Query 018073
Match_columns 361
No_of_seqs 366 out of 1650
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 05:55:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018073.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018073hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 5.9E-52 1.3E-56 408.4 18.3 280 69-357 2-283 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 7.9E-38 1.7E-42 300.4 12.9 205 140-353 145-355 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 3.9E-37 8.5E-42 284.5 9.5 196 138-337 181-405 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 5.8E-28 1.3E-32 216.2 8.2 195 137-338 217-437 (446)
5 smart00647 IBR In Between Ring 99.4 4.4E-13 9.6E-18 96.5 6.0 63 213-275 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 4E-13 8.7E-18 96.7 -0.0 63 213-275 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.7 1.3E-08 2.8E-13 66.5 2.5 40 144-190 1-40 (42)
8 KOG0320 Predicted E3 ubiquitin 98.5 1.1E-07 2.3E-12 80.0 3.3 58 137-205 127-184 (187)
9 PF13639 zf-RING_2: Ring finge 98.4 1.3E-07 2.9E-12 62.4 1.8 34 143-176 2-36 (44)
10 PF01485 IBR: IBR domain; Int 98.4 1.5E-07 3.3E-12 67.3 2.2 38 298-336 17-58 (64)
11 PF13923 zf-C3HC4_2: Zinc fing 98.4 1.8E-07 3.9E-12 60.1 2.2 32 144-176 1-32 (39)
12 smart00647 IBR In Between Ring 98.4 4.8E-07 1E-11 64.7 4.3 38 298-336 17-58 (64)
13 PF00097 zf-C3HC4: Zinc finger 98.3 4.2E-07 9.2E-12 59.0 3.0 39 144-190 1-39 (41)
14 PLN03208 E3 ubiquitin-protein 98.3 6.6E-07 1.4E-11 77.3 3.7 65 139-207 16-87 (193)
15 PF13445 zf-RING_UBOX: RING-ty 98.3 6.4E-07 1.4E-11 58.5 2.5 41 144-190 1-43 (43)
16 PF14634 zf-RING_5: zinc-RING 98.1 1.8E-06 3.8E-11 57.0 2.6 42 143-195 1-43 (44)
17 cd00162 RING RING-finger (Real 98.1 3.6E-06 7.8E-11 55.1 3.1 44 143-197 1-44 (45)
18 PF13920 zf-C3HC4_3: Zinc fing 98.1 3.2E-06 6.9E-11 57.4 2.8 46 141-199 2-48 (50)
19 KOG0823 Predicted E3 ubiquitin 98.0 3.9E-06 8.3E-11 73.9 2.5 59 138-206 44-102 (230)
20 KOG0317 Predicted E3 ubiquitin 97.9 1.5E-05 3.2E-10 72.4 4.1 52 139-203 237-288 (293)
21 PHA02929 N1R/p28-like protein; 97.8 2.2E-05 4.8E-10 70.7 3.8 50 139-199 172-227 (238)
22 KOG2177 Predicted E3 ubiquitin 97.7 1.4E-05 3E-10 74.9 2.5 106 139-277 11-124 (386)
23 smart00184 RING Ring finger. E 97.7 2.3E-05 5E-10 49.3 2.6 30 144-175 1-30 (39)
24 PHA02926 zinc finger-like prot 97.7 2.6E-05 5.7E-10 68.2 3.6 57 138-199 167-230 (242)
25 smart00504 Ubox Modified RING 97.7 4.2E-05 9.2E-10 54.4 3.7 48 142-202 2-49 (63)
26 KOG2164 Predicted E3 ubiquitin 97.7 2.5E-05 5.4E-10 76.1 3.0 59 141-207 186-244 (513)
27 TIGR00599 rad18 DNA repair pro 97.6 4.2E-05 9.1E-10 73.9 3.7 65 139-216 24-89 (397)
28 KOG0978 E3 ubiquitin ligase in 97.3 0.00022 4.8E-09 72.9 4.7 55 140-206 642-696 (698)
29 KOG0287 Postreplication repair 97.3 0.00021 4.5E-09 66.1 3.4 63 140-215 22-85 (442)
30 KOG4628 Predicted E3 ubiquitin 97.2 0.00051 1.1E-08 64.9 5.0 47 142-198 230-277 (348)
31 COG5540 RING-finger-containing 97.0 0.0005 1.1E-08 62.8 2.8 51 140-200 322-373 (374)
32 TIGR00570 cdk7 CDK-activating 97.0 0.0014 3.1E-08 61.0 5.8 51 142-202 4-57 (309)
33 PF14555 UBA_4: UBA-like domai 97.0 0.002 4.3E-08 42.1 4.9 40 80-119 1-40 (43)
34 PF11789 zf-Nse: Zinc-finger o 97.0 0.0006 1.3E-08 47.5 2.5 47 141-195 11-57 (57)
35 COG5243 HRD1 HRD ubiquitin lig 96.7 0.0044 9.5E-08 58.3 7.0 94 95-199 238-345 (491)
36 KOG1002 Nucleotide excision re 96.7 0.00096 2.1E-08 65.2 2.8 57 137-201 532-588 (791)
37 COG5574 PEX10 RING-finger-cont 96.7 0.0015 3.2E-08 58.8 3.4 54 139-203 213-266 (271)
38 PF12678 zf-rbx1: RING-H2 zinc 96.6 0.0015 3.2E-08 48.1 2.5 35 142-176 20-65 (73)
39 PF11793 FANCL_C: FANCL C-term 96.6 0.0014 2.9E-08 47.8 2.2 58 141-200 2-67 (70)
40 PF14835 zf-RING_6: zf-RING of 96.4 0.00073 1.6E-08 47.5 -0.2 43 142-199 8-51 (65)
41 PF04564 U-box: U-box domain; 96.1 0.01 2.2E-07 43.6 4.4 50 140-201 3-52 (73)
42 KOG2879 Predicted E3 ubiquitin 96.0 0.017 3.6E-07 52.4 6.3 52 138-199 236-287 (298)
43 PF14570 zf-RING_4: RING/Ubox 96.0 0.0059 1.3E-07 40.6 2.5 44 144-197 1-46 (48)
44 COG5432 RAD18 RING-finger-cont 95.9 0.0044 9.5E-08 56.4 2.2 48 140-200 24-71 (391)
45 KOG4367 Predicted Zn-finger pr 95.9 0.0029 6.4E-08 60.5 0.9 35 140-176 3-37 (699)
46 KOG0824 Predicted E3 ubiquitin 95.1 0.011 2.4E-07 54.2 1.9 55 138-204 4-58 (324)
47 KOG1814 Predicted E3 ubiquitin 95.1 0.0061 1.3E-07 58.2 0.1 41 297-338 271-313 (445)
48 KOG1039 Predicted E3 ubiquitin 94.9 0.02 4.4E-07 54.5 3.2 59 136-198 156-220 (344)
49 PF10571 UPF0547: Uncharacteri 94.4 0.021 4.6E-07 32.9 1.2 24 300-328 1-24 (26)
50 KOG2660 Locus-specific chromos 94.4 0.019 4.1E-07 53.5 1.5 49 140-200 14-62 (331)
51 KOG0006 E3 ubiquitin-protein l 94.0 0.093 2E-06 48.6 5.1 94 160-271 341-437 (446)
52 COG5152 Uncharacterized conser 94.0 0.031 6.7E-07 48.2 1.8 32 141-174 196-227 (259)
53 KOG4159 Predicted E3 ubiquitin 93.8 0.068 1.5E-06 52.0 4.1 49 139-200 82-130 (398)
54 KOG1734 Predicted RING-contain 93.0 0.097 2.1E-06 47.4 3.4 74 121-203 204-285 (328)
55 PF12861 zf-Apc11: Anaphase-pr 92.9 0.12 2.5E-06 38.9 3.1 32 159-198 50-81 (85)
56 KOG1645 RING-finger-containing 92.8 0.12 2.7E-06 49.4 4.0 49 141-198 4-55 (463)
57 KOG0802 E3 ubiquitin ligase [P 92.4 0.063 1.4E-06 54.9 1.6 46 141-197 291-339 (543)
58 PF07191 zinc-ribbons_6: zinc- 92.3 0.1 2.2E-06 37.6 2.1 58 301-361 3-65 (70)
59 smart00744 RINGv The RING-vari 91.7 0.18 3.9E-06 33.8 2.7 36 143-178 1-41 (49)
60 smart00661 RPOL9 RNA polymeras 91.5 0.16 3.4E-06 34.3 2.3 28 300-328 1-30 (52)
61 KOG1428 Inhibitor of type V ad 91.4 0.34 7.3E-06 53.4 5.6 74 141-217 3486-3561(3738)
62 KOG0311 Predicted E3 ubiquitin 91.2 0.03 6.6E-07 52.6 -2.0 48 140-198 42-89 (381)
63 PF15227 zf-C3HC4_4: zinc fing 91.1 0.11 2.4E-06 33.6 1.1 40 302-350 1-40 (42)
64 KOG0826 Predicted E3 ubiquitin 90.9 0.81 1.7E-05 42.8 6.9 47 141-197 300-346 (357)
65 KOG4265 Predicted E3 ubiquitin 90.6 0.22 4.7E-06 47.2 3.0 48 139-199 288-336 (349)
66 PF13248 zf-ribbon_3: zinc-rib 90.5 0.15 3.2E-06 29.3 1.2 11 300-310 3-13 (26)
67 KOG4739 Uncharacterized protei 90.4 0.091 2E-06 47.0 0.3 45 142-199 4-48 (233)
68 KOG4692 Predicted E3 ubiquitin 90.3 0.22 4.8E-06 46.8 2.8 52 136-200 417-468 (489)
69 KOG2817 Predicted E3 ubiquitin 90.2 0.98 2.1E-05 43.4 7.0 56 139-202 332-388 (394)
70 PF05883 Baculo_RING: Baculovi 90.2 0.11 2.4E-06 42.3 0.7 36 141-176 26-68 (134)
71 KOG0317 Predicted E3 ubiquitin 90.1 0.047 1E-06 50.0 -1.7 38 297-341 237-274 (293)
72 PF13240 zinc_ribbon_2: zinc-r 89.9 0.17 3.6E-06 28.2 1.1 10 301-310 1-10 (23)
73 KOG4185 Predicted E3 ubiquitin 89.8 0.51 1.1E-05 44.3 4.9 56 141-206 3-64 (296)
74 PF09297 zf-NADH-PPase: NADH p 89.7 0.45 9.8E-06 28.7 3.0 29 298-327 2-30 (32)
75 PHA00626 hypothetical protein 89.3 0.31 6.7E-06 33.2 2.1 28 301-329 2-34 (59)
76 KOG0828 Predicted E3 ubiquitin 89.2 0.21 4.5E-06 49.1 1.7 50 140-199 570-634 (636)
77 KOG1812 Predicted E3 ubiquitin 89.1 0.68 1.5E-05 45.2 5.3 42 228-273 304-345 (384)
78 PRK14559 putative protein seri 89.1 0.28 6E-06 51.0 2.7 12 325-336 40-51 (645)
79 KOG0297 TNF receptor-associate 89.0 0.44 9.5E-06 46.7 3.9 37 138-176 18-55 (391)
80 PRK00432 30S ribosomal protein 88.8 0.22 4.7E-06 33.6 1.2 29 297-328 18-47 (50)
81 PF14952 zf-tcix: Putative tre 88.6 0.34 7.3E-06 31.3 1.8 32 293-328 5-37 (44)
82 PF10367 Vps39_2: Vacuolar sor 88.5 0.52 1.1E-05 36.8 3.4 31 141-171 78-108 (109)
83 KOG0804 Cytoplasmic Zn-finger 88.5 0.23 5.1E-06 48.2 1.6 116 70-198 86-221 (493)
84 PF08274 PhnA_Zn_Ribbon: PhnA 88.5 0.4 8.7E-06 28.6 2.0 27 300-328 3-29 (30)
85 PF04931 DNA_pol_phi: DNA poly 88.2 1.4 3E-05 47.4 7.3 20 96-115 764-783 (784)
86 KOG0827 Predicted E3 ubiquitin 87.5 0.27 5.9E-06 46.9 1.3 46 142-195 5-52 (465)
87 KOG1813 Predicted E3 ubiquitin 87.3 0.22 4.8E-06 45.8 0.6 45 141-198 241-285 (313)
88 PF00097 zf-C3HC4: Zinc finger 87.3 0.18 3.9E-06 32.1 0.0 32 302-339 1-32 (41)
89 KOG4172 Predicted E3 ubiquitin 86.0 0.29 6.3E-06 33.2 0.5 45 142-198 8-53 (62)
90 PHA03096 p28-like protein; Pro 85.4 0.44 9.5E-06 44.4 1.5 38 142-179 179-222 (284)
91 KOG1815 Predicted E3 ubiquitin 85.2 0.47 1E-05 47.4 1.7 39 299-339 158-199 (444)
92 KOG1001 Helicase-like transcri 85.0 0.33 7.1E-06 50.8 0.5 51 142-204 455-505 (674)
93 PF13923 zf-C3HC4_2: Zinc fing 84.9 0.31 6.8E-06 30.7 0.3 32 302-339 1-32 (39)
94 KOG1785 Tyrosine kinase negati 84.9 0.37 7.9E-06 46.1 0.7 35 140-176 368-402 (563)
95 TIGR00622 ssl1 transcription f 84.5 0.83 1.8E-05 36.2 2.5 40 231-272 56-102 (112)
96 COG5220 TFB3 Cdk activating ki 84.2 0.27 5.9E-06 43.8 -0.4 49 142-198 11-63 (314)
97 TIGR02098 MJ0042_CXXC MJ0042 f 84.1 0.66 1.4E-05 29.1 1.5 27 300-328 3-35 (38)
98 PF13719 zinc_ribbon_5: zinc-r 83.7 0.82 1.8E-05 28.7 1.8 29 231-261 3-35 (37)
99 KOG1941 Acetylcholine receptor 83.1 1.9 4.1E-05 41.3 4.7 48 141-197 365-414 (518)
100 PF00627 UBA: UBA/TS-N domain; 83.0 4 8.8E-05 25.3 4.8 33 80-113 3-35 (37)
101 PF14835 zf-RING_6: zf-RING of 82.9 0.79 1.7E-05 32.4 1.6 35 300-335 8-49 (65)
102 PF04931 DNA_pol_phi: DNA poly 82.5 1.7 3.7E-05 46.6 4.8 8 85-92 707-714 (784)
103 KOG2114 Vacuolar assembly/sort 82.5 1.4 3E-05 46.3 3.8 69 111-197 813-881 (933)
104 PRK00398 rpoP DNA-directed RNA 82.4 1.2 2.6E-05 29.3 2.3 29 300-329 4-32 (46)
105 PLN03208 E3 ubiquitin-protein 81.8 0.5 1.1E-05 41.2 0.3 31 300-337 19-49 (193)
106 KOG4445 Uncharacterized conser 81.3 3.5 7.6E-05 38.2 5.5 39 139-177 113-152 (368)
107 KOG2038 CAATT-binding transcri 81.1 1.1 2.5E-05 46.5 2.6 13 3-15 882-894 (988)
108 KOG2807 RNA polymerase II tran 80.6 0.6 1.3E-05 43.6 0.4 23 249-271 342-365 (378)
109 TIGR00570 cdk7 CDK-activating 80.4 0.91 2E-05 42.6 1.5 52 232-312 5-56 (309)
110 PHA02926 zinc finger-like prot 80.2 0.84 1.8E-05 40.5 1.2 54 298-351 169-224 (242)
111 KOG0823 Predicted E3 ubiquitin 80.0 0.58 1.3E-05 41.7 0.1 20 318-340 62-81 (230)
112 KOG4275 Predicted E3 ubiquitin 79.5 1 2.2E-05 41.5 1.5 29 141-171 300-329 (350)
113 PF02150 RNA_POL_M_15KD: RNA p 79.0 2.1 4.5E-05 26.5 2.3 28 230-260 1-29 (35)
114 cd00194 UBA Ubiquitin Associat 78.4 7.4 0.00016 24.0 4.9 35 81-116 3-37 (38)
115 PF09538 FYDLN_acid: Protein o 78.2 1.4 2.9E-05 34.9 1.7 26 300-328 10-36 (108)
116 KOG0320 Predicted E3 ubiquitin 77.9 0.81 1.8E-05 39.1 0.4 30 255-310 149-178 (187)
117 COG5222 Uncharacterized conser 77.5 2.3 5.1E-05 39.2 3.2 44 142-196 275-318 (427)
118 COG5219 Uncharacterized conser 77.3 0.87 1.9E-05 48.3 0.5 53 138-199 1466-1523(1525)
119 PF14803 Nudix_N_2: Nudix N-te 77.1 2 4.3E-05 26.4 1.8 26 300-326 1-30 (34)
120 PF09026 CENP-B_dimeris: Centr 77.0 4.1 8.9E-05 31.2 3.8 9 70-78 44-52 (101)
121 PF07282 OrfB_Zn_ribbon: Putat 76.7 2 4.3E-05 30.8 2.1 29 298-327 27-55 (69)
122 KOG3039 Uncharacterized conser 76.5 1.8 3.8E-05 39.0 2.1 53 140-203 220-274 (303)
123 KOG3579 Predicted E3 ubiquitin 76.2 1.5 3.3E-05 40.2 1.6 52 139-196 266-322 (352)
124 PF06677 Auto_anti-p27: Sjogre 75.7 5.5 0.00012 25.6 3.7 30 292-325 11-41 (41)
125 PLN03086 PRLI-interacting fact 75.4 2.8 6.2E-05 42.8 3.5 57 185-261 406-463 (567)
126 TIGR03655 anti_R_Lar restricti 74.8 2.7 5.8E-05 28.6 2.2 30 300-330 2-38 (53)
127 KOG1493 Anaphase-promoting com 74.8 0.93 2E-05 33.1 -0.1 48 143-198 22-80 (84)
128 PRK14559 putative protein seri 74.7 2.3 5E-05 44.3 2.7 10 231-242 2-11 (645)
129 PF13717 zinc_ribbon_4: zinc-r 74.3 2.5 5.5E-05 26.2 1.8 29 231-261 3-35 (36)
130 KOG1991 Nuclear transport rece 73.7 7.3 0.00016 41.9 6.0 35 68-105 953-987 (1010)
131 KOG3002 Zn finger protein [Gen 73.4 2.2 4.9E-05 40.1 2.1 47 138-199 45-91 (299)
132 KOG3800 Predicted E3 ubiquitin 73.1 4.9 0.00011 37.1 4.1 47 143-199 2-51 (300)
133 KOG2906 RNA polymerase III sub 73.0 2.6 5.5E-05 32.4 1.9 29 301-330 3-33 (105)
134 smart00165 UBA Ubiquitin assoc 72.7 11 0.00025 23.0 4.6 32 82-114 4-35 (37)
135 PF04641 Rtf2: Rtf2 RING-finge 71.8 6 0.00013 36.5 4.5 68 138-217 110-180 (260)
136 COG5175 MOT2 Transcriptional r 71.3 2.5 5.5E-05 39.7 1.8 54 140-203 13-68 (480)
137 smart00661 RPOL9 RNA polymeras 71.0 3.6 7.8E-05 27.5 2.2 28 231-260 1-29 (52)
138 PRK05654 acetyl-CoA carboxylas 71.0 1 2.2E-05 42.2 -0.8 28 300-328 28-56 (292)
139 COG1997 RPL43A Ribosomal prote 70.5 3.7 8E-05 30.8 2.2 28 300-328 36-63 (89)
140 PRK00420 hypothetical protein; 69.6 8 0.00017 30.8 4.1 21 299-321 23-44 (112)
141 PRK08665 ribonucleotide-diphos 69.1 3 6.5E-05 44.5 2.1 27 300-329 725-751 (752)
142 KOG1952 Transcription factor N 68.9 3.7 8E-05 43.3 2.6 54 139-196 189-244 (950)
143 TIGR01384 TFS_arch transcripti 68.8 3.4 7.3E-05 32.3 1.9 25 301-328 2-26 (104)
144 PF14447 Prok-RING_4: Prokaryo 68.8 2 4.3E-05 29.4 0.5 45 141-200 7-51 (55)
145 COG1998 RPS31 Ribosomal protei 68.5 3.7 8.1E-05 27.3 1.7 27 299-326 19-45 (51)
146 COG2888 Predicted Zn-ribbon RN 67.5 2.9 6.2E-05 29.0 1.0 12 301-312 29-41 (61)
147 KOG2034 Vacuolar sorting prote 67.5 3.8 8.2E-05 43.5 2.4 39 140-178 816-854 (911)
148 KOG0978 E3 ubiquitin ligase in 66.8 2.4 5.2E-05 44.2 0.8 29 256-309 660-688 (698)
149 PF02845 CUE: CUE domain; Int 66.7 22 0.00047 22.6 5.1 37 81-117 3-40 (42)
150 PF07800 DUF1644: Protein of u 65.1 8.7 0.00019 32.3 3.6 86 141-244 2-121 (162)
151 CHL00174 accD acetyl-CoA carbo 65.0 1.5 3.2E-05 41.1 -1.0 28 300-328 39-67 (296)
152 PF14445 Prok-RING_2: Prokaryo 64.6 1.6 3.5E-05 29.1 -0.6 34 140-173 6-40 (57)
153 PF03119 DNA_ligase_ZBD: NAD-d 64.6 6.5 0.00014 23.0 2.0 21 301-321 1-21 (28)
154 KOG0825 PHD Zn-finger protein 64.6 1.8 3.8E-05 45.2 -0.6 16 160-175 143-158 (1134)
155 PRK09710 lar restriction allev 64.4 6.1 0.00013 27.9 2.2 29 298-327 5-36 (64)
156 PF07975 C1_4: TFIIH C1-like d 64.3 2.8 6.1E-05 28.3 0.5 23 250-272 19-42 (51)
157 COG5151 SSL1 RNA polymerase II 64.2 1.3 2.9E-05 41.0 -1.4 42 228-271 360-408 (421)
158 PF05290 Baculo_IE-1: Baculovi 64.0 6.7 0.00015 32.0 2.7 51 139-198 78-131 (140)
159 TIGR00515 accD acetyl-CoA carb 63.8 1.7 3.7E-05 40.6 -0.9 28 300-328 27-55 (285)
160 KOG3970 Predicted E3 ubiquitin 63.2 6.2 0.00013 35.1 2.5 54 142-198 51-104 (299)
161 PF02891 zf-MIZ: MIZ/SP-RING z 62.7 6.5 0.00014 26.4 2.1 47 142-196 3-49 (50)
162 PF14569 zf-UDP: Zinc-binding 62.4 4.1 8.9E-05 29.9 1.1 59 231-317 10-69 (80)
163 PF06827 zf-FPG_IleRS: Zinc fi 62.3 5 0.00011 23.6 1.3 24 300-324 2-27 (30)
164 KOG1571 Predicted E3 ubiquitin 62.1 12 0.00027 35.6 4.5 43 140-198 304-346 (355)
165 KOG1940 Zn-finger protein [Gen 61.5 5.5 0.00012 36.9 2.0 47 139-196 156-204 (276)
166 KOG2906 RNA polymerase III sub 61.3 7.6 0.00017 29.8 2.4 29 231-261 2-31 (105)
167 PRK04023 DNA polymerase II lar 61.2 6.7 0.00015 42.4 2.8 32 227-268 623-660 (1121)
168 PF10446 DUF2457: Protein of u 61.2 10 0.00022 37.2 3.9 12 136-147 189-200 (458)
169 PF13834 DUF4193: Domain of un 61.1 3.8 8.2E-05 31.6 0.7 32 138-169 67-98 (99)
170 COG5574 PEX10 RING-finger-cont 60.6 2.3 5E-05 38.7 -0.6 35 300-341 216-251 (271)
171 KOG3161 Predicted E3 ubiquitin 60.4 2.6 5.7E-05 43.0 -0.2 36 141-176 11-48 (861)
172 smart00804 TAP_C C-terminal do 60.2 36 0.00079 24.0 5.6 41 76-116 9-49 (63)
173 PRK14714 DNA polymerase II lar 60.0 6.1 0.00013 43.8 2.4 10 328-337 711-720 (1337)
174 TIGR02300 FYDLN_acid conserved 59.6 6 0.00013 32.0 1.7 27 300-328 10-36 (129)
175 PRK14892 putative transcriptio 59.6 7.1 0.00015 30.4 2.1 29 299-328 21-52 (99)
176 PF12773 DZR: Double zinc ribb 59.2 4.8 0.0001 26.7 0.9 12 299-310 12-23 (50)
177 PF01599 Ribosomal_S27: Riboso 58.8 6.3 0.00014 26.1 1.4 27 299-326 18-46 (47)
178 PF03115 Astro_capsid: Astrovi 58.6 3.2 7E-05 44.0 0.0 11 62-72 709-719 (787)
179 PF03943 TAP_C: TAP C-terminal 58.0 13 0.00027 25.1 2.8 37 81-117 2-38 (51)
180 COG5236 Uncharacterized conser 58.0 8.6 0.00019 36.4 2.7 49 138-197 58-106 (493)
181 COG1594 RPB9 DNA-directed RNA 57.6 8 0.00017 30.8 2.1 28 300-328 3-32 (113)
182 COG0777 AccD Acetyl-CoA carbox 56.7 3.4 7.5E-05 38.0 -0.1 28 300-328 29-57 (294)
183 TIGR00686 phnA alkylphosphonat 56.6 8.7 0.00019 30.1 2.1 26 300-327 3-28 (109)
184 COG0266 Nei Formamidopyrimidin 56.1 8.7 0.00019 35.6 2.4 26 299-325 245-272 (273)
185 COG1645 Uncharacterized Zn-fin 55.3 8.9 0.00019 31.3 2.0 24 299-333 28-51 (131)
186 PF08746 zf-RING-like: RING-li 55.1 9.9 0.00021 24.6 1.9 34 144-177 1-35 (43)
187 TIGR01206 lysW lysine biosynth 54.6 13 0.00027 25.5 2.4 28 300-328 3-32 (54)
188 PF04147 Nop14: Nop14-like fam 54.1 51 0.0011 35.8 8.2 16 64-79 417-435 (840)
189 PF14446 Prok-RING_1: Prokaryo 53.4 14 0.00029 25.3 2.4 32 141-172 5-38 (54)
190 PF13453 zf-TFIIB: Transcripti 53.1 9.7 0.00021 24.2 1.6 33 301-340 1-33 (41)
191 PF09788 Tmemb_55A: Transmembr 52.6 14 0.00029 33.7 2.9 20 228-247 121-140 (256)
192 COG1198 PriA Primosomal protei 52.6 11 0.00024 40.0 2.7 36 299-335 444-484 (730)
193 PF09723 Zn-ribbon_8: Zinc rib 52.0 18 0.00039 23.2 2.7 12 300-311 27-39 (42)
194 PF12906 RINGv: RING-variant d 52.0 11 0.00023 24.9 1.7 33 144-176 1-38 (47)
195 PHA02929 N1R/p28-like protein; 52.0 7.4 0.00016 35.4 1.2 40 299-340 174-216 (238)
196 PF08271 TF_Zn_Ribbon: TFIIB z 50.2 18 0.00039 23.2 2.5 21 301-321 2-23 (43)
197 PF01363 FYVE: FYVE zinc finge 50.1 10 0.00022 26.9 1.5 36 299-337 9-44 (69)
198 PF05715 zf-piccolo: Piccolo Z 50.1 6.6 0.00014 27.2 0.5 41 300-341 3-45 (61)
199 PF09889 DUF2116: Uncharacteri 49.9 3.4 7.5E-05 28.8 -1.0 12 300-311 4-15 (59)
200 PRK14811 formamidopyrimidine-D 49.6 13 0.00028 34.4 2.5 26 299-325 235-262 (269)
201 PF05605 zf-Di19: Drought indu 49.5 14 0.0003 25.0 2.0 42 141-200 2-43 (54)
202 PF14149 YhfH: YhfH-like prote 49.4 1.3 2.9E-05 27.6 -2.7 26 298-324 12-37 (37)
203 KOG3039 Uncharacterized conser 49.2 13 0.00029 33.6 2.3 38 141-180 43-80 (303)
204 PRK11827 hypothetical protein; 49.0 16 0.00034 25.6 2.2 27 300-327 9-35 (60)
205 PF08792 A2L_zn_ribbon: A2L zi 48.9 17 0.00037 22.1 2.1 27 300-327 4-30 (33)
206 smart00546 CUE Domain that may 48.7 62 0.0013 20.5 4.9 38 80-117 3-41 (43)
207 PF12861 zf-Apc11: Anaphase-pr 48.6 9.6 0.00021 28.7 1.2 48 300-355 33-80 (85)
208 PF04050 Upf2: Up-frameshift s 48.5 13 0.00029 31.8 2.2 11 73-83 63-73 (170)
209 KOG3053 Uncharacterized conser 47.8 18 0.00038 33.0 2.9 55 140-197 19-80 (293)
210 PF00098 zf-CCHC: Zinc knuckle 47.7 14 0.00031 19.1 1.4 16 261-276 2-17 (18)
211 PRK10220 hypothetical protein; 47.7 15 0.00033 28.9 2.1 26 300-327 4-29 (111)
212 KOG2932 E3 ubiquitin ligase in 47.5 5.2 0.00011 37.3 -0.5 54 227-316 87-140 (389)
213 PF05320 Pox_RNA_Pol_19: Poxvi 47.3 7.1 0.00015 32.6 0.3 8 64-71 43-50 (167)
214 PF06844 DUF1244: Protein of u 47.1 13 0.00028 26.4 1.5 17 164-180 11-27 (68)
215 COG2816 NPY1 NTP pyrophosphohy 46.8 19 0.00041 33.4 3.0 36 291-328 104-139 (279)
216 PF02042 RWP-RK: RWP-RK domain 46.6 34 0.00073 23.2 3.5 37 69-105 4-40 (52)
217 KOG2141 Protein involved in hi 46.6 16 0.00034 38.2 2.7 38 73-110 313-356 (822)
218 KOG3268 Predicted E3 ubiquitin 46.4 20 0.00043 30.7 2.8 57 141-200 165-229 (234)
219 PF06906 DUF1272: Protein of u 46.0 19 0.00041 24.7 2.1 43 143-198 7-51 (57)
220 PF12760 Zn_Tnp_IS1595: Transp 45.8 34 0.00073 22.3 3.4 28 298-326 17-45 (46)
221 PF01396 zf-C4_Topoisom: Topoi 45.8 11 0.00024 23.8 1.0 10 300-309 2-11 (39)
222 PRK01103 formamidopyrimidine/5 45.7 17 0.00036 33.8 2.6 26 299-325 245-272 (274)
223 PRK14714 DNA polymerase II lar 45.0 14 0.00031 41.1 2.2 33 299-338 667-704 (1337)
224 TIGR00577 fpg formamidopyrimid 44.7 17 0.00038 33.7 2.5 25 299-324 245-271 (272)
225 PF02724 CDC45: CDC45-like pro 44.7 43 0.00093 35.1 5.6 7 172-178 322-328 (622)
226 PRK10445 endonuclease VIII; Pr 44.5 18 0.00038 33.4 2.5 26 299-325 235-262 (263)
227 PRK14810 formamidopyrimidine-D 44.4 17 0.00038 33.7 2.5 25 299-324 244-270 (272)
228 COG5194 APC11 Component of SCF 44.2 17 0.00036 26.9 1.8 17 160-176 53-69 (88)
229 PLN02638 cellulose synthase A 44.1 17 0.00036 40.0 2.6 60 232-319 19-79 (1079)
230 smart00659 RPOLCX RNA polymera 43.8 21 0.00045 23.3 2.1 10 300-309 20-29 (44)
231 PRK13945 formamidopyrimidine-D 43.8 18 0.00039 33.8 2.5 26 299-325 254-281 (282)
232 PRK04023 DNA polymerase II lar 43.6 13 0.00028 40.4 1.6 33 297-336 624-661 (1121)
233 PF14569 zf-UDP: Zinc-binding 43.4 38 0.00082 25.0 3.5 51 138-198 6-61 (80)
234 KOG2979 Protein involved in DN 43.3 27 0.00059 31.8 3.4 48 141-196 176-223 (262)
235 TIGR00599 rad18 DNA repair pro 42.6 8.2 0.00018 37.8 -0.0 32 300-338 27-58 (397)
236 COG1594 RPB9 DNA-directed RNA 42.1 26 0.00056 27.9 2.8 30 230-261 2-32 (113)
237 PLN02189 cellulose synthase 42.0 21 0.00045 39.1 2.9 61 231-319 35-96 (1040)
238 PRK08115 ribonucleotide-diphos 41.9 13 0.00029 40.0 1.4 26 300-328 828-854 (858)
239 PF07754 DUF1610: Domain of un 40.6 24 0.00051 19.9 1.6 6 301-306 18-23 (24)
240 KOG1701 Focal adhesion adaptor 40.4 11 0.00025 36.7 0.6 25 300-325 428-459 (468)
241 PF03604 DNA_RNApol_7kD: DNA d 40.4 18 0.00039 21.9 1.3 10 300-309 18-27 (32)
242 PF02318 FYVE_2: FYVE-type zin 40.4 43 0.00093 26.7 3.9 36 298-335 53-88 (118)
243 KOG2930 SCF ubiquitin ligase, 40.4 19 0.00042 28.0 1.7 17 160-176 80-96 (114)
244 PRK12286 rpmF 50S ribosomal pr 40.3 19 0.00041 24.9 1.5 23 298-326 26-48 (57)
245 PRK11426 hypothetical protein; 39.8 50 0.0011 27.1 4.1 37 68-104 59-96 (132)
246 PF05129 Elf1: Transcription e 39.8 15 0.00033 27.4 1.1 29 299-328 22-56 (81)
247 PRK00241 nudC NADH pyrophospha 39.7 31 0.00067 31.7 3.3 34 293-328 94-127 (256)
248 KOG4684 Uncharacterized conser 39.5 26 0.00056 31.0 2.5 18 228-245 136-153 (275)
249 PRK06319 DNA topoisomerase I/S 39.4 29 0.00063 37.8 3.5 27 328-354 647-673 (860)
250 PF10122 Mu-like_Com: Mu-like 39.0 13 0.00027 25.1 0.5 24 301-325 6-31 (51)
251 PF15616 TerY-C: TerY-C metal 38.7 21 0.00045 29.3 1.8 24 299-330 77-100 (131)
252 COG3809 Uncharacterized protei 38.4 26 0.00056 25.8 2.0 34 300-340 2-35 (88)
253 TIGR02443 conserved hypothetic 38.2 29 0.00062 24.2 2.1 27 300-327 10-40 (59)
254 KOG4362 Transcriptional regula 37.9 7.7 0.00017 40.3 -1.0 51 140-200 20-70 (684)
255 cd00021 BBOX B-Box-type zinc f 37.9 24 0.00051 21.6 1.6 25 250-274 10-35 (39)
256 PRK09521 exosome complex RNA-b 37.9 23 0.0005 30.8 2.1 25 301-327 151-175 (189)
257 COG3024 Uncharacterized protei 37.7 17 0.00036 25.7 0.9 13 299-311 7-19 (65)
258 COG5220 TFB3 Cdk activating ki 36.8 21 0.00045 32.2 1.6 54 187-244 11-65 (314)
259 PLN02400 cellulose synthase 36.6 34 0.00073 37.7 3.4 59 232-318 38-97 (1085)
260 TIGR00264 alpha-NAC-related pr 36.2 81 0.0018 25.2 4.7 35 78-112 77-111 (116)
261 TIGR03826 YvyF flagellar opero 35.5 39 0.00084 27.9 2.9 12 299-310 81-92 (137)
262 PRK06369 nac nascent polypepti 35.2 1E+02 0.0023 24.6 5.2 35 79-113 76-110 (115)
263 PF14471 DUF4428: Domain of un 35.1 31 0.00068 23.2 1.9 30 143-173 1-30 (51)
264 PF05764 YL1: YL1 nuclear prot 35.0 35 0.00075 31.1 2.8 6 19-24 41-46 (240)
265 PF00643 zf-B_box: B-box zinc 34.5 12 0.00027 23.6 -0.1 23 251-273 14-37 (42)
266 PHA02325 hypothetical protein 34.2 18 0.0004 25.4 0.7 12 298-309 2-13 (72)
267 PF09526 DUF2387: Probable met 34.0 35 0.00076 24.8 2.2 27 300-327 9-39 (71)
268 PF06056 Terminase_5: Putative 33.8 54 0.0012 22.7 3.0 32 82-113 15-46 (58)
269 PLN02915 cellulose synthase A 33.6 33 0.00072 37.6 2.8 55 238-318 21-76 (1044)
270 PRK12495 hypothetical protein; 33.6 56 0.0012 29.2 3.7 29 299-338 42-70 (226)
271 KOG2164 Predicted E3 ubiquitin 33.5 17 0.00036 36.4 0.5 30 299-335 186-215 (513)
272 smart00834 CxxC_CXXC_SSSS Puta 33.5 27 0.00058 21.7 1.4 13 300-312 27-39 (41)
273 TIGR01031 rpmF_bact ribosomal 33.2 26 0.00057 24.0 1.3 23 298-326 25-47 (55)
274 TIGR00595 priA primosomal prot 32.9 35 0.00077 34.7 2.8 35 300-335 223-262 (505)
275 PF01783 Ribosomal_L32p: Ribos 32.9 26 0.00055 24.1 1.2 22 298-325 25-46 (56)
276 PF01428 zf-AN1: AN1-like Zinc 32.8 19 0.00041 23.2 0.6 28 233-267 1-29 (43)
277 KOG2879 Predicted E3 ubiquitin 32.7 20 0.00044 33.0 0.9 31 299-335 239-269 (298)
278 PHA02825 LAP/PHD finger-like p 32.7 50 0.0011 28.0 3.1 50 140-199 7-59 (162)
279 COG1096 Predicted RNA-binding 32.7 29 0.00063 30.1 1.8 25 300-327 150-174 (188)
280 COG2824 PhnA Uncharacterized Z 32.5 34 0.00073 26.8 1.9 29 300-339 4-33 (112)
281 PF03615 GCM: GCM motif protei 32.4 44 0.00096 27.3 2.7 22 300-327 83-106 (143)
282 COG5109 Uncharacterized conser 32.4 47 0.001 31.2 3.2 51 140-198 335-386 (396)
283 KOG2789 Putative Zn-finger pro 32.3 16 0.00035 35.3 0.2 36 139-174 72-107 (482)
284 COG5243 HRD1 HRD ubiquitin lig 32.0 42 0.00091 32.3 2.9 45 258-310 286-345 (491)
285 COG5432 RAD18 RING-finger-cont 31.8 14 0.00029 34.3 -0.4 30 300-336 26-55 (391)
286 TIGR01053 LSD1 zinc finger dom 31.6 51 0.0011 19.7 2.2 25 301-326 3-27 (31)
287 KOG0298 DEAD box-containing he 31.5 15 0.00032 40.9 -0.2 38 140-178 1152-1189(1394)
288 PLN02436 cellulose synthase A 31.3 40 0.00087 37.1 2.9 61 231-319 37-98 (1094)
289 PF06044 DRP: Dam-replacing fa 31.3 45 0.00097 30.3 2.8 40 287-328 20-63 (254)
290 KOG0801 Predicted E3 ubiquitin 31.2 16 0.00035 30.8 -0.0 27 140-166 176-203 (205)
291 KOG1991 Nuclear transport rece 31.2 59 0.0013 35.3 4.1 26 74-99 967-993 (1010)
292 PF10497 zf-4CXXC_R1: Zinc-fin 30.9 55 0.0012 25.7 3.0 34 162-197 37-70 (105)
293 smart00064 FYVE Protein presen 30.7 22 0.00048 25.0 0.7 36 141-176 10-47 (68)
294 PF10426 zf-RAG1: Recombinatio 30.6 16 0.00034 21.7 -0.1 19 186-204 2-20 (30)
295 PF14354 Lar_restr_allev: Rest 30.4 58 0.0013 22.3 2.8 12 229-242 2-13 (61)
296 COG4530 Uncharacterized protei 30.0 62 0.0013 25.5 3.0 10 19-28 77-86 (129)
297 cd00065 FYVE FYVE domain; Zinc 29.6 35 0.00076 23.0 1.5 35 142-176 3-39 (57)
298 PF03854 zf-P11: P-11 zinc fin 29.5 20 0.00043 23.8 0.2 44 142-200 3-47 (50)
299 COG4647 AcxC Acetone carboxyla 29.1 1.7E+02 0.0036 23.9 5.4 60 251-311 69-132 (165)
300 smart00336 BBOX B-Box-type zin 28.5 46 0.001 20.6 1.8 25 249-273 12-37 (42)
301 smart00154 ZnF_AN1 AN1-like Zi 28.3 40 0.00087 21.2 1.5 13 317-330 12-24 (39)
302 KOG4739 Uncharacterized protei 28.1 28 0.00061 31.4 1.0 17 256-272 22-38 (233)
303 PF12668 DUF3791: Protein of u 28.1 82 0.0018 21.9 3.2 25 81-105 6-30 (62)
304 PF15135 UPF0515: Uncharacteri 28.1 36 0.00079 30.9 1.7 21 92-112 8-28 (278)
305 PF06943 zf-LSD1: LSD1 zinc fi 26.8 72 0.0016 18.1 2.1 24 302-326 1-24 (25)
306 PRK14890 putative Zn-ribbon RN 26.7 65 0.0014 22.4 2.4 25 302-327 10-34 (59)
307 PF08209 Sgf11: Sgf11 (transcr 26.6 30 0.00065 21.1 0.6 13 300-312 5-17 (33)
308 PF11781 RRN7: RNA polymerase 26.3 40 0.00087 20.9 1.2 9 300-308 9-17 (36)
309 PLN03086 PRLI-interacting fact 26.2 38 0.00081 34.9 1.6 30 298-328 432-463 (567)
310 COG2051 RPS27A Ribosomal prote 25.8 78 0.0017 22.6 2.6 31 230-263 19-50 (67)
311 PRK14873 primosome assembly pr 25.7 50 0.0011 34.9 2.5 40 299-339 392-436 (665)
312 PRK05580 primosome assembly pr 25.7 54 0.0012 34.7 2.8 35 300-335 391-430 (679)
313 PF14353 CpXC: CpXC protein 25.6 21 0.00045 28.9 -0.3 46 187-244 2-50 (128)
314 PF04703 FaeA: FaeA-like prote 25.5 1E+02 0.0022 21.7 3.3 22 82-103 17-38 (62)
315 TIGR02159 PA_CoA_Oxy4 phenylac 25.3 54 0.0012 27.4 2.1 93 76-173 41-140 (146)
316 PF01780 Ribosomal_L37ae: Ribo 24.9 45 0.00097 25.4 1.4 35 300-338 36-70 (90)
317 PF11682 DUF3279: Protein of u 24.6 44 0.00094 27.3 1.4 12 300-311 111-122 (128)
318 PF04216 FdhE: Protein involve 24.2 37 0.00081 31.7 1.1 35 300-335 173-220 (290)
319 PF13913 zf-C2HC_2: zinc-finge 24.1 43 0.00093 18.8 0.9 10 300-309 3-12 (25)
320 COG3492 Uncharacterized protei 24.1 41 0.00088 25.5 1.1 17 164-180 42-58 (104)
321 KOG0824 Predicted E3 ubiquitin 24.1 28 0.00061 32.5 0.2 30 299-335 7-36 (324)
322 PF04710 Pellino: Pellino; In 24.0 26 0.00056 34.1 0.0 57 141-199 328-401 (416)
323 PF03884 DUF329: Domain of unk 23.8 24 0.00053 24.4 -0.2 15 299-313 2-16 (57)
324 PF13384 HTH_23: Homeodomain-l 23.0 84 0.0018 20.3 2.4 26 80-105 17-42 (50)
325 PF12959 DUF3848: Protein of u 23.0 1.7E+02 0.0036 22.8 4.2 47 69-116 23-74 (101)
326 PF02954 HTH_8: Bacterial regu 22.8 1.3E+02 0.0028 19.0 3.2 23 82-104 20-42 (42)
327 PF15387 DUF4611: Domain of un 22.6 44 0.00096 25.5 1.0 13 31-43 62-74 (96)
328 PF09151 DUF1936: Domain of un 22.6 44 0.00095 19.9 0.8 10 300-309 2-11 (36)
329 PF14851 FAM176: FAM176 family 22.3 1.6E+02 0.0034 24.9 4.3 8 74-81 120-127 (153)
330 COG3813 Uncharacterized protei 22.2 56 0.0012 23.7 1.4 44 143-199 7-52 (84)
331 smart00734 ZnF_Rad18 Rad18-lik 22.2 45 0.00098 19.0 0.8 20 187-208 2-21 (26)
332 KOG0309 Conserved WD40 repeat- 22.2 65 0.0014 34.1 2.4 37 140-176 1027-1063(1081)
333 PRK02935 hypothetical protein; 22.0 39 0.00086 26.4 0.6 11 300-310 71-81 (110)
334 PRK03976 rpl37ae 50S ribosomal 21.4 59 0.0013 24.8 1.5 37 299-339 36-72 (90)
335 TIGR01299 synapt_SV2 synaptic 21.3 56 0.0012 35.0 1.9 17 80-96 149-165 (742)
336 KOG2932 E3 ubiquitin ligase in 21.3 38 0.00083 31.7 0.6 32 141-173 90-121 (389)
337 KOG2807 RNA polymerase II tran 21.2 49 0.0011 31.3 1.2 9 161-169 351-359 (378)
338 KOG2463 Predicted RNA-binding 21.2 70 0.0015 30.3 2.2 79 69-164 183-266 (376)
339 TIGR00280 L37a ribosomal prote 21.1 61 0.0013 24.7 1.5 36 299-338 35-70 (91)
340 cd04476 RPA1_DBD_C RPA1_DBD_C: 21.0 66 0.0014 27.1 1.9 26 300-327 35-60 (166)
341 KOG1999 RNA polymerase II tran 20.9 1.5E+02 0.0032 32.4 4.7 6 141-146 169-174 (1024)
342 PF10245 MRP-S22: Mitochondria 20.8 1.2E+02 0.0025 27.7 3.5 32 64-95 34-65 (243)
343 PF10013 DUF2256: Uncharacteri 20.6 54 0.0012 21.1 1.0 12 299-310 8-19 (42)
344 PF08595 RXT2_N: RXT2-like, N- 20.5 1.8E+02 0.0039 24.4 4.4 6 108-113 139-144 (149)
345 KOG0825 PHD Zn-finger protein 20.3 81 0.0018 33.6 2.6 41 141-181 96-141 (1134)
346 COG1996 RPC10 DNA-directed RNA 20.1 62 0.0013 21.7 1.2 11 300-310 25-35 (49)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.9e-52 Score=408.44 Aligned_cols=280 Identities=50% Similarity=1.027 Sum_probs=258.1
Q ss_pred eeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhhhcHHHHHHHcCCCCCCCCCCCCCCcccccccc
Q 018073 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPDGEEMTCGICF 148 (361)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~C~IC~ 148 (361)
+|+.++|...|.+.|.+|+++|++++.+|++||.+|.|+..++++.|+.+++.++..+|+...+ ......+|.||+
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~----~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWP----KKKGDVQCGICV 77 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccC----CCCccccCCccc
Confidence 6889999999999999999999999999999999999999999999999999999999987653 345578899999
Q ss_pred ccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCCh-HHHHHHHHHHHHHHHhhC
Q 018073 149 ENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSD-EDKVKYNRYFIRSYVEDN 227 (361)
Q Consensus 149 e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~~-~~~~~y~~~~~~~~i~~~ 227 (361)
+.++. .+..+.|||.||..||..|+..+|..+.... |+||.+.|.+.+..+.|..++++ +...+|.++++++|++.+
T Consensus 78 ~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~-i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~ 155 (444)
T KOG1815|consen 78 ESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK-IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-hhhhcCCCcHHHHHHHHHHhhheeecccccc-ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 98865 6778899999999999999999999986433 99999999999999999999988 599999999999999999
Q ss_pred CCccccCCCCCCcceeeecCCCCceEEeccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCc
Q 018073 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKR 307 (361)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~ 307 (361)
..++|||+|+|++++.+. ......|.|.|++.|||.|+.+||.|.+|....+|+++...++++.+||.+|+|+||+|.+
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~ 234 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKV 234 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCccc
Confidence 999999999999998864 4456889999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecCCCCceeec-CCCccceeccccccccccCCCCCCcccCCCccchhc
Q 018073 308 PIEKNQGCMHMTCT-PPCKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQ 357 (361)
Q Consensus 308 ~IeK~~GCnhm~C~-~~C~~~FCw~C~~~~~~h~~~~g~~y~C~~~~~~~~ 357 (361)
+|||++|||||+|. +.|+++|||+|++.|..|+..+ +|.|++|...+.
T Consensus 235 ~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~--~~~c~~~~~~~~ 283 (444)
T KOG1815|consen 235 PIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSST--GYSCNRYVDGKS 283 (444)
T ss_pred chhccCCccccccccCCcCCeeceeeecccccccccc--eeeeeeeechhh
Confidence 99999999999998 2399999999999999999865 999999977653
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.9e-38 Score=300.39 Aligned_cols=205 Identities=26% Similarity=0.687 Sum_probs=176.4
Q ss_pred CccccccccccccC-Ccccc-ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCChHHHHHHHH
Q 018073 140 EEMTCGICFENYPS-DRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (361)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~ 217 (361)
...+|.||+...+. ..++. +.|+|.||.+||++|++.+...| ..++||..+|+..++.+....++++.++++|++
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~---~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG---TVIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC---CCccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 46789999954443 34444 56999999999999999995555 489999999999999999999999999999999
Q ss_pred HHHHHHHhhCCCccccCCCCCCcceeeecC---CCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHH
Q 018073 218 YFIRSYVEDNRKTKWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMN 293 (361)
Q Consensus 218 ~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~ 293 (361)
++.+.++.....+ +||.|+|...+....- .......| .|+..||.+|+.+||.+.+|+++++|......+..+.+
T Consensus 222 ~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~ 300 (384)
T KOG1812|consen 222 RLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLK 300 (384)
T ss_pred HHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHH
Confidence 9999999888877 9999999987654321 22344568 89999999999999999999999999876666677788
Q ss_pred HHHhhcCCCCCCCcceeecCCCCceeecCCCccceeccccccccccCCCCCCcccCCCcc
Q 018073 294 WILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYE 353 (361)
Q Consensus 294 ~i~~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~y~C~~~~ 353 (361)
|+.+++|+||+|+..|++++|||||+|+ ||++|||.|+++|..|+. .+|.|.|+.
T Consensus 301 ~la~~wr~CpkC~~~ie~~~GCnhm~Cr--C~~~fcy~C~~~~~~~~~---~~~~~~r~~ 355 (384)
T KOG1812|consen 301 YLAKRWRQCPKCKFMIELSEGCNHMTCR--CGHQFCYMCGGDWKTHNG---ECYECCRYK 355 (384)
T ss_pred HHHHhcCcCcccceeeeecCCcceEEee--ccccchhhcCcchhhCCc---cccCccccc
Confidence 8888899999999999999999999998 999999999999999885 677787765
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.9e-37 Score=284.54 Aligned_cols=196 Identities=30% Similarity=0.697 Sum_probs=170.5
Q ss_pred CCCccccccccccccC-CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCChHHHHHHH
Q 018073 138 DGEEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYN 216 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~ 216 (361)
..+.+.|.|||+.... ..+..++|+|.||+.|++.|+...|++|. +..++||+++|+...+...|+.++..++++||+
T Consensus 181 ~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~-v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQ-VSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcce-eeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 3457899999998765 66788999999999999999999999997 578999999999999999999999999999999
Q ss_pred HHHHHHHHhhCCCccccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhH--------HHHHH----
Q 018073 217 RYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTV--------AKWVL---- 283 (361)
Q Consensus 217 ~~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~--------~~~~~---- 283 (361)
++++.+.++...+.++||++.|..++.. ..+...+.| +|..+||+-|+..||...+|.-- ..|..
T Consensus 260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~--d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRACCQLPVKQ--DPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCcccc--CchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 9999999999999999999999988743 345667899 99999999999999999899743 11211
Q ss_pred ---------------hhhhhhHHHHHHHhhcCCCCCCCcceeecCCCCceeecCCCccceecccccccc
Q 018073 284 ---------------KNSAESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (361)
Q Consensus 284 ---------------~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (361)
....+..+..|+..|.|+||+|+++|||++|||||+|. .|++.|||+|+....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~-~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT-KCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec-cccccceeehhhhcC
Confidence 11123345589999999999999999999999999999 899999999998776
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=5.8e-28 Score=216.16 Aligned_cols=195 Identities=31% Similarity=0.727 Sum_probs=151.5
Q ss_pred CCCCccccccccccccCCccccccCC--CcccHhhHHHHHHhhhcCCC------CeeeeccCCCcCCCccchh-HHhhcC
Q 018073 137 PDGEEMTCGICFENYPSDRLLAAACG--HPFCSSCWTGYISTAINDGP------GCLMLRCPDPSCGAAVGQD-MIYLLS 207 (361)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~~i~~~i~~~~------~~~~i~CP~~~C~~~i~~~-~i~~ll 207 (361)
.|.+..+|..|-+.- +.+..++|. |..|.+|++.|..+.+++.. ....+.||. +|...+-.+ .-.+++
T Consensus 217 ~N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 217 TNSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred cccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 356788999998753 345567887 99999999999999997753 125688885 787765433 445788
Q ss_pred ChHHHHHHHHHHHHHHHhhCCCccccCCCCCCcceeeecCCCCceEEe--ccCCccccccCCcCCCCCCchhHHH-----
Q 018073 208 SDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC--RCSYSFCWNCTEEAHRPVDCDTVAK----- 280 (361)
Q Consensus 208 ~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C--~C~~~fC~~C~~~~H~~~~C~~~~~----- 280 (361)
..+.+.+|+++..+.++.... -+-||+|+|+..+...+ ....|+| .|++.||..|.+.+|.+ .|...-.
T Consensus 294 g~e~Y~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~ 369 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTT 369 (446)
T ss_pred chhHHHHHHHhhhhhheeecC-CEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhccc-cceeeecccccc
Confidence 999999999999999988766 56999999998876654 5678999 59999999999999987 3431100
Q ss_pred ---H-HHhhhh-----hhHHHHHHHhhcCCCCCCCcceeecCCCCceeec-CCCccceeccccccccc
Q 018073 281 ---W-VLKNSA-----ESENMNWILANSKPCPRCKRPIEKNQGCMHMTCT-PPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 281 ---~-~~~~~~-----~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~-~~C~~~FCw~C~~~~~~ 338 (361)
+ ...+.+ +..+..-|+..||+||+|+++.||||||+||.|+ ++||.+|||.|+-.|+.
T Consensus 370 tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 370 TCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 0 001111 2233445888999999999999999999999998 46999999999999985
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.40 E-value=4.4e-13 Score=96.46 Aligned_cols=63 Identities=46% Similarity=1.028 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHhhCCCccccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCc
Q 018073 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (361)
Q Consensus 213 ~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C 275 (361)
++|++++++++|+.++.++|||+|+|+.++......+...|.| .|++.||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4799999999999989999999999999987753346678999 99999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.29 E-value=4e-13 Score=96.67 Aligned_cols=63 Identities=35% Similarity=0.964 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHhhCCCccccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCc
Q 018073 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (361)
Q Consensus 213 ~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C 275 (361)
++|++++++.+++.++.++|||+|+|+.++..........|+| .|++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 4788899999998888999999999999998764443335999 69999999999999999887
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.67 E-value=1.3e-08 Score=66.49 Aligned_cols=40 Identities=30% Similarity=0.848 Sum_probs=29.3
Q ss_pred cccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccC
Q 018073 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (361)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP 190 (361)
|+||++.+ .++++++|||.||..|+..++...-.. .+.||
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~-----~~~CP 40 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGS-----GFSCP 40 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSS-----T---S
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCc-----CCCCc
Confidence 89999987 688999999999999999999764322 37888
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=1.1e-07 Score=80.04 Aligned_cols=58 Identities=22% Similarity=0.636 Sum_probs=46.5
Q ss_pred CCCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhh
Q 018073 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYL 205 (361)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ 205 (361)
.+...+.||||++.+....+++..|||.||+.|++.-+.. ..+|| .|...|...++-.
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~---------~~~CP--~C~kkIt~k~~~r 184 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN---------TNKCP--TCRKKITHKQFHR 184 (187)
T ss_pred ccccccCCCceecchhhccccccccchhHHHHHHHHHHHh---------CCCCC--Ccccccchhhhee
Confidence 3455789999999987666788999999999999988865 45799 8888777665543
No 9
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.39 E-value=1.3e-07 Score=62.45 Aligned_cols=34 Identities=29% Similarity=0.885 Sum_probs=30.1
Q ss_pred cccccccccc-CCccccccCCCcccHhhHHHHHHh
Q 018073 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
+|+||++.+. ...++.++|||.||.+|+..|++.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh
Confidence 5999999985 466778899999999999999977
No 10
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.39 E-value=1.5e-07 Score=67.30 Aligned_cols=38 Identities=45% Similarity=1.097 Sum_probs=29.3
Q ss_pred hcCCCCC--CCcceeecCCCCc--eeecCCCccceeccccccc
Q 018073 298 NSKPCPR--CKRPIEKNQGCMH--MTCTPPCKFEFCWLCLGQW 336 (361)
Q Consensus 298 ~~k~CP~--C~~~IeK~~GCnh--m~C~~~C~~~FCw~C~~~~ 336 (361)
+.+.||+ |...|++..|.++ |+|. .|++.|||.|+++|
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~-~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCP-SCGTEFCFKCGEPW 58 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTT-SCCSEECSSSTSES
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECC-CCCCcCccccCccc
Confidence 3479987 9999999999999 9998 79999999999999
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.39 E-value=1.8e-07 Score=60.12 Aligned_cols=32 Identities=34% Similarity=1.053 Sum_probs=26.5
Q ss_pred cccccccccCCccccccCCCcccHhhHHHHHHh
Q 018073 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
|+||++.+. +.++.++|||.||.+||.+|++.
T Consensus 1 C~iC~~~~~-~~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELR-DPVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-S-SEEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCccc-CcCEECCCCCchhHHHHHHHHHC
Confidence 899998764 33467899999999999999987
No 12
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.36 E-value=4.8e-07 Score=64.73 Aligned_cols=38 Identities=39% Similarity=1.046 Sum_probs=34.5
Q ss_pred hcCCCC--CCCcceeecC--CCCceeecCCCccceeccccccc
Q 018073 298 NSKPCP--RCKRPIEKNQ--GCMHMTCTPPCKFEFCWLCLGQW 336 (361)
Q Consensus 298 ~~k~CP--~C~~~IeK~~--GCnhm~C~~~C~~~FCw~C~~~~ 336 (361)
+.+.|| +|+..|+... |..+|+|. .|++.|||.|+.+|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~-~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCP-KCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECC-CCCCeECCCCCCcC
Confidence 458899 9999999864 99999996 69999999999998
No 13
>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=98.33 E-value=4.2e-07 Score=59.01 Aligned_cols=39 Identities=33% Similarity=1.022 Sum_probs=31.2
Q ss_pred cccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccC
Q 018073 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (361)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP 190 (361)
|+||++.+. .....++|||.||..||.+++.. . ..++||
T Consensus 1 C~iC~~~~~-~~~~~~~C~H~fC~~C~~~~~~~---~----~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFE-DPVILLPCGHSFCRDCLRKWLEN---S----GSVKCP 39 (41)
T ss_dssp ETTTSSBCS-SEEEETTTSEEEEHHHHHHHHHH---T----SSSBTT
T ss_pred CCcCCcccc-CCCEEecCCCcchHHHHHHHHHh---c----CCccCC
Confidence 899999764 23347899999999999999997 2 257798
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.27 E-value=6.6e-07 Score=77.27 Aligned_cols=65 Identities=23% Similarity=0.589 Sum_probs=47.2
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCC-------CCeeeeccCCCcCCCccchhHHhhcC
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDG-------PGCLMLRCPDPSCGAAVGQDMIYLLS 207 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~-------~~~~~i~CP~~~C~~~i~~~~i~~ll 207 (361)
...++|+||++.+ .+++.+.|||.||..|+..|+...-... ......+|| .|+..+....+..+.
T Consensus 16 ~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiy 87 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIY 87 (193)
T ss_pred CCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEee
Confidence 4568999999976 5667788999999999999986431100 011257999 999999876665544
No 15
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.25 E-value=6.4e-07 Score=58.52 Aligned_cols=41 Identities=29% Similarity=0.812 Sum_probs=22.9
Q ss_pred cccccccccC--CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccC
Q 018073 144 CGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (361)
Q Consensus 144 C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP 190 (361)
|+||.+ +.. +.+..|+|||.||++|+.+.+..... ..++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~-----~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDR-----NRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S------S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCC-----CeeeCc
Confidence 899999 632 23577899999999999999986431 268887
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.12 E-value=1.8e-06 Score=57.04 Aligned_cols=42 Identities=40% Similarity=1.036 Sum_probs=33.7
Q ss_pred cccccccccc-CCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCC
Q 018073 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (361)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~ 195 (361)
.|+||++.+. ...++.++|||.||..|+.... + ..+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~------~---~~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK------G---KSVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc------C---CCCCCc--CCC
Confidence 4999999993 3456778999999999999888 2 267899 675
No 17
>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=98.06 E-value=3.6e-06 Score=55.11 Aligned_cols=44 Identities=34% Similarity=0.986 Sum_probs=33.4
Q ss_pred ccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 143 TCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
+|+||++.+ ...+...+|||.||..|+..|+.. + ..+|| .|+..
T Consensus 1 ~C~iC~~~~-~~~~~~~~C~H~~c~~C~~~~~~~----~----~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF-REPVVLLPCGHVFCRSCIDKWLKS----G----KNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh-hCceEecCCCChhcHHHHHHHHHh----C----cCCCC--CCCCc
Confidence 499999887 233444569999999999999876 1 45798 78754
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.05 E-value=3.2e-06 Score=57.45 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=36.4
Q ss_pred ccccccccccccCCccccccCCCc-ccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
...|.||++.. ..++.++|||. ||..|+..++.. ..+|| .|+..|.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~---------~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR---------KKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT---------TSBBT--TTTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc---------CCCCC--cCChhhc
Confidence 35799999874 46778899999 999999999982 46899 8988764
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=3.9e-06 Score=73.88 Aligned_cols=59 Identities=34% Similarity=0.730 Sum_probs=47.6
Q ss_pred CCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhc
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLL 206 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~l 206 (361)
....++|.||++.- .+++...|||.||..||-+|+..+.+. -.|| .|+..|+.+.|-.|
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~------~~cP--VCK~~Vs~~~vvPl 102 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNS------KECP--VCKAEVSIDTVVPL 102 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCC------eeCC--ccccccccceEEee
Confidence 45689999999864 677888899999999999999886553 3578 99999877765444
No 20
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=1.5e-05 Score=72.38 Aligned_cols=52 Identities=31% Similarity=0.705 Sum_probs=42.0
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHH
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i 203 (361)
.....|.+|++.. ..+..++|||.||..|+..|...+- .|| .|+..+....+
T Consensus 237 ~a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek~---------eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEKA---------ECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHcccc---------CCC--cccccCCCcce
Confidence 3457899999875 5778899999999999999998742 399 89988766543
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.76 E-value=2.2e-05 Score=70.74 Aligned_cols=50 Identities=24% Similarity=0.615 Sum_probs=37.4
Q ss_pred CCccccccccccccCCc------cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 139 GEEMTCGICFENYPSDR------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
....+|+||++.+.... .+.++|+|.||..|+..|+.. ...|| .|+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~---------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE---------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc---------CCCCC--CCCCEee
Confidence 34678999999864322 234579999999999999864 23799 8988764
No 22
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.4e-05 Score=74.85 Aligned_cols=106 Identities=25% Similarity=0.507 Sum_probs=64.1
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCChHHHHHHHHH
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRY 218 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~~ 218 (361)
...++|+||++.+. .+..++|||.||..|+...+. + .+.|| .|+. ... .+...-.....
T Consensus 11 ~~~~~C~iC~~~~~--~p~~l~C~H~~c~~C~~~~~~-----~----~~~Cp--~cr~-~~~----~~~~n~~l~~~--- 69 (386)
T KOG2177|consen 11 QEELTCPICLEYFR--EPVLLPCGHNFCRACLTRSWE-----G----PLSCP--VCRP-PSR----NLRPNVLLANL--- 69 (386)
T ss_pred cccccChhhHHHhh--cCccccccchHhHHHHHHhcC-----C----CcCCc--ccCC-chh----ccCccHHHHHH---
Confidence 35688999999985 337889999999999999998 1 58999 8884 222 22111111111
Q ss_pred HHHHHHhhCCC------ccccCCCCCCcceeeecCCCCceEEe-ccCCccccccC-CcCCCCCCchh
Q 018073 219 FIRSYVEDNRK------TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCT-EEAHRPVDCDT 277 (361)
Q Consensus 219 ~~~~~i~~~~~------~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~-~~~H~~~~C~~ 277 (361)
...+-..... ...|+. ......+.| .|....|..|. ...|..+.-..
T Consensus 70 -~~~~~~~~~~~~~~~~~~~c~~-----------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~ 124 (386)
T KOG2177|consen 70 -VERLRQLRLSRPLGSKEELCEK-----------HGEELKLFCEEDEKLLCVLCRESGEHRGHPVLP 124 (386)
T ss_pred -HHHHHhcCCcccccccchhhhh-----------cCCcceEEecccccccCCCCCCcccccCCcccc
Confidence 1111111100 002221 111256789 89999999998 66777665433
No 23
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.74 E-value=2.3e-05 Score=49.33 Aligned_cols=30 Identities=37% Similarity=0.986 Sum_probs=26.1
Q ss_pred cccccccccCCccccccCCCcccHhhHHHHHH
Q 018073 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (361)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~ 175 (361)
|+||++. ...++.++|+|.||..|+..|+.
T Consensus 1 C~iC~~~--~~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEE--LKDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccC--CCCcEEecCCChHHHHHHHHHHH
Confidence 7899987 35677789999999999999987
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=97.73 E-value=2.6e-05 Score=68.24 Aligned_cols=57 Identities=35% Similarity=0.679 Sum_probs=40.6
Q ss_pred CCCccccccccccccC-----Cc--cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 138 DGEEMTCGICFENYPS-----DR--LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~-----~~--~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
.+...+|+||++..-. .. .+..+|+|.||..|++.|..++...| ..-.|| .|+..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~---~~rsCP--iCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG---ASDNCP--ICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC---cCCcCC--CCcceee
Confidence 3456889999987521 11 23457999999999999998754333 245799 8987653
No 25
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.69 E-value=4.2e-05 Score=54.37 Aligned_cols=48 Identities=13% Similarity=0.252 Sum_probs=38.2
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhH
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~ 202 (361)
+.|+||.+.+ .+++.++|||.||+.|+..|+.. . ..|| .|+..++...
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~---~------~~cP--~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS---H------GTDP--VTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH---C------CCCC--CCcCCCChhh
Confidence 5799999876 45677899999999999999976 1 3688 6877775544
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=2.5e-05 Score=76.11 Aligned_cols=59 Identities=27% Similarity=0.634 Sum_probs=45.2
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcC
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLS 207 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll 207 (361)
...|||||+..+ -...+.|||.||..|+-+|+......+ ..+|| -|...|....+..+.
T Consensus 186 ~~~CPICL~~~~--~p~~t~CGHiFC~~CiLqy~~~s~~~~----~~~CP--iC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPS--VPVRTNCGHIFCGPCILQYWNYSAIKG----PCSCP--ICRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCC--cccccccCceeeHHHHHHHHhhhcccC----CccCC--chhhhccccceeeee
Confidence 678999998743 334455999999999999999873322 67899 899988776665544
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.63 E-value=4.2e-05 Score=73.92 Aligned_cols=65 Identities=25% Similarity=0.543 Sum_probs=45.7
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHh-hcCChHHHHHHH
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY-LLSSDEDKVKYN 216 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~-~ll~~~~~~~y~ 216 (361)
...+.|+||++.+ ..++.++|||.||..|+..|+.. ...|| .|+..+....+. ..+-.++.+.|.
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~---------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSN---------QPKCP--LCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhC---------CCCCC--CCCCccccccCccchHHHHHHHHHH
Confidence 3468999999877 45667899999999999999864 13699 899887654222 222234555554
No 28
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=0.00022 Score=72.90 Aligned_cols=55 Identities=29% Similarity=0.699 Sum_probs=44.7
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhc
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLL 206 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~l 206 (361)
..++||+|... ..+.+...|+|.||..|++..+.++ .-+|| .|+..++...|..+
T Consensus 642 ~~LkCs~Cn~R--~Kd~vI~kC~H~FC~~Cvq~r~etR--------qRKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTR--WKDAVITKCGHVFCEECVQTRYETR--------QRKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCc--hhhHHHHhcchHHHHHHHHHHHHHh--------cCCCC--CCCCCCCccccccc
Confidence 36799999943 3567788899999999999999885 34899 99999988776543
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.27 E-value=0.00021 Score=66.11 Aligned_cols=63 Identities=30% Similarity=0.657 Sum_probs=46.9
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhh-cCChHHHHHH
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYL-LSSDEDKVKY 215 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~-ll~~~~~~~y 215 (361)
..+.|.||++.|. -+...+|+|.||.-|++.|+.. ...|| .|...+....++. .+-.++++.|
T Consensus 22 ~lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~---------~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSY---------KPQCP--TCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHhc--CceeccccchHHHHHHHHHhcc---------CCCCC--ceecccchhhhhhhhHHHHHHHHH
Confidence 3567999999874 4456779999999999999976 45799 8999887766643 2334555554
No 30
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.17 E-value=0.00051 Score=64.91 Aligned_cols=47 Identities=32% Similarity=0.810 Sum_probs=39.6
Q ss_pred cccccccccccC-CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 142 MTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 142 ~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
.+|.||+|.|.. +.+..|+|.|.|...|+..|+... .-.|| .|+..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~--------r~~CP--vCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT--------RTFCP--VCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc--------CccCC--CCCCcC
Confidence 699999999975 567889999999999999999874 23599 888755
No 31
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.0005 Score=62.78 Aligned_cols=51 Identities=29% Similarity=0.735 Sum_probs=42.5
Q ss_pred CccccccccccccC-CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
...+|.||++.+.. ++...++|.|.|...|+.+|+.. ...+|| .|+..+++
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~--------y~~~CP--vCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG--------YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh--------hcccCC--ccCCCCCC
Confidence 45799999998854 45678899999999999999974 367899 99988764
No 32
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.96 E-value=0.0014 Score=60.98 Aligned_cols=51 Identities=25% Similarity=0.612 Sum_probs=35.6
Q ss_pred cccccccccccC-Ccc--ccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhH
Q 018073 142 MTCGICFENYPS-DRL--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (361)
Q Consensus 142 ~~C~IC~e~~~~-~~~--~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~ 202 (361)
..||+|....-. ..+ ....|||.||..|+...+.. + +..|| .|+..+....
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~----~~~CP--~C~~~lrk~~ 57 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G----SGSCP--ECDTPLRKNN 57 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C----CCCCC--CCCCccchhh
Confidence 569999985322 222 22279999999999999742 2 35899 9998775443
No 33
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=96.96 E-value=0.002 Score=42.11 Aligned_cols=40 Identities=20% Similarity=0.408 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhhhcH
Q 018073 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADE 119 (361)
Q Consensus 80 ~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~~~~ 119 (361)
++.|.+.+++.++++..|..+|...+||++..++.||.++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 4678999999999999999999999999999999999864
No 34
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.95 E-value=0.0006 Score=47.47 Aligned_cols=47 Identities=28% Similarity=0.641 Sum_probs=30.2
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCC
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~ 195 (361)
.+.|||-...+. +.+.+..|||.|-++.+.+||. .+ ..++||..+|.
T Consensus 11 ~~~CPiT~~~~~-~PV~s~~C~H~fek~aI~~~i~----~~---~~~~CPv~GC~ 57 (57)
T PF11789_consen 11 SLKCPITLQPFE-DPVKSKKCGHTFEKEAILQYIQ----RN---GSKRCPVAGCN 57 (57)
T ss_dssp -SB-TTTSSB-S-SEEEESSS--EEEHHHHHHHCT----TT---S-EE-SCCC-S
T ss_pred ccCCCCcCChhh-CCcCcCCCCCeecHHHHHHHHH----hc---CCCCCCCCCCC
Confidence 578999998763 4445668999999999999992 22 36899998884
No 35
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.0044 Score=58.25 Aligned_cols=94 Identities=18% Similarity=0.324 Sum_probs=56.5
Q ss_pred HHHHHHHHHcCCChHHHHHHhhhcHHHHHHHcCCCC---CCCCCCCCCCcccccccccc-ccCC----------cccccc
Q 018073 95 VAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLE---KPAVQFPDGEEMTCGICFEN-YPSD----------RLLAAA 160 (361)
Q Consensus 95 ~~a~~LL~~~~w~~~~l~e~~~~~~~~~~~~~~l~~---~~~~~~~~~~~~~C~IC~e~-~~~~----------~~~~l~ 160 (361)
..-..|+|.--|....|..+..+--.-.|....+.. ...+..-.....+|.||+++ +... .+..++
T Consensus 238 r~Pi~l~r~~~t~~~AL~~~i~~~~~~~r~~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp 317 (491)
T COG5243 238 RVPIYLIRQMYTCFYALFRRIREHARFRRATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP 317 (491)
T ss_pred hchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCccccc
Confidence 345667777777777766554322111111111110 00011113346789999998 3322 246789
Q ss_pred CCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 161 CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 161 CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
|||.+...|++.|++.+ -.|| -|+.++-
T Consensus 318 CGHilHl~CLknW~ERq---------QTCP--ICr~p~i 345 (491)
T COG5243 318 CGHILHLHCLKNWLERQ---------QTCP--ICRRPVI 345 (491)
T ss_pred ccceeeHHHHHHHHHhc---------cCCC--cccCccc
Confidence 99999999999999873 3688 8988753
No 36
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.73 E-value=0.00096 Score=65.21 Aligned_cols=57 Identities=25% Similarity=0.781 Sum_probs=45.8
Q ss_pred CCCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchh
Q 018073 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (361)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~ 201 (361)
.+.....|.+|-++- .+.+...|.|.||+-|++.|+....... .+.|| .|...++.+
T Consensus 532 enk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~----nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN----NVTCP--VCHIGLSID 588 (791)
T ss_pred cccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc----CCCCc--ccccccccc
Confidence 355678999998753 5677788999999999999999876643 48999 898876544
No 37
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.68 E-value=0.0015 Score=58.83 Aligned_cols=54 Identities=28% Similarity=0.528 Sum_probs=40.6
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHH
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i 203 (361)
...+.|.||++.- ..+..++|||.||..|+-..+..+ ..-.|| .|++.+....|
T Consensus 213 ~~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~-------k~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKK-------KYEFCP--LCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeeccc--CCcccccccchhhHHHHHHHHHhh-------ccccCc--hhhhhccchhh
Confidence 4467899999863 667788999999999998854332 134599 89988766554
No 38
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.61 E-value=0.0015 Score=48.06 Aligned_cols=35 Identities=26% Similarity=0.630 Sum_probs=26.2
Q ss_pred cccccccccccCC-----------ccccccCCCcccHhhHHHHHHh
Q 018073 142 MTCGICFENYPSD-----------RLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 142 ~~C~IC~e~~~~~-----------~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
-.|.||++.+... .+....|||.|...|+.+|+..
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc
Confidence 3599999988211 1233469999999999999965
No 39
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.60 E-value=0.0014 Score=47.81 Aligned_cols=58 Identities=21% Similarity=0.632 Sum_probs=27.5
Q ss_pred cccccccccccc-CCcc--cc---ccCCCcccHhhHHHHHHhhhcCCCCe--eeeccCCCcCCCccch
Q 018073 141 EMTCGICFENYP-SDRL--LA---AACGHPFCSSCWTGYISTAINDGPGC--LMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 141 ~~~C~IC~e~~~-~~~~--~~---l~CgH~fC~~Cl~~~i~~~i~~~~~~--~~i~CP~~~C~~~i~~ 200 (361)
+..|+||+..+. .... +. ..|++.|...||.+|+.+.-+..... ..=.|| .|+..|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 467999998754 2222 11 25899999999999998765543221 223799 89988754
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.41 E-value=0.00073 Score=47.53 Aligned_cols=43 Identities=35% Similarity=0.874 Sum_probs=20.8
Q ss_pred cccccccccccCCcccc-ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 142 MTCGICFENYPSDRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
+.|++|.+.+ ..++. ..|.|.||..|++..+. -.|| .|..+.-
T Consensus 8 LrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~-----------~~CP--vC~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG-----------SECP--VCHTPAW 51 (65)
T ss_dssp TS-SSS-S----SS-B---SSS--B-TTTGGGGTT-----------TB-S--SS--B-S
T ss_pred cCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC-----------CCCC--CcCChHH
Confidence 5699999876 55655 46999999999966332 2499 8987653
No 41
>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=96.08 E-value=0.01 Score=43.56 Aligned_cols=50 Identities=16% Similarity=0.208 Sum_probs=36.7
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~ 201 (361)
..+.|+|+.+-+ .+++.+++||.|++.++..|+.. + ...|| .++..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~----~----~~~~P--~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ----N----GGTDP--FTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT----T----SSB-T--TT-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc----C----CCCCC--CCCCcCCcc
Confidence 368899999876 67888999999999999999987 1 35788 677777654
No 42
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.017 Score=52.44 Aligned_cols=52 Identities=27% Similarity=0.620 Sum_probs=39.3
Q ss_pred CCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
.+...+|++|-+. |....+..+|||.||--|+..-+... ..+.|| .|+..+.
T Consensus 236 ~t~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~-------asf~Cp--~Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWD-------ASFTCP--LCGENVE 287 (298)
T ss_pred ccCCceeeccCCC-CCCCeeeccccceeehhhhhhhhcch-------hhcccC--ccCCCCc
Confidence 4457899999864 44455566799999999998877653 258999 8998765
No 43
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.01 E-value=0.0059 Score=40.60 Aligned_cols=44 Identities=25% Similarity=0.742 Sum_probs=21.5
Q ss_pred cccccccccCCc--cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 144 CGICFENYPSDR--LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 144 C~IC~e~~~~~~--~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
|++|.+.+.... +...+||+.+|+.||..-.+. + .=+|| +|+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~----~----~g~CP--gCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN----E----GGRCP--GCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS----S-----SB-T--TT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc----c----CCCCC--CCCCC
Confidence 789999875443 344569999999999877652 1 23699 89865
No 44
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.93 E-value=0.0044 Score=56.36 Aligned_cols=48 Identities=29% Similarity=0.618 Sum_probs=36.7
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
....|-||-+.+ .-+...+|||.||.-|++.|+.. ...|| .|....-.
T Consensus 24 s~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~---------qp~CP--~Cr~~~~e 71 (391)
T COG5432 24 SMLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGT---------QPFCP--VCREDPCE 71 (391)
T ss_pred hHHHhhhhhhee--ecceecccccchhHHHHHHHhcC---------CCCCc--cccccHHh
Confidence 356799998876 34566789999999999999976 34588 78776533
No 45
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.87 E-value=0.0029 Score=60.48 Aligned_cols=35 Identities=26% Similarity=0.707 Sum_probs=29.3
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
+++.|+||..-| .+++.|+|+|..|+.|.+..+.+
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhccc
Confidence 357799998766 67889999999999999977654
No 46
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.14 E-value=0.011 Score=54.20 Aligned_cols=55 Identities=20% Similarity=0.509 Sum_probs=41.5
Q ss_pred CCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHh
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY 204 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~ 204 (361)
....-+|.||+.+- .-++.+.|+|.||.-|+++-+... ...|+ .|...|+...+.
T Consensus 4 ~~~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~nd--------k~~Ca--vCR~pids~i~~ 58 (324)
T KOG0824|consen 4 RTKKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKND--------KKTCA--VCRFPIDSTIDF 58 (324)
T ss_pred cccCCcceeeeccC--CcCccccccchhhhhhhcchhhcC--------CCCCc--eecCCCCcchhc
Confidence 34456899999864 456889999999999999866542 34588 899988766543
No 47
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.10 E-value=0.0061 Score=58.18 Aligned_cols=41 Identities=34% Similarity=0.957 Sum_probs=36.7
Q ss_pred hhcCCCCC--CCcceeecCCCCceeecCCCccceeccccccccc
Q 018073 297 ANSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 297 ~~~k~CP~--C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (361)
++.+-||+ |..|+-...|++-..|. +|++.||.+|...|..
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~Cs-kCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICS-KCNFAFCTLCKLTWHG 313 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhc-cCccHHHHHHHHhhcC
Confidence 45789998 99999777999999999 8999999999988864
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.94 E-value=0.02 Score=54.45 Aligned_cols=59 Identities=24% Similarity=0.584 Sum_probs=39.9
Q ss_pred CCCCCccccccccccccCCc-----ccc-ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 136 FPDGEEMTCGICFENYPSDR-----LLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 136 ~~~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
.+.....+|+||++...... +-. .+|.|.||..|+++|=...-... ...-.|| .|+...
T Consensus 156 ~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~--~~sksCP--~CRv~s 220 (344)
T KOG1039|consen 156 LQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFES--KTSKSCP--FCRVPS 220 (344)
T ss_pred cCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcccc--ccccCCC--cccCcc
Confidence 34567889999999865333 222 45999999999999874432211 1356799 787653
No 49
>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=94.43 E-value=0.021 Score=32.90 Aligned_cols=24 Identities=29% Similarity=0.945 Sum_probs=15.7
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
|.||.|+..|-.+ -+.|. .|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp-~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCP-HCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCC-CCCCCC
Confidence 5788888888422 24565 577766
No 50
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=94.41 E-value=0.019 Score=53.48 Aligned_cols=49 Identities=29% Similarity=0.706 Sum_probs=37.2
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
...+|.+|-.-+- +......|-|.||+.||-.|++. ...|| .|...|..
T Consensus 14 ~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~---------~~~CP--~C~i~ih~ 62 (331)
T KOG2660|consen 14 PHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEE---------SKYCP--TCDIVIHK 62 (331)
T ss_pred cceehhhccceee-cchhHHHHHHHHHHHHHHHHHHH---------hccCC--ccceeccC
Confidence 3578999986552 44445569999999999999988 24699 88877643
No 51
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.04 E-value=0.093 Score=48.57 Aligned_cols=94 Identities=23% Similarity=0.620 Sum_probs=55.7
Q ss_pred cCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCChHHHHHHHHHHHHHHHhhCCCccccCCCCCC
Q 018073 160 ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCD 239 (361)
Q Consensus 160 ~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~ 239 (361)
.||-.||+.|+..|-.-.-..+.+... -..|...+.+.. ....+|...... .| ....+.||. |.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~----t~tc~y~vde~~-------a~~arwd~as~~-TI--k~tTkpCPk--Ch 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASG----TTTCAYRVDERA-------AEQARWDAASKE-TI--KKTTKPCPK--CH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeecccc----ccceeeecChhh-------hhhhhhhhhhhh-hh--hhccCCCCC--cc
Confidence 499999999999987543322210000 013444443321 123344443322 12 234678884 98
Q ss_pred cceeeecCCCCceEEe-c--cCCccccccCCcCCC
Q 018073 240 YAVDFVVGSGNYDVTC-R--CSYSFCWNCTEEAHR 271 (361)
Q Consensus 240 ~~i~~~~~~~~~~v~C-~--C~~~fC~~C~~~~H~ 271 (361)
.+... ..+...+.| . ||..+||+|+-+|..
T Consensus 405 vptEr--nGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 405 VPTER--NGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred Ccccc--CCceEEeecCCCCCCceeEeccCChhhh
Confidence 76654 345678899 3 999999999998864
No 52
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.99 E-value=0.031 Score=48.20 Aligned_cols=32 Identities=38% Similarity=0.943 Sum_probs=26.7
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHH
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYI 174 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i 174 (361)
.|.|.||-.+| ..++...|||.||..|...-+
T Consensus 196 PF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 196 PFLCGICKKDY--ESPVVTECGHSFCSLCAIRKY 227 (259)
T ss_pred ceeehhchhhc--cchhhhhcchhHHHHHHHHHh
Confidence 58899999887 567788999999999976544
No 53
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.81 E-value=0.068 Score=52.00 Aligned_cols=49 Identities=24% Similarity=0.714 Sum_probs=37.1
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
.+.+.|.||+..+ ..+++++|||.||..|+.. .+.. ...|| .|+..+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r----~ld~-----~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDR----SLDQ-----ETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHH----Hhcc-----CCCCc--cccccccc
Confidence 5579999999876 5677789999999999766 2222 35688 68887753
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.98 E-value=0.097 Score=47.41 Aligned_cols=74 Identities=18% Similarity=0.445 Sum_probs=50.7
Q ss_pred HHHHHcCCCCCCCCCCCCCCccccccccccccCC--------ccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCC
Q 018073 121 RVRKAVGLLEKPAVQFPDGEEMTCGICFENYPSD--------RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDP 192 (361)
Q Consensus 121 ~~~~~~~l~~~~~~~~~~~~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~ 192 (361)
.+-..+|.-.....+....+...|.||-..+..+ ++..|+|+|.|...|+++|... |+ .-.||
T Consensus 204 ~mAs~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK---kqtCP-- 274 (328)
T KOG1734|consen 204 YMASTIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK---KQTCP-- 274 (328)
T ss_pred HHHHHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC---CCCCc--
Confidence 3344555544434444445567899998766432 4678999999999999999865 22 45799
Q ss_pred cCCCccchhHH
Q 018073 193 SCGAAVGQDMI 203 (361)
Q Consensus 193 ~C~~~i~~~~i 203 (361)
-|+..+....+
T Consensus 275 YCKekVdl~rm 285 (328)
T KOG1734|consen 275 YCKEKVDLKRM 285 (328)
T ss_pred hHHHHhhHhhh
Confidence 89998865433
No 55
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.86 E-value=0.12 Score=38.88 Aligned_cols=32 Identities=28% Similarity=0.630 Sum_probs=25.1
Q ss_pred ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 159 AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 159 l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
-.|+|.|...|+.+++.++-. .-.|| -|+...
T Consensus 50 g~C~H~FH~hCI~kWl~~~~~------~~~CP--mCR~~w 81 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQSS------KGQCP--MCRQPW 81 (85)
T ss_pred ccCccHHHHHHHHHHHccccC------CCCCC--CcCCee
Confidence 359999999999999998632 23699 788764
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.78 E-value=0.12 Score=49.43 Aligned_cols=49 Identities=31% Similarity=0.844 Sum_probs=38.2
Q ss_pred ccccccccccccC---CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 141 EMTCGICFENYPS---DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 141 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
..+||||++.+.. ..++++.|||.|=.+|+++|+. ++ ...+|| .|...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~------~~~~cp--~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK------TKMQCP--LCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh------hhhhCc--ccCChh
Confidence 3689999998643 3467889999999999999994 32 357899 787653
No 57
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.36 E-value=0.063 Score=54.95 Aligned_cols=46 Identities=30% Similarity=0.723 Sum_probs=36.0
Q ss_pred ccccccccccccCC-c--cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 141 EMTCGICFENYPSD-R--LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 141 ~~~C~IC~e~~~~~-~--~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
...|.||.+.+... + +..++|+|.|+..|++.|++.+ -.|| .|+..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~---------qtCP--~CR~~ 339 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ---------QTCP--TCRTV 339 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHh---------CcCC--cchhh
Confidence 57899999987531 1 5678999999999999999882 2588 67663
No 58
>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=92.30 E-value=0.1 Score=37.59 Aligned_cols=58 Identities=24% Similarity=0.454 Sum_probs=34.1
Q ss_pred CCCCCCcceeecCCCCceeecCCCcc-----ceeccccccccccCCCCCCcccCCCccchhcccCC
Q 018073 301 PCPRCKRPIEKNQGCMHMTCTPPCKF-----EFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVV 361 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~-----~FCw~C~~~~~~h~~~~g~~y~C~~~~~~~~~~~~ 361 (361)
.||.|+.+++..+ .+..|. .|.. -||--|+.+......--..-|.|+.-..-+.+.+|
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~-~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiSKkrV 65 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE-ACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLISKKRV 65 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET-TT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE-TTTS
T ss_pred cCCCCCCccEEeC--CEEECc-cccccceecccCCCcccHHHHHHHhcccceeeccCCceeecceE
Confidence 6999999999888 799998 7975 46999998876543211145778877665555443
No 59
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=91.71 E-value=0.18 Score=33.82 Aligned_cols=36 Identities=19% Similarity=0.462 Sum_probs=27.3
Q ss_pred ccccccccccCCccccccCC-----CcccHhhHHHHHHhhh
Q 018073 143 TCGICFENYPSDRLLAAACG-----HPFCSSCWTGYISTAI 178 (361)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~Cl~~~i~~~i 178 (361)
.|-||++.....++...+|. |.+...|+..|+..+-
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC
Confidence 38899984444555667774 8899999999998753
No 60
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.49 E-value=0.16 Score=34.30 Aligned_cols=28 Identities=25% Similarity=0.647 Sum_probs=21.2
Q ss_pred CCCCCCCcceeecC--CCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQ--GCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~--GCnhm~C~~~C~~~F 328 (361)
+-||.|+.++.... +-++..|. .|++++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~-~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCR-KCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECC-cCCCeE
Confidence 46999999887553 35689998 798764
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=91.41 E-value=0.34 Score=53.37 Aligned_cols=74 Identities=19% Similarity=0.351 Sum_probs=53.5
Q ss_pred ccccccccccc-cCCccccccCCCcccHhhHHHHHHhhhcCCCC-eeeeccCCCcCCCccchhHHhhcCChHHHHHHHH
Q 018073 141 EMTCGICFENY-PSDRLLAAACGHPFCSSCWTGYISTAINDGPG-CLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (361)
Q Consensus 141 ~~~C~IC~e~~-~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~-~~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~ 217 (361)
.-.|.|||.+- ..-.-+.|.|+|.|...|.+..++.+-..... ...|.|| -|...|..-.++.|+.+ +++.|+.
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP-iKel~ed 3561 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP-IKELYED 3561 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH-HHHHHHH
Confidence 45699999753 33445678999999999999999887654321 2368999 89999988888877753 3444443
No 62
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.22 E-value=0.03 Score=52.56 Aligned_cols=48 Identities=25% Similarity=0.662 Sum_probs=34.3
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
..+.|+||++-+. .-+....|.|+||.+|+-.-+.. | .-.|| .|+..+
T Consensus 42 ~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~----g----n~ecp--tcRk~l 89 (381)
T KOG0311|consen 42 IQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS----G----NNECP--TCRKKL 89 (381)
T ss_pred hhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh----c----CCCCc--hHHhhc
Confidence 4678999998764 23444569999999998766654 2 23588 788754
No 63
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=91.07 E-value=0.11 Score=33.64 Aligned_cols=40 Identities=25% Similarity=0.657 Sum_probs=23.1
Q ss_pred CCCCCcceeecCCCCceeecCCCccceeccccccccccCCCCCCcccCC
Q 018073 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACN 350 (361)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~y~C~ 350 (361)
||-|...+. +.++= .|||.||..|+..|...... ..+.|+
T Consensus 1 CpiC~~~~~-----~Pv~l--~CGH~FC~~Cl~~~~~~~~~--~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSL--PCGHSFCRSCLERLWKEPSG--SGFSCP 40 (42)
T ss_dssp ETTTTSB-S-----SEEE---SSSSEEEHHHHHHHHCCSSS--ST---S
T ss_pred CCccchhhC-----Ccccc--CCcCHHHHHHHHHHHHccCC--cCCCCc
Confidence 555665554 34555 49999999999987655442 115565
No 64
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=90.89 E-value=0.81 Score=42.83 Aligned_cols=47 Identities=23% Similarity=0.611 Sum_probs=33.2
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
...|+||+.... +..+..-=|-.||-.|+-.|+.. .| +||-.+|...
T Consensus 300 ~~~CpvClk~r~-Nptvl~vSGyVfCY~Ci~~Yv~~---~~------~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLKKRQ-NPTVLEVSGYVFCYPCIFSYVVN---YG------HCPVTGYPAS 346 (357)
T ss_pred cccChhHHhccC-CCceEEecceEEeHHHHHHHHHh---cC------CCCccCCcch
Confidence 467999997653 33333346899999999999984 22 5886666544
No 65
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.64 E-value=0.22 Score=47.15 Aligned_cols=48 Identities=23% Similarity=0.573 Sum_probs=36.6
Q ss_pred CCccccccccccccCCccccccCCCc-ccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
....+|.||+.+- .+.+.|+|.|. .|.+|.+..--. .=+|| -|+..|.
T Consensus 288 ~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr~q---------~n~CP--ICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLRYQ---------TNNCP--ICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCC--cceEEecchhhehhHhHHHHHHHh---------hcCCC--ccccchH
Confidence 4467899999864 67888999997 899998866521 12599 8998764
No 66
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.51 E-value=0.15 Score=29.33 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=8.5
Q ss_pred CCCCCCCccee
Q 018073 300 KPCPRCKRPIE 310 (361)
Q Consensus 300 k~CP~C~~~Ie 310 (361)
+.||+|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 67888888775
No 67
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.37 E-value=0.091 Score=47.05 Aligned_cols=45 Identities=29% Similarity=0.721 Sum_probs=33.1
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
+.|..|+---+...++.++|+|.||..|.+.-. +-.|| .|+..+.
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~-----------~~~C~--lCkk~ir 48 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS-----------PDVCP--LCKKSIR 48 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC-----------ccccc--cccceee
Confidence 568989875555667788899999999985321 22788 8998753
No 68
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.28 E-value=0.22 Score=46.80 Aligned_cols=52 Identities=31% Similarity=0.646 Sum_probs=37.2
Q ss_pred CCCCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 136 FPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 136 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
.|.++...|+||+.. +..-+..+|+|.-|.+|+.+|+... -+|- .|+..+..
T Consensus 417 lp~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN~---------k~CF--fCktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMNC---------KRCF--FCKTTVID 468 (489)
T ss_pred CCCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhcC---------Ceee--Eecceeee
Confidence 455677899999953 2344567899999999999998642 2454 67776543
No 69
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.20 E-value=0.98 Score=43.42 Aligned_cols=56 Identities=16% Similarity=0.346 Sum_probs=39.5
Q ss_pred CCccccccccccccC-CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhH
Q 018073 139 GEEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~ 202 (361)
-+.|.|||=-+.-.. +.+..+.|||.++++=+...... |. ..++|| -|........
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~n----g~--~sfKCP--YCP~e~~~~~ 388 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKN----GS--QSFKCP--YCPVEQLASD 388 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhC----CC--eeeeCC--CCCcccCHHh
Confidence 346899996665443 45678999999999977665543 32 479999 8987655443
No 70
>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=90.20 E-value=0.11 Score=42.33 Aligned_cols=36 Identities=25% Similarity=0.660 Sum_probs=28.7
Q ss_pred ccccccccccccC-CccccccCC------CcccHhhHHHHHHh
Q 018073 141 EMTCGICFENYPS-DRLLAAACG------HPFCSSCWTGYIST 176 (361)
Q Consensus 141 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~Cl~~~i~~ 176 (361)
..+|.||++.+.. .-++.++|| |.||.+|++.|-..
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence 5789999999876 456667776 77999999999433
No 71
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=90.10 E-value=0.047 Score=49.99 Aligned_cols=38 Identities=26% Similarity=0.829 Sum_probs=29.7
Q ss_pred hhcCCCCCCCcceeecCCCCceeecCCCccceeccccccccccCC
Q 018073 297 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 341 (361)
Q Consensus 297 ~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~ 341 (361)
.++.+|--|-...+ |-+|+ +|||-|||-|.-.|-....
T Consensus 237 ~a~~kC~LCLe~~~------~pSaT-pCGHiFCWsCI~~w~~ek~ 274 (293)
T KOG0317|consen 237 EATRKCSLCLENRS------NPSAT-PCGHIFCWSCILEWCSEKA 274 (293)
T ss_pred CCCCceEEEecCCC------CCCcC-cCcchHHHHHHHHHHcccc
Confidence 34667777766665 67899 6999999999999986654
No 72
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.95 E-value=0.17 Score=28.23 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=7.6
Q ss_pred CCCCCCccee
Q 018073 301 PCPRCKRPIE 310 (361)
Q Consensus 301 ~CP~C~~~Ie 310 (361)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 4788888886
No 73
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.78 E-value=0.51 Score=44.29 Aligned_cols=56 Identities=27% Similarity=0.617 Sum_probs=40.7
Q ss_pred ccccccccccccCC----ccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc--cchhHHhhc
Q 018073 141 EMTCGICFENYPSD----RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA--VGQDMIYLL 206 (361)
Q Consensus 141 ~~~C~IC~e~~~~~----~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~--i~~~~i~~l 206 (361)
...|.||-++|... -+..|.|||.+|..|....+.. ..+.|| .|+.. ++...+..+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~--------~~i~cp--fcR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN--------SRILCP--FCRETTEIPDGDVKSL 64 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC--------ceeecc--CCCCcccCCchhHhhh
Confidence 35799999998754 2456779999999999988865 256777 89887 444444443
No 74
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=89.74 E-value=0.45 Score=28.73 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=18.9
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCccc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
+.+-||+|+.+.+...+=--|.|. .|+++
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~-~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCP-SCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEES-SSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECC-CCcCE
Confidence 357899999999988887889997 78875
No 75
>PHA00626 hypothetical protein
Probab=89.27 E-value=0.31 Score=33.24 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=21.3
Q ss_pred CCCCCCc-ceeecCCCCc----eeecCCCcccee
Q 018073 301 PCPRCKR-PIEKNQGCMH----MTCTPPCKFEFC 329 (361)
Q Consensus 301 ~CP~C~~-~IeK~~GCnh----m~C~~~C~~~FC 329 (361)
.||+|+. -|.|.+=|+. -.|. .||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCk-dCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCC-DCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcC-CCCCeec
Confidence 5999998 5888877754 6787 6888773
No 76
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.20 E-value=0.21 Score=49.06 Aligned_cols=50 Identities=24% Similarity=0.587 Sum_probs=37.3
Q ss_pred CccccccccccccCCc---------------cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 140 EEMTCGICFENYPSDR---------------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~---------------~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
....|.||+.+++... ....+|.|.|.+.|+.+|..+ ..+.|| .|+..++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~--------ykl~CP--vCR~pLP 634 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT--------YKLICP--VCRCPLP 634 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh--------hcccCC--ccCCCCC
Confidence 4678999998765311 113489999999999999975 257899 8887765
No 77
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.10 E-value=0.68 Score=45.21 Aligned_cols=42 Identities=26% Similarity=0.827 Sum_probs=34.2
Q ss_pred CCccccCCCCCCcceeeecCCCCceEEeccCCccccccCCcCCCCC
Q 018073 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPV 273 (361)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~ 273 (361)
...+.||. |...|... .+...++|.||+.||+.|+.+|+...
T Consensus 304 ~~wr~Cpk--C~~~ie~~--~GCnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCPK--CKFMIELS--EGCNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCcc--cceeeeec--CCcceEEeeccccchhhcCcchhhCC
Confidence 56789995 99888654 45888999999999999998886543
No 78
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=89.09 E-value=0.28 Score=51.00 Aligned_cols=12 Identities=17% Similarity=0.163 Sum_probs=8.8
Q ss_pred ccceeccccccc
Q 018073 325 KFEFCWLCLGQW 336 (361)
Q Consensus 325 ~~~FCw~C~~~~ 336 (361)
+..||-.||.+.
T Consensus 40 ~~~fC~~CG~~~ 51 (645)
T PRK14559 40 DEAHCPNCGAET 51 (645)
T ss_pred ccccccccCCcc
Confidence 455999998764
No 79
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=88.99 E-value=0.44 Score=46.69 Aligned_cols=37 Identities=30% Similarity=0.738 Sum_probs=29.7
Q ss_pred CCCccccccccccccCCcccc-ccCCCcccHhhHHHHHHh
Q 018073 138 DGEEMTCGICFENYPSDRLLA-AACGHPFCSSCWTGYIST 176 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~~i~~ 176 (361)
......|++|...+. +++. +.|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc
Confidence 455689999998763 4444 689999999999998876
No 80
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=88.80 E-value=0.22 Score=33.60 Aligned_cols=29 Identities=24% Similarity=0.594 Sum_probs=21.4
Q ss_pred hhcCCCCCCCc-ceeecCCCCceeecCCCccce
Q 018073 297 ANSKPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 297 ~~~k~CP~C~~-~IeK~~GCnhm~C~~~C~~~F 328 (361)
.+.+.||+|+. .+.... +.++|. .|++.+
T Consensus 18 ~~~~fCP~Cg~~~m~~~~--~r~~C~-~Cgyt~ 47 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHL--DRWHCG-KCGYTE 47 (50)
T ss_pred EccCcCcCCCcchheccC--CcEECC-CcCCEE
Confidence 34579999998 444333 799999 799875
No 81
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=88.65 E-value=0.34 Score=31.31 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=23.7
Q ss_pred HHHHhhcCCCCCCCcceeecCCCCceeecC-CCccce
Q 018073 293 NWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFEF 328 (361)
Q Consensus 293 ~~i~~~~k~CP~C~~~IeK~~GCnhm~C~~-~C~~~F 328 (361)
.|.+...|.||+|++.- |+--+.|.+ .|.+.|
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchhh
Confidence 46666789999999875 777788872 566654
No 82
>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=88.54 E-value=0.52 Score=36.82 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=26.4
Q ss_pred ccccccccccccCCccccccCCCcccHhhHH
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWT 171 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~ 171 (361)
...|++|...+....+...+|||.|...|.+
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 4569999999877777788999999999975
No 83
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=88.49 E-value=0.23 Score=48.19 Aligned_cols=116 Identities=22% Similarity=0.346 Sum_probs=64.9
Q ss_pred eCHHHHHHHHHHHHHHHHHHhCCCHH--HHHHHHHHcCCChHH--HHHHhhhc-----HHHHHH-----HcCCCCC-CCC
Q 018073 70 LTEADIRQRQEEDITRISTVLSISKV--AASILLRFYNWSVSK--VHDEWFAD-----EERVRK-----AVGLLEK-PAV 134 (361)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~~l~i~~~--~a~~LL~~~~w~~~~--l~e~~~~~-----~~~~~~-----~~~l~~~-~~~ 134 (361)
||..||.+.+...+.+|+.+.=|..+ .-..+|.+|+=..+. ..++|-.. +..+-. .+.+... +..
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Chll~V~~ve~~~s~d~a 165 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCHLLYVDRVEVTESEDGA 165 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCccceeEEEEEEEEEEecccCC
Confidence 78999999999888888877665422 223444455433221 11222110 000110 0111110 111
Q ss_pred ---CCCCCCccccccccccccCC--ccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 135 ---QFPDGEEMTCGICFENYPSD--RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 135 ---~~~~~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
+.......+||||++....+ -+.+..|.|.|-..|+..|.- ..|| .|+...
T Consensus 166 s~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~-----------~scp--vcR~~q 221 (493)
T KOG0804|consen 166 SEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD-----------SSCP--VCRYCQ 221 (493)
T ss_pred CCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc-----------CcCh--hhhhhc
Confidence 11224467999999987643 345667999999999988763 4677 676543
No 84
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=88.47 E-value=0.4 Score=28.59 Aligned_cols=27 Identities=26% Similarity=0.766 Sum_probs=14.9
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
-+||+|+....-..|.+ |.|. .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp-~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCP-ECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEET-TTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCC-cccccC
Confidence 47999999888878876 8898 788875
No 85
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=88.17 E-value=1.4 Score=47.35 Aligned_cols=20 Identities=10% Similarity=0.069 Sum_probs=13.1
Q ss_pred HHHHHHHHcCCChHHHHHHh
Q 018073 96 AASILLRFYNWSVSKVHDEW 115 (361)
Q Consensus 96 ~a~~LL~~~~w~~~~l~e~~ 115 (361)
.++.++.||+-.+-.|++-|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56677777776666666554
No 86
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.52 E-value=0.27 Score=46.87 Aligned_cols=46 Identities=33% Similarity=0.810 Sum_probs=33.6
Q ss_pred cccccccccccCC-cccccc-CCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCC
Q 018073 142 MTCGICFENYPSD-RLLAAA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (361)
Q Consensus 142 ~~C~IC~e~~~~~-~~~~l~-CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~ 195 (361)
..|.||-+-++.. ++...+ |||.|...|+.+|++..-.. -.|| .|.
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~------R~cp--ic~ 52 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN------RGCP--ICQ 52 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc------CCCC--cee
Confidence 5799996655543 445555 99999999999999886543 2477 565
No 87
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.32 E-value=0.22 Score=45.83 Aligned_cols=45 Identities=27% Similarity=0.611 Sum_probs=34.6
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
.+-|.||-..| ..++...|+|+||..|....+.. .-+|+ .|...+
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk---------~~~c~--vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK---------GEKCY--VCSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc---------CCcce--eccccc
Confidence 46799999887 56788899999999998776643 23576 777654
No 88
>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=87.29 E-value=0.18 Score=32.11 Aligned_cols=32 Identities=38% Similarity=1.003 Sum_probs=22.3
Q ss_pred CCCCCcceeecCCCCceeecCCCccceecccccccccc
Q 018073 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (361)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (361)
||-|........ +=. .|+|.||..|+..|...
T Consensus 1 C~iC~~~~~~~~-----~~~-~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPV-----ILL-PCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEE-----EET-TTSEEEEHHHHHHHHHH
T ss_pred CCcCCccccCCC-----EEe-cCCCcchHHHHHHHHHh
Confidence 555665555332 344 69999999999998764
No 89
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.96 E-value=0.29 Score=33.21 Aligned_cols=45 Identities=29% Similarity=0.690 Sum_probs=32.7
Q ss_pred cccccccccccCCccccccCCCc-ccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 142 MTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
-+|.||++. +.+.+...|||. .|.+|-...++. . .=.|| -|+++|
T Consensus 8 dECTICye~--pvdsVlYtCGHMCmCy~Cg~rl~~~-~-------~g~CP--iCRapi 53 (62)
T KOG4172|consen 8 DECTICYEH--PVDSVLYTCGHMCMCYACGLRLKKA-L-------HGCCP--ICRAPI 53 (62)
T ss_pred cceeeeccC--cchHHHHHcchHHhHHHHHHHHHHc-c-------CCcCc--chhhHH
Confidence 579999985 234556679997 899998887765 1 23588 787765
No 90
>PHA03096 p28-like protein; Provisional
Probab=85.40 E-value=0.44 Score=44.42 Aligned_cols=38 Identities=24% Similarity=0.542 Sum_probs=28.7
Q ss_pred cccccccccccCC----ccc-cc-cCCCcccHhhHHHHHHhhhc
Q 018073 142 MTCGICFENYPSD----RLL-AA-ACGHPFCSSCWTGYISTAIN 179 (361)
Q Consensus 142 ~~C~IC~e~~~~~----~~~-~l-~CgH~fC~~Cl~~~i~~~i~ 179 (361)
..|+||++..... ..+ .| .|.|.||..|++.|..++..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 6799999975422 122 33 59999999999999988764
No 91
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.21 E-value=0.47 Score=47.37 Aligned_cols=39 Identities=26% Similarity=0.641 Sum_probs=32.3
Q ss_pred cCCCC--CCCcceee-cCCCCceeecCCCccceecccccccccc
Q 018073 299 SKPCP--RCKRPIEK-NQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (361)
Q Consensus 299 ~k~CP--~C~~~IeK-~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (361)
.|-|| .|+..+.- .+.+.-+.|. |++.|||.|+.+|...
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~--~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCG--CGHEFCFACGEESHSP 199 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCC--CCchhHhhccccccCC
Confidence 35566 79999987 7889999997 9999999998887643
No 92
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=85.00 E-value=0.33 Score=50.76 Aligned_cols=51 Identities=29% Similarity=0.740 Sum_probs=39.5
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHh
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY 204 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~ 204 (361)
++|.||.+ ....+...|+|.||.+||..+|...-. ..|| .|...+....+.
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~-------~~~~--~cr~~l~~~~l~ 505 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN-------APCP--LCRNVLKEKKLL 505 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC-------CCCc--HHHHHHHHHHHh
Confidence 78999998 467788899999999999999976322 2677 888876554443
No 93
>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=84.94 E-value=0.31 Score=30.75 Aligned_cols=32 Identities=28% Similarity=0.860 Sum_probs=22.2
Q ss_pred CCCCCcceeecCCCCceeecCCCccceecccccccccc
Q 018073 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (361)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (361)
||-|...+.. .++-. +|||.||+.|...|...
T Consensus 1 C~iC~~~~~~-----~~~~~-~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD-----PVVVT-PCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS-----EEEEC-TTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC-----cCEEC-CCCCchhHHHHHHHHHC
Confidence 4556555442 44566 69999999999888655
No 94
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=84.87 E-value=0.37 Score=46.13 Aligned_cols=35 Identities=31% Similarity=0.718 Sum_probs=28.1
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
....|.||.+.- .++...+|||..|..|+..|-.+
T Consensus 368 TFeLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s 402 (563)
T KOG1785|consen 368 TFELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS 402 (563)
T ss_pred hHHHHHHhhccC--CCcccccccchHHHHHHHhhccc
Confidence 345799999853 56677899999999999998654
No 95
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.53 E-value=0.83 Score=36.21 Aligned_cols=40 Identities=23% Similarity=0.546 Sum_probs=26.3
Q ss_pred cccCCCCCCcceeeecC------CCCceEEe-ccCCccccccCCcCCCC
Q 018073 231 KWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAHRP 272 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~~ 272 (361)
+.|- +|...+...+. .......| .|+..||..|..-+|.-
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 4577 48776542211 12235679 99999999998777753
No 96
>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=84.22 E-value=0.27 Score=43.79 Aligned_cols=49 Identities=27% Similarity=0.621 Sum_probs=35.7
Q ss_pred cccccccccccC-Ccccc--cc-CCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 142 MTCGICFENYPS-DRLLA--AA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 142 ~~C~IC~e~~~~-~~~~~--l~-CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
..||||-.+.-. .++.. -+ |-|+.|.+|+...++. | +-.||.++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G----pAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G----PAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C----CCCCCCccHHHHH
Confidence 359999875322 22322 23 9999999999988865 2 6789999999764
No 97
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=84.13 E-value=0.66 Score=29.08 Aligned_cols=27 Identities=26% Similarity=0.705 Sum_probs=16.9
Q ss_pred CCCCCCCcceeec------CCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKN------QGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~------~GCnhm~C~~~C~~~F 328 (361)
..||+|+..+.-. .| ..++|. .|++.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~-~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCG-KCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECC-CCCCEE
Confidence 3688888855422 12 278887 677765
No 98
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.69 E-value=0.82 Score=28.65 Aligned_cols=29 Identities=28% Similarity=0.670 Sum_probs=20.9
Q ss_pred cccCCCCCCcceeeecC---CCCceEEe-ccCCcc
Q 018073 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (361)
+.||+ |+..+.+... .+...|.| .|++.|
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 56885 9988876543 34568899 898876
No 99
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=83.07 E-value=1.9 Score=41.32 Aligned_cols=48 Identities=33% Similarity=0.759 Sum_probs=37.7
Q ss_pred ccccccccccccC--CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
.+.|..|-+.+.. +.+..++|.|.|...|+..|+.. .+ +-.|| .|+..
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~----~rsCP--~Crkl 414 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG----TRSCP--NCRKL 414 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC----CCCCc--cHHHH
Confidence 5779999998754 45678899999999999999943 22 45799 78743
No 100
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=83.00 E-value=4 Score=25.29 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHH
Q 018073 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (361)
Q Consensus 80 ~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e 113 (361)
.+.|.++.+. |.+...++..|+..+||++..++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 3567888888 99999999999999999988664
No 101
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=82.85 E-value=0.79 Score=32.43 Aligned_cols=35 Identities=26% Similarity=0.720 Sum_probs=14.9
Q ss_pred CCCCCCCcceeec---CCCCceeecCCCccce----ecccccc
Q 018073 300 KPCPRCKRPIEKN---QGCMHMTCTPPCKFEF----CWLCLGQ 335 (361)
Q Consensus 300 k~CP~C~~~IeK~---~GCnhm~C~~~C~~~F----Cw~C~~~ 335 (361)
-+|++|....... +||-|+.|+ .|-..+ |-+|..|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs-~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCS-SCIRDCIGSECPVCHTP 49 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-T-TTGGGGTTTB-SSS--B
T ss_pred cCCcHHHHHhcCCceeccCccHHHH-HHhHHhcCCCCCCcCCh
Confidence 6899999877543 788888887 563332 5666544
No 102
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=82.54 E-value=1.7 Score=46.63 Aligned_cols=8 Identities=13% Similarity=0.173 Sum_probs=3.6
Q ss_pred HHHHHhCC
Q 018073 85 RISTVLSI 92 (361)
Q Consensus 85 ~v~~~l~i 92 (361)
+++.+|+.
T Consensus 707 ~l~~aL~~ 714 (784)
T PF04931_consen 707 ALAKALGD 714 (784)
T ss_pred HHHHHhcc
Confidence 34444554
No 103
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.53 E-value=1.4 Score=46.33 Aligned_cols=69 Identities=23% Similarity=0.469 Sum_probs=43.1
Q ss_pred HHHHhhhcHHHHHHHcCCCCCCCCCCCCCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccC
Q 018073 111 VHDEWFADEERVRKAVGLLEKPAVQFPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (361)
Q Consensus 111 l~e~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP 190 (361)
.++.|..+-++.++.++.+....... ....|..|--++. -.++...|||.|...|+. ++ .-+||
T Consensus 813 ~Ie~yk~~i~e~r~~l~~lr~sa~i~---q~skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~----~~~CP 876 (933)
T KOG2114|consen 813 AIEVYKKDIEEKRQELETLRTSAQIF---QVSKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK----EDKCP 876 (933)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccee---eeeeecccCCccc-cceeeeecccHHHHHhhc--------cC----cccCC
Confidence 34444444455555555544322211 2357999976653 245667899999999998 22 46899
Q ss_pred CCcCCCc
Q 018073 191 DPSCGAA 197 (361)
Q Consensus 191 ~~~C~~~ 197 (361)
.|...
T Consensus 877 --~C~~e 881 (933)
T KOG2114|consen 877 --KCLPE 881 (933)
T ss_pred --ccchh
Confidence 88763
No 104
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.36 E-value=1.2 Score=29.26 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=19.7
Q ss_pred CCCCCCCcceeecCCCCceeecCCCcccee
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 329 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FC 329 (361)
-.||+|+..++-..+=..++|. .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp-~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCP-YCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECC-CCCCeEE
Confidence 3689999888755433378887 6776553
No 105
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=81.75 E-value=0.5 Score=41.21 Aligned_cols=31 Identities=29% Similarity=0.890 Sum_probs=24.0
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceecccccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (361)
-.||-|.-.+. .-.-+ .|||.|||.|+..|.
T Consensus 19 ~~CpICld~~~------dPVvT-~CGH~FC~~CI~~wl 49 (193)
T PLN03208 19 FDCNICLDQVR------DPVVT-LCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCccCCCcCC------CcEEc-CCCchhHHHHHHHHH
Confidence 57999988764 12335 599999999999985
No 106
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=81.35 E-value=3.5 Score=38.23 Aligned_cols=39 Identities=23% Similarity=0.564 Sum_probs=31.0
Q ss_pred CCccccccccccccCCc-cccccCCCcccHhhHHHHHHhh
Q 018073 139 GEEMTCGICFENYPSDR-LLAAACGHPFCSSCWTGYISTA 177 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~~i~~~ 177 (361)
.....|.||+--|.... +...+|.|+|...||..|+...
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 34567999987776555 6677899999999999999754
No 107
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=81.09 E-value=1.1 Score=46.52 Aligned_cols=13 Identities=15% Similarity=0.279 Sum_probs=6.2
Q ss_pred CcchhhhhhhhcC
Q 018073 3 SEDEFDMQDANAS 15 (361)
Q Consensus 3 ~~~~~~~~~~~~~ 15 (361)
.+||+|+.+.+++
T Consensus 882 eddd~d~~s~~~~ 894 (988)
T KOG2038|consen 882 EDDDEDENSLGSE 894 (988)
T ss_pred cccccchhcccCc
Confidence 3344455555543
No 108
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=80.59 E-value=0.6 Score=43.59 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=18.6
Q ss_pred CCceEEe-ccCCccccccCCcCCC
Q 018073 249 GNYDVTC-RCSYSFCWNCTEEAHR 271 (361)
Q Consensus 249 ~~~~v~C-~C~~~fC~~C~~~~H~ 271 (361)
.....+| .|+..||..|..-.|.
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred CCCcEEchhccceeeccchHHHHh
Confidence 3456899 9999999999876664
No 109
>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=80.40 E-value=0.91 Score=42.59 Aligned_cols=52 Identities=27% Similarity=0.619 Sum_probs=31.5
Q ss_pred ccCCCCCCcceeeecCCCCceEEeccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcceee
Q 018073 232 WCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEK 311 (361)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 311 (361)
-||. |.......+. ....+. .|||.||..|.... | .....+||.|+.++-|
T Consensus 5 ~CP~--Ck~~~y~np~-~kl~i~-~CGH~~C~sCv~~l------------------------~-~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPR--CKTTKYRNPS-LKLMVN-VCGHTLCESCVDLL------------------------F-VRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCc--CCCCCccCcc-cccccC-CCCCcccHHHHHHH------------------------h-cCCCCCCCCCCCccch
Confidence 5885 8754322211 122344 79999999996321 1 1123589999998876
Q ss_pred c
Q 018073 312 N 312 (361)
Q Consensus 312 ~ 312 (361)
+
T Consensus 56 ~ 56 (309)
T TIGR00570 56 N 56 (309)
T ss_pred h
Confidence 5
No 110
>PHA02926 zinc finger-like protein; Provisional
Probab=80.20 E-value=0.84 Score=40.52 Aligned_cols=54 Identities=22% Similarity=0.502 Sum_probs=33.8
Q ss_pred hcCCCCCCCcce-eec-CCCCceeecCCCccceeccccccccccCCCCCCcccCCC
Q 018073 298 NSKPCPRCKRPI-EKN-QGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNR 351 (361)
Q Consensus 298 ~~k~CP~C~~~I-eK~-~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~y~C~~ 351 (361)
.-+.|+-|--.+ +|. .++...-=.+.|+|-||+.|...|......+|.-..|+-
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi 224 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCC
Confidence 348899999665 442 222111111269999999999999875434455566764
No 111
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.04 E-value=0.58 Score=41.71 Aligned_cols=20 Identities=45% Similarity=1.105 Sum_probs=16.8
Q ss_pred eeecCCCccceeccccccccccC
Q 018073 318 MTCTPPCKFEFCWLCLGQWSDHG 340 (361)
Q Consensus 318 m~C~~~C~~~FCw~C~~~~~~h~ 340 (361)
+|| |||-|||-|+-.|....
T Consensus 62 vTl---CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL---CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee---cccceehHHHHHHHhhc
Confidence 455 99999999999997654
No 112
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.50 E-value=1 Score=41.47 Aligned_cols=29 Identities=28% Similarity=0.755 Sum_probs=22.6
Q ss_pred ccccccccccccCCccccccCCCc-ccHhhHH
Q 018073 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWT 171 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~ 171 (361)
...|.||++. +.+-+.|+|||. -|..|=+
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhcc
Confidence 5789999975 356788999996 6887743
No 113
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=79.04 E-value=2.1 Score=26.50 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=17.2
Q ss_pred ccccCCCCCCcceeeecCCCCceEEe-ccCCc
Q 018073 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (361)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (361)
+++|| .|+..+.+........ .| .|++.
T Consensus 1 m~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 1 MRFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp --BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred CeeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 36899 5999987765444333 77 77764
No 114
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=78.45 E-value=7.4 Score=24.03 Aligned_cols=35 Identities=20% Similarity=0.237 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhh
Q 018073 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (361)
Q Consensus 81 ~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~ 116 (361)
+.|.++.+ +|.+...++..|+..+||+++..+-++
T Consensus 3 ~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 34555554 589999999999999999998876544
No 115
>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=78.21 E-value=1.4 Score=34.95 Aligned_cols=26 Identities=31% Similarity=0.777 Sum_probs=19.6
Q ss_pred CCCCCCCccee-ecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (361)
+.||+|++..- .|- +.++|. +||+.|
T Consensus 10 R~Cp~CG~kFYDLnk--~PivCP-~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK--DPIVCP-KCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC--CCccCC-CCCCcc
Confidence 68999998776 344 889997 677665
No 116
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.91 E-value=0.81 Score=39.13 Aligned_cols=30 Identities=33% Similarity=0.988 Sum_probs=21.9
Q ss_pred eccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCccee
Q 018073 255 CRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (361)
Q Consensus 255 C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 310 (361)
=+||+.||..|.+. .+.++.+||-|+..|-
T Consensus 149 TkCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 38999999998632 1234589999997664
No 117
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.46 E-value=2.3 Score=39.24 Aligned_cols=44 Identities=25% Similarity=0.791 Sum_probs=32.0
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCC
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~ 196 (361)
+.|++|-.-+ .+.+....|+|.||.+|+..-+.. ..+.|| .|..
T Consensus 275 LkCplc~~Ll-rnp~kT~cC~~~fc~eci~~al~d--------sDf~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLL-RNPMKTPCCGHTFCDECIGTALLD--------SDFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhh-hCcccCccccchHHHHHHhhhhhh--------ccccCC--Cccc
Confidence 7899997643 233444469999999999876654 257899 7875
No 118
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.30 E-value=0.87 Score=48.32 Aligned_cols=53 Identities=23% Similarity=0.574 Sum_probs=37.4
Q ss_pred CCCccccccccccccC-Cc--c--ccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 138 DGEEMTCGICFENYPS-DR--L--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~-~~--~--~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
-+...+|+||+..+.. +. + .-..|.|.|...|+-+|+.+.- .-+|| -|+..++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~-------~s~CP--lCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA-------RSNCP--LCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC-------CCCCC--ccccccc
Confidence 3456789999986642 11 1 1224999999999999998843 34799 8986654
No 119
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=77.06 E-value=2 Score=26.41 Aligned_cols=26 Identities=35% Similarity=0.972 Sum_probs=14.1
Q ss_pred CCCCCCCcceeec----CCCCceeecCCCcc
Q 018073 300 KPCPRCKRPIEKN----QGCMHMTCTPPCKF 326 (361)
Q Consensus 300 k~CP~C~~~IeK~----~GCnhm~C~~~C~~ 326 (361)
|-||.|+.+++.. ++=..+.|. .|++
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~-~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCP-ACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEET-TTTE
T ss_pred CccccccChhhhhcCCCCCccceECC-CCCC
Confidence 4699999998854 455678887 6875
No 120
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=76.98 E-value=4.1 Score=31.15 Aligned_cols=9 Identities=0% Similarity=-0.278 Sum_probs=2.7
Q ss_pred eCHHHHHHH
Q 018073 70 LTEADIRQR 78 (361)
Q Consensus 70 l~~~~i~~~ 78 (361)
++-....+.
T Consensus 44 p~fgea~~~ 52 (101)
T PF09026_consen 44 PEFGEAMAY 52 (101)
T ss_dssp --HHHHHHH
T ss_pred hhHHHHHhh
Confidence 333333333
No 121
>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=76.68 E-value=2 Score=30.76 Aligned_cols=29 Identities=38% Similarity=0.828 Sum_probs=22.4
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCccc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
+++.||.|+....+...=..++|. .||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~-~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCP-NCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcC-CCCCE
Confidence 468999999999985555578887 67765
No 122
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.45 E-value=1.8 Score=38.97 Aligned_cols=53 Identities=13% Similarity=0.238 Sum_probs=38.2
Q ss_pred CccccccccccccCCcc--ccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHH
Q 018073 140 EEMTCGICFENYPSDRL--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i 203 (361)
..+.|+||-+.+...-. +.-+|||.||.+|...+|.. ...|| .|..++....|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~---------D~v~p--v~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK---------DMVDP--VTDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc---------ccccc--CCCCcCcccce
Confidence 56889999998753222 33469999999999999865 34466 67777765544
No 123
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.21 E-value=1.5 Score=40.18 Aligned_cols=52 Identities=25% Similarity=0.609 Sum_probs=38.7
Q ss_pred CCccccccccccccCCccccccC----CCcccHhhHHHHHHhhhcCCCCeeeeccCC-CcCCC
Q 018073 139 GEEMTCGICFENYPSDRLLAAAC----GHPFCSSCWTGYISTAINDGPGCLMLRCPD-PSCGA 196 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~C----gH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~-~~C~~ 196 (361)
...+-|.+|.|.+. +...+.| .|.||..|-++.|+.+-..| .+.||. ..|..
T Consensus 266 ~apLcCTLC~ERLE--DTHFVQCPSVp~HKFCFPCSResIK~Qg~sg----evYCPSGdkCPL 322 (352)
T KOG3579|consen 266 SAPLCCTLCHERLE--DTHFVQCPSVPSHKFCFPCSRESIKQQGASG----EVYCPSGDKCPL 322 (352)
T ss_pred CCceeehhhhhhhc--cCceeecCCCcccceecccCHHHHHhhcCCC----ceeCCCCCcCcc
Confidence 34588999999874 4444455 79999999999999876655 477885 35654
No 124
>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=75.73 E-value=5.5 Score=25.62 Aligned_cols=30 Identities=27% Similarity=0.967 Sum_probs=20.4
Q ss_pred HHHHHhhcCCCCCCCcceee-cCCCCceeecCCCc
Q 018073 292 MNWILANSKPCPRCKRPIEK-NQGCMHMTCTPPCK 325 (361)
Q Consensus 292 ~~~i~~~~k~CP~C~~~IeK-~~GCnhm~C~~~C~ 325 (361)
..|... ...||.|+.|+-+ ..| .+.|. .|+
T Consensus 11 ~G~~ML-~~~Cp~C~~PL~~~k~g--~~~Cv-~C~ 41 (41)
T PF06677_consen 11 QGWTML-DEHCPDCGTPLMRDKDG--KIYCV-SCG 41 (41)
T ss_pred HhHhHh-cCccCCCCCeeEEecCC--CEECC-CCC
Confidence 345333 3689999999987 455 57776 563
No 125
>PLN03086 PRLI-interacting factor K; Provisional
Probab=75.36 E-value=2.8 Score=42.76 Aligned_cols=57 Identities=25% Similarity=0.571 Sum_probs=35.3
Q ss_pred eeeccCCCcCCCccchhHHhhcCChHHHHHHHHHHHHHHHhhCCCccccCCCCCCcceeeecCCCCceEEe-ccCCcc
Q 018073 185 LMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (361)
Q Consensus 185 ~~i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (361)
..+.|| .|...++...+...+. + =....+-||+.+|+..+.... -...+.| .|+..|
T Consensus 406 ~~V~C~--NC~~~i~l~~l~lHe~--------------~--C~r~~V~Cp~~~Cg~v~~r~e--l~~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECR--NCKHYIPSRSIALHEA--------------Y--CSRHNVVCPHDGCGIVLRVEE--AKNHVHCEKCGQAF 463 (567)
T ss_pred CeEECC--CCCCccchhHHHHHHh--------------h--CCCcceeCCcccccceeeccc--cccCccCCCCCCcc
Confidence 467899 5998887665543221 1 112456799878999885542 2334567 677665
No 126
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=74.81 E-value=2.7 Score=28.57 Aligned_cols=30 Identities=27% Similarity=0.445 Sum_probs=19.7
Q ss_pred CCCCCCCccee------ecCCCCcee-ecCCCccceec
Q 018073 300 KPCPRCKRPIE------KNQGCMHMT-CTPPCKFEFCW 330 (361)
Q Consensus 300 k~CP~C~~~Ie------K~~GCnhm~-C~~~C~~~FCw 330 (361)
|+||.|+-.-+ .+.+..++. |. .|++...+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~-~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS-TCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC-CCCCCccc
Confidence 89999996555 234555554 77 67776543
No 127
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=74.80 E-value=0.93 Score=33.06 Aligned_cols=48 Identities=33% Similarity=0.753 Sum_probs=33.6
Q ss_pred ccccccccccC---------Cc-cccc-cCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 143 TCGICFENYPS---------DR-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 143 ~C~IC~e~~~~---------~~-~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
+|+||.-.|.. ++ +..+ .|.|.|-.-|+.+++.+.-+++ .|| -|+...
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~------~CP--mcRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG------QCP--MCRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc------cCC--cchhee
Confidence 68888766543 21 2223 4999999999999999877765 488 676543
No 128
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.68 E-value=2.3 Score=44.33 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=6.3
Q ss_pred cccCCCCCCcce
Q 018073 231 KWCPAPGCDYAV 242 (361)
Q Consensus 231 ~~CP~p~C~~~i 242 (361)
+.||. |+..+
T Consensus 2 ~~Cp~--Cg~~n 11 (645)
T PRK14559 2 LICPQ--CQFEN 11 (645)
T ss_pred CcCCC--CCCcC
Confidence 46874 87654
No 129
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.31 E-value=2.5 Score=26.25 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=19.9
Q ss_pred cccCCCCCCcceeeecC---CCCceEEe-ccCCcc
Q 018073 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (361)
+.||+ |+..+.+... .....|.| .|++.|
T Consensus 3 i~Cp~--C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN--CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC--CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 46885 9987766532 23467899 888875
No 130
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=73.73 E-value=7.3 Score=41.88 Aligned_cols=35 Identities=26% Similarity=0.202 Sum_probs=19.6
Q ss_pred EeeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcC
Q 018073 68 TVLTEADIRQRQEEDITRISTVLSISKVAASILLRFYN 105 (361)
Q Consensus 68 ~~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (361)
+.|.+-+..+.+.+.+..+++ -.+.....|+++-.
T Consensus 953 t~LD~VD~f~~f~~~i~~lq~---~d~~~yq~l~~~L~ 987 (1010)
T KOG1991|consen 953 TPLDQVDPFQLFKEAITNLQS---SDAVRYQKLISTLT 987 (1010)
T ss_pred CcccccchHHHHHHHHHhhhc---cChHHHHHHHhcCC
Confidence 446666777777776666543 23344444554443
No 131
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=73.38 E-value=2.2 Score=40.06 Aligned_cols=47 Identities=32% Similarity=0.796 Sum_probs=34.1
Q ss_pred CCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
....++||||++.+. ..+++..=||..|..|-. + ..-+|| .|+..++
T Consensus 45 ~~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~-----~-------~~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRT-----K-------VSNKCP--TCRLPIG 91 (299)
T ss_pred chhhccCchhhccCc-ccceecCCCcEehhhhhh-----h-------hcccCC--ccccccc
Confidence 445789999998764 233344448999999986 1 245899 7998887
No 132
>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=73.07 E-value=4.9 Score=37.12 Aligned_cols=47 Identities=30% Similarity=0.674 Sum_probs=32.1
Q ss_pred ccccccccc-cCCcccc--ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 143 TCGICFENY-PSDRLLA--AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 143 ~C~IC~e~~-~~~~~~~--l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
.||+|-... -...++. -+|+|..|.+|+-..+.. | +-.|| .|..++.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g----~~~Cp--eC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G----PAQCP--ECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C----CCCCC--cccchhh
Confidence 388886542 1122222 279999999999988865 2 45799 9998764
No 133
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=72.98 E-value=2.6 Score=32.36 Aligned_cols=29 Identities=28% Similarity=0.839 Sum_probs=22.2
Q ss_pred CCCCCCcce--eecCCCCceeecCCCccceec
Q 018073 301 PCPRCKRPI--EKNQGCMHMTCTPPCKFEFCW 330 (361)
Q Consensus 301 ~CP~C~~~I--eK~~GCnhm~C~~~C~~~FCw 330 (361)
-||.|+.++ ++.+-||...|+ .|.|.|=-
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~-tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCR-TCPYVFPI 33 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcC-CCCceeeE
Confidence 599999754 455559999999 79987743
No 134
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=72.68 E-value=11 Score=23.00 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHH
Q 018073 82 DITRISTVLSISKVAASILLRFYNWSVSKVHDE 114 (361)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~ 114 (361)
.|.++.+ +|.++..|+..|+..+||+++..+-
T Consensus 4 ~v~~L~~-mGf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 4 KIDQLLE-MGFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHH
Confidence 3444443 4899999999999999998887653
No 135
>PF04641 Rtf2: Rtf2 RING-finger
Probab=71.78 E-value=6 Score=36.48 Aligned_cols=68 Identities=18% Similarity=0.442 Sum_probs=45.0
Q ss_pred CCCccccccccccccCC-cccc-ccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHHhhcCC-hHHHHH
Q 018073 138 DGEEMTCGICFENYPSD-RLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS-DEDKVK 214 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~-~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i~~ll~-~~~~~~ 214 (361)
....+.|||....+... .++. .+|||.|+..+++..- . .-.|| .|...+....|-.|.+ .+.++.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~------~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~ 177 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K------SKKCP--VCGKPFTEEDIIPLNPPEEELEK 177 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c------ccccc--ccCCccccCCEEEecCCccHHHH
Confidence 35578999999888542 3444 4799999999998871 1 12498 8999987665544433 233444
Q ss_pred HHH
Q 018073 215 YNR 217 (361)
Q Consensus 215 y~~ 217 (361)
...
T Consensus 178 l~~ 180 (260)
T PF04641_consen 178 LRE 180 (260)
T ss_pred HHH
Confidence 333
No 136
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=71.25 E-value=2.5 Score=39.74 Aligned_cols=54 Identities=28% Similarity=0.735 Sum_probs=38.4
Q ss_pred CccccccccccccC--CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccchhHH
Q 018073 140 EEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (361)
Q Consensus 140 ~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~~~i 203 (361)
..-.|++|++++.. .+++..+||-.+|+-||.. |+..++ =+|| .|+.....+-|
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~ln-------grcp--acrr~y~denv 68 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNLN-------GRCP--ACRRKYDDENV 68 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhcc-------CCCh--Hhhhhccccce
Confidence 34459999998754 4567778999999999965 333333 3799 89987655443
No 137
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=71.00 E-value=3.6 Score=27.48 Aligned_cols=28 Identities=29% Similarity=0.767 Sum_probs=16.9
Q ss_pred cccCCCCCCcceeeecCCCCceEEe-ccCCc
Q 018073 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (361)
++||. |+..+............| .|++.
T Consensus 1 ~FCp~--Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 1 KFCPK--CGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCC--CCCccccccCCCCCEEECCcCCCe
Confidence 37884 998776553323235667 67654
No 138
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=70.99 E-value=1 Score=42.22 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=23.3
Q ss_pred CCCCCCCccee-ecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (361)
.+||+|+..|- |.-.=|.+.|. +|+|+|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCP-KCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCC-CCCCCe
Confidence 89999999987 44556778998 799998
No 139
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=70.46 E-value=3.7 Score=30.85 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=23.7
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
-.||.|+....|..+=--=.|. +||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~-kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCR-KCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcC-CCCCee
Confidence 5899999999988887777888 688776
No 140
>PRK00420 hypothetical protein; Validated
Probab=69.56 E-value=8 Score=30.75 Aligned_cols=21 Identities=38% Similarity=0.939 Sum_probs=15.5
Q ss_pred cCCCCCCCcceee-cCCCCceeec
Q 018073 299 SKPCPRCKRPIEK-NQGCMHMTCT 321 (361)
Q Consensus 299 ~k~CP~C~~~IeK-~~GCnhm~C~ 321 (361)
...||.|+.++.+ ..| +..|.
T Consensus 23 ~~~CP~Cg~pLf~lk~g--~~~Cp 44 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG--EVVCP 44 (112)
T ss_pred cCCCCCCCCcceecCCC--ceECC
Confidence 4899999999986 444 45554
No 141
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=69.11 E-value=3 Score=44.46 Aligned_cols=27 Identities=33% Similarity=1.123 Sum_probs=23.8
Q ss_pred CCCCCCCcceeecCCCCceeecCCCcccee
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 329 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FC 329 (361)
..||.|+..+...+||. +|. .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~-~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH-SCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC-CCCCCCC
Confidence 35999999999999998 998 7998765
No 142
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=68.89 E-value=3.7 Score=43.31 Aligned_cols=54 Identities=24% Similarity=0.568 Sum_probs=40.1
Q ss_pred CCccccccccccccCCc-cccc-cCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCC
Q 018073 139 GEEMTCGICFENYPSDR-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~-~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~ 196 (361)
...++|.||++.+.... +.+. .|-|.|-..|++.|..+.-..+. ..-+|| .|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~--~~WrCP--~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ--DGWRCP--ACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC--ccccCC--cccc
Confidence 34689999999886543 4444 49999999999999988444443 467899 7763
No 143
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=68.81 E-value=3.4 Score=32.26 Aligned_cols=25 Identities=24% Similarity=0.684 Sum_probs=18.1
Q ss_pred CCCCCCcceeecCCCCceeecCCCccce
Q 018073 301 PCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
.||+|+.++...+ +.+.|. .|++.+
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~-~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCP-SCGYEK 26 (104)
T ss_pred CCcccCcccccCC--CeEECc-CCCCcc
Confidence 5888888886554 378887 677663
No 144
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=68.76 E-value=2 Score=29.41 Aligned_cols=45 Identities=29% Similarity=0.659 Sum_probs=29.9
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
...|-.|... ......++|||.+|..||-..= .-.|| .|...+..
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~r-----------YngCP--fC~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGER-----------YNGCP--FCGTPFEF 51 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChhh-----------ccCCC--CCCCcccC
Confidence 3456666543 2455678999999999995321 23588 78887754
No 145
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=68.55 E-value=3.7 Score=27.32 Aligned_cols=27 Identities=22% Similarity=0.595 Sum_probs=16.1
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCcc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
.+.||+|+--+.-..-=+.-.|. +||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CG-kCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACG-KCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEec-cccc
Confidence 37899999533322222366777 6775
No 146
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.52 E-value=2.9 Score=29.02 Aligned_cols=12 Identities=42% Similarity=1.030 Sum_probs=6.4
Q ss_pred CCCCCC-cceeec
Q 018073 301 PCPRCK-RPIEKN 312 (361)
Q Consensus 301 ~CP~C~-~~IeK~ 312 (361)
+||+|+ ..|-+-
T Consensus 29 ~CPnCGe~~I~Rc 41 (61)
T COG2888 29 PCPNCGEVEIYRC 41 (61)
T ss_pred eCCCCCceeeehh
Confidence 566666 444433
No 147
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.46 E-value=3.8 Score=43.46 Aligned_cols=39 Identities=18% Similarity=0.416 Sum_probs=32.1
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAI 178 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i 178 (361)
+.-.|.+|...+-...++..+|||.|..+|+..++....
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHccc
Confidence 345799999887766777889999999999999887643
No 148
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=66.81 E-value=2.4 Score=44.16 Aligned_cols=29 Identities=24% Similarity=0.844 Sum_probs=20.9
Q ss_pred ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcce
Q 018073 256 RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (361)
Q Consensus 256 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~I 309 (361)
+|+|.||..|.+.. +....+.||+|+.+.
T Consensus 660 kC~H~FC~~Cvq~r-------------------------~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 660 KCGHVFCEECVQTR-------------------------YETRQRKCPKCNAAF 688 (698)
T ss_pred hcchHHHHHHHHHH-------------------------HHHhcCCCCCCCCCC
Confidence 79999999996321 112238999999875
No 149
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=66.68 E-value=22 Score=22.63 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=29.5
Q ss_pred HHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHhhh
Q 018073 81 EDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWFA 117 (361)
Q Consensus 81 ~~i~~v~~~l-~i~~~~a~~LL~~~~w~~~~l~e~~~~ 117 (361)
+.|..+.+++ +++++.....|+.+++|++..++.+..
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 5677777777 568889999999999999998887654
No 150
>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=65.05 E-value=8.7 Score=32.35 Aligned_cols=86 Identities=24% Similarity=0.563 Sum_probs=48.9
Q ss_pred ccccccccccccCCccccc------cCCCccc------HhhHHHHHHhhhcCC----------------------CCeee
Q 018073 141 EMTCGICFENYPSDRLLAA------ACGHPFC------SSCWTGYISTAINDG----------------------PGCLM 186 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l------~CgH~fC------~~Cl~~~i~~~i~~~----------------------~~~~~ 186 (361)
..+|+||++ +|.+.+..+ +|.-+.| .+||.+|-.+..+.. .....
T Consensus 2 d~~CpICme-~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (162)
T PF07800_consen 2 DVTCPICME-HPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE 80 (162)
T ss_pred CccCceecc-CCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence 467999997 454433221 3444444 578888877543221 11236
Q ss_pred eccCCCcCCCccchhHHhhcCChHHHHHHHHHHHHHHHhhCCCccccCCCCCCcceee
Q 018073 187 LRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (361)
Q Consensus 187 i~CP~~~C~~~i~~~~i~~ll~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~ 244 (361)
+.|| .|+..|.--.+-. . .+.|+ |.+.+-|+.-+|.+...+
T Consensus 81 L~CP--LCRG~V~GWtvve----~---------AR~~L--N~K~RsC~~e~C~F~GtY 121 (162)
T PF07800_consen 81 LACP--LCRGEVKGWTVVE----P---------ARRFL--NAKKRSCSQESCSFSGTY 121 (162)
T ss_pred ccCc--cccCceeceEEch----H---------HHHHh--ccCCccCcccccccccCH
Confidence 8898 8887663322210 1 12233 345678999899876544
No 151
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=64.98 E-value=1.5 Score=41.06 Aligned_cols=28 Identities=18% Similarity=0.371 Sum_probs=20.2
Q ss_pred CCCCCCCccee-ecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (361)
.+||+|+..|. |.-.=|...|. .|+|+|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp-~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICE-QCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCC-CCCCCc
Confidence 67888888776 33445677887 688876
No 152
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=64.61 E-value=1.6 Score=29.10 Aligned_cols=34 Identities=29% Similarity=0.787 Sum_probs=27.8
Q ss_pred CccccccccccccCCccccc-cCCCcccHhhHHHH
Q 018073 140 EEMTCGICFENYPSDRLLAA-ACGHPFCSSCWTGY 173 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~~ 173 (361)
..++|.+|-..++...+... -||.--|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 35789999999887777665 49999999999853
No 153
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=64.58 E-value=6.5 Score=22.96 Aligned_cols=21 Identities=24% Similarity=0.833 Sum_probs=14.2
Q ss_pred CCCCCCcceeecCCCCceeec
Q 018073 301 PCPRCKRPIEKNQGCMHMTCT 321 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~ 321 (361)
.||.|+..+.+..|=-+..|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999998888887
No 154
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=64.56 E-value=1.8 Score=45.16 Aligned_cols=16 Identities=25% Similarity=0.652 Sum_probs=9.5
Q ss_pred cCCCcccHhhHHHHHH
Q 018073 160 ACGHPFCSSCWTGYIS 175 (361)
Q Consensus 160 ~CgH~fC~~Cl~~~i~ 175 (361)
.|+|+||..|+..|-.
T Consensus 143 ~c~H~FC~~Ci~sWsR 158 (1134)
T KOG0825|consen 143 HTAHYFCEECVGSWSR 158 (1134)
T ss_pred ccccccHHHHhhhhhh
Confidence 3666666666665554
No 155
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=64.40 E-value=6.1 Score=27.94 Aligned_cols=29 Identities=34% Similarity=0.762 Sum_probs=19.2
Q ss_pred hcCCCCCCCcceeec---CCCCceeecCCCccc
Q 018073 298 NSKPCPRCKRPIEKN---QGCMHMTCTPPCKFE 327 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~---~GCnhm~C~~~C~~~ 327 (361)
+.|+||-|+..+.+. +|=-...|. +|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~-~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCN-GCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcC-CCCcC
Confidence 459999999766533 554456666 56664
No 156
>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=64.30 E-value=2.8 Score=28.34 Aligned_cols=23 Identities=26% Similarity=0.752 Sum_probs=13.7
Q ss_pred CceEEe-ccCCccccccCCcCCCC
Q 018073 250 NYDVTC-RCSYSFCWNCTEEAHRP 272 (361)
Q Consensus 250 ~~~v~C-~C~~~fC~~C~~~~H~~ 272 (361)
.....| .|+..||..|-.-.|..
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTT
T ss_pred CCeEECCCCCCccccCcChhhhcc
Confidence 356789 99999999998777764
No 157
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=64.18 E-value=1.3 Score=41.00 Aligned_cols=42 Identities=21% Similarity=0.441 Sum_probs=25.7
Q ss_pred CCccccCCCCCCcceeeecC------CCCceEEe-ccCCccccccCCcCCC
Q 018073 228 RKTKWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAHR 271 (361)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~ 271 (361)
+....|-. |+..+...+. .....-.| .|+..||..|..-.|.
T Consensus 360 ~ks~~Cf~--CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 360 PKSTHCFV--CQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred CCCcccee--ccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 34445653 6654443321 12345689 8999999999765553
No 158
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=63.98 E-value=6.7 Score=31.98 Aligned_cols=51 Identities=24% Similarity=0.626 Sum_probs=38.3
Q ss_pred CCccccccccccccCCcccccc---CCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 139 GEEMTCGICFENYPSDRLLAAA---CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~---CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
....+|.||-|... ++.+.-| ||=..|.-|....|...- ....|| .|+..+
T Consensus 78 ~~lYeCnIC~etS~-ee~FLKPneCCgY~iCn~Cya~LWK~~~------~ypvCP--vCkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSA-EERFLKPNECCGYSICNACYANLWKFCN------LYPVCP--VCKTSF 131 (140)
T ss_pred CCceeccCcccccc-hhhcCCcccccchHHHHHHHHHHHHHcc------cCCCCC--cccccc
Confidence 36789999998754 3333322 999999999999998754 256899 898765
No 159
>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=63.75 E-value=1.7 Score=40.64 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=22.4
Q ss_pred CCCCCCCcceeec-CCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~-~GCnhm~C~~~C~~~F 328 (361)
.+||+|+..|-+. -.=|.+.|. +|+|+|
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCP-KCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCC-CCCCcC
Confidence 7899999988743 445678998 799986
No 160
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.15 E-value=6.2 Score=35.07 Aligned_cols=54 Identities=19% Similarity=0.402 Sum_probs=41.9
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
..|.+|--++...+.+.|.|-|.|...|+......--.... -...+|| .|...|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTA-PaGyqCP--~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTA-PAGYQCP--CCSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCC-CCcccCC--CCCCcc
Confidence 35999998888788899999999999999988765433321 1357899 898865
No 161
>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=62.74 E-value=6.5 Score=26.37 Aligned_cols=47 Identities=17% Similarity=0.521 Sum_probs=24.8
Q ss_pred cccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCC
Q 018073 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~ 196 (361)
+.|+|-+..+. .......|.|.-|.+ +..|+....+.+ ..+|| .|++
T Consensus 3 L~CPls~~~i~-~P~Rg~~C~H~~CFD-l~~fl~~~~~~~----~W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR-IPVRGKNCKHLQCFD-LESFLESNQRTP----KWKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-S-SEEEETT--SS--EE-HHHHHHHHHHS-------B-T--TT--
T ss_pred eeCCCCCCEEE-eCccCCcCcccceEC-HHHHHHHhhccC----CeECc--CCcC
Confidence 56888876653 344566799998876 778888776654 47899 7864
No 162
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=62.43 E-value=4.1 Score=29.89 Aligned_cols=59 Identities=24% Similarity=0.674 Sum_probs=20.4
Q ss_pred cccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcce
Q 018073 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~I 309 (361)
.-|-. |+--|-.. ..+...|-| .|++..|..|. ++. ++..++-||+|+++.
T Consensus 10 qiCqi--CGD~VGl~-~~Ge~FVAC~eC~fPvCr~Cy----------EYE---------------rkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 10 QICQI--CGDDVGLT-ENGEVFVACHECAFPVCRPCY----------EYE---------------RKEGNQVCPQCKTRY 61 (80)
T ss_dssp -B-SS--S--B--B--SSSSB--S-SSS-----HHHH----------HHH---------------HHTS-SB-TTT--B-
T ss_pred ccccc--ccCccccC-CCCCEEEEEcccCCccchhHH----------HHH---------------hhcCcccccccCCCc
Confidence 34553 76665544 346677889 89998887664 222 123358999999999
Q ss_pred eecCCCCc
Q 018073 310 EKNQGCMH 317 (361)
Q Consensus 310 eK~~GCnh 317 (361)
.+..|+..
T Consensus 62 kr~kgsp~ 69 (80)
T PF14569_consen 62 KRHKGSPR 69 (80)
T ss_dssp ---TT---
T ss_pred ccccCCCC
Confidence 88887754
No 163
>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=62.27 E-value=5 Score=23.61 Aligned_cols=24 Identities=38% Similarity=0.819 Sum_probs=13.0
Q ss_pred CCCCCCCcceeec--CCCCceeecCCC
Q 018073 300 KPCPRCKRPIEKN--QGCMHMTCTPPC 324 (361)
Q Consensus 300 k~CP~C~~~IeK~--~GCnhm~C~~~C 324 (361)
++||+|+.+|++. +|=+...|. .|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~-rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP-RC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T-TT
T ss_pred CcCccCCCcceEeEecCCCCeECc-CC
Confidence 6899999999744 455555555 44
No 164
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.10 E-value=12 Score=35.65 Aligned_cols=43 Identities=23% Similarity=0.692 Sum_probs=29.2
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
....|.||.++. .+...++|||.-| |..-+ .+ ...|| .|...|
T Consensus 304 ~p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs--~~--------l~~CP--vCR~rI 346 (355)
T KOG1571|consen 304 QPDLCVVCLDEP--KSAVFVPCGHVCC--CTLCS--KH--------LPQCP--VCRQRI 346 (355)
T ss_pred CCCceEEecCCc--cceeeecCCcEEE--chHHH--hh--------CCCCc--hhHHHH
Confidence 356799999875 4578899999966 54322 21 24599 787654
No 165
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=61.46 E-value=5.5 Score=36.89 Aligned_cols=47 Identities=30% Similarity=0.613 Sum_probs=36.1
Q ss_pred CCccccccccccccC--CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCC
Q 018073 139 GEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~ 196 (361)
.....||||.+.+.. ..+..++|||..-..|++.++-. ..+|| .|..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~---------~y~CP--~C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE---------GYTCP--ICSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc---------CCCCC--cccc
Confidence 345669999987643 34456789999999999998865 26899 7887
No 166
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=61.31 E-value=7.6 Score=29.82 Aligned_cols=29 Identities=28% Similarity=0.784 Sum_probs=19.4
Q ss_pred cccCCCCCCcceeeecCCCCceEEe-ccCCcc
Q 018073 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (361)
.+||. |++.+.+..+.....+.| .|.+.+
T Consensus 2 ~FCP~--Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCPT--CGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccCC--CCCEEEEecCCeEeeEEcCCCCcee
Confidence 47995 999887775544456666 665544
No 167
>PRK04023 DNA polymerase II large subunit; Validated
Probab=61.17 E-value=6.7 Score=42.41 Aligned_cols=32 Identities=25% Similarity=0.599 Sum_probs=20.5
Q ss_pred CCCccccCCCCCCcceeeecCCCCceEEe-ccCC-----ccccccCCc
Q 018073 227 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSY-----SFCWNCTEE 268 (361)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~-----~fC~~C~~~ 268 (361)
....+.||. |+... ....| .||. .||..|+..
T Consensus 623 EVg~RfCps--CG~~t--------~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 623 EIGRRKCPS--CGKET--------FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred cccCccCCC--CCCcC--------CcccCCCCCCCCCcceeCccccCc
Confidence 345678995 88642 34678 6875 377777543
No 168
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=61.15 E-value=10 Score=37.20 Aligned_cols=12 Identities=33% Similarity=0.969 Sum_probs=6.5
Q ss_pred CCCCCccccccc
Q 018073 136 FPDGEEMTCGIC 147 (361)
Q Consensus 136 ~~~~~~~~C~IC 147 (361)
.|.+..|.|+-=
T Consensus 189 LPDSTDFVCGTL 200 (458)
T PF10446_consen 189 LPDSTDFVCGTL 200 (458)
T ss_pred CCCcccccCCCc
Confidence 344556666643
No 169
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=61.06 E-value=3.8 Score=31.63 Aligned_cols=32 Identities=31% Similarity=0.752 Sum_probs=24.8
Q ss_pred CCCccccccccccccCCccccccCCCcccHhh
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSC 169 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 169 (361)
...+|+|.-||-....+.+....=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45689999999776666665555689999988
No 170
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.60 E-value=2.3 Score=38.72 Aligned_cols=35 Identities=34% Similarity=0.738 Sum_probs=27.6
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceecccccc-ccccCC
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ-WSDHGE 341 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~-~~~h~~ 341 (361)
.+|+-|--.+++ -.|+ .|||-|||.|+-. |.....
T Consensus 216 ~kC~lC~e~~~~------ps~t-~CgHlFC~~Cl~~~~t~~k~ 251 (271)
T COG5574 216 YKCFLCLEEPEV------PSCT-PCGHLFCLSCLLISWTKKKY 251 (271)
T ss_pred cceeeeecccCC------cccc-cccchhhHHHHHHHHHhhcc
Confidence 579998888863 5688 6999999999977 876553
No 171
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.38 E-value=2.6 Score=42.96 Aligned_cols=36 Identities=22% Similarity=0.655 Sum_probs=27.9
Q ss_pred ccccccccccccCC--ccccccCCCcccHhhHHHHHHh
Q 018073 141 EMTCGICFENYPSD--RLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 141 ~~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
.+.|+||+..|-.. .++++.|||..|+-|+......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 35699998766433 4678899999999999876654
No 172
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=60.24 E-value=36 Score=24.04 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhh
Q 018073 76 RQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (361)
Q Consensus 76 ~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~ 116 (361)
...+.+.|..++...++...-+..+|...+||.++.+..|.
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45678889999999999999999999999999999887764
No 173
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.00 E-value=6.1 Score=43.76 Aligned_cols=10 Identities=20% Similarity=0.238 Sum_probs=4.9
Q ss_pred eecccccccc
Q 018073 328 FCWLCLGQWS 337 (361)
Q Consensus 328 FCw~C~~~~~ 337 (361)
||-.|+.+..
T Consensus 711 ~CP~CGtplv 720 (1337)
T PRK14714 711 ECPRCDVELT 720 (1337)
T ss_pred cCCCCCCccc
Confidence 4555554443
No 174
>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=59.64 E-value=6 Score=32.02 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=19.1
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
+.||+|++..---.- +.++|. +||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP-~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSP-YTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCC-CcCCcc
Confidence 689999987762222 889997 576653
No 175
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=59.61 E-value=7.1 Score=30.35 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=20.1
Q ss_pred cCCCCCCCcce---eecCCCCceeecCCCccce
Q 018073 299 SKPCPRCKRPI---EKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 299 ~k~CP~C~~~I---eK~~GCnhm~C~~~C~~~F 328 (361)
.-.||+|+... .+..|=-|..|. .||+.+
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~-~CG~y~ 52 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCG-NCGLYT 52 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECC-CCCCcc
Confidence 35799999432 233466799998 788774
No 176
>PF12773 DZR: Double zinc ribbon
Probab=59.24 E-value=4.8 Score=26.71 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=8.5
Q ss_pred cCCCCCCCccee
Q 018073 299 SKPCPRCKRPIE 310 (361)
Q Consensus 299 ~k~CP~C~~~Ie 310 (361)
.+.||+|++++.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 467777777776
No 177
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=58.84 E-value=6.3 Score=26.13 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=19.9
Q ss_pred cCCCC--CCCcceeecCCCCceeecCCCcc
Q 018073 299 SKPCP--RCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 299 ~k~CP--~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
-+.|| +|+.-+.-..--+..+|. +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CG-KCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCG-KCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEET-TTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCC-Cccc
Confidence 47899 999987666666789998 7875
No 178
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=58.56 E-value=3.2 Score=44.05 Aligned_cols=11 Identities=9% Similarity=0.172 Sum_probs=0.0
Q ss_pred cCCcceEeeCH
Q 018073 62 RHQLNYTVLTE 72 (361)
Q Consensus 62 ~~~~~~~~l~~ 72 (361)
++...|..|=.
T Consensus 709 ~R~~L~nTLVN 719 (787)
T PF03115_consen 709 NRVTLFNTLVN 719 (787)
T ss_dssp -----------
T ss_pred hHHHHHHHHHH
Confidence 44444444433
No 179
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=58.04 E-value=13 Score=25.11 Aligned_cols=37 Identities=14% Similarity=0.170 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhhh
Q 018073 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFA 117 (361)
Q Consensus 81 ~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~~ 117 (361)
+.|..++...++...-+...|...+||.++.+..|..
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5688999999999999999999999999998877653
No 180
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.97 E-value=8.6 Score=36.41 Aligned_cols=49 Identities=29% Similarity=0.636 Sum_probs=33.1
Q ss_pred CCCccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
......|.||.+.+. -...++|+|..|.-|--..-..-. .-.|| .|+..
T Consensus 58 DEen~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~RlRALY~-------~K~C~--~CrTE 106 (493)
T COG5236 58 DEENMNCQICAGSTT--YSARYPCGHQICHACAVRLRALYM-------QKGCP--LCRTE 106 (493)
T ss_pred ccccceeEEecCCce--EEEeccCCchHHHHHHHHHHHHHh-------ccCCC--ccccc
Confidence 445788999998653 345679999999999765432211 23577 78764
No 181
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=57.59 E-value=8 Score=30.84 Aligned_cols=28 Identities=21% Similarity=0.645 Sum_probs=20.3
Q ss_pred CCCCCCCcceee--cCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK--~~GCnhm~C~~~C~~~F 328 (361)
+-||+|+.++.- .++=+-+.|+ +||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~-kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCR-KCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECC-CCCcch
Confidence 689999988874 1222388998 788865
No 182
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=56.70 E-value=3.4 Score=37.95 Aligned_cols=28 Identities=21% Similarity=0.554 Sum_probs=23.5
Q ss_pred CCCCCCCccee-ecCCCCceeecCCCccce
Q 018073 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~F 328 (361)
.+||+|+..+- |.-+=|...|. +|+|+|
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp-~c~~h~ 57 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCP-KCGHHM 57 (294)
T ss_pred eECCCccceeeHHHHHhhhhccc-ccCccc
Confidence 78999999887 55677888998 799987
No 183
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=56.58 E-value=8.7 Score=30.14 Aligned_cols=26 Identities=31% Similarity=0.986 Sum_probs=17.8
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
-+||+|+.-.-=..|=+ +.|. .|+|+
T Consensus 3 p~CP~C~seytY~dg~~-~iCp-eC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP-SCLYE 28 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc-ccccc
Confidence 57999998776555544 7787 45554
No 184
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=56.11 E-value=8.7 Score=35.58 Aligned_cols=26 Identities=42% Similarity=0.954 Sum_probs=21.5
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCCc
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (361)
.++|+.|+.+|+|. +|=+--.|. .|.
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP-~CQ 272 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCP-VCQ 272 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCC-CCC
Confidence 47999999999966 888888887 674
No 185
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=55.31 E-value=8.9 Score=31.30 Aligned_cols=24 Identities=33% Similarity=0.798 Sum_probs=17.5
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 333 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~ 333 (361)
.+-||.|+.|..+- =|.-||-+|+
T Consensus 28 ~~hCp~Cg~PLF~K-----------dG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRK-----------DGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceee-----------CCeEECCCCC
Confidence 37899999999753 3556666666
No 186
>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=55.09 E-value=9.9 Score=24.62 Aligned_cols=34 Identities=18% Similarity=0.478 Sum_probs=16.5
Q ss_pred cccccccccCCcccc-ccCCCcccHhhHHHHHHhh
Q 018073 144 CGICFENYPSDRLLA-AACGHPFCSSCWTGYISTA 177 (361)
Q Consensus 144 C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~~i~~~ 177 (361)
|.+|-+-+.....-. ..|+=.+...|++.|++.+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~ 35 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR 35 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC
Confidence 566765543222211 2477789999999999874
No 187
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=54.58 E-value=13 Score=25.52 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=19.1
Q ss_pred CCCCCCCcceeecCCC--CceeecCCCccce
Q 018073 300 KPCPRCKRPIEKNQGC--MHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~~IeK~~GC--nhm~C~~~C~~~F 328 (361)
..||.|+..|+-...= -.+.|. .||..|
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp-~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICD-ECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCC-CCCCEE
Confidence 4799999988865422 257787 677665
No 188
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=54.10 E-value=51 Score=35.82 Aligned_cols=16 Identities=13% Similarity=0.283 Sum_probs=8.7
Q ss_pred CcceEe---eCHHHHHHHH
Q 018073 64 QLNYTV---LTEADIRQRQ 79 (361)
Q Consensus 64 ~~~~~~---l~~~~i~~~~ 79 (361)
+..|++ -|.+++...+
T Consensus 417 elPftf~~P~s~eel~~lL 435 (840)
T PF04147_consen 417 ELPFTFPCPSSHEELLELL 435 (840)
T ss_pred CCCceecCCCCHHHHHHHH
Confidence 445664 4566665554
No 189
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.40 E-value=14 Score=25.34 Aligned_cols=32 Identities=25% Similarity=0.916 Sum_probs=25.2
Q ss_pred cccccccccccc-CCcccccc-CCCcccHhhHHH
Q 018073 141 EMTCGICFENYP-SDRLLAAA-CGHPFCSSCWTG 172 (361)
Q Consensus 141 ~~~C~IC~e~~~-~~~~~~l~-CgH~fC~~Cl~~ 172 (361)
...|++|-+.|. .++++..+ ||-.+.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999985 45666655 999999999964
No 190
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.08 E-value=9.7 Score=24.22 Aligned_cols=33 Identities=33% Similarity=0.732 Sum_probs=19.4
Q ss_pred CCCCCCcceeecCCCCceeecCCCccceeccccccccccC
Q 018073 301 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (361)
.||+|+..++...- . .=...-|-.|++-|-+.+
T Consensus 1 ~CP~C~~~l~~~~~-~------~~~id~C~~C~G~W~d~~ 33 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-G------DVEIDVCPSCGGIWFDAG 33 (41)
T ss_pred CcCCCCcccceEEE-C------CEEEEECCCCCeEEccHH
Confidence 59999998875433 1 122333456777775443
No 191
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=52.61 E-value=14 Score=33.71 Aligned_cols=20 Identities=20% Similarity=0.566 Sum_probs=15.8
Q ss_pred CCccccCCCCCCcceeeecC
Q 018073 228 RKTKWCPAPGCDYAVDFVVG 247 (361)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~ 247 (361)
...+-||+|+|.++|...+.
T Consensus 121 S~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred cccccCCCCCCcceEEeCCc
Confidence 34678999999999977543
No 192
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.55 E-value=11 Score=39.98 Aligned_cols=36 Identities=22% Similarity=0.695 Sum_probs=30.0
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccc-----eecccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (361)
+-.||+|..+..-...=|.|.|. .||++ .|..||+.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 34799999888766555999998 89988 99999987
No 193
>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=51.99 E-value=18 Score=23.17 Aligned_cols=12 Identities=33% Similarity=1.146 Sum_probs=9.0
Q ss_pred CCCCCCCc-ceee
Q 018073 300 KPCPRCKR-PIEK 311 (361)
Q Consensus 300 k~CP~C~~-~IeK 311 (361)
..||+|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 68888888 6655
No 194
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=51.98 E-value=11 Score=24.94 Aligned_cols=33 Identities=30% Similarity=0.615 Sum_probs=22.6
Q ss_pred cccccccccCCccccccCCC-----cccHhhHHHHHHh
Q 018073 144 CGICFENYPSDRLLAAACGH-----PFCSSCWTGYIST 176 (361)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH-----~fC~~Cl~~~i~~ 176 (361)
|-||++.-..+.....+|+- .....||..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 67999886655545556643 5789999999988
No 195
>PHA02929 N1R/p28-like protein; Provisional
Probab=51.98 E-value=7.4 Score=35.36 Aligned_cols=40 Identities=20% Similarity=0.553 Sum_probs=27.4
Q ss_pred cCCCCCCCcceeecCCCCc---eeecCCCccceeccccccccccC
Q 018073 299 SKPCPRCKRPIEKNQGCMH---MTCTPPCKFEFCWLCLGQWSDHG 340 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnh---m~C~~~C~~~FCw~C~~~~~~h~ 340 (361)
...||-|.-.+.....-+. +.- .|+|.||..|...|....
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~~~ 216 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKKEK 216 (238)
T ss_pred CCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHhcC
Confidence 4689999988764432221 222 499999999999997543
No 196
>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=50.24 E-value=18 Score=23.23 Aligned_cols=21 Identities=24% Similarity=0.596 Sum_probs=10.7
Q ss_pred CCCCCCcc-eeecCCCCceeec
Q 018073 301 PCPRCKRP-IEKNQGCMHMTCT 321 (361)
Q Consensus 301 ~CP~C~~~-IeK~~GCnhm~C~ 321 (361)
.||.|+.. |.-...=.-+.|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~ 23 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCP 23 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEET
T ss_pred CCcCCcCCceEEcCCCCeEECC
Confidence 47777764 2333333344555
No 197
>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=50.12 E-value=10 Score=26.92 Aligned_cols=36 Identities=19% Similarity=0.371 Sum_probs=20.1
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~ 337 (361)
+..|+.|++..- ---..-.|+ .||.-||-.|.....
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr-~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCR-NCGRVVCSSCSSQRI 44 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-T-TT--EEECCCS-EEE
T ss_pred CCcCcCcCCcCC--CceeeEccC-CCCCEECCchhCCEE
Confidence 578999999883 335567798 799999999986654
No 198
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=50.09 E-value=6.6 Score=27.22 Aligned_cols=41 Identities=32% Similarity=0.511 Sum_probs=30.6
Q ss_pred CCCCCCCcceeec--CCCCceeecCCCccceeccccccccccCC
Q 018073 300 KPCPRCKRPIEKN--QGCMHMTCTPPCKFEFCWLCLGQWSDHGE 341 (361)
Q Consensus 300 k~CP~C~~~IeK~--~GCnhm~C~~~C~~~FCw~C~~~~~~h~~ 341 (361)
+.||-|++...-. +-=|+-+|+ .|+...|-+||-.=.+|-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT-~Ck~~VCnlCGFNP~Phl~ 45 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCT-ECKSQVCNLCGFNPTPHLT 45 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHH-HHhhhhhcccCCCCCcccc
Confidence 5799999877311 234899999 7999999999855555543
No 199
>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=49.87 E-value=3.4 Score=28.81 Aligned_cols=12 Identities=50% Similarity=1.187 Sum_probs=10.3
Q ss_pred CCCCCCCcceee
Q 018073 300 KPCPRCKRPIEK 311 (361)
Q Consensus 300 k~CP~C~~~IeK 311 (361)
|-||.||.+|.-
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 679999999973
No 200
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=49.58 E-value=13 Score=34.43 Aligned_cols=26 Identities=46% Similarity=1.019 Sum_probs=18.0
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCCc
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (361)
.++||.|+.+|+|. +|=.--.|. .|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp-~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP-QCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC-CCc
Confidence 47999999999855 664444554 443
No 201
>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=49.54 E-value=14 Score=25.03 Aligned_cols=42 Identities=17% Similarity=0.393 Sum_probs=23.3
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
.+.||.|...+.... |..++...=.... ..+.|| .|...+..
T Consensus 2 ~f~CP~C~~~~~~~~--------------L~~H~~~~H~~~~--~~v~CP--iC~~~~~~ 43 (54)
T PF05605_consen 2 SFTCPYCGKGFSESS--------------LVEHCEDEHRSES--KNVVCP--ICSSRVTD 43 (54)
T ss_pred CcCCCCCCCccCHHH--------------HHHHHHhHCcCCC--CCccCC--Cchhhhhh
Confidence 478999987543211 2344443322221 268999 88865443
No 202
>PF14149 YhfH: YhfH-like protein
Probab=49.37 E-value=1.3 Score=27.63 Aligned_cols=26 Identities=31% Similarity=0.832 Sum_probs=20.9
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCC
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPC 324 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C 324 (361)
..|.||.||..|+-..-|-.++|. .|
T Consensus 12 p~K~C~~CG~~i~EQ~E~Y~n~C~-~C 37 (37)
T PF14149_consen 12 PPKKCTECGKEIEEQAECYGNECD-RC 37 (37)
T ss_pred CCcccHHHHHHHHHHHHHHhCcCC-CC
Confidence 359999999999887777777776 45
No 203
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.21 E-value=13 Score=33.56 Aligned_cols=38 Identities=13% Similarity=0.168 Sum_probs=30.5
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcC
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAIND 180 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~ 180 (361)
.--|++|+..+ .+++..+=||.||++|+.+||..+-++
T Consensus 43 FdcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 43 FDCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred cceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 34588898766 567777889999999999999887543
No 204
>PRK11827 hypothetical protein; Provisional
Probab=48.97 E-value=16 Score=25.61 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=20.4
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
-.||.|+.+.+-..+=+...|. .|+-.
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~-~~~la 35 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICK-LDNLA 35 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECC-ccCee
Confidence 6899999998866555678888 56643
No 205
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=48.94 E-value=17 Score=22.09 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=16.0
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
+.|++|+....-+.-=..+.|. .|+..
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~-~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCI-FCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcc-cCCcE
Confidence 6788888766543333355665 45543
No 206
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=48.68 E-value=62 Score=20.54 Aligned_cols=38 Identities=11% Similarity=0.225 Sum_probs=29.5
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHHcCCChHHHHHHhhh
Q 018073 80 EEDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWFA 117 (361)
Q Consensus 80 ~~~i~~v~~~l-~i~~~~a~~LL~~~~w~~~~l~e~~~~ 117 (361)
.+.|..+.+++ +++...++..|+.++++++..++.+..
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 34566666666 568889999999999999998877654
No 207
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=48.56 E-value=9.6 Score=28.68 Aligned_cols=48 Identities=23% Similarity=0.546 Sum_probs=33.6
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceeccccccccccCCCCCCcccCCCccch
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYETA 355 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~~~~g~~y~C~~~~~~ 355 (361)
.-||.|+.| ...|.-+... |++.|=..|...|-.... +.-.|+-....
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~--C~H~FH~hCI~kWl~~~~---~~~~CPmCR~~ 80 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK--CSHNFHMHCILKWLSTQS---SKGQCPMCRQP 80 (85)
T ss_pred cCCCCccCC---CCCCceeecc--CccHHHHHHHHHHHcccc---CCCCCCCcCCe
Confidence 458888887 3567777775 999999999999976542 12356655443
No 208
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=48.51 E-value=13 Score=31.83 Aligned_cols=11 Identities=9% Similarity=0.238 Sum_probs=5.1
Q ss_pred HHHHHHHHHHH
Q 018073 73 ADIRQRQEEDI 83 (361)
Q Consensus 73 ~~i~~~~~~~i 83 (361)
+++.+.+.+.+
T Consensus 63 ~dFeref~kmm 73 (170)
T PF04050_consen 63 EDFEREFQKMM 73 (170)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 34544444443
No 209
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.83 E-value=18 Score=33.01 Aligned_cols=55 Identities=27% Similarity=0.568 Sum_probs=38.1
Q ss_pred CccccccccccccCCcc--ccccCC-----CcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 140 EEMTCGICFENYPSDRL--LAAACG-----HPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~Cg-----H~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
.+-.|=|||.+-..+.. ..-||. |-....|+..||..+-. |.....+.|| .|...
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~-~n~~q~V~C~--QCqTE 80 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQR-GNPLQTVSCP--QCQTE 80 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhc-CCCCceeech--hhcch
Confidence 35679999987432222 123564 55899999999988766 3334689999 78864
No 210
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=47.69 E-value=14 Score=19.08 Aligned_cols=16 Identities=44% Similarity=0.978 Sum_probs=12.9
Q ss_pred cccccCCcCCCCCCch
Q 018073 261 FCWNCTEEAHRPVDCD 276 (361)
Q Consensus 261 fC~~C~~~~H~~~~C~ 276 (361)
.|++|++.-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5899999999876664
No 211
>PRK10220 hypothetical protein; Provisional
Probab=47.68 E-value=15 Score=28.86 Aligned_cols=26 Identities=23% Similarity=0.674 Sum_probs=17.3
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
-+||+|..-.-=..|= ...|. .|+|+
T Consensus 4 P~CP~C~seytY~d~~-~~vCp-eC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICP-ECAHE 29 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECC-cccCc
Confidence 5899999877655553 37776 45554
No 212
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.47 E-value=5.2 Score=37.26 Aligned_cols=54 Identities=24% Similarity=0.755 Sum_probs=37.9
Q ss_pred CCCccccCCCCCCcceeeecCCCCceEEeccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCC
Q 018073 227 NRKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCK 306 (361)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~ 306 (361)
++.+-+|-. |+..|..- + ..+ .|++.||..|... |. .|.||.|.
T Consensus 87 ~p~VHfCd~--Cd~PI~IY-G---RmI--PCkHvFCl~CAr~-~~---------------------------dK~Cp~C~ 130 (389)
T KOG2932|consen 87 GPRVHFCDR--CDFPIAIY-G---RMI--PCKHVFCLECARS-DS---------------------------DKICPLCD 130 (389)
T ss_pred CcceEeecc--cCCcceee-e---ccc--ccchhhhhhhhhc-Cc---------------------------cccCcCcc
Confidence 455778874 88776432 1 111 5899999999732 22 18999999
Q ss_pred cceeecCCCC
Q 018073 307 RPIEKNQGCM 316 (361)
Q Consensus 307 ~~IeK~~GCn 316 (361)
-.|+|.+-|.
T Consensus 131 d~VqrIeq~~ 140 (389)
T KOG2932|consen 131 DRVQRIEQIM 140 (389)
T ss_pred cHHHHHHHhc
Confidence 9999998774
No 213
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=47.34 E-value=7.1 Score=32.57 Aligned_cols=8 Identities=25% Similarity=0.522 Sum_probs=3.8
Q ss_pred CcceEeeC
Q 018073 64 QLNYTVLT 71 (361)
Q Consensus 64 ~~~~~~l~ 71 (361)
+.+|++.+
T Consensus 43 ~S~~ki~s 50 (167)
T PF05320_consen 43 QSDYKIES 50 (167)
T ss_pred ccchhhhh
Confidence 44555533
No 214
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=47.14 E-value=13 Score=26.43 Aligned_cols=17 Identities=24% Similarity=0.727 Sum_probs=12.2
Q ss_pred cccHhhHHHHHHhhhcC
Q 018073 164 PFCSSCWTGYISTAIND 180 (361)
Q Consensus 164 ~fC~~Cl~~~i~~~i~~ 180 (361)
-||+.||..|+..+-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999876654
No 215
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=46.77 E-value=19 Score=33.40 Aligned_cols=36 Identities=22% Similarity=0.554 Sum_probs=26.7
Q ss_pred HHHHHHhhcCCCCCCCcceeecCCCCceeecCCCccce
Q 018073 291 NMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 291 ~~~~i~~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
-..|.. +.|-||+|+.+.+-..|=-.+.|. .|++.+
T Consensus 104 l~~w~~-~~RFCg~CG~~~~~~~~g~~~~C~-~cg~~~ 139 (279)
T COG2816 104 LLEWYR-SHRFCGRCGTKTYPREGGWARVCP-KCGHEH 139 (279)
T ss_pred HHHHHh-hCcCCCCCCCcCccccCceeeeCC-CCCCcc
Confidence 345543 348999999999988777778887 687654
No 216
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=46.59 E-value=34 Score=23.22 Aligned_cols=37 Identities=22% Similarity=0.106 Sum_probs=31.3
Q ss_pred eeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcC
Q 018073 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYN 105 (361)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (361)
-|+.++|.+.+.--+.+++..|+|+...-.-+-+.++
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 4788999999999999999999999888777776654
No 217
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=46.55 E-value=16 Score=38.17 Aligned_cols=38 Identities=13% Similarity=0.205 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHH------HHhCCCHHHHHHHHHHcCCChHH
Q 018073 73 ADIRQRQEEDITRIS------TVLSISKVAASILLRFYNWSVSK 110 (361)
Q Consensus 73 ~~i~~~~~~~i~~v~------~~l~i~~~~a~~LL~~~~w~~~~ 110 (361)
.+..+++...|+.+- .+..|..+.|.+-...-+.++..
T Consensus 313 sE~l~rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~ 356 (822)
T KOG2141|consen 313 SEQLQRLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTS 356 (822)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHH
Confidence 445555555554433 33334444455444444444433
No 218
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.36 E-value=20 Score=30.75 Aligned_cols=57 Identities=25% Similarity=0.636 Sum_probs=37.0
Q ss_pred ccccccccccccCCc-----c-ccccCCCcccHhhHHHHHHhhhcCCCCe--eeeccCCCcCCCccch
Q 018073 141 EMTCGICFENYPSDR-----L-LAAACGHPFCSSCWTGYISTAINDGPGC--LMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~-----~-~~l~CgH~fC~~Cl~~~i~~~i~~~~~~--~~i~CP~~~C~~~i~~ 200 (361)
...|+||+.. ..+- + -...||..|..-|+..|++.-+....+. ..=.|| -|..+|..
T Consensus 165 ~~~cgicyay-qldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pial 229 (234)
T KOG3268|consen 165 LGACGICYAY-QLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIAL 229 (234)
T ss_pred hhcccceeee-ecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCccee
Confidence 4567777742 1111 1 1346999999999999998877655422 233688 78877654
No 219
>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=45.96 E-value=19 Score=24.74 Aligned_cols=43 Identities=30% Similarity=0.818 Sum_probs=30.8
Q ss_pred ccccccccccCCccccccCC--CcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 143 TCGICFENYPSDRLLAAACG--HPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
.|..|-.+++.+..-..-|. ..||.+|....+.. .|| .|+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~-----------~CP--NCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG-----------VCP--NCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC-----------cCc--CCCCcc
Confidence 48889888877664445565 47999999877632 488 787654
No 220
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=45.84 E-value=34 Score=22.30 Aligned_cols=28 Identities=18% Similarity=0.477 Sum_probs=17.3
Q ss_pred hcCCCCCCCcc-eeecCCCCceeecCCCcc
Q 018073 298 NSKPCPRCKRP-IEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 298 ~~k~CP~C~~~-IeK~~GCnhm~C~~~C~~ 326 (361)
+.-.||+|+.. +-+..+=..-.|. .|++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~-~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCK-ACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECC-CCCC
Confidence 44579999974 3344444556676 5765
No 221
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=45.80 E-value=11 Score=23.81 Aligned_cols=10 Identities=40% Similarity=1.404 Sum_probs=5.2
Q ss_pred CCCCCCCcce
Q 018073 300 KPCPRCKRPI 309 (361)
Q Consensus 300 k~CP~C~~~I 309 (361)
+.||+|+..+
T Consensus 2 ~~CP~Cg~~l 11 (39)
T PF01396_consen 2 EKCPKCGGPL 11 (39)
T ss_pred cCCCCCCcee
Confidence 3566665443
No 222
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=45.70 E-value=17 Score=33.80 Aligned_cols=26 Identities=42% Similarity=0.962 Sum_probs=18.3
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCCc
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (361)
.++||.|+.+|+|. +|=.-..|. .|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCP-RCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECc-CCC
Confidence 46999999999855 665555554 453
No 223
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.05 E-value=14 Score=41.10 Aligned_cols=33 Identities=24% Similarity=0.585 Sum_probs=25.9
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccce-----eccccccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEF-----CWLCLGQWSD 338 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~F-----Cw~C~~~~~~ 338 (361)
.++||+|+..+... .|. .||... |-.|+.....
T Consensus 667 ~rkCPkCG~~t~~~------fCP-~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 667 RRRCPSCGTETYEN------RCP-DCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EEECCCCCCccccc------cCc-ccCCcCCCceeCccCCCccCC
Confidence 37999999987532 898 799774 9999987654
No 224
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.70 E-value=17 Score=33.67 Aligned_cols=25 Identities=44% Similarity=0.923 Sum_probs=18.1
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCC
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPC 324 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C 324 (361)
.++||+|+.+|+|. +|=.-..|. .|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCP-QC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECC-CC
Confidence 36999999999865 765555554 45
No 225
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=44.65 E-value=43 Score=35.05 Aligned_cols=7 Identities=14% Similarity=0.776 Sum_probs=3.0
Q ss_pred HHHHhhh
Q 018073 172 GYISTAI 178 (361)
Q Consensus 172 ~~i~~~i 178 (361)
.|+.+++
T Consensus 322 ~yvaskL 328 (622)
T PF02724_consen 322 SYVASKL 328 (622)
T ss_pred hhhHhhc
Confidence 3444443
No 226
>PRK10445 endonuclease VIII; Provisional
Probab=44.50 E-value=18 Score=33.45 Aligned_cols=26 Identities=31% Similarity=0.653 Sum_probs=18.8
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCCc
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (361)
.++||.|+.+|++. +|=.-..|. .|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP-~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCP-GCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECC-CCc
Confidence 37999999999854 775555565 453
No 227
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.44 E-value=17 Score=33.65 Aligned_cols=25 Identities=36% Similarity=0.894 Sum_probs=17.7
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCC
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPC 324 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C 324 (361)
.++||+|+.+|++. +|=.--.|. .|
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP-~C 270 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCP-HC 270 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECc-CC
Confidence 47999999999854 664445554 44
No 228
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=44.18 E-value=17 Score=26.92 Aligned_cols=17 Identities=29% Similarity=0.804 Sum_probs=16.0
Q ss_pred cCCCcccHhhHHHHHHh
Q 018073 160 ACGHPFCSSCWTGYIST 176 (361)
Q Consensus 160 ~CgH~fC~~Cl~~~i~~ 176 (361)
.|.|.|-.-|+.+|+.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 39999999999999988
No 229
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=44.14 E-value=17 Score=39.95 Aligned_cols=60 Identities=23% Similarity=0.619 Sum_probs=40.6
Q ss_pred ccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCccee
Q 018073 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (361)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 310 (361)
-|-. |+--|... ..+...|-| .|+...|..|- ++.+ +..++-||+|++...
T Consensus 19 iCqI--CGD~vg~~-~~Ge~FVAC~eC~FPVCrpCY----------EYEr---------------~eG~q~CPqCktrYk 70 (1079)
T PLN02638 19 VCQI--CGDNVGKT-VDGEPFVACDVCAFPVCRPCY----------EYER---------------KDGNQSCPQCKTKYK 70 (1079)
T ss_pred eeee--cccccCcC-CCCCEEEEeccCCCccccchh----------hhhh---------------hcCCccCCccCCchh
Confidence 4553 77666554 346688999 89999998775 2211 112478999999988
Q ss_pred ecCCCCcee
Q 018073 311 KNQGCMHMT 319 (361)
Q Consensus 311 K~~GCnhm~ 319 (361)
+--|+..+-
T Consensus 71 r~kgsprv~ 79 (1079)
T PLN02638 71 RHKGSPAIL 79 (1079)
T ss_pred hhcCCCCcC
Confidence 777776543
No 230
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=43.83 E-value=21 Score=23.27 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=5.7
Q ss_pred CCCCCCCcce
Q 018073 300 KPCPRCKRPI 309 (361)
Q Consensus 300 k~CP~C~~~I 309 (361)
.+||.|+..|
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 4566666554
No 231
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.79 E-value=18 Score=33.78 Aligned_cols=26 Identities=38% Similarity=0.912 Sum_probs=19.1
Q ss_pred cCCCCCCCcceeec--CCCCceeecCCCc
Q 018073 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (361)
Q Consensus 299 ~k~CP~C~~~IeK~--~GCnhm~C~~~C~ 325 (361)
.++||+|+.+|+|. +|=.-..|. .|.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCP-NCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECC-CCc
Confidence 47999999999855 775556665 453
No 232
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.62 E-value=13 Score=40.36 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=24.3
Q ss_pred hhcCCCCCCCcceeecCCCCceeecCCCcc-----ceeccccccc
Q 018073 297 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKF-----EFCWLCLGQW 336 (361)
Q Consensus 297 ~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~-----~FCw~C~~~~ 336 (361)
...+.||.|+... ....|. .||. .||-.|+..-
T Consensus 624 Vg~RfCpsCG~~t------~~frCP-~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCP-FCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred ccCccCCCCCCcC------CcccCC-CCCCCCCcceeCccccCcC
Confidence 3468999999885 457887 7885 4888886553
No 233
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=43.44 E-value=38 Score=24.96 Aligned_cols=51 Identities=24% Similarity=0.626 Sum_probs=19.5
Q ss_pred CCCccccccccccccCC---ccccc--cCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 138 DGEEMTCGICFENYPSD---RLLAA--ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 138 ~~~~~~C~IC~e~~~~~---~~~~l--~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
+.....|.||-+.+... +++.+ .|+-..|+.|+.--. ++|. -.|| .|+...
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~----q~Cp--qCkt~y 61 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGN----QVCP--QCKTRY 61 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS-----SB-T--TT--B-
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCc----cccc--ccCCCc
Confidence 34467899999987542 33332 488999999986544 3443 3688 787543
No 234
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=43.30 E-value=27 Score=31.83 Aligned_cols=48 Identities=17% Similarity=0.387 Sum_probs=35.0
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCC
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~ 196 (361)
...|||=+..+. ..+++..|||.|=++=+..++... ..++||..+|..
T Consensus 176 s~rdPis~~~I~-nPviSkkC~HvydrDsI~~~l~~~-------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIV-NPVISKKCGHVYDRDSIMQILCDE-------ITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhh-chhhhcCcCcchhhhhHHHHhccC-------ceeecccccCCc
Confidence 356888654442 456677899999988777777552 368999999993
No 235
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.57 E-value=8.2 Score=37.79 Aligned_cols=32 Identities=28% Similarity=0.685 Sum_probs=22.5
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceeccccccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (361)
-.||-|.-.+. +.++ . .|+|.||..|...|..
T Consensus 27 l~C~IC~d~~~-----~Pvi-t-pCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-T-SCSHTFCSLCIRRCLS 58 (397)
T ss_pred cCCCcCchhhh-----CccC-C-CCCCchhHHHHHHHHh
Confidence 58999987764 2332 4 5888888888877654
No 236
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=42.08 E-value=26 Score=27.91 Aligned_cols=30 Identities=20% Similarity=0.586 Sum_probs=20.1
Q ss_pred ccccCCCCCCcceeeecCCCCceEEe-ccCCcc
Q 018073 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (361)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (361)
+++|| .|+.++.+........+.| +||+..
T Consensus 2 m~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 56899 4999887754333446677 677664
No 237
>PLN02189 cellulose synthase
Probab=41.99 E-value=21 Score=39.10 Aligned_cols=61 Identities=23% Similarity=0.680 Sum_probs=41.9
Q ss_pred cccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcce
Q 018073 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~I 309 (361)
.-|.. |+--|... ..+...|-| .|++..|..|-+ +.+ +..++.||.|++..
T Consensus 35 ~~C~i--Cgd~vg~~-~~g~~fvaC~~C~fpvCr~Cye----------yer---------------~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 35 QVCEI--CGDEIGLT-VDGDLFVACNECGFPVCRPCYE----------YER---------------REGTQNCPQCKTRY 86 (1040)
T ss_pred ccccc--cccccCcC-CCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCch
Confidence 45664 77666554 446678999 899999988761 111 11237899999999
Q ss_pred eecCCCCcee
Q 018073 310 EKNQGCMHMT 319 (361)
Q Consensus 310 eK~~GCnhm~ 319 (361)
.+--|++.+.
T Consensus 87 ~r~kgs~~v~ 96 (1040)
T PLN02189 87 KRLKGSPRVE 96 (1040)
T ss_pred hhccCCCCcC
Confidence 8777776553
No 238
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=41.89 E-value=13 Score=39.98 Aligned_cols=26 Identities=38% Similarity=1.026 Sum_probs=21.2
Q ss_pred CCCCCCCc-ceeecCCCCceeecCCCccce
Q 018073 300 KPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 300 k~CP~C~~-~IeK~~GCnhm~C~~~C~~~F 328 (361)
-.||-|+. .||..|||| ||+ .|+.+.
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~-~c~~~~ 854 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCT-NCGAQL 854 (858)
T ss_pred CCCCccCCCceeecCCCc--ccc-chhhhh
Confidence 47999996 678999999 798 788763
No 239
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=40.57 E-value=24 Score=19.89 Aligned_cols=6 Identities=67% Similarity=2.073 Sum_probs=3.9
Q ss_pred CCCCCC
Q 018073 301 PCPRCK 306 (361)
Q Consensus 301 ~CP~C~ 306 (361)
+||+|+
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 566665
No 240
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=40.41 E-value=11 Score=36.67 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=15.5
Q ss_pred CCCCCCCccee-e--cCCC----CceeecCCCc
Q 018073 300 KPCPRCKRPIE-K--NQGC----MHMTCTPPCK 325 (361)
Q Consensus 300 k~CP~C~~~Ie-K--~~GC----nhm~C~~~C~ 325 (361)
-.|-.|+..+. + ..|| ||+.|+ .|+
T Consensus 428 Y~CEDCg~~LS~e~e~qgCyPld~HllCk-~Ch 459 (468)
T KOG1701|consen 428 YKCEDCGLLLSSEEEGQGCYPLDGHLLCK-TCH 459 (468)
T ss_pred eehhhcCccccccCCCCcceeccCceeec-hhh
Confidence 46677777765 3 3556 577776 564
No 241
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=40.40 E-value=18 Score=21.85 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=5.2
Q ss_pred CCCCCCCcce
Q 018073 300 KPCPRCKRPI 309 (361)
Q Consensus 300 k~CP~C~~~I 309 (361)
.+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 4666666554
No 242
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=40.37 E-value=43 Score=26.74 Aligned_cols=36 Identities=25% Similarity=0.534 Sum_probs=26.3
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCccceecccccc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (361)
+.+.|..|+.+.-...+.. ..|. .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~-~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCV-DCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEET-TTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCC-cCCccccCccCCc
Confidence 4578999998765555544 7888 7999999999866
No 243
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=40.36 E-value=19 Score=27.95 Aligned_cols=17 Identities=29% Similarity=0.798 Sum_probs=15.9
Q ss_pred cCCCcccHhhHHHHHHh
Q 018073 160 ACGHPFCSSCWTGYIST 176 (361)
Q Consensus 160 ~CgH~fC~~Cl~~~i~~ 176 (361)
.|.|.|..-|+..|+.+
T Consensus 80 ~CNHaFH~hCisrWlkt 96 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT 96 (114)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 39999999999999987
No 244
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.28 E-value=19 Score=24.92 Aligned_cols=23 Identities=30% Similarity=0.846 Sum_probs=16.8
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCcc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
+...||.|+.++. .|-.|. .||+
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~-~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCP-SCGY 48 (57)
T ss_pred cceECCCCCCccC-----CeEECC-CCCc
Confidence 4468999999987 477776 5664
No 245
>PRK11426 hypothetical protein; Provisional
Probab=39.84 E-value=50 Score=27.08 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=32.7
Q ss_pred EeeCHHHHHHHHH-HHHHHHHHHhCCCHHHHHHHHHHc
Q 018073 68 TVLTEADIRQRQE-EDITRISTVLSISKVAASILLRFY 104 (361)
Q Consensus 68 ~~l~~~~i~~~~~-~~i~~v~~~l~i~~~~a~~LL~~~ 104 (361)
..+++++|.+.+- +.|.+++..+++++.++...|..+
T Consensus 59 ~pIs~~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA~~ 96 (132)
T PRK11426 59 QSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQ 96 (132)
T ss_pred CCCCHHHHHHHhChHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 6789999999986 789999999999999999888655
No 246
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=39.83 E-value=15 Score=27.36 Aligned_cols=29 Identities=31% Similarity=0.723 Sum_probs=15.7
Q ss_pred cCCCCCCCc------ceeecCCCCceeecCCCccce
Q 018073 299 SKPCPRCKR------PIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 299 ~k~CP~C~~------~IeK~~GCnhm~C~~~C~~~F 328 (361)
+=.||.|+. -|.|..|=.+++|+ .|+..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~-~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCR-VCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEES-SS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEec-CCCCeE
Confidence 348999992 23456777889999 687666
No 247
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=39.68 E-value=31 Score=31.71 Aligned_cols=34 Identities=18% Similarity=0.565 Sum_probs=24.6
Q ss_pred HHHHhhcCCCCCCCcceeecCCCCceeecCCCccce
Q 018073 293 NWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 293 ~~i~~~~k~CP~C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
.|- .+.+-||+|+.++....|=..+.|. .|+..+
T Consensus 94 ~w~-~~~~fC~~CG~~~~~~~~~~~~~C~-~c~~~~ 127 (256)
T PRK00241 94 EFY-RSHRFCGYCGHPMHPSKTEWAMLCP-HCRERY 127 (256)
T ss_pred HHh-hcCccccccCCCCeecCCceeEECC-CCCCEE
Confidence 452 3468999999998866555678898 787543
No 248
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=39.51 E-value=26 Score=31.04 Aligned_cols=18 Identities=22% Similarity=0.661 Sum_probs=14.6
Q ss_pred CCccccCCCCCCcceeee
Q 018073 228 RKTKWCPAPGCDYAVDFV 245 (361)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~ 245 (361)
...+-||+|+|..+|...
T Consensus 136 SqRIACPRpnCkRiInL~ 153 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLD 153 (275)
T ss_pred cceeccCCCCcceeeecC
Confidence 346789999999998764
No 249
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=39.37 E-value=29 Score=37.78 Aligned_cols=27 Identities=33% Similarity=0.644 Sum_probs=20.6
Q ss_pred eeccccccccccCCCCCCcccCCCccc
Q 018073 328 FCWLCLGQWSDHGERTGGFYACNRYET 354 (361)
Q Consensus 328 FCw~C~~~~~~h~~~~g~~y~C~~~~~ 354 (361)
-|-.|++.......+.|.|+.|+.|..
T Consensus 647 ~CP~Cg~~m~lK~gr~G~Fl~Cs~yP~ 673 (860)
T PRK06319 647 PCPLCGGEMKVRHGRFGTFLGCENYPE 673 (860)
T ss_pred cCccCCCeeEEecCCCCceeeCCCCcc
Confidence 488888776655567788999998854
No 250
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=39.00 E-value=13 Score=25.08 Aligned_cols=24 Identities=25% Similarity=0.797 Sum_probs=11.1
Q ss_pred CCCCCCcceeecCCC--CceeecCCCc
Q 018073 301 PCPRCKRPIEKNQGC--MHMTCTPPCK 325 (361)
Q Consensus 301 ~CP~C~~~IeK~~GC--nhm~C~~~C~ 325 (361)
+|++|++.+-+.++= -.|.|. +|+
T Consensus 6 RC~~CnklLa~~g~~~~leIKCp-RC~ 31 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCP-RCK 31 (51)
T ss_pred eccchhHHHhhhcCccEEEEECC-CCC
Confidence 555555555543222 245554 444
No 251
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.74 E-value=21 Score=29.28 Aligned_cols=24 Identities=29% Similarity=0.819 Sum_probs=15.8
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceec
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCW 330 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw 330 (361)
.--||.|+...- ...|. |+.-|||
T Consensus 77 ~PgCP~CGn~~~------fa~C~--CGkl~Ci 100 (131)
T PF15616_consen 77 APGCPHCGNQYA------FAVCG--CGKLFCI 100 (131)
T ss_pred CCCCCCCcChhc------EEEec--CCCEEEe
Confidence 468999998852 34454 6666664
No 252
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.38 E-value=26 Score=25.84 Aligned_cols=34 Identities=29% Similarity=0.767 Sum_probs=22.5
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceeccccccccccC
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h~ 340 (361)
..||.|++-+. |.=+..=-...|-.|++-|-+-|
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWLDrG 35 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWLDRG 35 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEeecch
Confidence 57999998876 33331234556778888886544
No 253
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=38.23 E-value=29 Score=24.17 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.4
Q ss_pred CCCCCCCcc----eeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRP----IEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~----IeK~~GCnhm~C~~~C~~~ 327 (361)
-.||+|+.+ +-+..|=.++.|. .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv-~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECV-ECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-cCCCc
Confidence 479999964 3355677899999 78875
No 254
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=37.95 E-value=7.7 Score=40.33 Aligned_cols=51 Identities=20% Similarity=0.492 Sum_probs=38.1
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
...+|+||+..+. ....+.|.|.||..||..-+...-. ...|| .|+..+..
T Consensus 20 k~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~------~~~~~--lc~~~~eK 70 (684)
T KOG4362|consen 20 KILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG------PKQCA--LCKSDIEK 70 (684)
T ss_pred hhccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc------cccch--hhhhhhhh
Confidence 3578999998763 3467889999999999988766432 46787 77765543
No 255
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=37.89 E-value=24 Score=21.57 Aligned_cols=25 Identities=16% Similarity=0.359 Sum_probs=20.3
Q ss_pred CceEEe-ccCCccccccCCcCCCCCC
Q 018073 250 NYDVTC-RCSYSFCWNCTEEAHRPVD 274 (361)
Q Consensus 250 ~~~v~C-~C~~~fC~~C~~~~H~~~~ 274 (361)
...+.| .|+...|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 457899 9999999999876687653
No 256
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=37.87 E-value=23 Score=30.83 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=20.6
Q ss_pred CCCCCCcceeecCCCCceeecCCCccc
Q 018073 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
.||+|+.++.+ .+.|+|.|. .|++.
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~-~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCP-NCGNI 175 (189)
T ss_pred EccccCCceEE-CCCCEEECC-CCCCE
Confidence 79999999987 455999998 68754
No 257
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.70 E-value=17 Score=25.70 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=11.5
Q ss_pred cCCCCCCCcceee
Q 018073 299 SKPCPRCKRPIEK 311 (361)
Q Consensus 299 ~k~CP~C~~~IeK 311 (361)
+.+||.|+++++.
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5899999999985
No 258
>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=36.81 E-value=21 Score=32.16 Aligned_cols=54 Identities=22% Similarity=0.352 Sum_probs=35.0
Q ss_pred eccCCCcCCCcc-chhHHhhcCChHHHHHHHHHHHHHHHhhCCCccccCCCCCCcceee
Q 018073 187 LRCPDPSCGAAV-GQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (361)
Q Consensus 187 i~CP~~~C~~~i-~~~~i~~ll~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~ 244 (361)
-+|| .|+.-. ....+..|++++-+.+.-+--....+. .....||.|+|+.+++.
T Consensus 11 ~~CP--vCksDrYLnPdik~linPECyHrmCESCvdRIFs--~GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCP--VCKSDRYLNPDIKILINPECYHRMCESCVDRIFS--RGPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCC--ccccccccCCCeEEEECHHHHHHHHHHHHHHHhc--CCCCCCCCccHHHHHHH
Confidence 4799 888743 333566778888776655444433332 34568999999987654
No 259
>PLN02400 cellulose synthase
Probab=36.63 E-value=34 Score=37.75 Aligned_cols=59 Identities=25% Similarity=0.707 Sum_probs=39.9
Q ss_pred ccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCccee
Q 018073 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (361)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 310 (361)
-|-. |+--|... ..+...|-| .|+...|..|-+ + .+ +..++-||+|++...
T Consensus 38 iCqI--CGD~VG~t-~dGe~FVAC~eCaFPVCRpCYE-Y---------ER---------------keGnq~CPQCkTrYk 89 (1085)
T PLN02400 38 ICQI--CGDDVGVT-ETGDVFVACNECAFPVCRPCYE-Y---------ER---------------KDGTQCCPQCKTRYR 89 (1085)
T ss_pred eeee--cccccCcC-CCCCEEEEEccCCCccccchhh-e---------ec---------------ccCCccCcccCCccc
Confidence 4553 77655544 346688999 899999988862 1 10 112378999999888
Q ss_pred ecCCCCce
Q 018073 311 KNQGCMHM 318 (361)
Q Consensus 311 K~~GCnhm 318 (361)
+--|+..+
T Consensus 90 R~KgsprV 97 (1085)
T PLN02400 90 RHKGSPRV 97 (1085)
T ss_pred cccCCCCC
Confidence 77777654
No 260
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=36.19 E-value=81 Score=25.23 Aligned_cols=35 Identities=20% Similarity=0.136 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHH
Q 018073 78 RQEEDITRISTVLSISKVAASILLRFYNWSVSKVH 112 (361)
Q Consensus 78 ~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~ 112 (361)
.=.++|+-|++..+++...|+-.|...+|++-..+
T Consensus 77 i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI 111 (116)
T TIGR00264 77 ITEDDIELVMKQCNVSKEEARRALEECGGDLAEAI 111 (116)
T ss_pred CCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHH
Confidence 44678899999999999999999999999976544
No 261
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=35.53 E-value=39 Score=27.94 Aligned_cols=12 Identities=42% Similarity=1.016 Sum_probs=10.3
Q ss_pred cCCCCCCCccee
Q 018073 299 SKPCPRCKRPIE 310 (361)
Q Consensus 299 ~k~CP~C~~~Ie 310 (361)
.-+|.+||.+|.
T Consensus 81 ~~~CE~CG~~I~ 92 (137)
T TIGR03826 81 GYPCERCGTSIR 92 (137)
T ss_pred cCcccccCCcCC
Confidence 469999999995
No 262
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=35.19 E-value=1e+02 Score=24.61 Aligned_cols=35 Identities=23% Similarity=0.147 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHH
Q 018073 79 QEEDITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (361)
Q Consensus 79 ~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e 113 (361)
=.++|.-|++..+++...|+-.|...++++-..+-
T Consensus 76 ~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~ 110 (115)
T PRK06369 76 PEEDIELVAEQTGVSEEEARKALEEANGDLAEAIL 110 (115)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHH
Confidence 46788999999999999999999999999866543
No 263
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=35.12 E-value=31 Score=23.20 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=21.9
Q ss_pred ccccccccccCCccccccCCCcccHhhHHHH
Q 018073 143 TCGICFENYPSDRLLAAACGHPFCSSCWTGY 173 (361)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~ 173 (361)
.|.||-..+..-..+.+.=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 48999988755433445566 7999999876
No 264
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.96 E-value=35 Score=31.07 Aligned_cols=6 Identities=17% Similarity=0.512 Sum_probs=2.3
Q ss_pred CCCcCC
Q 018073 19 DDFYSG 24 (361)
Q Consensus 19 ~~~~~~ 24 (361)
|+.|+.
T Consensus 41 D~ef~~ 46 (240)
T PF05764_consen 41 DEEFES 46 (240)
T ss_pred CccccC
Confidence 333343
No 265
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=34.52 E-value=12 Score=23.56 Aligned_cols=23 Identities=26% Similarity=0.730 Sum_probs=20.1
Q ss_pred ceEEe-ccCCccccccCCcCCCCC
Q 018073 251 YDVTC-RCSYSFCWNCTEEAHRPV 273 (361)
Q Consensus 251 ~~v~C-~C~~~fC~~C~~~~H~~~ 273 (361)
..+.| .|+..+|..|....|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 67899 999999999998778774
No 266
>PHA02325 hypothetical protein
Probab=34.21 E-value=18 Score=25.41 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=9.1
Q ss_pred hcCCCCCCCcce
Q 018073 298 NSKPCPRCKRPI 309 (361)
Q Consensus 298 ~~k~CP~C~~~I 309 (361)
++|.||+|++.-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 468899998653
No 267
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=34.02 E-value=35 Score=24.75 Aligned_cols=27 Identities=22% Similarity=0.770 Sum_probs=20.6
Q ss_pred CCCCCCCcc----eeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRP----IEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~----IeK~~GCnhm~C~~~C~~~ 327 (361)
-.||+|+.+ +-+..|=.++.|. .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV-~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECV-ECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEec-CCCCe
Confidence 479999964 2355778899999 79875
No 268
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=33.81 E-value=54 Score=22.68 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChHHHHH
Q 018073 82 DITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (361)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e 113 (361)
.+.+|++.|+++......=...++|+...-.+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~~ 46 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLPIE 46 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCchh
Confidence 46889999999999988888999999765443
No 269
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=33.64 E-value=33 Score=37.65 Aligned_cols=55 Identities=25% Similarity=0.704 Sum_probs=36.8
Q ss_pred CCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcceeecCCCC
Q 018073 238 CDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCM 316 (361)
Q Consensus 238 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 316 (361)
|+--|... ..+.+.|-| .|+...|..|-+ +.. +...+-||+|+++..+--|++
T Consensus 21 CGd~vg~~-~~Ge~FVAC~eC~fpvCr~cye----------ye~---------------~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 21 CGDEVGVK-EDGQPFVACHVCGFPVCKPCYE----------YER---------------SEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred cccccCcC-CCCCEEEEeccCCCccccchhh----------hhh---------------hcCCccCCccCCchhhhcCCC
Confidence 66555443 346688999 899999988761 110 112378999999888666666
Q ss_pred ce
Q 018073 317 HM 318 (361)
Q Consensus 317 hm 318 (361)
.+
T Consensus 75 ~~ 76 (1044)
T PLN02915 75 RV 76 (1044)
T ss_pred Cc
Confidence 54
No 270
>PRK12495 hypothetical protein; Provisional
Probab=33.56 E-value=56 Score=29.18 Aligned_cols=29 Identities=31% Similarity=0.728 Sum_probs=20.2
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceeccccccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (361)
.+-||.|+.||.+..| ..||-.|......
T Consensus 42 a~hC~~CG~PIpa~pG-----------~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFRHDG-----------QEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccCCCC-----------eeECCCCCCcccc
Confidence 5789999999985444 4456677655543
No 271
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.53 E-value=17 Score=36.42 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=19.8
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (361)
--.||-|-.+-. .-+.-.|||-|||-|+=.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 368999987654 222214888888888744
No 272
>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=33.47 E-value=27 Score=21.74 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=10.6
Q ss_pred CCCCCCCcceeec
Q 018073 300 KPCPRCKRPIEKN 312 (361)
Q Consensus 300 k~CP~C~~~IeK~ 312 (361)
..||.|+..++|.
T Consensus 27 ~~CP~Cg~~~~r~ 39 (41)
T smart00834 27 ATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCcceec
Confidence 6899999987764
No 273
>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=33.20 E-value=26 Score=24.01 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=15.9
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCcc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
+...||.|+.+.. .|-.|. .||+
T Consensus 25 ~l~~C~~cG~~~~-----~H~vc~-~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKL-----PHRVCP-SCGY 47 (55)
T ss_pred cceECCCCCCccc-----CeeECC-ccCe
Confidence 3467999998886 566665 4653
No 274
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.89 E-value=35 Score=34.67 Aligned_cols=35 Identities=20% Similarity=0.579 Sum_probs=24.5
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc-----eecccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (361)
-.||+|..+..--..=|.+.|. .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCH-YCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcC-CCcCcCCCCCCCCCCCCC
Confidence 4688888777633333478888 78876 58888865
No 275
>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=32.88 E-value=26 Score=24.09 Aligned_cols=22 Identities=36% Similarity=0.857 Sum_probs=16.0
Q ss_pred hcCCCCCCCcceeecCCCCceeecCCCc
Q 018073 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 325 (361)
Q Consensus 298 ~~k~CP~C~~~IeK~~GCnhm~C~~~C~ 325 (361)
+...||.|+.+.. .|..|. .||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~-~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCP-SCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCT-TTB
T ss_pred ceeeeccCCCEec-----ccEeeC-CCC
Confidence 4568999998876 567776 565
No 276
>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=32.79 E-value=19 Score=23.16 Aligned_cols=28 Identities=32% Similarity=0.759 Sum_probs=15.0
Q ss_pred cCCCCCCcceeeecCCCCceEEe-ccCCccccccCC
Q 018073 233 CPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTE 267 (361)
Q Consensus 233 CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~ 267 (361)
|..++|..... ..+.| .|+..||...+.
T Consensus 1 C~~~~C~~~~~-------~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 1 CSFPGCKKKDF-------LPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp -SSTTT--BCT-------SHEE-TTTS-EE-TTTHS
T ss_pred CccCcCcCccC-------CCeECCCCCcccCccccC
Confidence 44456765431 45899 699999998874
No 277
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.73 E-value=20 Score=32.99 Aligned_cols=31 Identities=23% Similarity=0.788 Sum_probs=19.1
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (361)
++.||.|+.+=. +.|+=. +|+|-|||.|.+.
T Consensus 239 ~~~C~~Cg~~Pt-----iP~~~~-~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPT-----IPHVIG-KCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCC-----CCeeec-cccceeehhhhhh
Confidence 578999997532 122222 3777777777644
No 278
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=32.68 E-value=50 Score=27.96 Aligned_cols=50 Identities=20% Similarity=0.428 Sum_probs=33.7
Q ss_pred CccccccccccccCCccccccCCC---cccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 140 EEMTCGICFENYPSDRLLAAACGH---PFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH---~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
....|-||++... .......|.. ....+|++.|+..+ + ..+|+ .|.....
T Consensus 7 ~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s---~----~~~Ce--iC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTS---K----NKSCK--ICNGPYN 59 (162)
T ss_pred CCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcC---C----CCccc--ccCCeEE
Confidence 3567999998753 2222223444 46999999999863 2 56898 8887653
No 279
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=32.68 E-value=29 Score=30.14 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=18.8
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
-.|++|+.++++ .=+.|+|. +|++.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp-~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCP-NCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECC-CCCCE
Confidence 378999999888 44678887 67653
No 280
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=32.47 E-value=34 Score=26.79 Aligned_cols=29 Identities=28% Similarity=1.038 Sum_probs=20.0
Q ss_pred CCCCCCCccee-ecCCCCceeecCCCccceecccccccccc
Q 018073 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (361)
Q Consensus 300 k~CP~C~~~Ie-K~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (361)
-+||+|..-.- ..++ +|.|. .|+.+|++.
T Consensus 4 p~cp~c~sEytYed~~--~~~cp---------ec~~ew~~~ 33 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICP---------ECAHEWNEN 33 (112)
T ss_pred CCCCccCCceEEecCc--eEeCc---------hhccccccc
Confidence 68999976554 5566 89997 455567643
No 281
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=32.44 E-value=44 Score=27.27 Aligned_cols=22 Identities=41% Similarity=1.115 Sum_probs=11.7
Q ss_pred CCCCC--CCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPR--CKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~--C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
|+||+ |.-.++ +|-|+..|||-
T Consensus 83 k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 83 KPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp SB-SS--S--BEE------EE---TBTTB-
T ss_pred CCCCccccCCcee------EEeccCcCCCc
Confidence 99999 999888 78887446653
No 282
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=32.41 E-value=47 Score=31.24 Aligned_cols=51 Identities=20% Similarity=0.447 Sum_probs=33.9
Q ss_pred CccccccccccccC-CccccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCcc
Q 018073 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (361)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i 198 (361)
+.++||+=-+.-.. +.++.+.|||.+=+.=+...- ++| ...++|| -|...-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG--~~~FKCP--YCP~~~ 386 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNG--VLSFKCP--YCPEMS 386 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcC--cEEeeCC--CCCcch
Confidence 46899985544332 556889999998776554322 233 4689999 787653
No 283
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=32.26 E-value=16 Score=35.27 Aligned_cols=36 Identities=31% Similarity=0.826 Sum_probs=28.1
Q ss_pred CCccccccccccccCCccccccCCCcccHhhHHHHH
Q 018073 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYI 174 (361)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i 174 (361)
.++.+|+|||-.++...-...-|...+|.+|+..+=
T Consensus 72 rr~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNLVRCCSETICGECFAPFG 107 (482)
T ss_pred cccccCceeeeecccccchhhhhccchhhhheeccc
Confidence 356899999988875444555699999999997653
No 284
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=32.00 E-value=42 Score=32.33 Aligned_cols=45 Identities=29% Similarity=0.620 Sum_probs=25.9
Q ss_pred CCccccccCCc-CCCCC--------------CchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCccee
Q 018073 258 SYSFCWNCTEE-AHRPV--------------DCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (361)
Q Consensus 258 ~~~fC~~C~~~-~H~~~--------------~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~Ie 310 (361)
+-.+|..|+.+ .|.|+ +|...- .-.-..+|+.. .+.||-|+.|+.
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHil-------Hl~CLknW~ER-qQTCPICr~p~i 345 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHIL-------HLHCLKNWLER-QQTCPICRRPVI 345 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCccccccccee-------eHHHHHHHHHh-ccCCCcccCccc
Confidence 55788888876 66652 333210 01112355443 278999999954
No 285
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=31.82 E-value=14 Score=34.30 Aligned_cols=30 Identities=30% Similarity=0.843 Sum_probs=21.4
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceeccccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~ 336 (361)
-+|--|.-.|- +-|.-.|||.||++|-+..
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~h 55 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRH 55 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHH
Confidence 47877777664 6664259999999997654
No 286
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=31.57 E-value=51 Score=19.72 Aligned_cols=25 Identities=20% Similarity=0.608 Sum_probs=20.7
Q ss_pred CCCCCCcceeecCCCCceeecCCCcc
Q 018073 301 PCPRCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 301 ~CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
.|+.|++++.-..|=.++.|. .|++
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs-~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCA-LCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECC-CCCe
Confidence 688999999888888888888 6754
No 287
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=31.47 E-value=15 Score=40.90 Aligned_cols=38 Identities=24% Similarity=0.556 Sum_probs=29.6
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHhhh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAI 178 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i 178 (361)
..+.|+||.+.+. ..-....|||.+|..|...+...+.
T Consensus 1152 ~~~~c~ic~dil~-~~~~I~~cgh~~c~~c~~~~l~~~s 1189 (1394)
T KOG0298|consen 1152 GHFVCEICLDILR-NQGGIAGCGHEPCCRCDELWLYASS 1189 (1394)
T ss_pred cccchHHHHHHHH-hcCCeeeechhHhhhHHHHHHHHhc
Confidence 4668999998764 2334467999999999999998753
No 288
>PLN02436 cellulose synthase A
Probab=31.31 E-value=40 Score=37.13 Aligned_cols=61 Identities=23% Similarity=0.675 Sum_probs=41.1
Q ss_pred cccCCCCCCcceeeecCCCCceEEe-ccCCccccccCCcCCCCCCchhHHHHHHhhhhhhHHHHHHHhhcCCCCCCCcce
Q 018073 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI 309 (361)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~i~~~~k~CP~C~~~I 309 (361)
.-|.- |+--|... ..+...|-| .|++..|..|-+ +.+ +..++.||.|++..
T Consensus 37 ~iCqI--CGD~Vg~t-~dGe~FVACn~C~fpvCr~Cye----------yer---------------~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 37 QTCQI--CGDEIELT-VDGEPFVACNECAFPVCRPCYE----------YER---------------REGNQACPQCKTRY 88 (1094)
T ss_pred ccccc--cccccCcC-CCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCch
Confidence 34554 77655444 346688999 899999988861 110 11237899999999
Q ss_pred eecCCCCcee
Q 018073 310 EKNQGCMHMT 319 (361)
Q Consensus 310 eK~~GCnhm~ 319 (361)
.+--|++.+.
T Consensus 89 ~r~kgs~~~~ 98 (1094)
T PLN02436 89 KRIKGSPRVE 98 (1094)
T ss_pred hhccCCCCcC
Confidence 8777776554
No 289
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.25 E-value=45 Score=30.27 Aligned_cols=40 Identities=28% Similarity=0.670 Sum_probs=0.0
Q ss_pred hhhHHHHHHHhhcCCCCCCCcc----eeecCCCCceeecCCCccce
Q 018073 287 AESENMNWILANSKPCPRCKRP----IEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 287 ~~~~~~~~i~~~~k~CP~C~~~----IeK~~GCnhm~C~~~C~~~F 328 (361)
+...+..|+..|. .||.|+.. .+-|.-=.-..|. .|+.+|
T Consensus 20 aRVltE~Wv~~n~-yCP~Cg~~~L~~f~NN~PVaDF~C~-~C~eey 63 (254)
T PF06044_consen 20 ARVLTEDWVAENM-YCPNCGSKPLSKFENNRPVADFYCP-NCNEEY 63 (254)
T ss_dssp HHHHHHHHHHHH----TTT--SS-EE--------EEE-T-TT--EE
T ss_pred hHHHHHHHHHHCC-cCCCCCChhHhhccCCCccceeECC-CCchHH
No 290
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.24 E-value=16 Score=30.83 Aligned_cols=27 Identities=22% Similarity=0.544 Sum_probs=19.6
Q ss_pred CccccccccccccC-CccccccCCCccc
Q 018073 140 EEMTCGICFENYPS-DRLLAAACGHPFC 166 (361)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC 166 (361)
...+|.||+|++.. +.+..|+|-..|-
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEee
Confidence 46789999998865 4456788876654
No 291
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.21 E-value=59 Score=35.33 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHh-CCCHHHHHH
Q 018073 74 DIRQRQEEDITRISTVL-SISKVAASI 99 (361)
Q Consensus 74 ~i~~~~~~~i~~v~~~l-~i~~~~a~~ 99 (361)
-|...|..+-.+.+.++ +++++....
T Consensus 967 ~i~~lq~~d~~~yq~l~~~L~~~q~~~ 993 (1010)
T KOG1991|consen 967 AITNLQSSDAVRYQKLISTLTPEQQDS 993 (1010)
T ss_pred HHHhhhccChHHHHHHHhcCCHHHHHH
Confidence 34444444444444444 345554443
No 292
>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=30.93 E-value=55 Score=25.67 Aligned_cols=34 Identities=18% Similarity=0.479 Sum_probs=22.4
Q ss_pred CCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCc
Q 018073 162 GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (361)
Q Consensus 162 gH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~ 197 (361)
.=.||..||..-+...+.+-.....-.|| .|...
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECC--CCCCe
Confidence 66799999998877655432111256798 66653
No 293
>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 PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=30.59 E-value=16 Score=21.73 Aligned_cols=19 Identities=26% Similarity=0.599 Sum_probs=9.9
Q ss_pred eeccCCCcCCCccchhHHh
Q 018073 186 MLRCPDPSCGAAVGQDMIY 204 (361)
Q Consensus 186 ~i~CP~~~C~~~i~~~~i~ 204 (361)
.++||...|...|......
T Consensus 2 ~vrCPvkdC~EEv~lgKY~ 20 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYS 20 (30)
T ss_dssp EEE--STT---EEEHHHHH
T ss_pred ccccccccCcchhhhhhhc
Confidence 5899999999887655433
No 295
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.38 E-value=58 Score=22.32 Aligned_cols=12 Identities=42% Similarity=0.670 Sum_probs=7.9
Q ss_pred CccccCCCCCCcce
Q 018073 229 KTKWCPAPGCDYAV 242 (361)
Q Consensus 229 ~~~~CP~p~C~~~i 242 (361)
.++.||. |+...
T Consensus 2 ~LkPCPF--CG~~~ 13 (61)
T PF14354_consen 2 ELKPCPF--CGSAD 13 (61)
T ss_pred CCcCCCC--CCCcc
Confidence 4678996 76443
No 296
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.04 E-value=62 Score=25.52 Aligned_cols=10 Identities=60% Similarity=0.684 Sum_probs=5.4
Q ss_pred CCCcCCCCCC
Q 018073 19 DDFYSGGDDD 28 (361)
Q Consensus 19 ~~~~~~~~~~ 28 (361)
|+..+||.+-
T Consensus 77 D~d~~GgDDl 86 (129)
T COG4530 77 DDDPKGGDDL 86 (129)
T ss_pred cCCccCCCcc
Confidence 5566665443
No 297
>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=29.56 E-value=35 Score=22.97 Aligned_cols=35 Identities=29% Similarity=0.592 Sum_probs=24.2
Q ss_pred cccccccccccCC--ccccccCCCcccHhhHHHHHHh
Q 018073 142 MTCGICFENYPSD--RLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 142 ~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
..|.+|-..|... ...-..||+.||..|+......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 3588888776542 1222359999999999877554
No 298
>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=29.48 E-value=20 Score=23.77 Aligned_cols=44 Identities=30% Similarity=0.678 Sum_probs=21.2
Q ss_pred cccccccccccCCccccccC-CCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccch
Q 018073 142 MTCGICFENYPSDRLLAAAC-GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (361)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~C-gH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~~ 200 (361)
+.|--|.-. .. -.+.| .|+.|..|+...+.. .-.|| .|+.+++.
T Consensus 3 ~nCKsCWf~--~k--~Li~C~dHYLCl~CLt~ml~~---------s~~C~--iC~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFA--NK--GLIKCSDHYLCLNCLTLMLSR---------SDRCP--ICGKPLPT 47 (50)
T ss_dssp ----SS-S----S--SEEE-SS-EEEHHHHHHT-SS---------SSEET--TTTEE---
T ss_pred ccChhhhhc--CC--CeeeecchhHHHHHHHHHhcc---------ccCCC--cccCcCcc
Confidence 346667522 11 23456 599999999887754 34688 78877653
No 299
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.11 E-value=1.7e+02 Score=23.86 Aligned_cols=60 Identities=18% Similarity=0.323 Sum_probs=31.0
Q ss_pred ceEEeccCCccccccCCcC--CCCCCchhHHHHHHh--hhhhhHHHHHHHhhcCCCCCCCcceee
Q 018073 251 YDVTCRCSYSFCWNCTEEA--HRPVDCDTVAKWVLK--NSAESENMNWILANSKPCPRCKRPIEK 311 (361)
Q Consensus 251 ~~v~C~C~~~fC~~C~~~~--H~~~~C~~~~~~~~~--~~~~~~~~~~i~~~~k~CP~C~~~IeK 311 (361)
..+.|.||++||.- ++.| |....-.....-+.. -..+....+|+...--.||.|+.+.+-
T Consensus 69 rv~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~ev 132 (165)
T COG4647 69 RVIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHEV 132 (165)
T ss_pred cEEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceeee
Confidence 45689999999853 2233 222111111110100 011122346766655689999998773
No 300
>smart00336 BBOX B-Box-type zinc finger.
Probab=28.54 E-value=46 Score=20.58 Aligned_cols=25 Identities=28% Similarity=0.678 Sum_probs=19.9
Q ss_pred CCceEEe-ccCCccccccCCcCCCCC
Q 018073 249 GNYDVTC-RCSYSFCWNCTEEAHRPV 273 (361)
Q Consensus 249 ~~~~v~C-~C~~~fC~~C~~~~H~~~ 273 (361)
....+.| .|....|..|....|.++
T Consensus 12 ~~~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 12 EPAEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred CceEEECCCCCcccccccChhhcCCC
Confidence 3456889 899999999997777654
No 301
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.26 E-value=40 Score=21.24 Aligned_cols=13 Identities=31% Similarity=0.756 Sum_probs=10.2
Q ss_pred ceeecCCCccceec
Q 018073 317 HMTCTPPCKFEFCW 330 (361)
Q Consensus 317 hm~C~~~C~~~FCw 330 (361)
-++|. .|+..||-
T Consensus 12 ~f~C~-~C~~~FC~ 24 (39)
T smart00154 12 GFKCR-HCGNLFCG 24 (39)
T ss_pred CeECC-ccCCcccc
Confidence 47887 79999884
No 302
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=28.12 E-value=28 Score=31.42 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=15.0
Q ss_pred ccCCccccccCCcCCCC
Q 018073 256 RCSYSFCWNCTEEAHRP 272 (361)
Q Consensus 256 ~C~~~fC~~C~~~~H~~ 272 (361)
.|.+.||..|....|.+
T Consensus 22 aC~HvfC~~C~k~~~~~ 38 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSPD 38 (233)
T ss_pred echhhhhhhhcccCCcc
Confidence 79999999999888865
No 303
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=28.12 E-value=82 Score=21.92 Aligned_cols=25 Identities=20% Similarity=0.049 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcC
Q 018073 81 EDITRISTVLSISKVAASILLRFYN 105 (361)
Q Consensus 81 ~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (361)
--|+..+..+++++.+|.-+|.+++
T Consensus 6 ~~Ie~~A~~~~~s~~ea~~~~~~~~ 30 (62)
T PF12668_consen 6 FCIEEFAKKLNISGEEAYNYFKRSG 30 (62)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcC
Confidence 4688999999999999999998776
No 304
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.10 E-value=36 Score=30.88 Aligned_cols=21 Identities=24% Similarity=0.270 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHHcCCChHHHH
Q 018073 92 ISKVAASILLRFYNWSVSKVH 112 (361)
Q Consensus 92 i~~~~a~~LL~~~~w~~~~l~ 112 (361)
|+...|.+|++.|.=|...+-
T Consensus 8 vs~~~a~~lmRrf~~~h~~v~ 28 (278)
T PF15135_consen 8 VSSEKAGALMRRFGSNHTGVG 28 (278)
T ss_pred cchHHHHHHHHhccccccchH
Confidence 567788999999987765544
No 305
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=26.76 E-value=72 Score=18.14 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=18.5
Q ss_pred CCCCCcceeecCCCCceeecCCCcc
Q 018073 302 CPRCKRPIEKNQGCMHMTCTPPCKF 326 (361)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~ 326 (361)
|-+|++++.-..|=.++.|. .|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa-~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCA-CCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECC-ccCc
Confidence 56788888888888888887 5654
No 306
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.72 E-value=65 Score=22.44 Aligned_cols=25 Identities=20% Similarity=0.554 Sum_probs=11.3
Q ss_pred CCCCCcceeecCCCCceeecCCCccc
Q 018073 302 CPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 302 CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
|-.|++.|.-.+.--+..|. .||..
T Consensus 10 CtSCg~~i~~~~~~~~F~CP-nCG~~ 34 (59)
T PRK14890 10 CTSCGIEIAPREKAVKFLCP-NCGEV 34 (59)
T ss_pred ccCCCCcccCCCccCEeeCC-CCCCe
Confidence 44444444434434444444 34443
No 307
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=26.57 E-value=30 Score=21.08 Aligned_cols=13 Identities=38% Similarity=1.114 Sum_probs=9.3
Q ss_pred CCCCCCCcceeec
Q 018073 300 KPCPRCKRPIEKN 312 (361)
Q Consensus 300 k~CP~C~~~IeK~ 312 (361)
-.||+|+++|..+
T Consensus 5 ~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 5 VECPNCGRPVAAS 17 (33)
T ss_dssp EE-TTTSSEEEGG
T ss_pred EECCCCcCCcchh
Confidence 4799999998643
No 308
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=26.33 E-value=40 Score=20.89 Aligned_cols=9 Identities=44% Similarity=1.302 Sum_probs=6.0
Q ss_pred CCCCCCCcc
Q 018073 300 KPCPRCKRP 308 (361)
Q Consensus 300 k~CP~C~~~ 308 (361)
-+||.|+..
T Consensus 9 ~~C~~C~~~ 17 (36)
T PF11781_consen 9 EPCPVCGSR 17 (36)
T ss_pred CcCCCCCCe
Confidence 457777765
No 309
>PLN03086 PRLI-interacting factor K; Provisional
Probab=26.22 E-value=38 Score=34.86 Aligned_cols=30 Identities=23% Similarity=0.634 Sum_probs=25.4
Q ss_pred hcCCCCC--CCcceeecCCCCceeecCCCccce
Q 018073 298 NSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEF 328 (361)
Q Consensus 298 ~~k~CP~--C~~~IeK~~GCnhm~C~~~C~~~F 328 (361)
+...||+ |+..+.+...=+|..|. .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~-~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCE-KCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCC-CCCCcc
Confidence 4578995 99999999999999998 797765
No 310
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.76 E-value=78 Score=22.59 Aligned_cols=31 Identities=23% Similarity=0.445 Sum_probs=20.7
Q ss_pred ccccCCCCCCcceeeecCCCCceEEe-ccCCcccc
Q 018073 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (361)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (361)
.+.|| +|++.-..- +..+..|.| .||...+.
T Consensus 19 ~VkCp--dC~N~q~vF-shast~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVF-SHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEe-ccCceEEEecccccEEEe
Confidence 46788 698753322 345677899 89888764
No 311
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.71 E-value=50 Score=34.86 Aligned_cols=40 Identities=18% Similarity=0.331 Sum_probs=27.1
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccc----eecccccc-cccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFE----FCWLCLGQ-WSDH 339 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~----FCw~C~~~-~~~h 339 (361)
+-.||+|..+..--.+=+.+.|. .||+. .|-.|++. +...
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch-~CG~~~~p~~Cp~Cgs~~l~~~ 436 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCR-WCGRAAPDWRCPRCGSDRLRAV 436 (665)
T ss_pred eeECCCCCCceeEecCCCeeECC-CCcCCCcCccCCCCcCCcceee
Confidence 34788888777754445678898 78864 57778765 4433
No 312
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.69 E-value=54 Score=34.67 Aligned_cols=35 Identities=20% Similarity=0.610 Sum_probs=26.4
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc-----eecccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~-----FCw~C~~~ 335 (361)
-.||+|..+..--..=+.++|. .||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCH-HCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECC-CCcCCCCCCCCCCCCcCC
Confidence 3689998887633334779998 89986 59999875
No 313
>PF14353 CpXC: CpXC protein
Probab=25.64 E-value=21 Score=28.87 Aligned_cols=46 Identities=22% Similarity=0.478 Sum_probs=26.7
Q ss_pred eccCCCcCCCccchhHHhhc---CChHHHHHHHHHHHHHHHhhCCCccccCCCCCCcceee
Q 018073 187 LRCPDPSCGAAVGQDMIYLL---SSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (361)
Q Consensus 187 i~CP~~~C~~~i~~~~i~~l---l~~~~~~~y~~~~~~~~i~~~~~~~~CP~p~C~~~i~~ 244 (361)
|+|| .|+..+.......+ ..++++++ .+...-....||+ |+..+..
T Consensus 2 itCP--~C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP~--Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCP--HCGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCPS--CGHKFRL 50 (128)
T ss_pred cCCC--CCCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECCC--CCCceec
Confidence 6899 89998765544333 33333322 2223335678995 9876544
No 314
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=25.55 E-value=1e+02 Score=21.67 Aligned_cols=22 Identities=23% Similarity=0.212 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCHHHHHHHHHH
Q 018073 82 DITRISTVLSISKVAASILLRF 103 (361)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~ 103 (361)
...+|++.++|+...|+.+|..
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3578999999999999998843
No 315
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=25.26 E-value=54 Score=27.41 Aligned_cols=93 Identities=13% Similarity=0.205 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhhhcHHHHHHHcCCCCCCCCCCCC----CCccccccccccc
Q 018073 76 RQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPD----GEEMTCGICFENY 151 (361)
Q Consensus 76 ~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~~~~~~~~~~~~l~~~~~~~~~~----~~~~~C~IC~e~~ 151 (361)
...+.++|++....+++..... .+-.+=-|+.+.+.++ ..+.+++.||-.......+. .....||-|-...
T Consensus 41 ~e~L~~~I~~aL~~~Gv~~V~V-~i~~~p~Wt~d~it~~----gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s~~ 115 (146)
T TIGR02159 41 LEVIRQDIRDAVRALGVEVVEV-STSLDPPWTTDWITED----AREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGSAD 115 (146)
T ss_pred HHHHHHHHHHHHHhcCCCeEEE-eEeeCCCCChHHCCHH----HHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCCCC
Confidence 3444444444333345543222 2233456888877653 22234456774432211101 1247899998754
Q ss_pred c--CCccccccCC-CcccHhhHHHH
Q 018073 152 P--SDRLLAAACG-HPFCSSCWTGY 173 (361)
Q Consensus 152 ~--~~~~~~l~Cg-H~fC~~Cl~~~ 173 (361)
. .+.+-+..|. .++|.+|..-+
T Consensus 116 t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 116 TTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred cEeecCCCChhhHHHhhhhhhCCcH
Confidence 3 2344556787 56899998643
No 316
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=24.94 E-value=45 Score=25.42 Aligned_cols=35 Identities=23% Similarity=0.501 Sum_probs=26.6
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccceeccccccccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (361)
-.||.|+..-.|..+---=.|. .|+..|= |+.|.+
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~-~C~~~~A---GGAy~~ 70 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCK-KCGKKFA---GGAYTP 70 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEET-TTTEEEE----BSSSS
T ss_pred CcCCCCCCceeEEeeeEEeecC-CCCCEEe---CCCccc
Confidence 4899999999888888778898 7887763 444543
No 317
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=24.59 E-value=44 Score=27.28 Aligned_cols=12 Identities=42% Similarity=0.885 Sum_probs=9.5
Q ss_pred CCCCCCCcceee
Q 018073 300 KPCPRCKRPIEK 311 (361)
Q Consensus 300 k~CP~C~~~IeK 311 (361)
|.||+|+.-|--
T Consensus 111 K~C~~C~tGiYS 122 (128)
T PF11682_consen 111 KYCPKCGTGIYS 122 (128)
T ss_pred EecCCCCCcccc
Confidence 789999887753
No 318
>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=24.16 E-value=37 Score=31.69 Aligned_cols=35 Identities=29% Similarity=0.737 Sum_probs=17.0
Q ss_pred CCCCCCCcc-----eeecC--CCCceeecCCCccce------ecccccc
Q 018073 300 KPCPRCKRP-----IEKNQ--GCMHMTCTPPCKFEF------CWLCLGQ 335 (361)
Q Consensus 300 k~CP~C~~~-----IeK~~--GCnhm~C~~~C~~~F------Cw~C~~~ 335 (361)
..||-||.+ |...+ |=-++.|+ -|+++| |-.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs-~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCS-LCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEET-TT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcC-CCCCeeeecCCCCcCCCCC
Confidence 689999975 23333 78999998 798877 7788754
No 319
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.13 E-value=43 Score=18.79 Aligned_cols=10 Identities=50% Similarity=1.268 Sum_probs=6.5
Q ss_pred CCCCCCCcce
Q 018073 300 KPCPRCKRPI 309 (361)
Q Consensus 300 k~CP~C~~~I 309 (361)
.+||.|++..
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5677777654
No 320
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.13 E-value=41 Score=25.52 Aligned_cols=17 Identities=24% Similarity=0.698 Sum_probs=14.2
Q ss_pred cccHhhHHHHHHhhhcC
Q 018073 164 PFCSSCWTGYISTAIND 180 (361)
Q Consensus 164 ~fC~~Cl~~~i~~~i~~ 180 (361)
-||+.|+..|+..+-..
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999877654
No 321
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.06 E-value=28 Score=32.51 Aligned_cols=30 Identities=23% Similarity=0.569 Sum_probs=18.7
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~ 335 (361)
++.||-|... |||-+= ..|+|.|||+|.+-
T Consensus 7 ~~eC~IC~nt------~n~Pv~-l~C~HkFCyiCiKG 36 (324)
T KOG0824|consen 7 KKECLICYNT------GNCPVN-LYCFHKFCYICIKG 36 (324)
T ss_pred CCcceeeecc------CCcCcc-ccccchhhhhhhcc
Confidence 3567766532 122222 26999999999865
No 322
>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=24.03 E-value=26 Score=34.05 Aligned_cols=57 Identities=19% Similarity=0.400 Sum_probs=0.0
Q ss_pred ccccccccccccCCc-----------------cccccCCCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 141 EMTCGICFENYPSDR-----------------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~-----------------~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
..+||+|...-+... ....+|||..=....+-|-...|-.|...+.-.|| .|...+.
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CP--FCa~~L~ 401 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACP--FCATPLD 401 (416)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCC--cccCccc
Confidence 678999996432211 12347999887777777777778777656778899 8988774
No 323
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=23.78 E-value=24 Score=24.40 Aligned_cols=15 Identities=33% Similarity=0.900 Sum_probs=8.2
Q ss_pred cCCCCCCCcceeecC
Q 018073 299 SKPCPRCKRPIEKNQ 313 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~ 313 (361)
+.+||.|+++++-..
T Consensus 2 ~v~CP~C~k~~~~~~ 16 (57)
T PF03884_consen 2 TVKCPICGKPVEWSP 16 (57)
T ss_dssp EEE-TTT--EEE-SS
T ss_pred cccCCCCCCeecccC
Confidence 368999999998543
No 324
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.05 E-value=84 Score=20.30 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcC
Q 018073 80 EEDITRISTVLSISKVAASILLRFYN 105 (361)
Q Consensus 80 ~~~i~~v~~~l~i~~~~a~~LL~~~~ 105 (361)
...+.+|+..|++++....-.++.|+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 45788999999999999988887775
No 325
>PF12959 DUF3848: Protein of unknown function (DUF3848); InterPro: IPR024380 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences[].
Probab=23.03 E-value=1.7e+02 Score=22.83 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=33.7
Q ss_pred eeCHHHHH-----HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhh
Q 018073 69 VLTEADIR-----QRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (361)
Q Consensus 69 ~l~~~~i~-----~~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~ 116 (361)
..++++|. -.++++|-.+.+.+.++...|.+||..=+ =.+.+.+.|.
T Consensus 23 ~qpPeeIl~~AYEy~VkeDi~m~~ee~~l~~~qa~ALl~sp~-PL~~iY~~w~ 74 (101)
T PF12959_consen 23 SQPPEEILNHAYEYTVKEDILMAMEELELPDQQAKALLKSPS-PLADIYREWE 74 (101)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHcCCC-hHHHHHHHHH
Confidence 35677774 45788899999999999999999995432 3444555554
No 326
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=22.82 E-value=1.3e+02 Score=18.96 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHc
Q 018073 82 DITRISTVLSISKVAASILLRFY 104 (361)
Q Consensus 82 ~i~~v~~~l~i~~~~a~~LL~~~ 104 (361)
.+.+++..|||++..-.--|++|
T Consensus 20 n~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHC
T ss_pred CHHHHHHHHCCCHHHHHHHHHhC
Confidence 56889999999998877666654
No 327
>PF15387 DUF4611: Domain of unknown function (DUF4611)
Probab=22.60 E-value=44 Score=25.47 Aligned_cols=13 Identities=54% Similarity=0.711 Sum_probs=6.4
Q ss_pred CCCCCCCCCcccc
Q 018073 31 PAYAFDSDDADVA 43 (361)
Q Consensus 31 ~~~~~~~~~~~~~ 43 (361)
|+++++++|+||+
T Consensus 62 p~E~ldg~dedda 74 (96)
T PF15387_consen 62 PDEALDGDDEDDA 74 (96)
T ss_pred chhhccCcccccc
Confidence 4455555555444
No 328
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.59 E-value=44 Score=19.91 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=6.4
Q ss_pred CCCCCCCcce
Q 018073 300 KPCPRCKRPI 309 (361)
Q Consensus 300 k~CP~C~~~I 309 (361)
..||+|++-+
T Consensus 2 hlcpkcgvgv 11 (36)
T PF09151_consen 2 HLCPKCGVGV 11 (36)
T ss_dssp -B-TTTSSSB
T ss_pred ccCCccCceE
Confidence 3699999765
No 329
>PF14851 FAM176: FAM176 family
Probab=22.32 E-value=1.6e+02 Score=24.88 Aligned_cols=8 Identities=50% Similarity=0.530 Sum_probs=3.3
Q ss_pred HHHHHHHH
Q 018073 74 DIRQRQEE 81 (361)
Q Consensus 74 ~i~~~~~~ 81 (361)
+..+++++
T Consensus 120 e~A~rlEe 127 (153)
T PF14851_consen 120 ERAQRLEE 127 (153)
T ss_pred HHHHHHHH
Confidence 33444444
No 330
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.25 E-value=56 Score=23.66 Aligned_cols=44 Identities=30% Similarity=0.760 Sum_probs=30.7
Q ss_pred ccccccccccCCccccccC--CCcccHhhHHHHHHhhhcCCCCeeeeccCCCcCCCccc
Q 018073 143 TCGICFENYPSDRLLAAAC--GHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (361)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~C--gH~fC~~Cl~~~i~~~i~~~~~~~~i~CP~~~C~~~i~ 199 (361)
.|..|-.++++...-.+-| .|.||.+|...-+.- .|| .|+..+.
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g-----------~CP--nCGGelv 52 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLHG-----------LCP--NCGGELV 52 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC-----------cCC--CCCchhh
Confidence 4888887887765555556 589999998765432 488 7887653
No 331
>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=22.24 E-value=45 Score=18.96 Aligned_cols=20 Identities=25% Similarity=0.544 Sum_probs=14.7
Q ss_pred eccCCCcCCCccchhHHhhcCC
Q 018073 187 LRCPDPSCGAAVGQDMIYLLSS 208 (361)
Q Consensus 187 i~CP~~~C~~~i~~~~i~~ll~ 208 (361)
+.|| .|...+....++..+.
T Consensus 2 v~CP--iC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCP--VCFREVPENLINSHLD 21 (26)
T ss_pred CcCC--CCcCcccHHHHHHHHH
Confidence 5798 8998887777766553
No 332
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=22.23 E-value=65 Score=34.05 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=29.5
Q ss_pred CccccccccccccCCccccccCCCcccHhhHHHHHHh
Q 018073 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIST 176 (361)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~ 176 (361)
..+.|.||--.+.....+-..|+|.-..+|...|++.
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc
Confidence 3567888876665566666789999999999999987
No 333
>PRK02935 hypothetical protein; Provisional
Probab=21.97 E-value=39 Score=26.39 Aligned_cols=11 Identities=36% Similarity=1.156 Sum_probs=8.6
Q ss_pred CCCCCCCccee
Q 018073 300 KPCPRCKRPIE 310 (361)
Q Consensus 300 k~CP~C~~~Ie 310 (361)
..||+|+++.-
T Consensus 71 V~CP~C~K~TK 81 (110)
T PRK02935 71 VICPSCEKPTK 81 (110)
T ss_pred eECCCCCchhh
Confidence 37999998774
No 334
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.36 E-value=59 Score=24.79 Aligned_cols=37 Identities=30% Similarity=0.638 Sum_probs=27.5
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceecccccccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~h 339 (361)
.-.||.|+..-.|..+---=.|. +|+..|= |+.|.+.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~-~C~~~~A---GGAy~~~ 72 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECR-KCGAKFA---GGAYTPE 72 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcC-CCCCEEe---CCccccc
Confidence 35899999988888887778888 6888763 4455543
No 335
>TIGR01299 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam model pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices.
Probab=21.32 E-value=56 Score=34.98 Aligned_cols=17 Identities=6% Similarity=-0.005 Sum_probs=9.4
Q ss_pred HHHHHHHHHHhCCCHHH
Q 018073 80 EEDITRISTVLSISKVA 96 (361)
Q Consensus 80 ~~~i~~v~~~l~i~~~~ 96 (361)
.++.+.+.+.++.++-.
T Consensus 149 ~~~~d~~l~~~~~~~~~ 165 (742)
T TIGR01299 149 AQQYELIIQECGHGRFQ 165 (742)
T ss_pred HHHHHHHHHHcCCCHHH
Confidence 34445555556666644
No 336
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=21.31 E-value=38 Score=31.74 Aligned_cols=32 Identities=22% Similarity=0.300 Sum_probs=20.7
Q ss_pred ccccccccccccCCccccccCCCcccHhhHHHH
Q 018073 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGY 173 (361)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~ 173 (361)
...|.-|--.+. .--...+|.|.||.+|-+..
T Consensus 90 VHfCd~Cd~PI~-IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcce-eeecccccchhhhhhhhhcC
Confidence 456777753321 11235689999999998653
No 337
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.22 E-value=49 Score=31.32 Aligned_cols=9 Identities=44% Similarity=1.412 Sum_probs=5.1
Q ss_pred CCCcccHhh
Q 018073 161 CGHPFCSSC 169 (361)
Q Consensus 161 CgH~fC~~C 169 (361)
|.+.||.+|
T Consensus 351 Ck~~FCldC 359 (378)
T KOG2807|consen 351 CKNVFCLDC 359 (378)
T ss_pred ccceeeccc
Confidence 555555555
No 338
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=21.21 E-value=70 Score=30.34 Aligned_cols=79 Identities=18% Similarity=0.186 Sum_probs=39.0
Q ss_pred eeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChHHHHHHhhhcHHHHHHHcCCCCCCCC--C--CCCCCcccc
Q 018073 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAV--Q--FPDGEEMTC 144 (361)
Q Consensus 69 ~l~~~~i~~~~~~~i~~v~~~l~i~~~~a~~LL~~~~w~~~~l~e~~~~~~~~~~~~~~l~~~~~~--~--~~~~~~~~C 144 (361)
++|+..|.+.+.+.. .|.++.......| ...| + .+.|+...||..-+.. . .-..-.+-|
T Consensus 183 witp~ni~~~~~e~~-----al~~pe~~~Vac~----------TtDf-a-mQNVlLqm~L~l~~~~G~~Ir~~r~~iLRC 245 (376)
T KOG2463|consen 183 WITPSNITEAIIELG-----ALNRPENQLVACL----------TTDF-A-MQNVLLQMNLNLLAMSGMKIRSVRSYILRC 245 (376)
T ss_pred ccccchHHHHHHhhh-----cccccccceeeee----------cccH-H-HHHHHHHhcccccCccchhhhhhhhheeEe
Confidence 778888888877765 4444443311111 1111 0 2334444444332111 1 111224679
Q ss_pred ccccccccCC-ccccccCCCc
Q 018073 145 GICFENYPSD-RLLAAACGHP 164 (361)
Q Consensus 145 ~IC~e~~~~~-~~~~l~CgH~ 164 (361)
--||..++.. ..+-..|||.
T Consensus 246 h~Cfsit~~m~k~FCp~CG~~ 266 (376)
T KOG2463|consen 246 HGCFSITSEMPKDFCPSCGHK 266 (376)
T ss_pred eeeeEecCccchhcccccCCC
Confidence 9999887532 3344458876
No 339
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=21.15 E-value=61 Score=24.74 Aligned_cols=36 Identities=25% Similarity=0.507 Sum_probs=26.9
Q ss_pred cCCCCCCCcceeecCCCCceeecCCCccceeccccccccc
Q 018073 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (361)
Q Consensus 299 ~k~CP~C~~~IeK~~GCnhm~C~~~C~~~FCw~C~~~~~~ 338 (361)
.-.||.|+..-.|..+---=.|. +|+..|= |+.|.+
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~-~C~~~~A---GGAy~p 70 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCR-KCGAKFA---GGAYTP 70 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcC-CCCCEEe---CCcccc
Confidence 35899999888888777778888 6888763 445544
No 340
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.98 E-value=66 Score=27.14 Aligned_cols=26 Identities=19% Similarity=0.650 Sum_probs=18.0
Q ss_pred CCCCCCCcceeecCCCCceeecCCCccc
Q 018073 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (361)
Q Consensus 300 k~CP~C~~~IeK~~GCnhm~C~~~C~~~ 327 (361)
.-||+|++.+...+. ....|. +|+..
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~-~C~~~ 60 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCE-KCNKS 60 (166)
T ss_pred ccccccCcccEeCCC-CcEECC-CCCCc
Confidence 679999988876653 556676 56554
No 341
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.93 E-value=1.5e+02 Score=32.41 Aligned_cols=6 Identities=33% Similarity=0.744 Sum_probs=2.5
Q ss_pred cccccc
Q 018073 141 EMTCGI 146 (361)
Q Consensus 141 ~~~C~I 146 (361)
..-|.|
T Consensus 169 ~VKC~i 174 (1024)
T KOG1999|consen 169 IVKCKI 174 (1024)
T ss_pred EEEecc
Confidence 334444
No 342
>PF10245 MRP-S22: Mitochondrial 28S ribosomal protein S22; InterPro: IPR019374 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is the conserved N terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them [].
Probab=20.76 E-value=1.2e+02 Score=27.66 Aligned_cols=32 Identities=19% Similarity=0.433 Sum_probs=29.6
Q ss_pred CcceEeeCHHHHHHHHHHHHHHHHHHhCCCHH
Q 018073 64 QLNYTVLTEADIRQRQEEDITRISTVLSISKV 95 (361)
Q Consensus 64 ~~~~~~l~~~~i~~~~~~~i~~v~~~l~i~~~ 95 (361)
...|+.||.+++...+.+.+.+....|++||.
T Consensus 34 ~p~yklMTdeql~~~~~~~~~~a~~~LqMPPV 65 (243)
T PF10245_consen 34 PPTYKLMTDEQLEEALEKAIEKAKKLLQMPPV 65 (243)
T ss_pred CCeeEeCCHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 45799999999999999999999999999984
No 343
>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=20.62 E-value=54 Score=21.14 Aligned_cols=12 Identities=58% Similarity=1.207 Sum_probs=9.9
Q ss_pred cCCCCCCCccee
Q 018073 299 SKPCPRCKRPIE 310 (361)
Q Consensus 299 ~k~CP~C~~~Ie 310 (361)
+|.||.|++++.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 489999998874
No 344
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=20.53 E-value=1.8e+02 Score=24.38 Aligned_cols=6 Identities=17% Similarity=0.429 Sum_probs=2.3
Q ss_pred hHHHHH
Q 018073 108 VSKVHD 113 (361)
Q Consensus 108 ~~~l~e 113 (361)
..+|++
T Consensus 139 ~~kLl~ 144 (149)
T PF08595_consen 139 LKKLLE 144 (149)
T ss_pred HHHHHH
Confidence 334443
No 345
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.34 E-value=81 Score=33.56 Aligned_cols=41 Identities=12% Similarity=0.159 Sum_probs=26.5
Q ss_pred ccccccccccccC--Ccccccc---CCCcccHhhHHHHHHhhhcCC
Q 018073 141 EMTCGICFENYPS--DRLLAAA---CGHPFCSSCWTGYISTAINDG 181 (361)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~---CgH~fC~~Cl~~~i~~~i~~~ 181 (361)
..+|.+|.-++.. +..-.++ |+|.+|..||..+....+...
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~ 141 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESE 141 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccc
Confidence 3456666544432 1222333 999999999999998776543
No 346
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.08 E-value=62 Score=21.68 Aligned_cols=11 Identities=36% Similarity=0.751 Sum_probs=7.4
Q ss_pred CCCCCCCccee
Q 018073 300 KPCPRCKRPIE 310 (361)
Q Consensus 300 k~CP~C~~~Ie 310 (361)
.+||.|+..|-
T Consensus 25 irCp~Cg~rIl 35 (49)
T COG1996 25 IRCPYCGSRIL 35 (49)
T ss_pred eeCCCCCcEEE
Confidence 57777776653
Done!