877885
No 193
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.05 E-value=8.2 Score=41.89 Aligned_cols=37 Identities=22% Similarity=0.592 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCC----CceeccCccccccHHHHHHHhhcCCCCC
Q 016213 336 RTICPLCSQKRA----NPSVVTVSGFVFCYACIFKYVSQYKRCP 375 (393)
Q Consensus 336 ~~~CpiC~~~~~----np~~~~~~G~vfCy~Ci~~~~~~~~~CP 375 (393)
-..|+||..... .|+-+. |||+-|..|+..- .+..||
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~-cghtic~~c~~~l--yn~scp 51 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQ-CGHTICGHCVQLL--YNASCP 51 (861)
T ss_pred HhhchHHHHHHHHHhcCccccc-ccchHHHHHHHhH--hhccCC
Confidence 457999966543 466666 9999999999754 356777
No 194
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=41.25 E-value=2.4 Score=34.24 Aligned_cols=35 Identities=23% Similarity=0.613 Sum_probs=28.2
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..|-||.+.+-.| |-.||..|++ +.+.|-+||+.+
T Consensus 55 ~kC~iCk~~vHQ~------GshYC~tCAY----~KgiCAMCGKki 89 (100)
T KOG3476|consen 55 AKCRICKQLVHQP------GSHYCQTCAY----KKGICAMCGKKI 89 (100)
T ss_pred chhHHHHHHhcCC------cchhHhHhhh----hhhHHHHhhhHh
Confidence 4799998876544 7789999998 568999999875
No 195
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=41.06 E-value=22 Score=34.59 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=37.4
Q ss_pred CCCCCCCCCCCC--------CCCCceeccCccccccHHHHHHHhh--cCCCCCCCCCCC
Q 016213 333 PPDRTICPLCSQ--------KRANPSVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPA 381 (393)
Q Consensus 333 p~~~~~CpiC~~--------~~~np~~~~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~ 381 (393)
|.+...|-||.. .+..|+.|.-+....-..|+..|+. +...|.+|....
T Consensus 75 ~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~ 133 (323)
T KOG1609|consen 75 PSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF 133 (323)
T ss_pred CCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence 444578999988 4566777766666668999999998 557899998754
No 196
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=40.93 E-value=9.2 Score=23.84 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=5.6
Q ss_pred CCCCCCCCCC
Q 016213 373 RCPVTLMPAT 382 (393)
Q Consensus 373 ~CPv~~~~~~ 382 (393)
.||||++.++
T Consensus 3 ~CPiC~~~v~ 12 (26)
T smart00734 3 QCPVCFREVP 12 (26)
T ss_pred cCCCCcCccc
Confidence 3666665553
No 197
>PRK12496 hypothetical protein; Provisional
Probab=40.82 E-value=6.6 Score=35.50 Aligned_cols=12 Identities=17% Similarity=0.338 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCc
Q 016213 372 KRCPVTLMPATV 383 (393)
Q Consensus 372 ~~CPv~~~~~~~ 383 (393)
..||+||.++.-
T Consensus 144 ~~C~~CG~~~~r 155 (164)
T PRK12496 144 DVCEICGSPVKR 155 (164)
T ss_pred CcCCCCCChhhh
Confidence 468888877643
No 198
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.35 E-value=14 Score=38.13 Aligned_cols=34 Identities=24% Similarity=0.487 Sum_probs=26.3
Q ss_pred CCCCCCCCCCCCCCc-----eeccCccccccHHHHHHHh
Q 016213 335 DRTICPLCSQKRANP-----SVVTVSGFVFCYACIFKYV 368 (393)
Q Consensus 335 ~~~~CpiC~~~~~np-----~~~~~~G~vfCy~Ci~~~~ 368 (393)
+...||-|..+|.-. ..+..||+-|||-|...--
T Consensus 367 N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 367 NSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred cCCCCCcccceeecCCCccceeeccccccceeehhhhcC
Confidence 356799999887644 5777899999999986443
No 199
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=40.34 E-value=24 Score=35.29 Aligned_cols=50 Identities=2% Similarity=-0.242 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCCceeccCccc-cccHHHHHHHhhcCCCCCCCCCCCCcCCeeeCc
Q 016213 336 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~-vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~riy 390 (393)
+.+|-.|+.-...-.... ||| .||..|+- +.-...||+|. -...++++|.
T Consensus 343 ~~~~~~~~~~~~st~~~~-~~~n~~~~~~a~--~s~~~~~~~c~--~~~~~~~~i~ 393 (394)
T KOG2113|consen 343 SLKGTSAGFGLLSTIWSG-GNMNLSPGSLAS--ASASPTSSTCD--HNDHTLVPIN 393 (394)
T ss_pred hcccccccCceeeeEeec-CCcccChhhhhh--cccCCcccccc--ccceeeeecC
Confidence 678999998877655555 887 79999997 66678999997 3445666653
No 200
>PRK12495 hypothetical protein; Provisional
Probab=39.97 E-value=11 Score=35.77 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHH
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACI 364 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci 364 (393)
...|+.|+.+|- . .-|-+||-.|-
T Consensus 42 a~hC~~CG~PIp---a--~pG~~~Cp~CQ 65 (226)
T PRK12495 42 NAHCDECGDPIF---R--HDGQEFCPTCQ 65 (226)
T ss_pred hhhcccccCccc---C--CCCeeECCCCC
Confidence 467999999887 2 24666665554
No 201
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.92 E-value=18 Score=26.99 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCCceeccCccc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGF 357 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~ 357 (393)
.-..||-|++....-.+++.||+
T Consensus 26 ~l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCCeEECCCCCc
Confidence 34579999998888777766775
No 202
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=39.75 E-value=16 Score=27.50 Aligned_cols=16 Identities=13% Similarity=0.152 Sum_probs=10.5
Q ss_pred hcCCCCCCCCCCCCcC
Q 016213 369 SQYKRCPVTLMPATVE 384 (393)
Q Consensus 369 ~~~~~CPv~~~~~~~~ 384 (393)
..|.-||||++++..+
T Consensus 6 ~PH~HC~VCg~aIp~d 21 (64)
T COG4068 6 VPHRHCVVCGKAIPPD 21 (64)
T ss_pred CCCccccccCCcCCCc
Confidence 4566777777776544
No 203
>PHA00626 hypothetical protein
Probab=39.71 E-value=23 Score=26.44 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=5.8
Q ss_pred CCCCCCC
Q 016213 338 ICPLCSQ 344 (393)
Q Consensus 338 ~CpiC~~ 344 (393)
.||-|+.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 5888887
No 204
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=39.15 E-value=27 Score=38.17 Aligned_cols=53 Identities=19% Similarity=0.204 Sum_probs=49.7
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCee
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 387 (393)
|...-|+--..++||++++++|----..-|.-++-..+.-|.-++|++.+|+.
T Consensus 853 DeFlDPLmftimkdPV~Lp~S~i~IDRSTikahllsd~tDPFNRmPLtlddVt 905 (929)
T COG5113 853 DEFLDPLMFTIMKDPVKLPTSRITIDRSTIKAHLLSDGTDPFNRMPLTLDDVT 905 (929)
T ss_pred hhhhCchhhhcccCCeecccccccccHHHHHHHHhcCCCCccccCCCchhhcC
Confidence 67888999999999999999999999999999999999999999999988875
No 205
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=38.87 E-value=15 Score=28.18 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=22.2
Q ss_pred cccccHHHHHHHhhcCCCCCCCCCCCC---cCCeeeCcc
Q 016213 356 GFVFCYACIFKYVSQYKRCPVTLMPAT---VEQIRRLFH 391 (393)
Q Consensus 356 G~vfCy~Ci~~~~~~~~~CPv~~~~~~---~~~l~riy~ 391 (393)
++.-|..|- +|.+...||+|+-.-+ -+.++-|..
T Consensus 4 ~~~AC~~C~--~i~~~~~Cp~Cgs~~~S~~w~G~v~i~d 40 (64)
T PRK06393 4 QYRACKKCK--RLTPEKTCPVHGDEKTTTEWFGFLIITE 40 (64)
T ss_pred hhhhHhhCC--cccCCCcCCCCCCCcCCcCcceEEEEEC
Confidence 455677774 5556779999997643 345555554
No 206
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=38.56 E-value=26 Score=25.04 Aligned_cols=32 Identities=19% Similarity=0.441 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHH
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFK 366 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~ 366 (393)
+-..|-.|.+.+.+......-|.++|..|-.+
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 45788999998888754445889999988754
No 207
>PRK07217 replication factor A; Reviewed
Probab=38.21 E-value=23 Score=35.39 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=19.9
Q ss_pred CCCCC--CCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCee
Q 016213 337 TICPL--CSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 337 ~~Cpi--C~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 387 (393)
..||. |.+.+ +++.||.|+..-...||+
T Consensus 189 ~rCP~~~C~Rvl-----------------------~~g~C~~HG~ve~~~DLr 218 (311)
T PRK07217 189 KRCPEEDCTRVL-----------------------QNGRCSEHGKVEGEFDLR 218 (311)
T ss_pred ecCCccccCccc-----------------------cCCCCCCCCCcCCceeeE
Confidence 57999 99877 347888888655544543
No 208
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.49 E-value=19 Score=39.49 Aligned_cols=42 Identities=21% Similarity=0.395 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCCce-ecc--CccccccHHHHHHHhhcCCCCCCCCCCC
Q 016213 337 TICPLCSQKRANPS-VVT--VSGFVFCYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 337 ~~CpiC~~~~~np~-~~~--~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
..|-+|+.+-.-.+ |+. -|+-+||..|-.++ .+.||||+-..
T Consensus 655 r~C~vcq~pedse~~v~rt~~C~~~~C~~c~~~~---~~~~~vC~~~~ 699 (717)
T KOG3726|consen 655 RTCKVCQLPEDSETDVCRTTFCYTPYCVACSLDY---ASISEVCGPDA 699 (717)
T ss_pred HHHHHhcCCcCccccccCccccCCcchHhhhhhh---hccCcccCchh
Confidence 45778887655332 322 48888888987655 47899999654
No 209
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=35.53 E-value=24 Score=24.38 Aligned_cols=8 Identities=50% Similarity=1.219 Sum_probs=6.4
Q ss_pred CCCCCCCC
Q 016213 338 ICPLCSQK 345 (393)
Q Consensus 338 ~CpiC~~~ 345 (393)
+||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 68888885
No 210
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=35.20 E-value=21 Score=26.37 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCCCCceeccCccc
Q 016213 335 DRTICPLCSQKRANPSVVTVSGF 357 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~ 357 (393)
+-..||.|++...--.+++.|||
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTBB
T ss_pred ceeeeccCCCEecccEeeCCCCe
Confidence 34579999987666677766775
No 211
>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=34.94 E-value=12 Score=27.36 Aligned_cols=31 Identities=23% Similarity=0.552 Sum_probs=17.8
Q ss_pred CCCCC--CCCCCCC-----c--eeccCccccccHHHHHHH
Q 016213 337 TICPL--CSQKRAN-----P--SVVTVSGFVFCYACIFKY 367 (393)
Q Consensus 337 ~~Cpi--C~~~~~n-----p--~~~~~~G~vfCy~Ci~~~ 367 (393)
..||- |...+.- . +.++.||+.||+.|-..|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 46766 7765332 2 456679999999997655
No 212
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=34.77 E-value=19 Score=24.11 Aligned_cols=31 Identities=13% Similarity=0.194 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 379 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 379 (393)
....|+-|++...-..-.. . ...-.||.|+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~------------~--~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKIS------------D--DPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecC------------C--CCCCCCCCCCC
Confidence 3567877777654332211 0 23467999986
No 213
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.68 E-value=26 Score=24.75 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=5.5
Q ss_pred CCCCCCCCC
Q 016213 338 ICPLCSQKR 346 (393)
Q Consensus 338 ~CpiC~~~~ 346 (393)
.||-|+..+
T Consensus 2 FCp~Cg~~l 10 (52)
T smart00661 2 FCPKCGNML 10 (52)
T ss_pred CCCCCCCcc
Confidence 477776644
No 214
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=34.56 E-value=28 Score=23.83 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=18.4
Q ss_pred CCCCCCCCCC-ceeccCccccccH
Q 016213 339 CPLCSQKRAN-PSVVTVSGFVFCY 361 (393)
Q Consensus 339 CpiC~~~~~n-p~~~~~~G~vfCy 361 (393)
|-+|.+...- |-.+..||.+||.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccccCeECCccCCcccc
Confidence 6678887665 8888889999986
No 215
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=34.16 E-value=21 Score=34.70 Aligned_cols=55 Identities=24% Similarity=0.239 Sum_probs=47.5
Q ss_pred CCCCCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCC-CCCCCCCCCcCCeee
Q 016213 332 LPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPATVEQIRR 388 (393)
Q Consensus 332 ~p~~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~-CPv~~~~~~~~~l~r 388 (393)
+| +..-|.|-.+.+++|++.+ +|-.+-..=|.++++.-|+ -|||+.+++..+++.
T Consensus 208 vp-d~lcgkIt~el~~~pvi~p-sgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q~ip 263 (284)
T KOG4642|consen 208 VP-DYLCGKITLELMREPVITP-SGITYDRADIEEHLQRVGHFDPVTRWPLTEYQLIP 263 (284)
T ss_pred cc-chhhhhhhHHhhcCCccCc-cccchhHHHHHHHHHHhccCCchhcccCCHHhhcc
Confidence 45 4566788999999999987 9999999999999998764 799999999988875
No 216
>PHA02768 hypothetical protein; Provisional
Probab=34.06 E-value=28 Score=25.85 Aligned_cols=42 Identities=7% Similarity=0.131 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcC---CCCCCCCCCC-CcCCeeeC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPA-TVEQIRRL 389 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~-~~~~l~ri 389 (393)
...|+.|++.......+. .+.+.| -+|..|++.. ....|+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~------------~H~r~H~k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMI------------THLRKHNTNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHH------------HHHHhcCCcccCCcccceecccceeEEE
Confidence 468999999988876654 233333 4899998753 45566665
No 217
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=33.59 E-value=26 Score=35.04 Aligned_cols=14 Identities=43% Similarity=0.985 Sum_probs=12.2
Q ss_pred ccccccHHHHHHHh
Q 016213 355 SGFVFCYACIFKYV 368 (393)
Q Consensus 355 ~G~vfCy~Ci~~~~ 368 (393)
||++||..|...|-
T Consensus 342 Cgf~FCR~C~e~yh 355 (446)
T KOG0006|consen 342 CGFAFCRECKEAYH 355 (446)
T ss_pred chhHhHHHHHhhhc
Confidence 99999999998554
No 218
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=33.36 E-value=25 Score=38.18 Aligned_cols=18 Identities=28% Similarity=0.541 Sum_probs=12.5
Q ss_pred CCCCCCCCCCCcCCeeeCc
Q 016213 372 KRCPVTLMPATVEQIRRLF 390 (393)
Q Consensus 372 ~~CPv~~~~~~~~~l~riy 390 (393)
..||.|+.. +++.++||-
T Consensus 547 ~~CP~CGs~-~~ev~sRv~ 564 (586)
T TIGR02827 547 HRCPVCGSA-NIDYGTRVI 564 (586)
T ss_pred CcCcCCCCc-cceEEEeec
Confidence 699999963 455666663
No 219
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.73 E-value=38 Score=24.60 Aligned_cols=28 Identities=25% Similarity=0.696 Sum_probs=20.6
Q ss_pred CCCCCCCCCCC--ceeccCccccccHHHHHHH
Q 016213 338 ICPLCSQKRAN--PSVVTVSGFVFCYACIFKY 367 (393)
Q Consensus 338 ~CpiC~~~~~n--p~~~~~~G~vfCy~Ci~~~ 367 (393)
.|+||++.+-= ..-+. -|| -|-.|..+.
T Consensus 1 ~C~iCg~kigl~~~~k~~-DG~-iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIK-DGY-ICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceecc-Ccc-chHHHHHHh
Confidence 59999997443 34455 785 899999766
No 220
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=32.71 E-value=11 Score=38.76 Aligned_cols=15 Identities=13% Similarity=0.164 Sum_probs=11.2
Q ss_pred hcCCCCCCCCCCCCcC
Q 016213 369 SQYKRCPVTLMPATVE 384 (393)
Q Consensus 369 ~~~~~CPv~~~~~~~~ 384 (393)
+.+++|| ||.+++..
T Consensus 257 ~~~~~Cp-CG~~i~~G 271 (374)
T TIGR00375 257 TACANCP-CGGRIKKG 271 (374)
T ss_pred hcCCCCC-CCCcceec
Confidence 3468999 99997643
No 221
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=32.03 E-value=12 Score=34.34 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=8.2
Q ss_pred cCCCCCCCCCCC
Q 016213 370 QYKRCPVTLMPA 381 (393)
Q Consensus 370 ~~~~CPv~~~~~ 381 (393)
+++.||+||.++
T Consensus 152 ~~~~Cp~CG~~~ 163 (177)
T COG1439 152 PKDFCPICGSPL 163 (177)
T ss_pred CCCcCCCCCCce
Confidence 456778887663
No 222
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=31.69 E-value=16 Score=24.35 Aligned_cols=21 Identities=33% Similarity=0.838 Sum_probs=9.7
Q ss_pred CCCCCCCCCCC--c-------eeccCcccc
Q 016213 338 ICPLCSQKRAN--P-------SVVTVSGFV 358 (393)
Q Consensus 338 ~CpiC~~~~~n--p-------~~~~~~G~v 358 (393)
-||.|+.+++- | .+++.||+|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 48888877543 2 355666665
No 223
>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=31.45 E-value=26 Score=24.26 Aligned_cols=34 Identities=24% Similarity=0.554 Sum_probs=18.9
Q ss_pred CCC--CCCCCCCceeccCccccccHHHHHHHhhcCCCCC
Q 016213 339 CPL--CSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCP 375 (393)
Q Consensus 339 Cpi--C~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CP 375 (393)
|.+ |.+....|..++.||..||..-. ..+...|+
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~Hr---~~e~H~C~ 36 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKHR---LPEDHNCS 36 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTTH---STTTCT-S
T ss_pred CccCcCcCccCCCeECCCCCcccCcccc---CccccCCc
Confidence 555 89988899999889999997433 23445555
No 224
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=30.79 E-value=50 Score=22.56 Aligned_cols=32 Identities=22% Similarity=0.724 Sum_probs=22.6
Q ss_pred CCCCCCCCCC-ceeccCcc---ccccHHHHHHHhhc
Q 016213 339 CPLCSQKRAN-PSVVTVSG---FVFCYACIFKYVSQ 370 (393)
Q Consensus 339 CpiC~~~~~n-p~~~~~~G---~vfCy~Ci~~~~~~ 370 (393)
|-.|+++|.+ |.+...=| |..|-.|..++.++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHhh
Confidence 7789999884 77766333 34458999887653
No 225
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=30.76 E-value=16 Score=43.54 Aligned_cols=47 Identities=15% Similarity=0.490 Sum_probs=36.7
Q ss_pred CCCCCCCCCCCCC--ceeccCccccccHHHHHHHhhc----------CCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRAN--PSVVTVSGFVFCYACIFKYVSQ----------YKRCPVTLMPAT 382 (393)
Q Consensus 336 ~~~CpiC~~~~~n--p~~~~~~G~vfCy~Ci~~~~~~----------~~~CPv~~~~~~ 382 (393)
.+.|-||-...-. |++---|||+|-..|...-+++ ...||+|..++.
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 5789999886443 5663349999999999988874 248999999875
No 226
>PF07578 LAB_N: Lipid A Biosynthesis N-terminal domain; InterPro: IPR011499 This domain is found at the N terminus of a group of Chlamydial lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function.; GO: 0008915 lipid-A-disaccharide synthase activity, 0009245 lipid A biosynthetic process
Probab=30.55 E-value=43 Score=26.27 Aligned_cols=19 Identities=16% Similarity=0.462 Sum_probs=12.9
Q ss_pred HHHHHHHHH-HHHHhccccc
Q 016213 288 IAAVFFFKM-MEWWYQSAEE 306 (393)
Q Consensus 288 p~~iF~lkf-LeWWyss~~~ 306 (393)
.-.+|+.|| +|||+++..+
T Consensus 5 gq~lF~~Rf~~QW~~SEk~k 24 (72)
T PF07578_consen 5 GQLLFSSRFIVQWIYSEKAK 24 (72)
T ss_pred HHHHHHHHHHHHHHHHHHcC
Confidence 445677774 6999986443
No 227
>PRK11827 hypothetical protein; Provisional
Probab=30.50 E-value=32 Score=26.04 Aligned_cols=12 Identities=33% Similarity=0.719 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCC
Q 016213 336 RTICPLCSQKRA 347 (393)
Q Consensus 336 ~~~CpiC~~~~~ 347 (393)
-..||+|++++.
T Consensus 8 ILaCP~ckg~L~ 19 (60)
T PRK11827 8 IIACPVCNGKLW 19 (60)
T ss_pred heECCCCCCcCe
Confidence 457999998865
No 228
>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=30.13 E-value=36 Score=25.62 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRAN 348 (393)
Q Consensus 335 ~~~~CpiC~~~~~n 348 (393)
.+..||.|+.....
T Consensus 27 TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK 40 (69)
T ss_pred CccCccCccccccc
Confidence 46789999998877
No 229
>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=29.97 E-value=14 Score=23.45 Aligned_cols=27 Identities=19% Similarity=0.435 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHH
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACI 364 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci 364 (393)
..||.|...+.+-.+-. =+-.||..|.
T Consensus 2 ~~C~rC~~~~~~~~~~~-r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-RSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETT-EEEEE-TTTC
T ss_pred CcCccCCCcceEeEecC-CCCeECcCCc
Confidence 36999999987776644 5667777764
No 230
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.75 E-value=19 Score=25.82 Aligned_cols=13 Identities=31% Similarity=0.496 Sum_probs=6.0
Q ss_pred hhcCCCCCCCCCC
Q 016213 368 VSQYKRCPVTLMP 380 (393)
Q Consensus 368 ~~~~~~CPv~~~~ 380 (393)
|.++=+||+|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 31 LPDDWVCPVCGAP 43 (47)
T ss_dssp S-TT-B-TTTSSB
T ss_pred CCCCCcCcCCCCc
Confidence 3344577777754
No 231
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.34 E-value=17 Score=25.43 Aligned_cols=11 Identities=27% Similarity=0.392 Sum_probs=7.8
Q ss_pred CCCCCCCCCCC
Q 016213 372 KRCPVTLMPAT 382 (393)
Q Consensus 372 ~~CPv~~~~~~ 382 (393)
.+||-||.++.
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 57888887653
No 232
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.84 E-value=22 Score=39.59 Aligned_cols=44 Identities=18% Similarity=0.385 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCCc------eeccCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~np------~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
...|.-|+...+-| +.=...|...|..|-++ -..-..||-|+..
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 46788888887777 33445789999999876 3344799999966
No 233
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.43 E-value=49 Score=30.31 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
....||.|+...+---+ +...-.||+||.++.
T Consensus 116 ~~Y~Cp~C~~rytf~eA----------------~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEA----------------MEYGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHH----------------hhcCCcCCCCCCCCe
Confidence 46789999865443222 234679999998874
No 234
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=28.06 E-value=25 Score=34.13 Aligned_cols=38 Identities=18% Similarity=0.380 Sum_probs=30.8
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
+...|.-|++.++..+-. +-|-.||.+|-. ...||||+
T Consensus 162 yHFkCt~C~keL~sdaRe-vk~eLyClrChD-----~mgipiCg 199 (332)
T KOG2272|consen 162 YHFKCTTCGKELTSDARE-VKGELYCLRCHD-----KMGIPICG 199 (332)
T ss_pred cceecccccccccchhhh-hccceecccccc-----ccCCcccc
Confidence 688999999999887653 479999999974 46777776
No 235
>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=27.92 E-value=19 Score=25.08 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHH
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYAC 363 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~C 363 (393)
...||.|+.++-. ..-|.+||-.|
T Consensus 17 ~~~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 17 DEHCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred cCccCCCCCeeEE----ecCCCEECCCC
Confidence 3578888655433 23666666544
No 236
>PLN02720 complex II
Probab=27.87 E-value=29 Score=30.28 Aligned_cols=9 Identities=33% Similarity=1.391 Sum_probs=7.6
Q ss_pred HHHHHHHhc
Q 016213 294 FKMMEWWYQ 302 (393)
Q Consensus 294 lkfLeWWys 302 (393)
+||||||..
T Consensus 129 ~KFl~WWE~ 137 (140)
T PLN02720 129 VKFLDWWER 137 (140)
T ss_pred hHHHHHHHh
Confidence 589999974
No 237
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=27.18 E-value=59 Score=31.94 Aligned_cols=10 Identities=40% Similarity=1.016 Sum_probs=5.1
Q ss_pred CCCCCCCCCC
Q 016213 336 RTICPLCSQK 345 (393)
Q Consensus 336 ~~~CpiC~~~ 345 (393)
...|+-|++.
T Consensus 130 r~~c~eCgk~ 139 (279)
T KOG2462|consen 130 RYKCPECGKS 139 (279)
T ss_pred ceeccccccc
Confidence 4455555554
No 238
>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=27.04 E-value=35 Score=28.94 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=28.1
Q ss_pred CCCCCCCCCC---CCC-ceeccCccccccHHHHHHHhhcCC--CCCCCCC
Q 016213 336 RTICPLCSQK---RAN-PSVVTVSGFVFCYACIFKYVSQYK--RCPVTLM 379 (393)
Q Consensus 336 ~~~CpiC~~~---~~n-p~~~~~~G~vfCy~Ci~~~~~~~~--~CPv~~~ 379 (393)
...|.+|+++ +.| ..++..|++.+|-.|-.. ..+.+ .|-||.+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 4589999886 445 467888999999999865 22222 4766653
No 239
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.86 E-value=32 Score=26.11 Aligned_cols=20 Identities=35% Similarity=0.801 Sum_probs=12.8
Q ss_pred cHHHHHHHhhcCCCCCCCCCCC
Q 016213 360 CYACIFKYVSQYKRCPVTLMPA 381 (393)
Q Consensus 360 Cy~Ci~~~~~~~~~CPv~~~~~ 381 (393)
|..|- +|.+...||+|+...
T Consensus 6 C~~C~--~i~~~~~CP~Cgs~~ 25 (61)
T PRK08351 6 CRHCH--YITTEDRCPVCGSRD 25 (61)
T ss_pred hhhCC--cccCCCcCCCCcCCc
Confidence 44443 344566899999754
No 240
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.34 E-value=21 Score=39.11 Aligned_cols=31 Identities=16% Similarity=0.310 Sum_probs=17.3
Q ss_pred eeccCccccccHHHHHHHhhcCCCCCCCCCCCCcCCeeeC
Q 016213 350 SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 389 (393)
Q Consensus 350 ~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 389 (393)
++|..|||. ...++..||.||.. +++.++||
T Consensus 567 ~iC~~CG~~--------~~g~~~~CP~CGs~-~~ev~~RV 597 (623)
T PRK08271 567 TICNDCHHI--------DKRTGKRCPICGSE-NIDYYTRV 597 (623)
T ss_pred ccCCCCCCc--------CCCCCcCCcCCCCc-chhHHHHH
Confidence 356666665 12246789999853 23444444
No 241
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=26.24 E-value=85 Score=26.09 Aligned_cols=43 Identities=19% Similarity=0.335 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCCCceeccCccc---cccHHHHHH--HhhcCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGF---VFCYACIFK--YVSQYKRCPVTLM 379 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~---vfCy~Ci~~--~~~~~~~CPv~~~ 379 (393)
-+-||.|+.-....... .||. +||.++-.- +..++++|+.|+.
T Consensus 49 vggCp~CrvG~le~~ft-~~Gi~~AI~fFPiGilcc~~~r~~rC~nCG~ 96 (98)
T PF10164_consen 49 VGGCPACRVGVLEDSFT-CCGILCAIFFFPIGILCCLAMRERRCSNCGA 96 (98)
T ss_pred ecCCCCCceeeeccccc-HHHHHHHHHHHhhHHHHhhhcCccccCCCCc
Confidence 36799999865444332 2554 344444322 2357899999985
No 242
>PF04088 Peroxin-13_N: Peroxin 13, N-terminal region; InterPro: IPR007223 Peroxin-13 is a component of the peroxisomal translocation machinery with Peroxin-14 and Peroxin-17. Both termini of Peroxin-13 are oriented to the cytosol. It is required for peroxisomal association of peroxin-14 []. The proteins also contain an SH3 domain (IPR001452 from INTERPRO).; GO: 0016560 protein import into peroxisome matrix, docking, 0005777 peroxisome, 0016021 integral to membrane
Probab=26.12 E-value=83 Score=28.41 Aligned_cols=26 Identities=23% Similarity=0.289 Sum_probs=21.1
Q ss_pred CCCCCchhHHHHHHHHHhHHhHHHHH
Q 016213 106 HSGLEKRQRVLSVVFMVVLPYFKSKL 131 (393)
Q Consensus 106 ~~~Lt~~q~~~sLl~lV~~PYlk~KL 131 (393)
..+.+.+=...-+++.+++|||-.||
T Consensus 131 ~~~~s~~PlllF~~~v~G~PyLi~Kl 156 (158)
T PF04088_consen 131 RPKPSSKPLLLFLAAVFGLPYLIWKL 156 (158)
T ss_pred CCCCCcccHHHHHHHHHHHHHHHHHH
Confidence 45567777777888889999999997
No 243
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.02 E-value=23 Score=39.47 Aligned_cols=41 Identities=15% Similarity=0.417 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCC------Cce-eccCccccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRA------NPS-VVTVSGFVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~------np~-~~~~~G~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
...|..|.+++- +-. +.. |||+|-.+|+..+...++ |-+|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChhh
Confidence 568999999876 333 555 999999999999998776 66554
No 244
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.42 E-value=37 Score=34.65 Aligned_cols=54 Identities=13% Similarity=0.269 Sum_probs=41.6
Q ss_pred CCCCCCCCCCC--C-ceeccCccccccHHHHHHHhhcC-CCCCCCCCCCCcCCeeeCcc
Q 016213 337 TICPLCSQKRA--N-PSVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPATVEQIRRLFH 391 (393)
Q Consensus 337 ~~CpiC~~~~~--n-p~~~~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~~~~~l~riy~ 391 (393)
..|-|-++.+. | |.+.+ .|||+=+.-|..+=+.+ -.||++++-....+++++|.
T Consensus 331 Lvc~isge~md~~N~P~lfp-nG~Vyg~~~L~s~~~~~~i~dP~~~k~f~~~~l~kvy~ 388 (389)
T KOG0396|consen 331 LVCSISGELMDDDNPPHLFP-NGYVYGTKALESLNEDDGIGDPRTKKVFRYSELCKVYL 388 (389)
T ss_pred HHhhccccccCCCCCccccc-CceeehhHHHHhhcccCCCcCCCCCccccHHHHHHHhc
Confidence 44555444322 4 45665 99999999999988888 58999999999999999885
No 245
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.21 E-value=32 Score=40.44 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCceeccCcccc---------ccHHHHH
Q 016213 336 RTICPLCSQKRANPSVVTVSGFV---------FCYACIF 365 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~v---------fCy~Ci~ 365 (393)
...||-|+.....+..|+.||.. +|..|-.
T Consensus 679 ~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 679 ENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred cccCcccCCcCCCceeCccCCCccCCCccccccCCCCCC
Confidence 45788888887666677778874 7887754
No 246
>COG3647 Predicted membrane protein [Function unknown]
Probab=25.01 E-value=2.8e+02 Score=25.39 Aligned_cols=16 Identities=25% Similarity=1.068 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHhcc
Q 016213 288 IAAVFFFKMMEWWYQS 303 (393)
Q Consensus 288 p~~iF~lkfLeWWyss 303 (393)
....-+.-++||||.-
T Consensus 142 msiaA~YElIEWwyA~ 157 (205)
T COG3647 142 MSIAAMYELIEWWYAL 157 (205)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3334567899999985
No 247
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=24.62 E-value=42 Score=34.90 Aligned_cols=51 Identities=24% Similarity=0.438 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCC-ceeccCccccccHHHHHHHhhcCCCCCCCCCCC----CcCCeeeC
Q 016213 337 TICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA----TVEQIRRL 389 (393)
Q Consensus 337 ~~CpiC~~~~~n-p~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~----~~~~l~ri 389 (393)
.+|-+|.+.+.. |-.+...+-|+|-+|-++-+.- +|-+|+.|+ ..++.+||
T Consensus 361 F~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~P~~G~~etvRv 416 (468)
T KOG1701|consen 361 FTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPILPRDGKDETVRV 416 (468)
T ss_pred eEEEEeccccCCccccccCCCceeeehhhhhhcCc--chhhccCCccCCCCCcceEEE
No 248
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=24.29 E-value=29 Score=22.99 Aligned_cols=30 Identities=27% Similarity=0.619 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCceeccCccccccHHHHHH
Q 016213 337 TICPLCSQKRANPSVVTVSGFVFCYACIFK 366 (393)
Q Consensus 337 ~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~ 366 (393)
+.|-.|+++|-..-....=|-.+|.+|...
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 469999999888753333688999999764
No 249
>PF14353 CpXC: CpXC protein
Probab=24.27 E-value=36 Score=28.98 Aligned_cols=43 Identities=12% Similarity=0.188 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCc--eeccCccccccHHHHHHHhh-c---CCCCCCCCCCCCc
Q 016213 337 TICPLCSQKRANP--SVVTVSGFVFCYACIFKYVS-Q---YKRCPVTLMPATV 383 (393)
Q Consensus 337 ~~CpiC~~~~~np--~~~~~~G~vfCy~Ci~~~~~-~---~~~CPv~~~~~~~ 383 (393)
..||-|++...-. +.+.+... +=+.+-|- + .-.||-||....+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~----p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADED----PELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCC----HHHHHHHHcCCcCEEECCCCCCceec
Confidence 4799999875443 22221111 11112222 2 2489999977543
No 250
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=23.96 E-value=41 Score=29.67 Aligned_cols=36 Identities=25% Similarity=0.745 Sum_probs=12.8
Q ss_pred CCCCCCCCCCCCC-c----eeccCcc---ccccH-HHHHHHhhcC
Q 016213 336 RTICPLCSQKRAN-P----SVVTVSG---FVFCY-ACIFKYVSQY 371 (393)
Q Consensus 336 ~~~CpiC~~~~~n-p----~~~~~~G---~vfCy-~Ci~~~~~~~ 371 (393)
...||+|+-.+.+ | .+...-| +.||- .|++.|+.++
T Consensus 25 ~~~C~~CgM~i~d~p~~~aqi~~~~g~~~~~Fdsi~c~~~~~~~~ 69 (149)
T PF05573_consen 25 DDRCPVCGMVISDYPGFAAQIIYKDGEKVYKFDSIGCMFAYLKEP 69 (149)
T ss_dssp ------------------EEEEETT-SSEEEES-HHHHHHHHTTC
T ss_pred CCccCCCCCEeccCCCccEEEEECCCCEEEEECCHHHHHHHHhcc
Confidence 5789999999987 5 2333245 56665 7999999853
No 251
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.66 E-value=66 Score=35.10 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=32.9
Q ss_pred CCCCCCCCCCCCCce-eccCcc----ccccHHHHHHHhhcCCCCCCCC
Q 016213 336 RTICPLCSQKRANPS-VVTVSG----FVFCYACIFKYVSQYKRCPVTL 378 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-~~~~~G----~vfCy~Ci~~~~~~~~~CPv~~ 378 (393)
.+.|.-|....+-.= -.. +| +++|..|...-.++-.+-++|.
T Consensus 462 P~~caqcktdftp~wk~ek-stq~d~~i~cE~cvtSnqkkAlK~ehT~ 508 (706)
T KOG3740|consen 462 PYACAQCKTDFTPAWKKEK-STQADAAIVCENCVTSNQKKALKVEHTN 508 (706)
T ss_pred chhhhhccccccccccccc-ccCcchHHHHHhhhhhcccccccccchH
Confidence 688999998876542 344 78 9999999998888777777774
No 252
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=23.63 E-value=26 Score=26.74 Aligned_cols=24 Identities=25% Similarity=0.354 Sum_probs=15.4
Q ss_pred ccccccHHHHHHHhhcC--CCCCCCCCC
Q 016213 355 SGFVFCYACIFKYVSQY--KRCPVTLMP 380 (393)
Q Consensus 355 ~G~vfCy~Ci~~~~~~~--~~CPv~~~~ 380 (393)
+++--|..|- ++.+. ..||+|+.+
T Consensus 2 ~~~kAC~~Ck--~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 2 STEKACKNCK--RLTPEDTEICPVCGST 27 (64)
T ss_pred chhHHHhhcc--ccCCCCCccCCCCCCc
Confidence 3455677775 34443 459999977
No 253
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.60 E-value=8.7 Score=36.70 Aligned_cols=53 Identities=25% Similarity=0.392 Sum_probs=30.0
Q ss_pred CCCCCCCCCCCCCCceeccCcccccc--------HHHHHHHhhcCCCCCCCCCCCCcCCee
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFC--------YACIFKYVSQYKRCPVTLMPATVEQIR 387 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfC--------y~Ci~~~~~~~~~CPv~~~~~~~~~l~ 387 (393)
....||+|....+--.|.+-+|-.-- |.=|..++=.--.||.|...+-.+|..
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yAaf~sDFe 78 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYAAFKSDFE 78 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHHHhhHHHH
Confidence 46789999999988877653332211 111112222234799998765444433
No 254
>PRK01343 zinc-binding protein; Provisional
Probab=23.31 E-value=74 Score=23.86 Aligned_cols=35 Identities=23% Similarity=0.569 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCCceeccCccccccH-HHH----HHHhhcCCCCCC
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCY-ACI----FKYVSQYKRCPV 376 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy-~Ci----~~~~~~~~~CPv 376 (393)
...||+|+++..++. +-||- +|- -+|+.+..+=|.
T Consensus 9 ~~~CP~C~k~~~~~~------rPFCS~RC~~iDLg~W~~e~Y~Ip~ 48 (57)
T PRK01343 9 TRPCPECGKPSTREA------YPFCSERCRDIDLNRWLSGSYVIPG 48 (57)
T ss_pred CCcCCCCCCcCcCCC------CcccCHHHhhhhHHHHhCCCcccCC
Confidence 457999999876542 35775 574 467766655554
No 255
>PRK07726 DNA topoisomerase III; Provisional
Probab=23.30 E-value=47 Score=36.59 Aligned_cols=41 Identities=24% Similarity=0.331 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCC-----CceeccCccccccHHHHHHHhh--cCCCCCCCCC
Q 016213 336 RTICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVS--QYKRCPVTLM 379 (393)
Q Consensus 336 ~~~CpiC~~~~~-----np~~~~~~G~vfCy~Ci~~~~~--~~~~CPv~~~ 379 (393)
...||.|++.+. +-....++|+-.|.. .|+. ..++||-|+.
T Consensus 610 ~~~CP~C~~~~~~~~~~~~~f~~Cs~~~~~~~---~~~~~~~~~~~~~~~~ 657 (658)
T PRK07726 610 GPKCPDCGKPMLKVKGKNGKMLVCQDRECGKR---KNVSKKTNARCPNCKK 657 (658)
T ss_pred cccccccCccceeecccCCeeEecCCCccccc---cccccccCCCCCccCC
Confidence 367999998654 112223345444433 3333 2468999985
No 256
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.16 E-value=51 Score=23.03 Aligned_cols=25 Identities=24% Similarity=0.386 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCceeccCccccccHHH
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYAC 363 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~C 363 (393)
.|..|+..- +--++-.||+++|..-
T Consensus 1 ~C~~C~~~~-~l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIE-NLWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcC-CeEEecCCCCcccCCC
Confidence 478888544 3334445999999544
No 257
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.12 E-value=53 Score=26.76 Aligned_cols=12 Identities=25% Similarity=1.099 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKR 346 (393)
Q Consensus 335 ~~~~CpiC~~~~ 346 (393)
+...||.|+...
T Consensus 34 ~~~~Cp~C~~~~ 45 (89)
T COG1997 34 AKHVCPFCGRTT 45 (89)
T ss_pred cCCcCCCCCCcc
Confidence 467899999983
No 258
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.59 E-value=46 Score=29.31 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 382 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 382 (393)
....||-|+...+---+.. -+. -..+-.||.||.++.
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~-~~d----------~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQ-LLD----------MDGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHH-hcC----------CCCcEECCCCCCEEE
Confidence 4678999987655322221 000 012358999998874
No 259
>smart00746 TRASH metallochaperone-like domain.
Probab=21.81 E-value=94 Score=18.63 Aligned_cols=31 Identities=35% Similarity=0.836 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcee---ccCcccc--cc-HHHHHHHhh
Q 016213 339 CPLCSQKRANPSV---VTVSGFV--FC-YACIFKYVS 369 (393)
Q Consensus 339 CpiC~~~~~np~~---~~~~G~v--fC-y~Ci~~~~~ 369 (393)
|++|+..+.++.. ...-|.+ || -.|...|..
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~~~ 37 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKFKK 37 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHHHh
Confidence 8899988875421 1124544 34 357666654
No 260
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.68 E-value=56 Score=24.48 Aligned_cols=22 Identities=23% Similarity=0.629 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCCCceeccCccc
Q 016213 336 RTICPLCSQKRANPSVVTVSGF 357 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~ 357 (393)
-..||.|++...--.|+..||+
T Consensus 27 ~~~c~~cG~~~l~Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLPHRVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccCceEcCCCCC
Confidence 4578888887666666666674
No 261
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=21.66 E-value=30 Score=36.16 Aligned_cols=69 Identities=13% Similarity=0.171 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHhcccc-cccCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc---eeccCcccc
Q 016213 284 QTGLIAAVFFFKMMEWWYQSAE-ERMSA-PTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANP---SVVTVSGFV 358 (393)
Q Consensus 284 ~~~lp~~iF~lkfLeWWyss~~-~r~~~-~~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~~~np---~~~~~~G~v 358 (393)
.-..-+.|=+-|+++-|-+... .+... +.. .-|+. ++ .+-..||+|.+...-. -=|.-||-|
T Consensus 139 ve~nkLiiRl~rL~~~~~t~~d~~k~k~~Eqs-----vVpW~----DD----s~V~~CP~Ca~~F~l~rRrHHCRLCG~V 205 (505)
T KOG1842|consen 139 VETNKLIIRLKRLEEGLPTEKDSVKRKRLEQS-----VVPWL----DD----SSVQFCPECANSFGLTRRRHHCRLCGRV 205 (505)
T ss_pred HHHHHHHHHHHHHHccCccccchHHHHHHHhc-----ccccc----CC----CcccccccccchhhhHHHhhhhhhcchH
Confidence 3345666777788888886531 11111 111 11121 11 1234799999974332 234559999
Q ss_pred ccHHHHH
Q 016213 359 FCYACIF 365 (393)
Q Consensus 359 fCy~Ci~ 365 (393)
.|..|-.
T Consensus 206 mC~~C~k 212 (505)
T KOG1842|consen 206 MCRDCSK 212 (505)
T ss_pred HHHHHHH
Confidence 9999974
No 262
>COG3686 Predicted membrane protein [Function unknown]
Probab=21.37 E-value=3.9e+02 Score=23.14 Aligned_cols=46 Identities=20% Similarity=0.279 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhhHHHH--------------------HHHHHHHHHHHHHHhCCCCCCCHHHHHhcc
Q 016213 185 TKKIQKIIFACYPWLHA--------------------SCEGLSFTYQLLYLLDATGFYSVGLHALGI 231 (393)
Q Consensus 185 ~~~~k~~f~~~YP~i~~--------------------~~e~~~l~~~l~YL~g~t~y~sP~l~llgi 231 (393)
..+.++-|+..||.+-+ +|-...++|-.+||.| -+|-.-+.|+.|+
T Consensus 48 A~~A~~N~fE~fp~FaAavl~a~l~G~~~~~~~~~A~l~i~~RllYi~~Yla~-~p~lRSlvW~~gm 113 (125)
T COG3686 48 ANRAQQNFFETFPAFAAAVLVAHLTGNPSQAANTLAILFIAARLLYIPCYLAD-IPYLRSLVWLGGM 113 (125)
T ss_pred HHHHHhhhHHhhHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHcC-cHHHHHHHHHHHH
Confidence 44556667888887654 3455667777888888 5555556666554
No 263
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.23 E-value=37 Score=24.92 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCceecc--Cc---cccccHHHH
Q 016213 338 ICPLCSQKRANPSVVT--VS---GFVFCYACI 364 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~--~~---G~vfCy~Ci 364 (393)
-||.|+..-..-.... .. -+|+|..|-
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cg 36 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCG 36 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCC
Confidence 3999976533322111 12 467787763
No 264
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=21.20 E-value=33 Score=26.29 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCceeccCccccccHHHH
Q 016213 338 ICPLCSQKRANPSVVTVSGFVFCYACI 364 (393)
Q Consensus 338 ~CpiC~~~~~np~~~~~~G~vfCy~Ci 364 (393)
-||-|+...........-.+|.|-.|-
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~Cg 34 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCE 34 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCC
Confidence 499999987777654434456676664
No 265
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.19 E-value=41 Score=33.47 Aligned_cols=25 Identities=12% Similarity=0.254 Sum_probs=14.7
Q ss_pred CCCCCCCCCCCC------CceeccCcccccc
Q 016213 336 RTICPLCSQKRA------NPSVVTVSGFVFC 360 (393)
Q Consensus 336 ~~~CpiC~~~~~------np~~~~~~G~vfC 360 (393)
-.+||-|++.+- |--||+.|||.|=
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 357888887653 3345555666543
No 266
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=21.10 E-value=48 Score=24.97 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCceeccCccc
Q 016213 336 RTICPLCSQKRANPSVVTVSGF 357 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~ 357 (393)
-..||-|++...-..++. ||+
T Consensus 27 ~~~c~~cg~~~~pH~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPHHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccceecC-Ccc
Confidence 457888888887777777 774
No 267
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.04 E-value=37 Score=23.51 Aligned_cols=26 Identities=27% Similarity=0.567 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCceec--cCccccccHHH
Q 016213 338 ICPLCSQKRANPSVV--TVSGFVFCYAC 363 (393)
Q Consensus 338 ~CpiC~~~~~np~~~--~~~G~vfCy~C 363 (393)
-||+|+..=..-... .-.|+-+|..|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 499999853222111 12588999888
No 268
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=20.84 E-value=70 Score=33.47 Aligned_cols=13 Identities=8% Similarity=0.238 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHH
Q 016213 279 MLDYAQTGLIAAV 291 (393)
Q Consensus 279 ~~~~~~~~lp~~i 291 (393)
+-.+.+....+++
T Consensus 199 L~~YVk~hhtTGl 211 (480)
T KOG2675|consen 199 LQAYVKEHHTTGL 211 (480)
T ss_pred HHHHHHHhccccc
Confidence 3444455555544
No 269
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=20.79 E-value=73 Score=33.69 Aligned_cols=41 Identities=22% Similarity=0.567 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCCCCceeccCccccccHHHHHHHhh------------cCCCCCCCCCC
Q 016213 335 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS------------QYKRCPVTLMP 380 (393)
Q Consensus 335 ~~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~------------~~~~CPv~~~~ 380 (393)
..+.|.+|++ -++|..=|---|-.|- -|.+ .++.|||.+..
T Consensus 268 ~e~~CAVCgD----nAaCqHYGvRTCEGCK-GFFKRTVQKnaKYvClanKnCPVDKRr 320 (605)
T KOG4217|consen 268 AEGLCAVCGD----NAACQHYGVRTCEGCK-GFFKRTVQKNAKYVCLANKNCPVDKRR 320 (605)
T ss_pred ccceeeecCC----hHHhhhcCccccccch-HHHHHHHhcCCeeEeecCCCCCcchhh
Confidence 4789999986 3566667888888885 2332 35689987543
No 270
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=20.56 E-value=60 Score=34.47 Aligned_cols=43 Identities=19% Similarity=0.296 Sum_probs=27.5
Q ss_pred CCCCCCCCCCCCCceeccCccccccHHHHHHHhhcCCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 383 (393)
Q Consensus 336 ~~~CpiC~~~~~np~~~~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~ 383 (393)
.+.||.|+..-.+--+|..||+.+ ... --...+|..|+.++..
T Consensus 136 ~g~cp~c~~~~~~g~~ce~cg~~~--~~~---~l~~p~~~~~~~~~e~ 178 (530)
T TIGR00398 136 EGTCPKCGSEDARGDHCEVCGRHL--EPT---ELINPRCKICGAKPEL 178 (530)
T ss_pred cCCCCCCCCcccccchhhhccccC--CHH---HhcCCccccCCCcceE
Confidence 467999988655555666677753 111 1134789999887643
No 271
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.52 E-value=55 Score=23.02 Aligned_cols=9 Identities=44% Similarity=1.398 Sum_probs=4.3
Q ss_pred CCCCCCCCC
Q 016213 337 TICPLCSQK 345 (393)
Q Consensus 337 ~~CpiC~~~ 345 (393)
.+||+|+.+
T Consensus 9 K~C~~C~rp 17 (42)
T PF10013_consen 9 KICPVCGRP 17 (42)
T ss_pred CcCcccCCc
Confidence 345555444
No 272
>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=20.27 E-value=37 Score=33.54 Aligned_cols=24 Identities=25% Similarity=0.361 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCCCc------eeccCccccc
Q 016213 336 RTICPLCSQKRANP------SVVTVSGFVF 359 (393)
Q Consensus 336 ~~~CpiC~~~~~np------~~~~~~G~vf 359 (393)
-.+||-|++.+-.. -||+.|||.|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 45799999875443 4555566654
No 273
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.20 E-value=17 Score=39.82 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=14.8
Q ss_pred cccccHHHHHHHhhcCCCCCCCCCC
Q 016213 356 GFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 356 G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
+...|..|-+.+...+..||+|+..
T Consensus 567 ~~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 567 AITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred CCccCCCCCCccCCCCCcCcCCCCc
Confidence 3444555554334456789999853
No 274
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.14 E-value=33 Score=37.96 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCCce-----ec-cCccccccHHHHHHHhhcCCCCCCCCCC
Q 016213 336 RTICPLCSQKRANPS-----VV-TVSGFVFCYACIFKYVSQYKRCPVTLMP 380 (393)
Q Consensus 336 ~~~CpiC~~~~~np~-----~~-~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 380 (393)
...|.-|+...+-|. +. ...+...|-.|-+.. ....||.|+..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~--~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA--PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC--cCccCCCCcCC
Confidence 345766766666551 11 124567788898753 46799999865
No 275
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.10 E-value=48 Score=27.57 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=8.6
Q ss_pred CCCCCCCCCCC
Q 016213 335 DRTICPLCSQK 345 (393)
Q Consensus 335 ~~~~CpiC~~~ 345 (393)
.-..||-|+..
T Consensus 20 t~f~CP~Cge~ 30 (99)
T PRK14892 20 KIFECPRCGKV 30 (99)
T ss_pred cEeECCCCCCe
Confidence 46789999953
No 276
>PF07627 PSCyt3: Protein of unknown function (DUF1588); InterPro: IPR013039 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=20.09 E-value=61 Score=27.03 Aligned_cols=13 Identities=23% Similarity=0.866 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCCCc
Q 016213 336 RTICPLCSQKRANP 349 (393)
Q Consensus 336 ~~~CpiC~~~~~np 349 (393)
...|..|++ ..||
T Consensus 69 ~~~Ca~CH~-~iDP 81 (101)
T PF07627_consen 69 NPACASCHR-KIDP 81 (101)
T ss_pred CCcHHHHhh-hhCc
Confidence 567888888 5555
Done!