Query 016355
Match_columns 391
No_of_seqs 389 out of 1595
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 06:06:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016355.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016355hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 4.8E-42 1E-46 335.4 15.9 254 22-292 98-355 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 5.6E-36 1.2E-40 281.7 9.8 197 72-282 181-407 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 1.1E-33 2.4E-38 283.9 9.7 211 71-297 66-284 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 6E-28 1.3E-32 219.8 10.2 192 72-281 218-437 (446)
5 smart00647 IBR In Between Ring 99.2 3E-11 6.4E-16 88.4 5.2 63 145-217 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 2.2E-11 4.7E-16 89.1 1.1 63 145-217 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.4 8.1E-08 1.8E-12 63.8 1.3 41 78-123 1-41 (42)
8 smart00647 IBR In Between Ring 98.4 4.5E-07 9.8E-12 66.0 4.4 44 238-281 12-60 (64)
9 PF01485 IBR: IBR domain; Int 98.3 1.9E-07 4.1E-12 68.0 1.2 41 241-281 15-60 (64)
10 PF13639 zf-RING_2: Ring finge 98.2 7.4E-07 1.6E-11 59.9 2.7 40 77-123 2-42 (44)
11 KOG0320 Predicted E3 ubiquitin 98.2 1.1E-06 2.4E-11 75.3 3.0 57 72-137 128-184 (187)
12 PF00097 zf-C3HC4: Zinc finger 98.2 1.5E-06 3.1E-11 57.5 3.0 40 78-123 1-40 (41)
13 PF13923 zf-C3HC4_2: Zinc fing 98.1 1.3E-06 2.9E-11 57.0 2.1 38 78-123 1-38 (39)
14 PLN03208 E3 ubiquitin-protein 98.1 2.2E-06 4.8E-11 75.4 3.8 64 73-140 16-88 (193)
15 PF14634 zf-RING_5: zinc-RING 98.0 5.2E-06 1.1E-10 55.8 3.1 42 77-127 1-43 (44)
16 cd00162 RING RING-finger (Real 97.9 1.6E-05 3.4E-10 52.9 4.0 43 77-129 1-44 (45)
17 PHA02926 zinc finger-like prot 97.8 1.5E-05 3.3E-10 70.9 3.7 57 72-131 167-230 (242)
18 PF13445 zf-RING_UBOX: RING-ty 97.8 2.8E-05 6.1E-10 51.7 3.3 41 78-122 1-43 (43)
19 PF13920 zf-C3HC4_3: Zinc fing 97.7 2.8E-05 6.1E-10 53.7 3.2 46 75-131 2-48 (50)
20 smart00184 RING Ring finger. E 97.6 6.1E-05 1.3E-09 48.2 3.3 38 78-123 1-38 (39)
21 KOG0823 Predicted E3 ubiquitin 97.6 3.8E-05 8.2E-10 68.9 2.5 60 72-139 44-103 (230)
22 KOG2164 Predicted E3 ubiquitin 97.6 3.5E-05 7.5E-10 76.5 2.2 60 75-140 186-245 (513)
23 KOG2177 Predicted E3 ubiquitin 97.6 0.00012 2.7E-09 69.6 6.0 108 73-217 11-122 (386)
24 smart00504 Ubox Modified RING 97.4 0.0003 6.5E-09 50.8 4.6 49 76-135 2-50 (63)
25 PHA02929 N1R/p28-like protein; 97.4 0.00019 4.1E-09 65.9 4.2 50 73-131 172-227 (238)
26 TIGR00599 rad18 DNA repair pro 97.2 0.00028 6.2E-09 69.5 3.5 66 72-148 23-89 (397)
27 KOG0287 Postreplication repair 97.0 0.00038 8.3E-09 65.5 2.3 64 74-148 22-86 (442)
28 TIGR00570 cdk7 CDK-activating 97.0 0.0015 3.3E-08 61.9 6.3 54 76-137 4-60 (309)
29 KOG0978 E3 ubiquitin ligase in 97.0 0.00025 5.4E-09 73.8 0.8 56 73-138 641-696 (698)
30 KOG0317 Predicted E3 ubiquitin 96.9 0.00039 8.4E-09 64.4 1.7 52 72-134 236-287 (293)
31 COG5540 RING-finger-containing 96.8 0.00061 1.3E-08 63.3 2.3 55 70-132 318-373 (374)
32 KOG4628 Predicted E3 ubiquitin 96.4 0.0021 4.5E-08 62.0 3.0 48 75-130 229-277 (348)
33 PF11789 zf-Nse: Zinc-finger o 96.3 0.0039 8.4E-08 44.2 2.8 50 72-127 8-57 (57)
34 PF12678 zf-rbx1: RING-H2 zinc 96.2 0.0041 8.8E-08 46.5 2.7 41 76-123 20-71 (73)
35 KOG1002 Nucleotide excision re 96.1 0.0031 6.8E-08 62.8 2.4 58 71-134 532-589 (791)
36 PF14835 zf-RING_6: zf-RING of 96.1 0.00059 1.3E-08 48.9 -1.9 47 75-134 7-54 (65)
37 COG5574 PEX10 RING-finger-cont 95.6 0.0075 1.6E-07 55.4 2.5 54 73-135 213-266 (271)
38 PF11793 FANCL_C: FANCL C-term 95.3 0.0095 2.1E-07 44.1 1.6 56 75-132 2-67 (70)
39 COG5432 RAD18 RING-finger-cont 95.2 0.015 3.3E-07 53.9 2.8 67 71-148 21-88 (391)
40 COG5243 HRD1 HRD ubiquitin lig 95.1 0.038 8.2E-07 53.0 5.5 51 73-132 285-346 (491)
41 KOG2879 Predicted E3 ubiquitin 94.8 0.037 8E-07 51.1 4.3 52 72-131 236-287 (298)
42 KOG1039 Predicted E3 ubiquitin 94.7 0.023 4.9E-07 55.1 3.0 93 72-166 158-264 (344)
43 KOG1814 Predicted E3 ubiquitin 94.7 0.022 4.7E-07 55.5 2.8 44 242-286 271-317 (445)
44 PF10571 UPF0547: Uncharacteri 94.1 0.019 4.2E-07 33.7 0.6 23 245-271 1-24 (26)
45 KOG4367 Predicted Zn-finger pr 94.0 0.11 2.5E-06 50.8 5.9 79 191-281 174-255 (699)
46 KOG1812 Predicted E3 ubiquitin 93.8 0.015 3.2E-07 57.7 -0.5 43 159-216 304-346 (384)
47 KOG0824 Predicted E3 ubiquitin 93.7 0.034 7.5E-07 52.0 1.8 52 74-135 6-57 (324)
48 PF04564 U-box: U-box domain; 93.4 0.046 9.9E-07 40.8 1.7 50 74-133 3-52 (73)
49 PF14570 zf-RING_4: RING/Ubox 93.1 0.07 1.5E-06 36.2 2.1 45 78-130 1-47 (48)
50 KOG1428 Inhibitor of type V ad 92.8 0.16 3.5E-06 56.6 5.2 68 72-141 3483-3554(3738)
51 KOG0006 E3 ubiquitin-protein l 92.5 0.21 4.5E-06 47.1 5.0 96 91-214 336-438 (446)
52 KOG2660 Locus-specific chromos 91.9 0.081 1.7E-06 50.3 1.6 47 73-130 13-60 (331)
53 PF05883 Baculo_RING: Baculovi 91.7 0.079 1.7E-06 44.0 1.2 37 73-109 24-67 (134)
54 PHA00626 hypothetical protein 91.7 0.14 2.9E-06 35.6 2.1 27 246-272 2-34 (59)
55 COG5152 Uncharacterized conser 91.5 0.081 1.8E-06 46.5 1.0 35 72-108 193-227 (259)
56 KOG1645 RING-finger-containing 90.7 0.2 4.2E-06 49.0 2.9 50 75-131 4-56 (463)
57 KOG3002 Zn finger protein [Gen 90.6 0.15 3.3E-06 48.7 2.1 48 71-131 44-91 (299)
58 smart00661 RPOL9 RNA polymeras 90.4 0.19 4.1E-06 34.6 1.9 27 245-271 1-30 (52)
59 KOG4739 Uncharacterized protei 90.1 0.088 1.9E-06 48.0 0.0 59 75-144 3-61 (233)
60 KOG4159 Predicted E3 ubiquitin 89.6 0.46 9.9E-06 47.2 4.6 49 72-131 81-129 (398)
61 PF07975 C1_4: TFIIH C1-like d 89.6 0.22 4.7E-06 34.3 1.6 24 192-215 20-43 (51)
62 KOG4185 Predicted E3 ubiquitin 89.6 0.66 1.4E-05 44.3 5.6 56 75-138 3-64 (296)
63 PF12861 zf-Apc11: Anaphase-pr 89.5 0.28 6.1E-06 37.5 2.3 32 94-131 51-82 (85)
64 COG5220 TFB3 Cdk activating ki 89.4 0.12 2.5E-06 46.9 0.2 51 75-131 10-64 (314)
65 KOG4445 Uncharacterized conser 89.4 0.69 1.5E-05 43.4 5.2 85 15-112 68-153 (368)
66 KOG0311 Predicted E3 ubiquitin 88.8 0.063 1.4E-06 51.4 -2.0 47 74-129 42-88 (381)
67 KOG4265 Predicted E3 ubiquitin 88.7 0.48 1E-05 45.7 3.8 63 57-130 267-335 (349)
68 KOG1815 Predicted E3 ubiquitin 88.6 0.27 5.8E-06 50.0 2.2 42 241-282 155-199 (444)
69 PF13248 zf-ribbon_3: zinc-rib 88.4 0.24 5.2E-06 29.0 1.0 23 245-278 3-25 (26)
70 smart00744 RINGv The RING-vari 88.1 0.66 1.4E-05 31.7 3.2 42 77-123 1-47 (49)
71 KOG3579 Predicted E3 ubiquitin 87.7 0.42 9.1E-06 44.4 2.6 69 72-142 265-343 (352)
72 PRK00398 rpoP DNA-directed RNA 87.7 0.46 1E-05 31.9 2.2 29 245-273 4-33 (46)
73 PRK00432 30S ribosomal protein 87.6 0.36 7.9E-06 33.1 1.7 25 245-271 21-47 (50)
74 COG5175 MOT2 Transcriptional r 87.1 0.43 9.3E-06 45.4 2.4 51 78-136 17-69 (480)
75 PF13240 zinc_ribbon_2: zinc-r 87.0 0.27 5.9E-06 27.9 0.6 11 246-256 1-11 (23)
76 PRK14559 putative protein seri 86.9 0.36 7.8E-06 51.1 2.0 30 245-280 16-52 (645)
77 PF13719 zinc_ribbon_5: zinc-r 86.5 0.63 1.4E-05 29.7 2.2 33 162-203 3-35 (37)
78 PHA03096 p28-like protein; Pro 86.1 0.41 8.9E-06 45.4 1.8 38 76-113 179-222 (284)
79 KOG1734 Predicted RING-contain 86.1 0.23 4.9E-06 45.9 0.0 54 74-134 223-284 (328)
80 KOG0802 E3 ubiquitin ligase [P 86.1 0.47 1E-05 49.5 2.3 46 74-128 290-338 (543)
81 KOG4172 Predicted E3 ubiquitin 85.8 0.2 4.4E-06 34.5 -0.3 44 76-130 8-53 (62)
82 TIGR02098 MJ0042_CXXC MJ0042 f 85.7 0.65 1.4E-05 29.6 2.1 26 245-271 3-35 (38)
83 KOG0828 Predicted E3 ubiquitin 85.6 0.45 9.7E-06 47.6 1.7 52 72-131 568-634 (636)
84 PF13717 zinc_ribbon_4: zinc-r 85.4 0.83 1.8E-05 29.0 2.3 33 162-203 3-35 (36)
85 PF13719 zinc_ribbon_5: zinc-r 85.1 0.66 1.4E-05 29.6 1.8 27 245-271 3-35 (37)
86 KOG0317 Predicted E3 ubiquitin 85.0 0.18 3.9E-06 47.1 -1.2 36 245-286 240-276 (293)
87 KOG1952 Transcription factor N 84.1 0.91 2E-05 48.4 3.3 51 73-123 189-241 (950)
88 PF09297 zf-NADH-PPase: NADH p 82.7 1.6 3.6E-05 26.7 2.8 26 245-270 4-30 (32)
89 PLN03086 PRLI-interacting fact 82.6 1.7 3.7E-05 45.1 4.5 56 118-203 407-463 (567)
90 PF08274 PhnA_Zn_Ribbon: PhnA 81.8 1.1 2.3E-05 27.3 1.7 26 245-271 3-29 (30)
91 PF00097 zf-C3HC4: Zinc finger 81.7 0.25 5.5E-06 32.0 -1.2 38 247-289 1-39 (41)
92 PF15227 zf-C3HC4_4: zinc fing 81.4 0.66 1.4E-05 30.5 0.7 32 247-283 1-32 (42)
93 PF09538 FYDLN_acid: Protein o 80.3 0.85 1.8E-05 36.8 1.1 26 245-271 10-36 (108)
94 KOG1001 Helicase-like transcri 80.1 0.72 1.6E-05 49.1 0.9 51 76-136 455-505 (674)
95 KOG2807 RNA polymerase II tran 80.0 0.82 1.8E-05 43.4 1.1 23 192-214 344-366 (378)
96 COG1998 RPS31 Ribosomal protei 79.8 1.1 2.4E-05 30.3 1.4 25 245-269 20-45 (51)
97 PF10367 Vps39_2: Vacuolar sor 79.6 1.1 2.5E-05 35.5 1.7 32 74-105 77-108 (109)
98 PRK05654 acetyl-CoA carboxylas 79.1 0.37 8E-06 46.0 -1.5 30 242-271 25-56 (292)
99 PF05290 Baculo_IE-1: Baculovi 78.4 2 4.4E-05 35.5 2.8 53 73-131 78-132 (140)
100 PF14952 zf-tcix: Putative tre 77.8 1.1 2.4E-05 29.5 0.9 25 243-271 10-37 (44)
101 PRK14714 DNA polymerase II lar 77.8 1.1 2.4E-05 50.0 1.5 30 245-280 668-703 (1337)
102 KOG1785 Tyrosine kinase negati 77.7 0.77 1.7E-05 44.7 0.2 45 74-126 368-413 (563)
103 PRK04023 DNA polymerase II lar 76.9 1.4 3E-05 48.2 1.8 40 244-291 626-672 (1121)
104 PF14447 Prok-RING_4: Prokaryo 76.5 1.2 2.5E-05 31.1 0.8 46 75-133 7-52 (55)
105 KOG4692 Predicted E3 ubiquitin 76.5 1.9 4.2E-05 41.4 2.4 49 73-132 420-468 (489)
106 PF04641 Rtf2: Rtf2 RING-finge 76.3 3 6.5E-05 39.2 3.7 70 72-151 110-182 (260)
107 TIGR00515 accD acetyl-CoA carb 74.6 0.62 1.3E-05 44.3 -1.3 30 243-272 25-56 (285)
108 PRK14559 putative protein seri 74.6 2.4 5.2E-05 45.0 2.9 11 245-255 42-52 (645)
109 KOG3800 Predicted E3 ubiquitin 74.2 2.8 6.2E-05 39.3 2.9 52 77-136 2-56 (300)
110 CHL00174 accD acetyl-CoA carbo 73.7 0.59 1.3E-05 44.5 -1.7 31 243-273 37-69 (296)
111 KOG2817 Predicted E3 ubiquitin 73.3 3.6 7.9E-05 40.3 3.5 59 73-137 332-391 (394)
112 PF06677 Auto_anti-p27: Sjogre 73.2 3 6.4E-05 27.4 2.0 22 245-268 18-41 (41)
113 COG1997 RPL43A Ribosomal prote 73.1 4.7 0.0001 30.9 3.3 27 245-271 36-63 (89)
114 COG1198 PriA Primosomal protei 73.0 2.5 5.5E-05 45.3 2.6 34 245-278 445-484 (730)
115 PRK08665 ribonucleotide-diphos 72.8 1.9 4E-05 46.8 1.6 26 245-272 725-751 (752)
116 PF02150 RNA_POL_M_15KD: RNA p 72.7 3.2 7E-05 26.1 2.0 27 245-271 2-30 (35)
117 KOG2807 RNA polymerase II tran 72.6 3.6 7.7E-05 39.3 3.2 43 76-127 331-374 (378)
118 COG0777 AccD Acetyl-CoA carbox 72.6 1.2 2.5E-05 41.6 -0.0 34 241-274 25-60 (294)
119 COG5219 Uncharacterized conser 72.2 2.8 6E-05 45.5 2.6 50 74-131 1468-1523(1525)
120 KOG0823 Predicted E3 ubiquitin 72.1 1.1 2.4E-05 40.7 -0.3 19 266-284 64-82 (230)
121 PF03833 PolC_DP2: DNA polymer 71.5 1.3 2.8E-05 47.6 0.0 33 244-282 655-693 (900)
122 TIGR00622 ssl1 transcription f 71.3 2.8 6.1E-05 33.9 1.9 23 192-214 80-102 (112)
123 PRK14714 DNA polymerase II lar 71.1 3 6.6E-05 46.8 2.7 15 355-369 799-813 (1337)
124 KOG3039 Uncharacterized conser 70.9 3.5 7.5E-05 37.8 2.6 54 73-135 219-274 (303)
125 PF12773 DZR: Double zinc ribb 70.5 2.9 6.2E-05 28.3 1.6 11 245-255 13-23 (50)
126 KOG0297 TNF receptor-associate 69.9 2.5 5.4E-05 42.2 1.6 36 73-110 19-55 (391)
127 KOG1813 Predicted E3 ubiquitin 69.5 1.6 3.5E-05 41.0 0.2 46 74-130 240-285 (313)
128 KOG0978 E3 ubiquitin ligase in 69.5 1.4 3.1E-05 46.6 -0.2 13 198-210 660-672 (698)
129 KOG0320 Predicted E3 ubiquitin 69.4 2.1 4.7E-05 37.3 0.9 12 198-209 150-161 (187)
130 PF07191 zinc-ribbons_6: zinc- 68.9 4 8.7E-05 30.0 2.1 33 246-280 3-41 (70)
131 PF14149 YhfH: YhfH-like prote 68.6 0.55 1.2E-05 29.9 -2.1 29 239-267 8-37 (37)
132 PF01599 Ribosomal_S27: Riboso 68.4 3.1 6.8E-05 28.1 1.3 25 245-269 19-46 (47)
133 PF14803 Nudix_N_2: Nudix N-te 68.1 4.2 9.1E-05 25.5 1.8 25 245-269 1-30 (34)
134 TIGR01384 TFS_arch transcripti 67.8 3.1 6.8E-05 33.0 1.5 24 245-270 1-25 (104)
135 KOG0827 Predicted E3 ubiquitin 67.8 2.8 6.2E-05 40.9 1.5 47 75-127 4-52 (465)
136 PRK00420 hypothetical protein; 67.0 3.7 8.1E-05 33.2 1.8 27 245-280 24-51 (112)
137 PF10083 DUF2321: Uncharacteri 65.9 4.2 9.2E-05 34.7 2.0 33 245-280 40-79 (158)
138 PF07282 OrfB_Zn_ribbon: Putat 65.4 4.3 9.3E-05 29.5 1.7 26 245-270 29-55 (69)
139 KOG0804 Cytoplasmic Zn-finger 65.0 4.3 9.3E-05 40.4 2.1 47 73-130 173-221 (493)
140 KOG2906 RNA polymerase III sub 64.7 4.4 9.4E-05 31.7 1.7 29 246-274 3-34 (105)
141 KOG2034 Vacuolar sorting prote 64.5 8.2 0.00018 41.8 4.2 39 73-111 815-853 (911)
142 KOG1493 Anaphase-promoting com 63.8 1.6 3.4E-05 32.5 -0.9 48 77-130 22-80 (84)
143 COG1645 Uncharacterized Zn-fin 63.8 4.4 9.6E-05 33.6 1.7 24 245-277 29-52 (131)
144 PF14835 zf-RING_6: zf-RING of 63.0 3.6 7.8E-05 29.7 0.9 29 245-280 8-39 (65)
145 COG2888 Predicted Zn-ribbon RN 63.0 3.7 8.1E-05 29.0 0.9 16 245-260 28-44 (61)
146 PLN03208 E3 ubiquitin-protein 62.9 1.5 3.3E-05 38.9 -1.2 32 244-280 18-49 (193)
147 PRK04023 DNA polymerase II lar 62.9 4.9 0.00011 44.2 2.2 15 355-369 752-766 (1121)
148 KOG0826 Predicted E3 ubiquitin 62.6 9 0.0002 36.7 3.7 49 73-129 298-346 (357)
149 TIGR01206 lysW lysine biosynth 62.4 7 0.00015 27.3 2.2 28 245-272 3-33 (54)
150 TIGR00570 cdk7 CDK-activating 62.2 10 0.00022 36.3 4.1 35 245-279 4-38 (309)
151 PRK14892 putative transcriptio 62.0 5.6 0.00012 31.5 1.9 27 245-271 22-52 (99)
152 TIGR02300 FYDLN_acid conserved 61.4 4.3 9.3E-05 33.4 1.2 26 245-271 10-36 (129)
153 PF14569 zf-UDP: Zinc-binding 60.8 4.6 9.9E-05 30.2 1.1 45 190-262 25-69 (80)
154 PF03119 DNA_ligase_ZBD: NAD-d 60.2 8.7 0.00019 22.8 2.1 20 246-265 1-20 (28)
155 PF02891 zf-MIZ: MIZ/SP-RING z 60.2 7 0.00015 26.7 1.9 47 76-128 3-49 (50)
156 PF14353 CpXC: CpXC protein 59.8 7.2 0.00016 32.2 2.3 10 245-254 39-48 (128)
157 KOG4275 Predicted E3 ubiquitin 59.7 2.7 5.9E-05 39.4 -0.3 29 75-105 300-329 (350)
158 PHA02929 N1R/p28-like protein; 59.6 5 0.00011 37.1 1.5 43 244-286 174-219 (238)
159 PF08271 TF_Zn_Ribbon: TFIIB z 58.9 9.6 0.00021 25.0 2.4 24 246-269 2-27 (43)
160 PF09788 Tmemb_55A: Transmembr 58.9 12 0.00026 34.7 3.7 45 159-203 121-167 (256)
161 TIGR03655 anti_R_Lar restricti 57.7 7.9 0.00017 26.7 1.9 26 245-270 2-35 (53)
162 PF07975 C1_4: TFIIH C1-like d 56.2 7.8 0.00017 26.7 1.6 26 78-103 2-35 (51)
163 TIGR00686 phnA alkylphosphonat 55.9 8 0.00017 30.9 1.8 25 245-270 3-28 (109)
164 KOG2114 Vacuolar assembly/sort 55.6 12 0.00026 40.3 3.6 40 76-128 841-880 (933)
165 COG1594 RPB9 DNA-directed RNA 55.3 9.2 0.0002 31.1 2.2 27 245-271 3-32 (113)
166 COG5432 RAD18 RING-finger-cont 54.2 3.9 8.5E-05 38.4 -0.2 41 245-294 26-68 (391)
167 PF01428 zf-AN1: AN1-like Zinc 54.2 9.9 0.00021 25.0 1.8 25 193-219 13-37 (43)
168 COG1579 Zn-ribbon protein, pos 54.0 13 0.00027 34.4 3.1 62 133-202 166-230 (239)
169 KOG4684 Uncharacterized conser 53.1 15 0.00033 33.0 3.3 22 158-179 135-156 (275)
170 PRK09710 lar restriction allev 52.8 12 0.00026 27.0 2.1 27 243-269 5-35 (64)
171 KOG1941 Acetylcholine receptor 52.1 5 0.00011 39.2 0.2 48 74-128 364-413 (518)
172 TIGR00595 priA primosomal prot 51.8 10 0.00022 39.2 2.4 34 245-278 223-262 (505)
173 PF14569 zf-UDP: Zinc-binding 51.2 25 0.00053 26.4 3.6 50 73-130 7-61 (80)
174 KOG3970 Predicted E3 ubiquitin 51.1 17 0.00036 33.0 3.2 56 73-130 48-104 (299)
175 PF06827 zf-FPG_IleRS: Zinc fi 51.0 11 0.00023 22.6 1.5 23 245-267 2-27 (30)
176 PF10122 Mu-like_Com: Mu-like 50.5 5.9 0.00013 27.1 0.3 25 245-269 5-32 (51)
177 PF06906 DUF1272: Protein of u 49.9 14 0.00031 25.8 2.0 45 76-131 6-52 (57)
178 PF12906 RINGv: RING-variant d 49.9 12 0.00026 25.1 1.7 33 78-110 1-38 (47)
179 PF13453 zf-TFIIB: Transcripti 49.3 11 0.00023 24.5 1.3 30 246-280 1-30 (41)
180 PF13834 DUF4193: Domain of un 49.0 6.3 0.00014 31.0 0.3 33 71-103 66-98 (99)
181 KOG0825 PHD Zn-finger protein 48.9 5 0.00011 42.7 -0.4 21 94-114 120-140 (1134)
182 smart00659 RPOLCX RNA polymera 48.6 13 0.00029 24.7 1.7 23 246-269 4-27 (44)
183 KOG3053 Uncharacterized conser 48.6 14 0.0003 34.2 2.4 56 72-129 17-80 (293)
184 PF08792 A2L_zn_ribbon: A2L zi 48.5 16 0.00035 22.6 2.0 27 245-271 4-31 (33)
185 TIGR02443 conserved hypothetic 48.3 17 0.00037 25.7 2.3 27 245-271 10-41 (59)
186 PRK10220 hypothetical protein; 48.2 13 0.00028 29.8 1.8 25 245-270 4-29 (111)
187 COG3813 Uncharacterized protei 47.7 13 0.00028 27.4 1.6 44 77-131 7-52 (84)
188 PF09526 DUF2387: Probable met 47.7 17 0.00037 26.9 2.4 26 245-270 9-39 (71)
189 PLN03086 PRLI-interacting fact 47.5 29 0.00063 36.3 4.8 27 245-271 434-463 (567)
190 PF14471 DUF4428: Domain of un 46.9 17 0.00038 24.9 2.1 30 77-107 1-30 (51)
191 PRK14873 primosome assembly pr 46.8 13 0.00028 39.9 2.2 34 245-278 393-431 (665)
192 PF06844 DUF1244: Protein of u 46.5 15 0.00032 26.6 1.8 17 99-115 12-28 (68)
193 PF01363 FYVE: FYVE zinc finge 45.8 18 0.00039 26.1 2.3 34 245-280 10-44 (69)
194 PF14445 Prok-RING_2: Prokaryo 45.4 4.2 9.1E-05 27.7 -1.1 34 74-107 6-40 (57)
195 PRK11827 hypothetical protein; 45.1 16 0.00036 26.0 1.8 25 245-269 9-34 (60)
196 PF05129 Elf1: Transcription e 44.5 13 0.00029 28.2 1.4 27 245-271 23-56 (81)
197 smart00249 PHD PHD zinc finger 44.3 12 0.00025 24.1 1.0 32 77-108 1-33 (47)
198 PF12760 Zn_Tnp_IS1595: Transp 44.3 44 0.00094 22.2 3.8 25 245-269 19-45 (46)
199 COG2816 NPY1 NTP pyrophosphohy 44.2 21 0.00046 33.7 3.0 27 245-271 112-139 (279)
200 KOG0824 Predicted E3 ubiquitin 44.2 5.9 0.00013 37.5 -0.7 27 245-280 8-38 (324)
201 PF07754 DUF1610: Domain of un 43.4 16 0.00034 21.0 1.2 7 245-251 17-23 (24)
202 PRK05580 primosome assembly pr 42.8 17 0.00037 39.1 2.4 34 245-278 391-430 (679)
203 PF12677 DUF3797: Domain of un 42.7 20 0.00043 24.3 1.8 27 244-270 13-47 (49)
204 PF02318 FYVE_2: FYVE-type zin 42.3 34 0.00074 27.8 3.6 35 243-278 53-88 (118)
205 PF09723 Zn-ribbon_8: Zinc rib 42.2 27 0.00059 22.8 2.4 12 245-256 27-39 (42)
206 PF02318 FYVE_2: FYVE-type zin 41.6 18 0.00039 29.5 1.9 33 74-106 53-88 (118)
207 PLN02189 cellulose synthase 41.1 16 0.00034 40.7 1.9 46 190-263 50-95 (1040)
208 smart00834 CxxC_CXXC_SSSS Puta 40.6 14 0.00031 23.5 0.9 12 245-256 27-38 (41)
209 PRK09521 exosome complex RNA-b 40.2 18 0.00039 32.1 1.8 25 245-270 150-175 (189)
210 PF14354 Lar_restr_allev: Rest 39.9 23 0.00049 24.9 2.0 12 244-255 3-14 (61)
211 COG5574 PEX10 RING-finger-cont 39.3 7.4 0.00016 36.2 -0.8 37 73-109 93-132 (271)
212 KOG2930 SCF ubiquitin ligase, 38.7 22 0.00047 28.2 1.8 29 88-123 72-102 (114)
213 PF14446 Prok-RING_1: Prokaryo 37.7 43 0.00093 23.3 2.9 32 75-106 5-38 (54)
214 smart00531 TFIIE Transcription 37.4 27 0.00059 29.6 2.4 36 158-201 96-131 (147)
215 COG1096 Predicted RNA-binding 37.2 21 0.00045 31.6 1.6 24 245-270 150-174 (188)
216 PF10272 Tmpp129: Putative tra 37.0 68 0.0015 31.6 5.3 75 55-131 249-351 (358)
217 cd04476 RPA1_DBD_C RPA1_DBD_C: 36.8 33 0.00072 29.5 2.9 26 244-270 34-60 (166)
218 KOG2462 C2H2-type Zn-finger pr 36.7 9.2 0.0002 35.8 -0.6 110 73-204 128-254 (279)
219 PLN02189 cellulose synthase 36.6 31 0.00068 38.4 3.2 50 73-130 32-86 (1040)
220 PLN02436 cellulose synthase A 35.8 33 0.00071 38.4 3.2 50 73-130 34-88 (1094)
221 KOG1571 Predicted E3 ubiquitin 35.6 30 0.00065 33.7 2.6 45 72-130 302-346 (355)
222 PLN02638 cellulose synthase A 35.3 35 0.00076 38.2 3.4 50 73-130 15-69 (1079)
223 smart00064 FYVE Protein presen 35.3 32 0.00069 24.7 2.2 36 75-110 10-47 (68)
224 PLN02638 cellulose synthase A 35.0 20 0.00042 40.1 1.4 46 190-263 33-78 (1079)
225 COG0266 Nei Formamidopyrimidin 35.0 28 0.0006 32.9 2.2 24 245-268 246-272 (273)
226 KOG0309 Conserved WD40 repeat- 34.9 27 0.00059 37.3 2.3 50 72-128 1025-1075(1081)
227 PHA02926 zinc finger-like prot 34.9 20 0.00043 32.7 1.2 39 244-282 170-212 (242)
228 PF03604 DNA_RNApol_7kD: DNA d 34.8 15 0.00033 22.6 0.3 10 245-254 18-27 (32)
229 PRK14890 putative Zn-ribbon RN 34.6 25 0.00054 24.9 1.4 34 245-278 8-45 (59)
230 TIGR00622 ssl1 transcription f 34.4 22 0.00047 28.8 1.2 44 75-127 55-110 (112)
231 PRK08115 ribonucleotide-diphos 34.2 19 0.0004 39.6 1.1 24 245-270 828-853 (858)
232 PF05715 zf-piccolo: Piccolo Z 34.1 13 0.00028 26.3 -0.1 36 245-280 3-41 (61)
233 KOG2164 Predicted E3 ubiquitin 34.0 21 0.00045 36.4 1.3 35 198-256 203-237 (513)
234 cd00021 BBOX B-Box-type zinc f 34.0 25 0.00054 21.9 1.3 25 192-216 11-35 (39)
235 PLN02436 cellulose synthase A 33.7 25 0.00054 39.3 1.9 46 190-263 52-97 (1094)
236 PF03884 DUF329: Domain of unk 33.4 11 0.00024 26.6 -0.5 13 245-257 3-15 (57)
237 COG5175 MOT2 Transcriptional r 33.4 16 0.00034 35.2 0.3 50 246-296 16-68 (480)
238 PF03833 PolC_DP2: DNA polymer 33.2 14 0.00031 40.0 0.0 15 355-369 781-795 (900)
239 KOG3161 Predicted E3 ubiquitin 33.0 12 0.00026 39.1 -0.5 35 75-109 11-47 (861)
240 PF13901 DUF4206: Domain of un 32.8 97 0.0021 27.8 5.3 23 128-150 112-134 (202)
241 KOG3268 Predicted E3 ubiquitin 32.7 55 0.0012 28.6 3.5 58 72-131 162-228 (234)
242 KOG2979 Protein involved in DN 32.6 42 0.00092 31.2 2.9 48 75-128 176-223 (262)
243 COG5194 APC11 Component of SCF 32.5 35 0.00076 25.7 2.0 35 76-110 32-69 (88)
244 KOG2932 E3 ubiquitin ligase in 32.4 22 0.00047 33.9 1.1 31 75-107 90-121 (389)
245 PHA02825 LAP/PHD finger-like p 32.2 47 0.001 28.6 3.0 50 74-131 7-59 (162)
246 PF01396 zf-C4_Topoisom: Topoi 31.9 43 0.00093 21.5 2.1 20 245-265 2-24 (39)
247 PRK00241 nudC NADH pyrophospha 31.5 45 0.00098 31.2 3.1 27 244-270 99-126 (256)
248 PF00643 zf-B_box: B-box zinc 31.3 17 0.00037 23.3 0.2 24 192-215 14-37 (42)
249 PF12861 zf-Apc11: Anaphase-pr 31.3 25 0.00054 27.0 1.0 43 245-290 33-76 (85)
250 PF08746 zf-RING-like: RING-li 31.1 48 0.0011 21.8 2.3 41 78-123 1-42 (43)
251 COG3492 Uncharacterized protei 31.1 39 0.00085 26.1 2.1 16 99-114 43-58 (104)
252 COG5151 SSL1 RNA polymerase II 30.9 15 0.00033 34.9 -0.2 21 193-213 388-408 (421)
253 PRK14811 formamidopyrimidine-D 30.6 36 0.00078 32.1 2.2 21 245-265 236-258 (269)
254 KOG2789 Putative Zn-finger pro 30.5 18 0.00038 35.6 0.1 37 72-108 71-107 (482)
255 COG5222 Uncharacterized conser 30.3 44 0.00096 31.7 2.7 44 76-128 275-318 (427)
256 PRK06266 transcription initiat 30.2 37 0.0008 29.9 2.1 58 130-201 85-144 (178)
257 PF08882 Acetone_carb_G: Aceto 30.0 36 0.00078 27.4 1.8 13 261-273 23-35 (112)
258 PLN02400 cellulose synthase 29.8 35 0.00076 38.2 2.3 46 190-263 52-97 (1085)
259 TIGR00373 conserved hypothetic 29.6 36 0.00079 29.3 1.9 32 158-202 106-137 (158)
260 cd00065 FYVE FYVE domain; Zinc 29.6 37 0.0008 23.3 1.7 35 76-110 3-39 (57)
261 KOG2691 RNA polymerase II subu 29.3 49 0.0011 26.4 2.4 16 160-177 3-18 (113)
262 PF15616 TerY-C: TerY-C metal 28.9 34 0.00074 28.5 1.6 23 245-273 78-100 (131)
263 PLN02915 cellulose synthase A 28.9 58 0.0012 36.5 3.7 52 72-131 12-68 (1044)
264 COG2824 PhnA Uncharacterized Z 28.8 40 0.00086 26.9 1.8 25 245-270 4-29 (112)
265 PF13913 zf-C2HC_2: zinc-finge 28.7 28 0.0006 20.0 0.7 10 194-203 3-12 (25)
266 PF14369 zf-RING_3: zinc-finge 28.2 58 0.0013 20.4 2.2 29 162-203 3-31 (35)
267 COG5236 Uncharacterized conser 28.2 30 0.00064 33.5 1.2 34 72-107 58-91 (493)
268 COG1996 RPC10 DNA-directed RNA 28.1 31 0.00066 23.6 0.9 10 245-254 25-34 (49)
269 smart00336 BBOX B-Box-type zin 28.0 45 0.00098 21.0 1.8 24 192-215 14-37 (42)
270 PRK12286 rpmF 50S ribosomal pr 27.9 32 0.0007 24.2 1.1 21 243-268 26-47 (57)
271 PF01780 Ribosomal_L37ae: Ribo 27.7 60 0.0013 25.2 2.6 27 245-271 36-63 (90)
272 PF11023 DUF2614: Protein of u 27.4 40 0.00088 27.2 1.7 22 192-213 68-97 (114)
273 PLN02915 cellulose synthase A 27.4 34 0.00073 38.2 1.6 45 190-262 31-75 (1044)
274 KOG1940 Zn-finger protein [Gen 27.3 40 0.00087 31.8 1.9 50 70-128 153-204 (276)
275 PF01873 eIF-5_eIF-2B: Domain 26.9 89 0.0019 25.8 3.7 37 232-270 83-123 (125)
276 TIGR01053 LSD1 zinc finger dom 26.8 61 0.0013 19.8 2.0 24 246-269 3-27 (31)
277 PRK08332 ribonucleotide-diphos 26.8 36 0.00077 40.4 1.8 27 245-273 1705-1738(1740)
278 PRK01103 formamidopyrimidine/5 26.8 45 0.00099 31.4 2.2 21 245-265 246-268 (274)
279 PRK12495 hypothetical protein; 26.8 53 0.0012 29.8 2.5 30 244-282 42-71 (226)
280 KOG2932 E3 ubiquitin ligase in 26.2 17 0.00038 34.5 -0.7 17 245-261 124-140 (389)
281 TIGR00577 fpg formamidopyrimid 26.1 48 0.001 31.3 2.2 21 245-265 246-268 (272)
282 KOG4362 Transcriptional regula 26.0 15 0.00031 39.0 -1.4 56 74-137 20-75 (684)
283 PLN02400 cellulose synthase 25.9 48 0.001 37.2 2.4 50 73-130 34-88 (1085)
284 PF05605 zf-Di19: Drought indu 25.8 1.5E+02 0.0033 20.2 4.2 41 75-131 2-42 (54)
285 COG2051 RPS27A Ribosomal prote 25.6 44 0.00095 24.3 1.4 15 191-205 36-50 (67)
286 PLN02195 cellulose synthase A 25.5 68 0.0015 35.7 3.5 50 74-131 5-59 (977)
287 PRK14810 formamidopyrimidine-D 25.4 49 0.0011 31.2 2.2 21 245-265 245-267 (272)
288 PRK13945 formamidopyrimidine-D 25.4 48 0.001 31.4 2.1 23 245-267 255-280 (282)
289 PRK10445 endonuclease VIII; Pr 25.4 51 0.0011 30.9 2.3 21 245-265 236-258 (263)
290 PF10426 zf-RAG1: Recombinatio 25.2 19 0.00042 21.8 -0.4 18 118-135 2-19 (30)
291 KOG3039 Uncharacterized conser 25.2 61 0.0013 30.0 2.6 35 245-284 222-260 (303)
292 PF01783 Ribosomal_L32p: Ribos 25.0 29 0.00064 24.2 0.4 13 243-255 25-37 (56)
293 PF01927 Mut7-C: Mut7-C RNAse 25.0 1.6E+02 0.0035 24.8 5.1 33 141-175 68-103 (147)
294 TIGR01031 rpmF_bact ribosomal 24.9 39 0.00085 23.6 1.1 13 243-255 25-37 (55)
295 TIGR00280 L37a ribosomal prote 24.7 76 0.0016 24.7 2.7 27 245-271 36-63 (91)
296 PF07800 DUF1644: Protein of u 24.1 1.3E+02 0.0029 25.9 4.3 36 75-111 2-49 (162)
297 PF06943 zf-LSD1: LSD1 zinc fi 23.8 78 0.0017 18.4 2.0 23 247-269 1-24 (25)
298 PF00628 PHD: PHD-finger; Int 23.7 34 0.00074 22.9 0.6 33 77-109 1-34 (51)
299 PF09332 Mcm10: Mcm10 replicat 23.5 5.2 0.00011 39.0 -4.9 46 198-254 249-295 (344)
300 smart00154 ZnF_AN1 AN1-like Zi 23.4 52 0.0011 21.1 1.4 18 193-210 12-29 (39)
301 PRK03976 rpl37ae 50S ribosomal 23.1 83 0.0018 24.4 2.6 27 245-271 37-64 (90)
302 PF11682 DUF3279: Protein of u 23.1 45 0.00097 27.7 1.2 13 245-257 111-123 (128)
303 PF09889 DUF2116: Uncharacteri 22.9 35 0.00077 24.2 0.5 11 245-255 4-14 (59)
304 PF08646 Rep_fac-A_C: Replicat 22.8 60 0.0013 27.3 2.0 25 245-270 19-46 (146)
305 COG5109 Uncharacterized conser 22.5 84 0.0018 30.1 3.0 53 73-131 334-387 (396)
306 COG4647 AcxC Acetone carboxyla 22.3 47 0.001 27.4 1.2 20 80-101 62-81 (165)
307 KOG1873 Ubiquitin-specific pro 22.2 55 0.0012 35.1 1.9 43 232-274 54-106 (877)
308 PF03854 zf-P11: P-11 zinc fin 22.1 49 0.0011 22.4 1.0 44 76-132 3-47 (50)
309 PRK03824 hypA hydrogenase nick 21.8 91 0.002 26.1 2.9 14 160-175 69-82 (135)
310 COG4640 Predicted membrane pro 21.4 44 0.00094 33.1 1.0 7 245-251 2-8 (465)
311 PTZ00255 60S ribosomal protein 21.0 1E+02 0.0023 23.9 2.8 27 245-271 37-64 (90)
312 PF15135 UPF0515: Uncharacteri 20.7 59 0.0013 30.1 1.6 37 245-281 133-186 (278)
313 PF04216 FdhE: Protein involve 20.0 53 0.0011 31.3 1.2 35 245-279 173-221 (290)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.8e-42 Score=335.44 Aligned_cols=254 Identities=40% Similarity=0.826 Sum_probs=202.9
Q ss_pred hHHHHHHHHHHHHHhhhhhhhhccCCcc-ccchHhHHHHHHhcCCCCCCCCCCCcccccccccccCCC-Ceeec-cCCCc
Q 016355 22 PLLVALRQRILEYTSNLEAFVLKLVPSI-ELERPLRLAQIAVGIVSSPSQGDKSPENCSICCEDKPYP-MMITM-KCSHK 98 (391)
Q Consensus 22 ~~l~~l~~~i~~~~~~~~~~~l~l~~~~-~~~~~~~~~~~ai~~~~~~~~~~~~~~~C~IC~e~~~~~-~~~~l-~C~H~ 98 (391)
..|++..+++++ .+......++++. |...+.++|.+++.. .........+|.||+.+.+.. .++.. .|+|.
T Consensus 98 ~~l~~~v~~~r~---~l~~~~~i~~~~~~d~~~~~~lA~e~i~s---~~~~~~~~~~C~iC~~e~~~~~~~f~~~~C~H~ 171 (384)
T KOG1812|consen 98 VLLVELVQRIRE---QLTSSEPILVPKNADIKFAYKLAREAIVS---QLPSKLPKEECGICFVEDPEAEDMFSVLKCGHR 171 (384)
T ss_pred HHHHHHHHHHHH---HhhcccceecccchhhHHHHHHHHHhhcc---ccccccccccCccCccccccHhhhHHHhcccch
Confidence 334444444444 4434455566554 777789999998876 222345688999999555544 66666 99999
Q ss_pred ccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhCChhHHHHHHHHHHHHhcCCCCCccccCCCCCeeecCccc
Q 016355 99 FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANILHSDRIYCPFPNCSVLLDPREC 178 (391)
Q Consensus 99 fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l~~~~~e~~~~~~~~~~i~~~~~~~CP~p~C~~~~~~~~~ 178 (391)
||.+|+++|++++...| ..++||..+|+..++.+.+..+|++++.++|++++.+.++...+.+|||+|+|+..+...+.
T Consensus 172 fC~~C~k~~iev~~~~~-~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el 250 (384)
T KOG1812|consen 172 FCKDCVKQHIEVKLLSG-TVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLDRVYCPYPRCSSLMSKTEL 250 (384)
T ss_pred hhhHHhHHHhhhhhccC-CCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhhcccCCCCCchHhhhhhhh
Confidence 99999999999994444 44799999999999999999999999999999999999998666669999999999987544
Q ss_pred cccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecC
Q 016355 179 LSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTH 258 (391)
Q Consensus 179 ~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~ 258 (391)
.. ........|+.|+..||.+|+.+||.+.+|++|+++.. ....++.+++.++ ++||.||+|+..|++++
T Consensus 251 ~~-------~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~-~~~~d~~~~~~la--~~wr~CpkC~~~ie~~~ 320 (384)
T KOG1812|consen 251 SS-------EVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNP-EEYVDDITLKYLA--KRWRQCPKCKFMIELSE 320 (384)
T ss_pred cc-------chhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCC-cccccHHHHHHHH--HhcCcCcccceeeeecC
Confidence 31 12233456999999999999999999999999999987 3445577888888 78899999999999999
Q ss_pred CCcceEeccccceeccccccccCCCCcc-cccCCC
Q 016355 259 GCYHMTCWCGHEFCYSCGAEYRDGQQTC-QCAFWD 292 (391)
Q Consensus 259 GCnhMtC~C~~~FCw~C~~~~~~~~~~c-~C~~~~ 292 (391)
|||||||+||++|||.|+++|..+++.| .|.++.
T Consensus 321 GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~~r~~ 355 (384)
T KOG1812|consen 321 GCNHMTCRCGHQFCYMCGGDWKTHNGECYECCRYK 355 (384)
T ss_pred CcceEEeeccccchhhcCcchhhCCccccCccccc
Confidence 9999999999999999999998877643 344444
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.6e-36 Score=281.68 Aligned_cols=197 Identities=26% Similarity=0.622 Sum_probs=162.1
Q ss_pred CCCcccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCc-ccccCCCccCCccCHHHHHhhCChhHHHHHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQV-PIRCPQLRCKYFISTVECKSFLPLSSYESLET 149 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~-~i~CP~~~C~~~i~~~~i~~~l~~~~~e~~~~ 149 (391)
....+.|.|||++..+...+.+ +|+|+||+.|++.|++..|.+|.+ .++||+++|+...+...++.+++.+++++|++
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~ 260 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEK 260 (445)
T ss_pred HhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHH
Confidence 5678999999999998665555 999999999999999999999987 69999999999999999999999999999999
Q ss_pred HHHHHhcC-CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCCchhH--------
Q 016355 150 ALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEY-------- 220 (391)
Q Consensus 150 ~~~~~~i~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~-------- 220 (391)
.+.+..+. ..+.+|||++.|....-. .++...+.|.+|+.+||+.|+..||+...|.--
T Consensus 261 l~lqk~l~~msdv~yCPr~~Cq~p~~~------------d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~ 328 (445)
T KOG1814|consen 261 LMLQKTLELMSDVVYCPRACCQLPVKQ------------DPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELY 328 (445)
T ss_pred HHHHHHHHhhcccccCChhhccCcccc------------CchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHH
Confidence 99888877 678899999999987633 345567889999999999999999999999521
Q ss_pred hcCcccc--c------Chh----HHHH------HHHHhccCCCCCccccceeeecCCCcceEe-ccccceeccccccccC
Q 016355 221 QNLPLEE--R------DAG----DITL------HRLAQNKRWRRCQQCRRMIELTHGCYHMTC-WCGHEFCYSCGAEYRD 281 (391)
Q Consensus 221 ~~~~~~~--~------~~~----~~~~------~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~~~~ 281 (391)
..|.... + .-+ ++.+ +|+.++. |+||+|+++|||++|||||+| .|++.|||+|+..+.+
T Consensus 329 ~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~--krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~ 406 (445)
T KOG1814|consen 329 LEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNS--KRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYP 406 (445)
T ss_pred HHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcC--CCCCcccceeecCCCccceeeccccccceeehhhhcCC
Confidence 1111100 0 000 1111 2333333 999999999999999999999 9999999999999875
Q ss_pred C
Q 016355 282 G 282 (391)
Q Consensus 282 ~ 282 (391)
.
T Consensus 407 ~ 407 (445)
T KOG1814|consen 407 E 407 (445)
T ss_pred C
Confidence 3
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-33 Score=283.93 Aligned_cols=211 Identities=26% Similarity=0.590 Sum_probs=182.1
Q ss_pred CCCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcc-cccCCCccCCccCHHHHHhhCCh-hHHHHHH
Q 016355 71 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVP-IRCPQLRCKYFISTVECKSFLPL-SSYESLE 148 (391)
Q Consensus 71 ~~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~-i~CP~~~C~~~i~~~~i~~~l~~-~~~e~~~ 148 (391)
......+|.||++.++. .++.+.|+|.||..||..|+..+|.+|... |+||..+|...+..+.+..++++ +..++|.
T Consensus 66 ~~~~~~~c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 66 KKKGDVQCGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CCCccccCCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 34567899999999887 667779999999999999999999877653 89999999999999999999988 4899999
Q ss_pred HHHHHHhcC-CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccc
Q 016355 149 TALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEE 227 (391)
Q Consensus 149 ~~~~~~~i~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~ 227 (391)
+.+..+++. .....|||+|+|+.++... ......+.| .|++.||+.|+.+||.|.+|.....|.+ +
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~-----------~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~-k 211 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFG-----------SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLK-K 211 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeecc-----------CCCccceeC-CCCchhHhhccccccCCCcccchHHHHH-h
Confidence 999999998 4568899999999988762 123355789 5777999999999999999999999987 4
Q ss_pred cChhHHHHHHHHhccCCCCCccccceeeecCCCcceEe-c--cccceeccccccccCCCCc--ccccCCCCCchH
Q 016355 228 RDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHMTC-W--CGHEFCYSCGAEYRDGQQT--CQCAFWDEDNSE 297 (391)
Q Consensus 228 ~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC-~--C~~~FCw~C~~~~~~~~~~--c~C~~~~~~~~~ 297 (391)
..++++++.|+..++ ++||+|.++|||++|||||+| . |+++|||+|++.|..|+.. +.|++|+++...
T Consensus 212 ~~~~se~~~wi~~nt--k~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~~~~~~~ 284 (444)
T KOG1815|consen 212 CRDDSETINWILANT--KECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRYVDGKSK 284 (444)
T ss_pred hhhhhhhhhhhhccC--ccCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeeeeeeechhhh
Confidence 455567777777666 899999999999999999999 4 9999999999999998754 899999987764
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=6e-28 Score=219.76 Aligned_cols=192 Identities=25% Similarity=0.601 Sum_probs=147.9
Q ss_pred CCCcccccccccccCCCCeeeccCC--CcccHHHHHHHHHHHhhCCCc--------ccccCCCccCCccCHH-HHHhhCC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCS--HKFCSHCMRTYIDGKVQSSQV--------PIRCPQLRCKYFISTV-ECKSFLP 140 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~--H~fC~~Cl~~~i~~~i~~g~~--------~i~CP~~~C~~~i~~~-~i~~~l~ 140 (391)
+..+.+|..|-+... .++.++|. |..|.+|++.|..+.+++.++ .+.||. +|...+-.+ .-..+|+
T Consensus 218 N~~ni~C~~Ctdv~~--~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg 294 (446)
T KOG0006|consen 218 NSRNITCITCTDVRS--PVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCcc--ceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 566889999987543 34556887 999999999999999987753 578886 677765333 3347899
Q ss_pred hhHHHHHHHHHHHHhcCCCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCC-CCcccccccccCCCCCCCchh
Q 016355 141 LSSYESLETALAEANILHSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPV-CERFICVECGVPWHSSLSCEE 219 (391)
Q Consensus 141 ~~~~e~~~~~~~~~~i~~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~-C~~~fC~~C~~~~H~~~sC~e 219 (391)
.+.|.+|+++..+.++...+.+-||+|+|+..+.+ .++..+++|+. |++.||..|...+|.+. |.+
T Consensus 295 ~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~------------EPD~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~ 361 (446)
T KOG0006|consen 295 EEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLP------------EPDQRKVTCEGGCGFAFCRECKEAYHEGE-CSA 361 (446)
T ss_pred hhHHHHHHHhhhhhheeecCCEecCCCCCCccccc------------CCCCCcccCCCCchhHhHHHHHhhhcccc-cee
Confidence 99999999999999999888999999999988877 45778899986 99999999999999884 321
Q ss_pred Hh--------cCcccccChh-----HHHHHHHHhccCCCCCccccceeeecCCCcceEe---ccccceeccccccccC
Q 016355 220 YQ--------NLPLEERDAG-----DITLHRLAQNKRWRRCQQCRRMIELTHGCYHMTC---WCGHEFCYSCGAEYRD 281 (391)
Q Consensus 220 ~~--------~~~~~~~~~~-----~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC---~C~~~FCw~C~~~~~~ 281 (391)
.- ....+++..+ +..-..|.+ .+|+||+|+++.||||||+||.| .||.+|||.|+-.|+.
T Consensus 362 ~~~as~t~tc~y~vde~~a~~arwd~as~~TIk~--tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 362 VFEASGTTTCAYRVDERAAEQARWDAASKETIKK--TTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred eeccccccceeeecChhhhhhhhhhhhhhhhhhh--ccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 10 0001111111 111112222 34999999999999999999999 5999999999999985
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.18 E-value=3e-11 Score=88.40 Aligned_cols=63 Identities=38% Similarity=0.821 Sum_probs=52.3
Q ss_pred HHHHHHHHHHhcC-CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCCc
Q 016355 145 ESLETALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSC 217 (391)
Q Consensus 145 e~~~~~~~~~~i~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~sC 217 (391)
++|++++.+..+. +.+.+|||+|+|+.++.... ......+.|+.|+..||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~----------~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTE----------EEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecC----------CCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 3688888888887 46889999999999887731 123467899999999999999999999987
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=99.10 E-value=2.2e-11 Score=89.09 Aligned_cols=63 Identities=27% Similarity=0.824 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhcC-CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCCc
Q 016355 145 ESLETALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSC 217 (391)
Q Consensus 145 e~~~~~~~~~~i~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~sC 217 (391)
++|++++.+.++. +.+++|||+|+|+.++..... .....++|+.|+..||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~----------~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDG----------CNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SS----------TTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCC----------CCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 3566666666666 556789999999999988321 11124889999999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.42 E-value=8.1e-08 Score=63.83 Aligned_cols=41 Identities=29% Similarity=0.816 Sum_probs=28.6
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 78 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
|+||++.+..+ ++++|||.||..|+.++++..-+. .+.||.
T Consensus 1 CpiC~~~~~~P--v~l~CGH~FC~~Cl~~~~~~~~~~---~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDP--VSLPCGHSFCRSCLERLWKEPSGS---GFSCPE 41 (42)
T ss_dssp ETTTTSB-SSE--EE-SSSSEEEHHHHHHHHCCSSSS---T---SS
T ss_pred CCccchhhCCc--cccCCcCHHHHHHHHHHHHccCCc---CCCCcC
Confidence 89999988766 889999999999999998643221 268886
No 8
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.37 E-value=4.5e-07 Score=66.01 Aligned_cols=44 Identities=32% Similarity=0.906 Sum_probs=38.4
Q ss_pred HHhccCCCCCc--cccceeeecC--CCcceEe-ccccceeccccccccC
Q 016355 238 LAQNKRWRRCQ--QCRRMIELTH--GCYHMTC-WCGHEFCYSCGAEYRD 281 (391)
Q Consensus 238 l~~~~~~k~CP--~C~~~IeK~~--GCnhMtC-~C~~~FCw~C~~~~~~ 281 (391)
+..+..++.|| +|+..|+..+ |.++|+| .||+.|||.|+.+|..
T Consensus 12 i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 12 VESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred HhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 33446779999 9999999975 9999999 9999999999999964
No 9
>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=98.31 E-value=1.9e-07 Score=68.02 Aligned_cols=41 Identities=39% Similarity=1.077 Sum_probs=29.5
Q ss_pred ccCCCCCcc--ccceeeecCCCcc--eEe-ccccceeccccccccC
Q 016355 241 NKRWRRCQQ--CRRMIELTHGCYH--MTC-WCGHEFCYSCGAEYRD 281 (391)
Q Consensus 241 ~~~~k~CP~--C~~~IeK~~GCnh--MtC-~C~~~FCw~C~~~~~~ 281 (391)
+...+.||+ |...|++..|.++ |+| .|++.|||.|+.+|..
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 344589987 9999999999999 999 6999999999999954
No 10
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.24 E-value=7.4e-07 Score=59.93 Aligned_cols=40 Identities=25% Similarity=0.752 Sum_probs=32.5
Q ss_pred cccccccccC-CCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 77 NCSICCEDKP-YPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 77 ~C~IC~e~~~-~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
+|+||++++. ...++.++|+|.||.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence 6999999995 4566666999999999999999762 27886
No 11
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=1.1e-06 Score=75.33 Aligned_cols=57 Identities=25% Similarity=0.703 Sum_probs=45.2
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHh
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 137 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~ 137 (391)
..+.+.|+||++.+.....++..|||.||..|++..+.. ..+||. |...|...++..
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~-------~~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN-------TNKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHh-------CCCCCC--cccccchhhhee
Confidence 345689999999998766677799999999999988864 258999 777777666543
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.17 E-value=1.5e-06 Score=57.47 Aligned_cols=40 Identities=35% Similarity=1.021 Sum_probs=31.8
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 78 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
|+||++.+..+. ..++|||.||..|+.++++. ...++||.
T Consensus 1 C~iC~~~~~~~~-~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV-ILLPCGHSFCRDCLRKWLEN-----SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE-EETTTSEEEEHHHHHHHHHH-----TSSSBTTT
T ss_pred CCcCCccccCCC-EEecCCCcchHHHHHHHHHh-----cCCccCCc
Confidence 889999876552 35599999999999999987 23457886
No 13
>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=98.13 E-value=1.3e-06 Score=57.03 Aligned_cols=38 Identities=29% Similarity=0.954 Sum_probs=28.3
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 78 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
|+||++.... .++.++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEKN-------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred CCCCCCcccC-cCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence 8999997764 23455999999999999998642 47886
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.12 E-value=2.2e-06 Score=75.38 Aligned_cols=64 Identities=23% Similarity=0.567 Sum_probs=46.8
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhh---------CCCcccccCCCccCCccCHHHHHhhCC
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ---------SSQVPIRCPQLRCKYFISTVECKSFLP 140 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~---------~g~~~i~CP~~~C~~~i~~~~i~~~l~ 140 (391)
...++|+||++....+ +...|||.||..|+..|+...-. ......+||. |...++...+..+.+
T Consensus 16 ~~~~~CpICld~~~dP--VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 16 GGDFDCNICLDQVRDP--VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCccCCccCCCcCCCc--EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 4578999999987544 55699999999999999764211 1123468999 999998766655543
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.00 E-value=5.2e-06 Score=55.76 Aligned_cols=42 Identities=29% Similarity=0.866 Sum_probs=32.4
Q ss_pred cccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccC
Q 016355 77 NCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 127 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~ 127 (391)
.|+||++.+.....+.+ +|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC--CC
Confidence 49999999944433444 999999999999887 33478998 65
No 16
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.90 E-value=1.6e-05 Score=52.91 Aligned_cols=43 Identities=28% Similarity=0.812 Sum_probs=32.7
Q ss_pred cccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCc
Q 016355 77 NCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 129 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~ 129 (391)
+|+||++.+. ..+.+ +|+|.||..|+..|++. ...+||. |+..
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCCC--CCCc
Confidence 5999999873 23444 69999999999999875 2357987 7654
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=97.82 E-value=1.5e-05 Score=70.94 Aligned_cols=57 Identities=21% Similarity=0.551 Sum_probs=40.3
Q ss_pred CCCcccccccccccC-----CCCeee-c-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKP-----YPMMIT-M-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~-----~~~~~~-l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.+...+|+||++..- .+..+. + +|+|.||..|++.|.+++-..|.. -.||. |...+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~-rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGAS-DNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcC-CcCCC--Ccceee
Confidence 345689999999752 222233 3 999999999999999875333322 47999 887653
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.76 E-value=2.8e-05 Score=51.72 Aligned_cols=41 Identities=27% Similarity=0.732 Sum_probs=21.7
Q ss_pred ccccccccCC-CCe-eeccCCCcccHHHHHHHHHHHhhCCCcccccC
Q 016355 78 CSICCEDKPY-PMM-ITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCP 122 (391)
Q Consensus 78 C~IC~e~~~~-~~~-~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP 122 (391)
|+||.+ +.. .+. ..|+|||.||.+|+.+..+... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999 643 222 4459999999999999998532 2347887
No 19
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.73 E-value=2.8e-05 Score=53.68 Aligned_cols=46 Identities=30% Similarity=0.830 Sum_probs=34.8
Q ss_pred cccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 75 PENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
...|.||++... +.+.++|||. ||.+|+.+++. ...+||. |...+.
T Consensus 2 ~~~C~iC~~~~~--~~~~~pCgH~~~C~~C~~~~~~-------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--DVVLLPCGHLCFCEECAERLLK-------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--SEEEETTCEEEEEHHHHHHHHH-------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCC--ceEEeCCCChHHHHHHhHHhcc-------cCCCCCc--CChhhc
Confidence 457999999754 3455599999 99999999997 2358998 888764
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.61 E-value=6.1e-05 Score=48.16 Aligned_cols=38 Identities=32% Similarity=0.893 Sum_probs=28.7
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 78 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 78 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
|+||++.. ...+.++|+|.||..|+..|++ ....+||.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~------~~~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK------SGNNTCPI 38 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH------hCcCCCCC
Confidence 78999873 3445569999999999999987 12246875
No 21
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=3.8e-05 Score=68.91 Aligned_cols=60 Identities=27% Similarity=0.598 Sum_probs=46.7
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFL 139 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l 139 (391)
+...|+|.||+|....+ +..-|||.||-.|+.+|+.+..+. -.||. |+..++.+.+-.+.
T Consensus 44 ~~~~FdCNICLd~akdP--VvTlCGHLFCWpClyqWl~~~~~~----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP--VVTLCGHLFCWPCLYQWLQTRPNS----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCC--EEeecccceehHHHHHHHhhcCCC----eeCCc--cccccccceEEeee
Confidence 57899999999976544 444799999999999999875431 35788 99998877665554
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=3.5e-05 Score=76.46 Aligned_cols=60 Identities=27% Similarity=0.644 Sum_probs=46.7
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhCC
Q 016355 75 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLP 140 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l~ 140 (391)
...|+||++..+.+. .+.|||.||..|+-+|+..... ..+..||. |...|...++..+.-
T Consensus 186 ~~~CPICL~~~~~p~--~t~CGHiFC~~CiLqy~~~s~~--~~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV--RTNCGHIFCGPCILQYWNYSAI--KGPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCccc--ccccCceeeHHHHHHHHhhhcc--cCCccCCc--hhhhccccceeeeee
Confidence 788999999877663 2369999999999999987622 22568999 999988877765543
No 23
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=0.00012 Score=69.56 Aligned_cols=108 Identities=23% Similarity=0.498 Sum_probs=67.9
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhCChhHHHHHHHHHH
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALA 152 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l~~~~~e~~~~~~~ 152 (391)
...++|+||++.+..+ ..++|+|.||..|+...+. ..+.||. |.. ... .+.....+......+.
T Consensus 11 ~~~~~C~iC~~~~~~p--~~l~C~H~~c~~C~~~~~~-------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~~~~~ 74 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP--VLLPCGHNFCRACLTRSWE-------GPLSCPV--CRP-PSR----NLRPNVLLANLVERLR 74 (386)
T ss_pred cccccChhhHHHhhcC--ccccccchHhHHHHHHhcC-------CCcCCcc--cCC-chh----ccCccHHHHHHHHHHH
Confidence 4578999999999877 4559999999999999997 4489998 874 222 2223333333333332
Q ss_pred HHhcC-CCCC--ccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccc-cCCCCCCCc
Q 016355 153 EANIL-HSDR--IYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECG-VPWHSSLSC 217 (391)
Q Consensus 153 ~~~i~-~~~~--~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~-~~~H~~~sC 217 (391)
..... .... ..|+. ........|..|+...|..|. ...|..+.-
T Consensus 75 ~~~~~~~~~~~~~~c~~---------------------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 75 QLRLSRPLGSKEELCEK---------------------HGEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred hcCCcccccccchhhhh---------------------cCCcceEEecccccccCCCCCCcccccCCcc
Confidence 22221 1111 12321 011145679999999999998 667877754
No 24
>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=97.36 E-value=0.0003 Score=50.80 Aligned_cols=49 Identities=10% Similarity=0.139 Sum_probs=38.5
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHH
Q 016355 76 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 135 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i 135 (391)
+.|+||.+....+ +..+|||.||..|+.+|+.. ...||. |+..++.+++
T Consensus 2 ~~Cpi~~~~~~~P--v~~~~G~v~~~~~i~~~~~~-------~~~cP~--~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVMKDP--VILPSGQTYERRAIEKWLLS-------HGTDPV--TGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcCCCC--EECCCCCEEeHHHHHHHHHH-------CCCCCC--CcCCCChhhc
Confidence 5799999987654 55699999999999999975 137988 7777765543
No 25
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.36 E-value=0.00019 Score=65.93 Aligned_cols=50 Identities=24% Similarity=0.621 Sum_probs=37.3
Q ss_pred CCcccccccccccCCCC-----eeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 73 KSPENCSICCEDKPYPM-----MITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~-----~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
....+|+||++.+.... +..+ +|+|.||.+|+..|... ...||. |...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCCC--CCCEee
Confidence 45689999999865432 2234 89999999999999853 237998 887654
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.18 E-value=0.00028 Score=69.45 Aligned_cols=66 Identities=27% Similarity=0.588 Sum_probs=45.8
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH-hhCChhHHHHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK-SFLPLSSYESLE 148 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~-~~l~~~~~e~~~ 148 (391)
-...+.|+||.+.+..+ +.++|||.||..|+..|+.. ...||. |...+....+. +.+-.++++.|.
T Consensus 23 Le~~l~C~IC~d~~~~P--vitpCgH~FCs~CI~~~l~~-------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVP--VLTSCSHTFCSLCIRRCLSN-------QPKCPL--CRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred cccccCCCcCchhhhCc--cCCCCCCchhHHHHHHHHhC-------CCCCCC--CCCccccccCccchHHHHHHHHHH
Confidence 34578999999987654 44599999999999999853 127998 98877654332 233334455554
No 27
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.00 E-value=0.00038 Score=65.50 Aligned_cols=64 Identities=30% Similarity=0.636 Sum_probs=47.7
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH-hhCChhHHHHHH
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK-SFLPLSSYESLE 148 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~-~~l~~~~~e~~~ 148 (391)
...-|.||++-+..+ +..+|+|.||.=|++.|+..+ ..||. |...+....++ +.+-.++++.|.
T Consensus 22 ~lLRC~IC~eyf~ip--~itpCsHtfCSlCIR~~L~~~-------p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIP--MITPCSHTFCSLCIRKFLSYK-------PQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHhcCc--eeccccchHHHHHHHHHhccC-------CCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 456799999998766 334899999999999999642 47998 99888877776 344445555443
No 28
>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=96.99 E-value=0.0015 Score=61.88 Aligned_cols=54 Identities=22% Similarity=0.591 Sum_probs=39.0
Q ss_pred cccccccccc-CCCCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHh
Q 016355 76 ENCSICCEDK-PYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 137 (391)
Q Consensus 76 ~~C~IC~e~~-~~~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~ 137 (391)
..|++|..+. ..+.+.-+ .|||.||..|+...+. .| +..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~--~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG--SGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC--CCCCCC--CCCccchhhccc
Confidence 5799999974 33443222 7999999999999873 22 348997 999887776553
No 29
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.95 E-value=0.00025 Score=73.78 Aligned_cols=56 Identities=25% Similarity=0.656 Sum_probs=43.9
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhh
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSF 138 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~ 138 (391)
....+|++|.+- + .+++...|+|.||.+|++..+.+.-. +||. |+..|+..++..+
T Consensus 641 K~~LkCs~Cn~R-~-Kd~vI~kC~H~FC~~Cvq~r~etRqR------KCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTR-W-KDAVITKCGHVFCEECVQTRYETRQR------KCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCc-h-hhHHHHhcchHHHHHHHHHHHHHhcC------CCCC--CCCCCCccccccc
Confidence 457899999843 2 34444599999999999999977533 8998 9999988877654
No 30
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00039 Score=64.40 Aligned_cols=52 Identities=27% Similarity=0.758 Sum_probs=40.1
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 134 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~ 134 (391)
...+..|.+|++....+ ...+|||.||-.|+..|..++- -||. |...+.+..
T Consensus 236 ~~a~~kC~LCLe~~~~p--SaTpCGHiFCWsCI~~w~~ek~-------eCPl--CR~~~~psk 287 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNP--SATPCGHIFCWSCILEWCSEKA-------ECPL--CREKFQPSK 287 (293)
T ss_pred CCCCCceEEEecCCCCC--CcCcCcchHHHHHHHHHHcccc-------CCCc--ccccCCCcc
Confidence 34568899999986544 3449999999999999997642 3998 988776544
No 31
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.00061 Score=63.30 Aligned_cols=55 Identities=22% Similarity=0.562 Sum_probs=43.2
Q ss_pred CCCCCcccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCH
Q 016355 70 QGDKSPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 132 (391)
Q Consensus 70 ~~~~~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~ 132 (391)
.++....+|.||++++...+-+.+ +|.|.|...|+.+|+.. +..+||. |...+++
T Consensus 318 ~ea~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~------y~~~CPv--Crt~iPP 373 (374)
T COG5540 318 VEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG------YSNKCPV--CRTAIPP 373 (374)
T ss_pred HhcCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh------hcccCCc--cCCCCCC
Confidence 345667999999999865544444 99999999999999942 3468998 9988764
No 32
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.0021 Score=61.95 Aligned_cols=48 Identities=33% Similarity=0.735 Sum_probs=38.2
Q ss_pred cccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 75 PENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
+.+|.||+|+|...+.+.. +|+|.|...|+..|+... .-.||. |+..+
T Consensus 229 ~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPv--CK~di 277 (348)
T KOG4628|consen 229 TDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPV--CKRDI 277 (348)
T ss_pred CceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCC--CCCcC
Confidence 3799999999986655555 999999999999999653 125998 77744
No 33
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.26 E-value=0.0039 Score=44.21 Aligned_cols=50 Identities=26% Similarity=0.525 Sum_probs=31.5
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 127 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~ 127 (391)
....+.|+|....+..+ +.+..|+|.|-++-+.+|+ .+...++||..||+
T Consensus 8 ~~~~~~CPiT~~~~~~P-V~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDP-VKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE-EEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC-cCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 34568899999887644 3445999999999999999 23345799999985
No 34
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.18 E-value=0.0041 Score=46.54 Aligned_cols=41 Identities=32% Similarity=0.721 Sum_probs=29.0
Q ss_pred ccccccccccCC----------CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 76 ENCSICCEDKPY----------PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 76 ~~C~IC~e~~~~----------~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
-.|.||++.+.. .-.+.+ .|||.|...|+.+|++.. -.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence 349999999822 122334 899999999999999532 27887
No 35
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.13 E-value=0.0031 Score=62.76 Aligned_cols=58 Identities=26% Similarity=0.714 Sum_probs=44.2
Q ss_pred CCCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHH
Q 016355 71 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 134 (391)
Q Consensus 71 ~~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~ 134 (391)
++....+|.+|-+.-. +-+.-+|.|.||+-|++.|+........ +.||. |...++.+.
T Consensus 532 enk~~~~C~lc~d~ae--d~i~s~ChH~FCrlCi~eyv~~f~~~~n--vtCP~--C~i~LsiDl 589 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAE--DYIESSCHHKFCRLCIKEYVESFMENNN--VTCPV--CHIGLSIDL 589 (791)
T ss_pred cccCceeecccCChhh--hhHhhhhhHHHHHHHHHHHHHhhhcccC--CCCcc--ccccccccc
Confidence 4677899999987543 3355599999999999999987654322 79998 888776553
No 36
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.13 E-value=0.00059 Score=48.86 Aligned_cols=47 Identities=34% Similarity=0.755 Sum_probs=22.8
Q ss_pred cccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHH
Q 016355 75 PENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 134 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~ 134 (391)
..-|++|++-...+ +.+ .|.|.||..|++..+. -.||. |..+--..+
T Consensus 7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---------~~CPv--C~~Paw~qD 54 (65)
T PF14835_consen 7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---------SECPV--CHTPAWIQD 54 (65)
T ss_dssp TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT---------TB-SS--S--B-S-SS
T ss_pred hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---------CCCCC--cCChHHHHH
Confidence 45699999986655 566 9999999999976442 25998 877654333
No 37
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.63 E-value=0.0075 Score=55.37 Aligned_cols=54 Identities=24% Similarity=0.521 Sum_probs=37.8
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHH
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 135 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i 135 (391)
...+.|.||++.-..+ ...+|||.||..|+-..++.+ ..-.||. |.....+..+
T Consensus 213 ~~d~kC~lC~e~~~~p--s~t~CgHlFC~~Cl~~~~t~~-----k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEVP--SCTPCGHLFCLSCLLISWTKK-----KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCCc--ccccccchhhHHHHHHHHHhh-----ccccCch--hhhhccchhh
Confidence 4578899999864322 334999999999999853321 1236998 8887765554
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.29 E-value=0.0095 Score=44.14 Aligned_cols=56 Identities=27% Similarity=0.509 Sum_probs=26.6
Q ss_pred cccccccccccC-CCCe--eec---cCCCcccHHHHHHHHHHHhhCCC-c-c--cccCCCccCCccCH
Q 016355 75 PENCSICCEDKP-YPMM--ITM---KCSHKFCSHCMRTYIDGKVQSSQ-V-P--IRCPQLRCKYFIST 132 (391)
Q Consensus 75 ~~~C~IC~e~~~-~~~~--~~l---~C~H~fC~~Cl~~~i~~~i~~g~-~-~--i~CP~~~C~~~i~~ 132 (391)
..+|+||+.... .... ... .|++.|...||.+|+...-+... + + -.||. |+..|+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 457999998764 3222 222 68899999999999987654332 2 2 36998 9988754
No 39
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.16 E-value=0.015 Score=53.86 Aligned_cols=67 Identities=30% Similarity=0.492 Sum_probs=43.1
Q ss_pred CCCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH-hhCChhHHHHHH
Q 016355 71 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK-SFLPLSSYESLE 148 (391)
Q Consensus 71 ~~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~-~~l~~~~~e~~~ 148 (391)
+-....-|-||-+-+..+ ...+|||.||.=|++.|+.+ .+ .||. |....-...++ ..+..++.+.|.
T Consensus 21 ~LDs~lrC~IC~~~i~ip--~~TtCgHtFCslCIR~hL~~------qp-~CP~--Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 21 GLDSMLRCRICDCRISIP--CETTCGHTFCSLCIRRHLGT------QP-FCPV--CREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred cchhHHHhhhhhheeecc--eecccccchhHHHHHHHhcC------CC-CCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence 334567899998877654 33499999999999999943 33 6887 76654333332 233344444443
No 40
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.14 E-value=0.038 Score=53.04 Aligned_cols=51 Identities=22% Similarity=0.605 Sum_probs=37.5
Q ss_pred CCcccccccccccC-CC--------C--eeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCH
Q 016355 73 KSPENCSICCEDKP-YP--------M--MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 132 (391)
Q Consensus 73 ~~~~~C~IC~e~~~-~~--------~--~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~ 132 (391)
.....|.||+|+.- .+ + --.++|||.+..+|++.|.+.+ =.||. |+.++-.
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCPI--Cr~p~if 346 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCPI--CRRPVIF 346 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCCc--ccCcccc
Confidence 45678999999832 11 1 1356999999999999999753 27998 8887543
No 41
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.78 E-value=0.037 Score=51.11 Aligned_cols=52 Identities=27% Similarity=0.618 Sum_probs=38.2
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.....+|++|-+.-..+ ++...|+|.||.-|+........ ...||. |+....
T Consensus 236 ~t~~~~C~~Cg~~PtiP-~~~~~C~HiyCY~Ci~ts~~~~a-----sf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP-HVIGKCGHIYCYYCIATSRLWDA-----SFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCC-eeeccccceeehhhhhhhhcchh-----hcccCc--cCCCCc
Confidence 45678999998865444 33337999999999988875433 368998 887654
No 42
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.75 E-value=0.023 Score=55.11 Aligned_cols=93 Identities=23% Similarity=0.441 Sum_probs=54.5
Q ss_pred CCCcccccccccccCCCC-----eeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCH---HHH---HhhC
Q 016355 72 DKSPENCSICCEDKPYPM-----MITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST---VEC---KSFL 139 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~-----~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~---~~i---~~~l 139 (391)
.....+|+||++...... +-.+ +|.|.||..|+++|-...-.+....-.||. |...... ..+ ..--
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~~ 235 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVPSSFVNPSSFWVETKEE 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCccccccccceeeeeccc
Confidence 356889999999876443 3334 799999999999997543322333457998 7654321 111 0112
Q ss_pred ChhHHHHHHHHHHHHhcC--CCCCccccC
Q 016355 140 PLSSYESLETALAEANIL--HSDRIYCPF 166 (391)
Q Consensus 140 ~~~~~e~~~~~~~~~~i~--~~~~~~CP~ 166 (391)
...+++.|.+......-. ....-.||+
T Consensus 236 k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred ccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 233455665554322211 345567887
No 43
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.74 E-value=0.022 Score=55.45 Aligned_cols=44 Identities=20% Similarity=0.559 Sum_probs=38.2
Q ss_pred cCCCCCcc--ccceeeecCCCcceEe-ccccceeccccccccCCCCcc
Q 016355 242 KRWRRCQQ--CRRMIELTHGCYHMTC-WCGHEFCYSCGAEYRDGQQTC 286 (391)
Q Consensus 242 ~~~k~CP~--C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~~~~~~~~c 286 (391)
.+..-||+ |..++-...|++-..| .|.+.||.+|...|.+ ...|
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG-~s~C 317 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG-VSPC 317 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC-CCcc
Confidence 34589998 9999977899999999 9999999999999987 3344
No 44
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.08 E-value=0.019 Score=33.68 Aligned_cols=23 Identities=26% Similarity=0.820 Sum_probs=15.7
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
|.||.|+..|-.+ -+.| .|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5788888888432 3567 677766
No 45
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.96 E-value=0.11 Score=50.76 Aligned_cols=79 Identities=24% Similarity=0.516 Sum_probs=45.6
Q ss_pred CCeeeCCCCCcccccccccCCCCCCC-chhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcc-eEe-cc
Q 016355 191 NSCVECPVCERFICVECGVPWHSSLS-CEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYH-MTC-WC 267 (391)
Q Consensus 191 ~~~v~C~~C~~~fC~~C~~~~H~~~s-C~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnh-MtC-~C 267 (391)
...+.|..|...+|.-|+..-|++.. =......+. ..+. +.....-+.=-.|. --.|=|| |.| .|
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~---~~gr-----vs~~~s~r~~~~ct----~h~~e~~smyc~~c 241 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPP---AQGR-----VSRRLSPRKVSTCT----DHELENHSMYCVQC 241 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCc---ccCc-----eeeccchhhhhhcc----CCCCCCceEEEEec
Confidence 34577999999999999998888742 111111111 0000 00000001111222 1245566 999 99
Q ss_pred ccceeccccccccC
Q 016355 268 GHEFCYSCGAEYRD 281 (391)
Q Consensus 268 ~~~FCw~C~~~~~~ 281 (391)
+.-.||.|+.+.+.
T Consensus 242 k~pvc~~clee~kh 255 (699)
T KOG4367|consen 242 KMPVCYQCLEEGKH 255 (699)
T ss_pred CChHHHHHHHhhcc
Confidence 99999999998764
No 46
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.78 E-value=0.015 Score=57.70 Aligned_cols=43 Identities=21% Similarity=0.681 Sum_probs=34.2
Q ss_pred CCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccccccccCCCCCCC
Q 016355 159 SDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLS 216 (391)
Q Consensus 159 ~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~s 216 (391)
...+.|| .|...+.. ..+-+.++|. |++.||+.|+.+|+.+..
T Consensus 304 ~~wr~Cp--kC~~~ie~------------~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIEL------------SEGCNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred HhcCcCc--ccceeeee------------cCCcceEEee-ccccchhhcCcchhhCCc
Confidence 4678899 69988876 2246789997 999999999999966553
No 47
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.73 E-value=0.034 Score=52.00 Aligned_cols=52 Identities=25% Similarity=0.680 Sum_probs=39.8
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHH
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 135 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i 135 (391)
..-+|.||+.+-..+ +.+.|+|.||.-|+++.+... ...|+. |...|+...+
T Consensus 6 ~~~eC~IC~nt~n~P--v~l~C~HkFCyiCiKGsy~nd------k~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 6 KKKECLICYNTGNCP--VNLYCFHKFCYICIKGSYKND------KKTCAV--CRFPIDSTID 57 (324)
T ss_pred cCCcceeeeccCCcC--ccccccchhhhhhhcchhhcC------CCCCce--ecCCCCcchh
Confidence 456899999987655 778999999999998776432 236988 9888875543
No 48
>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=93.39 E-value=0.046 Score=40.80 Aligned_cols=50 Identities=14% Similarity=0.184 Sum_probs=34.8
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHH
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTV 133 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~ 133 (391)
..|.|+|+.+-...+ +.+++||.|++.++..|+.. ....||. ++..++..
T Consensus 3 ~~f~CpIt~~lM~dP--Vi~~~G~tyer~~I~~~l~~------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELMRDP--VILPSGHTYERSAIERWLEQ------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB-SSE--EEETTSEEEEHHHHHHHHCT------TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHhhCc--eeCCcCCEEcHHHHHHHHHc------CCCCCCC--CCCcCCcc
Confidence 468899999876544 66789999999999999964 2347888 67777654
No 49
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.11 E-value=0.07 Score=36.17 Aligned_cols=45 Identities=22% Similarity=0.660 Sum_probs=21.1
Q ss_pred ccccccccCC--CCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 78 CSICCEDKPY--PMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 78 C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
|++|.++... .++....|++.+|..||..-.+ ++. =+||. |+...
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----~~~--g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----NEG--GRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----SS---SB-TT--T--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----ccC--CCCCC--CCCCC
Confidence 6888887743 3445559999999999987664 222 27988 87653
No 50
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=92.82 E-value=0.16 Score=56.59 Aligned_cols=68 Identities=26% Similarity=0.558 Sum_probs=53.6
Q ss_pred CCCcccccccccccC-CCCeeeccCCCcccHHHHHHHHHHHhhCCCc---ccccCCCccCCccCHHHHHhhCCh
Q 016355 72 DKSPENCSICCEDKP-YPMMITMKCSHKFCSHCMRTYIDGKVQSSQV---PIRCPQLRCKYFISTVECKSFLPL 141 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~-~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~---~i~CP~~~C~~~i~~~~i~~~l~~ 141 (391)
....-.|.|||.+.. ....+.+.|+|.|-..|.+.-++..-..-.+ .|.||. |+..|....++.++++
T Consensus 3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 344567999998753 4566888999999999999988876542222 489999 9999999999998875
No 51
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=92.55 E-value=0.21 Score=47.14 Aligned_cols=96 Identities=23% Similarity=0.578 Sum_probs=55.6
Q ss_pred eec--cCCCcccHHHHHHHHHHHhhCC---CcccccCCCccCCccCHHHHHhhCChhHHHHHHHHHHHHhcCCCCCcccc
Q 016355 91 ITM--KCSHKFCSHCMRTYIDGKVQSS---QVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANILHSDRIYCP 165 (391)
Q Consensus 91 ~~l--~C~H~fC~~Cl~~~i~~~i~~g---~~~i~CP~~~C~~~i~~~~i~~~l~~~~~e~~~~~~~~~~i~~~~~~~CP 165 (391)
+++ .||-.||++|++.|....-..+ ...- .|...++... ....+|+....+ .| ....+.||
T Consensus 336 vtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t~-----tc~y~vde~~-------a~~arwd~as~~-TI-k~tTkpCP 401 (446)
T KOG0006|consen 336 VTCEGGCGFAFCRECKEAYHEGECSAVFEASGTT-----TCAYRVDERA-------AEQARWDAASKE-TI-KKTTKPCP 401 (446)
T ss_pred ccCCCCchhHhHHHHHhhhccccceeeecccccc-----ceeeecChhh-------hhhhhhhhhhhh-hh-hhccCCCC
Confidence 444 5999999999999975322111 1111 2444443321 112345544221 11 23445677
Q ss_pred CCCCCeeecCccccccccCCCCCCCCCeeeCC--CCCcccccccccCCCCC
Q 016355 166 FPNCSVLLDPRECLSARASSSSQSDNSCVECP--VCERFICVECGVPWHSS 214 (391)
Q Consensus 166 ~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~--~C~~~fC~~C~~~~H~~ 214 (391)
.|....+++ ..-..+.|+ .|+..+||+|+.+|...
T Consensus 402 --kChvptErn------------GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 402 --KCHVPTERN------------GGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred --CccCccccC------------CceEEeecCCCCCCceeEeccCChhhhh
Confidence 688776662 233457786 59999999999999653
No 52
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.90 E-value=0.081 Score=50.27 Aligned_cols=47 Identities=28% Similarity=0.750 Sum_probs=36.8
Q ss_pred CCcccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
..-.+|.+|-.-+-.. .++ .|-|.||+.|+-.|++. ...||. |+..+
T Consensus 13 n~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~-------~~~CP~--C~i~i 60 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEE-------SKYCPT--CDIVI 60 (331)
T ss_pred ccceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHH-------hccCCc--cceec
Confidence 4578999998776544 445 99999999999999987 248998 76554
No 53
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=91.74 E-value=0.079 Score=44.00 Aligned_cols=37 Identities=16% Similarity=0.502 Sum_probs=29.1
Q ss_pred CCcccccccccccCC-CCeeeccCC------CcccHHHHHHHHH
Q 016355 73 KSPENCSICCEDKPY-PMMITMKCS------HKFCSHCMRTYID 109 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~-~~~~~l~C~------H~fC~~Cl~~~i~ 109 (391)
....+|.||++.... .-++.++|+ |+||.+|+++|-.
T Consensus 24 ~~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 24 RCTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred ccCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 347899999999877 334555776 8899999999953
No 54
>PHA00626 hypothetical protein
Probab=91.71 E-value=0.14 Score=35.57 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=21.5
Q ss_pred CCccccc-eeeecCCCcc----eEe-cccccee
Q 016355 246 RCQQCRR-MIELTHGCYH----MTC-WCGHEFC 272 (391)
Q Consensus 246 ~CP~C~~-~IeK~~GCnh----MtC-~C~~~FC 272 (391)
.||+|+. .|.|++-|+. ..| .|||.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 6999999 5888887765 778 8888773
No 55
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.50 E-value=0.081 Score=46.46 Aligned_cols=35 Identities=37% Similarity=0.803 Sum_probs=28.1
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYI 108 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i 108 (391)
..-.|.|.||-.++..+ +...|||.||..|.-.-+
T Consensus 193 e~IPF~C~iCKkdy~sp--vvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 193 EKIPFLCGICKKDYESP--VVTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCCceeehhchhhccch--hhhhcchhHHHHHHHHHh
Confidence 34568999999999866 556999999999976544
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.73 E-value=0.2 Score=48.95 Aligned_cols=50 Identities=24% Similarity=0.714 Sum_probs=38.0
Q ss_pred cccccccccccCCC---CeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 75 PENCSICCEDKPYP---MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 75 ~~~C~IC~e~~~~~---~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
..+|+||++.+..+ .++++.|||.|=.+|+++|+. ++ ...+||. |+..-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~----~~~~cp~--c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK----TKMQCPL--CSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh----hhhhCcc--cCChhH
Confidence 46899999987532 466779999999999999993 22 2358998 876433
No 57
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=90.64 E-value=0.15 Score=48.66 Aligned_cols=48 Identities=27% Similarity=0.625 Sum_probs=37.0
Q ss_pred CCCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 71 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 71 ~~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.....++|+||++.+..+ .++.+=||..|..|-. ...-+||. |...++
T Consensus 44 ~~~~lleCPvC~~~l~~P-i~QC~nGHlaCssC~~----------~~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPP-IFQCDNGHLACSSCRT----------KVSNKCPT--CRLPIG 91 (299)
T ss_pred cchhhccCchhhccCccc-ceecCCCcEehhhhhh----------hhcccCCc--cccccc
Confidence 455689999999987655 3566779999999975 22358998 988876
No 58
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.43 E-value=0.19 Score=34.58 Aligned_cols=27 Identities=30% Similarity=0.661 Sum_probs=21.1
Q ss_pred CCCccccceeeecCC--CcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHG--CYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~G--CnhMtC-~C~~~F 271 (391)
+-||.|+.++...++ -+++.| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 469999998876543 568999 899864
No 59
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.15 E-value=0.088 Score=48.01 Aligned_cols=59 Identities=24% Similarity=0.491 Sum_probs=38.7
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhCChhHH
Q 016355 75 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSY 144 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l~~~~~ 144 (391)
-..|..|+---+...++-..|+|+||..|...-.. =.||. |+..+....+..-|+.++.
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~---------~~C~l--Ckk~ir~i~l~~slp~~ik 61 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSP---------DVCPL--CKKSIRIIQLNRSLPTDIK 61 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCCc---------ccccc--ccceeeeeecccccchhHH
Confidence 35689888765544444449999999999754331 17988 9988765554444444433
No 60
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.64 E-value=0.46 Score=47.18 Aligned_cols=49 Identities=27% Similarity=0.707 Sum_probs=36.9
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
....|+|.||+.....+ ++.+|||.||..|+.+-.. ..-.||. |...+.
T Consensus 81 ~~sef~c~vc~~~l~~p--v~tpcghs~c~~Cl~r~ld-------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYPP--VVTPCGHSFCLECLDRSLD-------QETECPL--CRDELV 129 (398)
T ss_pred ccchhhhhhhHhhcCCC--ccccccccccHHHHHHHhc-------cCCCCcc--cccccc
Confidence 36789999999877655 5669999999999777322 2246887 887765
No 61
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=89.62 E-value=0.22 Score=34.32 Aligned_cols=24 Identities=38% Similarity=0.958 Sum_probs=15.5
Q ss_pred CeeeCCCCCcccccccccCCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSSL 215 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~~ 215 (391)
....||.|+..||..|..-.|+..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 567899999999999988878653
No 62
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.57 E-value=0.66 Score=44.33 Aligned_cols=56 Identities=30% Similarity=0.670 Sum_probs=39.6
Q ss_pred cccccccccccCCC---Ceeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCc--cCHHHHHhh
Q 016355 75 PENCSICCEDKPYP---MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF--ISTVECKSF 138 (391)
Q Consensus 75 ~~~C~IC~e~~~~~---~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~--i~~~~i~~~ 138 (391)
...|.||-++|+.. ..... .|||.+|..|+...+. ...+.||. |... ++...++.+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~------~~~i~cpf--cR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG------NSRILCPF--CRETTEIPDGDVKSL 64 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc------CceeeccC--CCCcccCCchhHhhh
Confidence 46799999998754 23333 8999999999988873 33467877 8777 444444443
No 63
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=89.52 E-value=0.28 Score=37.49 Aligned_cols=32 Identities=31% Similarity=0.763 Sum_probs=25.0
Q ss_pred cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 94 KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 94 ~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.|+|.|...|+.++++++-. . =.||. |...+.
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~---~-~~CPm--CR~~w~ 82 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSS---K-GQCPM--CRQPWK 82 (85)
T ss_pred cCccHHHHHHHHHHHccccC---C-CCCCC--cCCeee
Confidence 89999999999999987521 1 27998 877653
No 64
>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=89.45 E-value=0.12 Score=46.86 Aligned_cols=51 Identities=24% Similarity=0.725 Sum_probs=38.1
Q ss_pred ccccccccccc-CCCCeeec---cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 75 PENCSICCEDK-PYPMMITM---KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 75 ~~~C~IC~e~~-~~~~~~~l---~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
..-|++|-.+. ..+++.-+ .|-|.+|-+|+..-++. .|..||.++|+..+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~------GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR------GPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC------CCCCCCCccHHHHHH
Confidence 34699999875 34454444 59999999999988852 356899999987653
No 65
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=89.40 E-value=0.69 Score=43.45 Aligned_cols=85 Identities=15% Similarity=0.298 Sum_probs=50.9
Q ss_pred hhhhcchhHHHHHHHHHHHHHhhhhhhhhccCCccccchHhHHHHHHhcCCCCCCCCCCCcccccccccccCCCCeeec-
Q 016355 15 REEKLDIPLLVALRQRILEYTSNLEAFVLKLVPSIELERPLRLAQIAVGIVSSPSQGDKSPENCSICCEDKPYPMMITM- 93 (391)
Q Consensus 15 ~ee~~~~~~l~~l~~~i~~~~~~~~~~~l~l~~~~~~~~~~~~~~~ai~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l- 93 (391)
...-+.++-+.++++.|.+....-. ...+ ..++.+..-..... .+.+...|.||+--+...+-|+.
T Consensus 68 nPRGl~d~~~~~i~~~~~~iikq~~--g~pi--------i~~lie~~~e~LT~---nn~p~gqCvICLygfa~~~~ft~T 134 (368)
T KOG4445|consen 68 NPRGLGDPEFREIQRQIQEIIKQNS--GMPI--------ICQLIEHCSEFLTE---NNHPNGQCVICLYGFASSPAFTVT 134 (368)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHhcC--CCch--------hHHHHHHHHHHccc---CCCCCCceEEEEEeecCCCceeee
Confidence 4445666666666666666554211 1111 12222222122221 24567789999988877764555
Q ss_pred cCCCcccHHHHHHHHHHHh
Q 016355 94 KCSHKFCSHCMRTYIDGKV 112 (391)
Q Consensus 94 ~C~H~fC~~Cl~~~i~~~i 112 (391)
.|.|+|-..|+.+|+....
T Consensus 135 ~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 135 ACDHYMHFACLARYLTECL 153 (368)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 9999999999999997643
No 66
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.85 E-value=0.063 Score=51.35 Aligned_cols=47 Identities=28% Similarity=0.648 Sum_probs=34.0
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCc
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 129 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~ 129 (391)
..+.|+||++-.... |....|.|.||.+|+-.-+.. |.- .||. |...
T Consensus 42 ~~v~c~icl~llk~t-mttkeClhrfc~~ci~~a~r~----gn~--ecpt--cRk~ 88 (381)
T KOG0311|consen 42 IQVICPICLSLLKKT-MTTKECLHRFCFDCIWKALRS----GNN--ECPT--CRKK 88 (381)
T ss_pred hhhccHHHHHHHHhh-cccHHHHHHHHHHHHHHHHHh----cCC--CCch--HHhh
Confidence 467899999976544 334499999999999776643 333 6887 7654
No 67
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.66 E-value=0.48 Score=45.69 Aligned_cols=63 Identities=30% Similarity=0.641 Sum_probs=43.3
Q ss_pred HHHHHhcCCCCCCCC-----CCCcccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 57 LAQIAVGIVSSPSQG-----DKSPENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 57 ~~~~ai~~~~~~~~~-----~~~~~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
+.++..|+-+.+.++ +....+|.||+++.. +.+.|+|.|. .|.+|.+..-- + .=+||. |...|
T Consensus 267 ~LqEiyGien~~v~~~~~~~~~~gkeCVIClse~r--dt~vLPCRHLCLCs~Ca~~Lr~-q------~n~CPI--CRqpi 335 (349)
T KOG4265|consen 267 LLQEIYGIENSTVEGTDADESESGKECVICLSESR--DTVVLPCRHLCLCSGCAKSLRY-Q------TNNCPI--CRQPI 335 (349)
T ss_pred eeehhhccccCCCCCCccccccCCCeeEEEecCCc--ceEEecchhhehhHhHHHHHHH-h------hcCCCc--cccch
Confidence 445666766544333 245789999999764 4466799998 89999876551 1 127998 98876
No 68
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.57 E-value=0.27 Score=49.99 Aligned_cols=42 Identities=31% Similarity=0.831 Sum_probs=35.7
Q ss_pred ccCCCCCc--cccceeee-cCCCcceEeccccceeccccccccCC
Q 016355 241 NKRWRRCQ--QCRRMIEL-THGCYHMTCWCGHEFCYSCGAEYRDG 282 (391)
Q Consensus 241 ~~~~k~CP--~C~~~IeK-~~GCnhMtC~C~~~FCw~C~~~~~~~ 282 (391)
+...+-|| .|+..+.- .+.+.-+.|.||+.|||.|+.+|...
T Consensus 155 ~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 155 NVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSP 199 (444)
T ss_pred CCccccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCC
Confidence 34457776 69999988 89999999999999999999999764
No 69
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.36 E-value=0.24 Score=29.00 Aligned_cols=23 Identities=35% Similarity=0.837 Sum_probs=15.0
Q ss_pred CCCccccceeeecCCCcceEeccccceecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~ 278 (391)
+.||+|+..|..+ ..||-.||.+
T Consensus 3 ~~Cp~Cg~~~~~~-----------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD-----------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc-----------cccChhhCCC
Confidence 6788888876543 4566666654
No 70
>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=88.12 E-value=0.66 Score=31.67 Aligned_cols=42 Identities=17% Similarity=0.437 Sum_probs=28.8
Q ss_pred cccccccccCCCCeeeccCC-----CcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 77 NCSICCEDKPYPMMITMKCS-----HKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l~C~-----H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
.|-||++.....+.+..+|. |.+-.+|+.+|+..+-. .+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~-----~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGN-----KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCC-----CcCCC
Confidence 38899983333333444664 88999999999976432 37876
No 71
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.68 E-value=0.42 Score=44.44 Aligned_cols=69 Identities=26% Similarity=0.467 Sum_probs=48.3
Q ss_pred CCCcccccccccccCCCCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCC-CccCC---ccCH----HHHHhhCCh
Q 016355 72 DKSPENCSICCEDKPYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ-LRCKY---FIST----VECKSFLPL 141 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~-~~C~~---~i~~----~~i~~~l~~ 141 (391)
.....-|.+|-+......++.+ -=.|.||+.|-+..|+.+-..| .+.||. ..|.. .++. .+|..+|..
T Consensus 265 ~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg--evYCPSGdkCPLvgS~vPWAFMQGEIatILag 342 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG--EVYCPSGDKCPLVGSNVPWAFMQGEIATILAG 342 (352)
T ss_pred CCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC--ceeCCCCCcCcccCCcccHHHhhhhHHHHhcc
Confidence 3456899999998887777766 3479999999999998875544 567886 45643 3333 345555554
Q ss_pred h
Q 016355 142 S 142 (391)
Q Consensus 142 ~ 142 (391)
+
T Consensus 343 d 343 (352)
T KOG3579|consen 343 D 343 (352)
T ss_pred c
Confidence 4
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.66 E-value=0.46 Score=31.89 Aligned_cols=29 Identities=28% Similarity=0.765 Sum_probs=22.6
Q ss_pred CCCccccceeeecCCCcceEe-ccccceec
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEFCY 273 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~FCw 273 (391)
-.||+|+..++.+.+=..++| .||+.+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 479999999887765558899 89887654
No 73
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=87.65 E-value=0.36 Score=33.13 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=19.4
Q ss_pred CCCccccc-eeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRR-MIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~-~IeK~~GCnhMtC-~C~~~F 271 (391)
+.||+|+. .+.... +.++| .||+.+
T Consensus 21 ~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcchheccC--CcEECCCcCCEE
Confidence 79999998 433333 79999 999875
No 74
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=87.06 E-value=0.43 Score=45.44 Aligned_cols=51 Identities=20% Similarity=0.577 Sum_probs=38.3
Q ss_pred ccccccccC--CCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH
Q 016355 78 CSICCEDKP--YPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK 136 (391)
Q Consensus 78 C~IC~e~~~--~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~ 136 (391)
|+.|.++.. ..+++.++||-.+|.-||..--+ .++ =+||. |......+.++
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~~~irq-~ln-----grcpa--crr~y~denv~ 69 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQ-NLN-----GRCPA--CRRKYDDENVR 69 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHHHHHHh-hcc-----CCChH--hhhhcccccee
Confidence 999999765 45677789999999999965433 232 38998 98877666655
No 75
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.98 E-value=0.27 Score=27.90 Aligned_cols=11 Identities=36% Similarity=0.658 Sum_probs=7.6
Q ss_pred CCccccceeee
Q 016355 246 RCQQCRRMIEL 256 (391)
Q Consensus 246 ~CP~C~~~IeK 256 (391)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 37777777764
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=86.92 E-value=0.36 Score=51.07 Aligned_cols=30 Identities=47% Similarity=1.044 Sum_probs=25.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccc------eecccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE------FCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~------FCw~C~~~~~ 280 (391)
|-||+|+.++. +.+| .||+. ||-.||.+..
T Consensus 16 kFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 16 RFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred ccccccCCCCC------CCcCCCCCCCCCcccccccccCCccc
Confidence 88999999884 4679 89876 9999998875
No 77
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.48 E-value=0.63 Score=29.72 Aligned_cols=33 Identities=27% Similarity=0.615 Sum_probs=21.1
Q ss_pred ccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCccc
Q 016355 162 IYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 203 (391)
Q Consensus 162 ~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~f 203 (391)
+.|| .|+..+..++.. -......+.|+.|+..|
T Consensus 3 i~CP--~C~~~f~v~~~~-------l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDK-------LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHH-------cccCCcEEECCCCCcEe
Confidence 5788 588776653221 01234578999999766
No 78
>PHA03096 p28-like protein; Provisional
Probab=86.15 E-value=0.41 Score=45.40 Aligned_cols=38 Identities=18% Similarity=0.496 Sum_probs=29.9
Q ss_pred ccccccccccCC----CCeeec--cCCCcccHHHHHHHHHHHhh
Q 016355 76 ENCSICCEDKPY----PMMITM--KCSHKFCSHCMRTYIDGKVQ 113 (391)
Q Consensus 76 ~~C~IC~e~~~~----~~~~~l--~C~H~fC~~Cl~~~i~~~i~ 113 (391)
..|.||++.... +..+.+ .|.|.||..|.+.|..+...
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 689999997643 233444 99999999999999988763
No 79
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.14 E-value=0.23 Score=45.87 Aligned_cols=54 Identities=22% Similarity=0.533 Sum_probs=41.1
Q ss_pred CcccccccccccCCC--------CeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHH
Q 016355 74 SPENCSICCEDKPYP--------MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 134 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~--------~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~ 134 (391)
+..-|.||-..+..+ +..+++|+|.|.-.|+++|.-. |..+ .||- |+..+....
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GKkq-tCPY--CKekVdl~r 284 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GKKQ-TCPY--CKEKVDLKR 284 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cCCC-CCch--HHHHhhHhh
Confidence 456799998766432 5788899999999999999742 4444 7998 998876544
No 80
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.12 E-value=0.47 Score=49.51 Aligned_cols=46 Identities=30% Similarity=0.729 Sum_probs=35.4
Q ss_pred CcccccccccccCCC-C--eeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 74 SPENCSICCEDKPYP-M--MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~-~--~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
....|.||.|+.... + ...++|+|.|+..|++.|++.+ -.||. |..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~--CR~ 338 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPT--CRT 338 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCc--chh
Confidence 367899999987542 1 2455999999999999999862 26888 655
No 81
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.84 E-value=0.2 Score=34.54 Aligned_cols=44 Identities=27% Similarity=0.641 Sum_probs=30.9
Q ss_pred ccccccccccCCCCeeec-cCCCc-ccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 76 ENCSICCEDKPYPMMITM-KCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l-~C~H~-fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
-+|.||++.-..+ .+ .|||+ .|.+|-....+. + .-.||. |..+|
T Consensus 8 dECTICye~pvds---VlYtCGHMCmCy~Cg~rl~~~----~--~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDS---VLYTCGHMCMCYACGLRLKKA----L--HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchH---HHHHcchHHhHHHHHHHHHHc----c--CCcCcc--hhhHH
Confidence 6899999853222 23 89998 899998877753 1 126887 87765
No 82
>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=85.75 E-value=0.65 Score=29.64 Aligned_cols=26 Identities=27% Similarity=0.852 Sum_probs=18.2
Q ss_pred CCCccccceeeec------CCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELT------HGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~------~GCnhMtC-~C~~~F 271 (391)
-.||+|+..+.-. .| ..++| +||+.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 4688998866544 23 37888 888766
No 83
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.56 E-value=0.45 Score=47.59 Aligned_cols=52 Identities=23% Similarity=0.650 Sum_probs=38.0
Q ss_pred CCCcccccccccccCCC-----Ce---------eec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKPYP-----MM---------ITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~-----~~---------~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
...+..|.||+.+.+.- .+ +.+ +|.|.|-..|+.+|..+ ..+.||. |..+++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT------YKLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh------hcccCCc--cCCCCC
Confidence 34577899999987531 11 223 89999999999999963 2368998 776664
No 84
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.36 E-value=0.83 Score=29.00 Aligned_cols=33 Identities=24% Similarity=0.554 Sum_probs=20.9
Q ss_pred ccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCccc
Q 016355 162 IYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 203 (391)
Q Consensus 162 ~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~f 203 (391)
+.|| +|+..+..++.. -.+....+.|+.|+..|
T Consensus 3 i~Cp--~C~~~y~i~d~~-------ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEK-------IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHH-------CCCCCcEEECCCCCCEe
Confidence 5788 588766553321 12344678999998765
No 85
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.08 E-value=0.66 Score=29.64 Aligned_cols=27 Identities=30% Similarity=0.802 Sum_probs=19.3
Q ss_pred CCCccccceeeec-----CCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELT-----HGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~-----~GCnhMtC-~C~~~F 271 (391)
..||+|++...-. .+=-++.| +|++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4799998877643 22338888 888876
No 86
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=84.95 E-value=0.18 Score=47.07 Aligned_cols=36 Identities=33% Similarity=0.819 Sum_probs=27.5
Q ss_pred CCCccccceeeecCCCcceEe-ccccceeccccccccCCCCcc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEFCYSCGAEYRDGQQTC 286 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~~~~~~~~c 286 (391)
.+|-=|-...+ |-+| .|||-|||-|...|-.....|
T Consensus 240 ~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~~ek~eC 276 (293)
T KOG0317|consen 240 RKCSLCLENRS------NPSATPCGHIFCWSCILEWCSEKAEC 276 (293)
T ss_pred CceEEEecCCC------CCCcCcCcchHHHHHHHHHHccccCC
Confidence 56666655543 6788 999999999999998766554
No 87
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=84.05 E-value=0.91 Score=48.43 Aligned_cols=51 Identities=24% Similarity=0.530 Sum_probs=40.7
Q ss_pred CCcccccccccccCC-CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 73 KSPENCSICCEDKPY-PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~-~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
...++|.||++.+.. ..+.+. +|-|+|-..|++.|....-.+|...-+||.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~ 241 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA 241 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc
Confidence 467899999998864 456777 899999999999999885455555568886
No 88
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=82.71 E-value=1.6 Score=26.73 Aligned_cols=26 Identities=35% Similarity=0.778 Sum_probs=18.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
+-||+|+.+.+...|=-.|.| .||++
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 789999999999988788999 89875
No 89
>PLN03086 PRLI-interacting factor K; Provisional
Probab=82.56 E-value=1.7 Score=45.09 Aligned_cols=56 Identities=21% Similarity=0.583 Sum_probs=36.4
Q ss_pred ccccCCCccCCccCHHHHHhhCChhHHHHHHHHHHHHhcC-CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeC
Q 016355 118 PIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVEC 196 (391)
Q Consensus 118 ~i~CP~~~C~~~i~~~~i~~~l~~~~~e~~~~~~~~~~i~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C 196 (391)
.+.||. |+..++...+...+ .. ....+-||..+|+..+...+. ...+.|
T Consensus 407 ~V~C~N--C~~~i~l~~l~lHe----------------~~C~r~~V~Cp~~~Cg~v~~r~el------------~~H~~C 456 (567)
T PLN03086 407 TVECRN--CKHYIPSRSIALHE----------------AYCSRHNVVCPHDGCGIVLRVEEA------------KNHVHC 456 (567)
T ss_pred eEECCC--CCCccchhHHHHHH----------------hhCCCcceeCCcccccceeecccc------------ccCccC
Confidence 478987 99888765544221 11 235577998789998866221 233579
Q ss_pred CCCCccc
Q 016355 197 PVCERFI 203 (391)
Q Consensus 197 ~~C~~~f 203 (391)
+.|+..|
T Consensus 457 ~~Cgk~f 463 (567)
T PLN03086 457 EKCGQAF 463 (567)
T ss_pred CCCCCcc
Confidence 9998766
No 90
>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=81.78 E-value=1.1 Score=27.26 Aligned_cols=26 Identities=31% Similarity=0.823 Sum_probs=13.6
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
-+||+|+....-.+|.+ |.| .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccccC
Confidence 37999999888877765 778 888875
No 91
>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=81.72 E-value=0.25 Score=31.98 Aligned_cols=38 Identities=26% Similarity=0.671 Sum_probs=23.6
Q ss_pred CccccceeeecCCCcceEe-ccccceeccccccccCCCCccccc
Q 016355 247 CQQCRRMIELTHGCYHMTC-WCGHEFCYSCGAEYRDGQQTCQCA 289 (391)
Q Consensus 247 CP~C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~~~~~~~~c~C~ 289 (391)
||-|...+.... += .|||.||..|...|-.....-.|+
T Consensus 1 C~iC~~~~~~~~-----~~~~C~H~fC~~C~~~~~~~~~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFEDPV-----ILLPCGHSFCRDCLRKWLENSGSVKCP 39 (41)
T ss_dssp ETTTSSBCSSEE-----EETTTSEEEEHHHHHHHHHHTSSSBTT
T ss_pred CCcCCccccCCC-----EEecCCCcchHHHHHHHHHhcCCccCC
Confidence 445555444333 45 899999999999986532233444
No 92
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=81.39 E-value=0.66 Score=30.54 Aligned_cols=32 Identities=28% Similarity=0.674 Sum_probs=21.2
Q ss_pred CccccceeeecCCCcceEeccccceeccccccccCCC
Q 016355 247 CQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDGQ 283 (391)
Q Consensus 247 CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~~~~ 283 (391)
||-|...+. +-++=.|||.||..|...|.+..
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERLWKEP 32 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHHHCCS
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHHHHcc
Confidence 444554443 34666899999999999986543
No 93
>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=80.30 E-value=0.85 Score=36.75 Aligned_cols=26 Identities=31% Similarity=0.675 Sum_probs=19.8
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
|.||+|++.+---.- +-++| .||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 799999988754333 78889 888765
No 94
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=80.12 E-value=0.72 Score=49.13 Aligned_cols=51 Identities=25% Similarity=0.783 Sum_probs=37.2
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH
Q 016355 76 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK 136 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~ 136 (391)
++|.+|.+ ....+...|+|.||.+|+..++...- ...||. |...+....+.
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~-----~~~~~~--cr~~l~~~~l~ 505 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE-----NAPCPL--CRNVLKEKKLL 505 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc-----CCCCcH--HHHHHHHHHHh
Confidence 89999999 33445559999999999999996422 226776 88776655544
No 95
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=79.95 E-value=0.82 Score=43.45 Aligned_cols=23 Identities=30% Similarity=0.803 Sum_probs=18.9
Q ss_pred CeeeCCCCCcccccccccCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSS 214 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~ 214 (391)
...+|+.|+..||..|..-.|..
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CcEEchhccceeeccchHHHHhh
Confidence 45779999999999998776643
No 96
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=79.80 E-value=1.1 Score=30.34 Aligned_cols=25 Identities=24% Similarity=0.541 Sum_probs=19.1
Q ss_pred CCCccccceeeecCCCcceEe-cccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
+.||+|+-.+....-=+...| +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 899999976655544458889 8986
No 97
>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=79.58 E-value=1.1 Score=35.47 Aligned_cols=32 Identities=19% Similarity=0.629 Sum_probs=25.6
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHH
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMR 105 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~ 105 (391)
....|.+|...+..+.+...+|||.|...|++
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 35569999998877665555999999999975
No 98
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=79.12 E-value=0.37 Score=45.99 Aligned_cols=30 Identities=23% Similarity=0.699 Sum_probs=24.6
Q ss_pred cCCCCCccccceeeec-CCCcceEe-ccccce
Q 016355 242 KRWRRCQQCRRMIELT-HGCYHMTC-WCGHEF 271 (391)
Q Consensus 242 ~~~k~CP~C~~~IeK~-~GCnhMtC-~C~~~F 271 (391)
..|.+||+|+..|-+. -.=|.+.| .|+|+|
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3589999999988654 45678899 899998
No 99
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=78.38 E-value=2 Score=35.53 Aligned_cols=53 Identities=21% Similarity=0.394 Sum_probs=42.3
Q ss_pred CCcccccccccccCCCCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 73 KSPENCSICCEDKPYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.+..+|.||-|....+.+..- -||-.+|.-|....++..- .. ..||. |+..+.
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~---~y-pvCPv--CkTSFK 132 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN---LY-PVCPV--CKTSFK 132 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc---cC-CCCCc--cccccc
Confidence 378999999999887776665 6899999999999997642 23 48999 887663
No 100
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=77.78 E-value=1.1 Score=29.47 Aligned_cols=25 Identities=28% Similarity=0.750 Sum_probs=18.8
Q ss_pred CCCCCccccceeeecCCCcceEe---ccccce
Q 016355 243 RWRRCQQCRRMIELTHGCYHMTC---WCGHEF 271 (391)
Q Consensus 243 ~~k~CP~C~~~IeK~~GCnhMtC---~C~~~F 271 (391)
++|+||+|++.= |+--+.| .|++.|
T Consensus 10 GirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 10 GIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred ccccCCcCcCcc----CcccccccCCccchhh
Confidence 459999999865 7777778 566654
No 101
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=77.78 E-value=1.1 Score=50.02 Aligned_cols=30 Identities=40% Similarity=0.852 Sum_probs=24.1
Q ss_pred CCCccccceeeecCCCcceEe-ccccce-----ecccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF-----CYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F-----Cw~C~~~~~ 280 (391)
++||+|+..+... .| .||.+. |-.||....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccC
Confidence 8999999987432 89 799764 999998765
No 102
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=77.72 E-value=0.77 Score=44.74 Aligned_cols=45 Identities=31% Similarity=0.849 Sum_probs=31.7
Q ss_pred CcccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCcc
Q 016355 74 SPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRC 126 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C 126 (391)
...-|-||-+... -+.+ +|||..|..|+..|-.+ ++. -.||...|
T Consensus 368 TFeLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~s---d~g--q~CPFCRc 413 (563)
T KOG1785|consen 368 TFELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDS---DEG--QTCPFCRC 413 (563)
T ss_pred hHHHHHHhhccCC---CcccccccchHHHHHHHhhccc---CCC--CCCCceee
Confidence 3456999987543 2566 99999999999988643 221 26888444
No 103
>PRK04023 DNA polymerase II large subunit; Validated
Probab=76.89 E-value=1.4 Score=48.16 Aligned_cols=40 Identities=30% Similarity=0.877 Sum_probs=29.7
Q ss_pred CCCCccccceeeecCCCcceEe-cccc-----ceeccccccccCCCCcc-cccCC
Q 016355 244 WRRCQQCRRMIELTHGCYHMTC-WCGH-----EFCYSCGAEYRDGQQTC-QCAFW 291 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC-~C~~-----~FCw~C~~~~~~~~~~c-~C~~~ 291 (391)
.+.||.|+... ....| .||. .||-.|+..-.. +.| +|..-
T Consensus 626 ~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~--y~CPKCG~E 672 (1121)
T PRK04023 626 RRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEE--DECEKCGRE 672 (1121)
T ss_pred CccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCC--CcCCCCCCC
Confidence 48999999985 66899 8996 499999877543 234 55543
No 104
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=76.51 E-value=1.2 Score=31.10 Aligned_cols=46 Identities=20% Similarity=0.426 Sum_probs=30.3
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHH
Q 016355 75 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTV 133 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~ 133 (391)
...|..|-.... .-..++|+|.+|..||...= + -.||. |...+...
T Consensus 7 ~~~~~~~~~~~~--~~~~~pCgH~I~~~~f~~~r--------Y-ngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVGT--KGTVLPCGHLICDNCFPGER--------Y-NGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEcccccc--ccccccccceeeccccChhh--------c-cCCCC--CCCcccCC
Confidence 456666655433 23456999999999984321 2 27999 98877543
No 105
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.46 E-value=1.9 Score=41.44 Aligned_cols=49 Identities=27% Similarity=0.572 Sum_probs=33.8
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCH
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 132 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~ 132 (391)
.+.-.|+||+-. +.+-+ -.+|+|.-|..|+.+++-+ .-+|-. |+..+..
T Consensus 420 sEd~lCpICyA~-pi~Av-f~PC~H~SC~~CI~qHlmN-------~k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 420 SEDNLCPICYAG-PINAV-FAPCSHRSCYGCITQHLMN-------CKRCFF--CKTTVID 468 (489)
T ss_pred cccccCcceecc-cchhh-ccCCCCchHHHHHHHHHhc-------CCeeeE--ecceeee
Confidence 456789999864 32322 1299999999999999843 135766 7776643
No 106
>PF04641 Rtf2: Rtf2 RING-finger
Probab=76.28 E-value=3 Score=39.18 Aligned_cols=70 Identities=14% Similarity=0.323 Sum_probs=49.0
Q ss_pred CCCcccccccccccCC-CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHhhCCh-hHHHHHH
Q 016355 72 DKSPENCSICCEDKPY-PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPL-SSYESLE 148 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~-~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~e~~~ 148 (391)
....+.|+|...++.. ..++.+ +|||+|+..+++..- .+ -.||. |+..+...+|-.+-+. +.++.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~----~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS----KKCPV--CGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc----ccccc--cCCccccCCEEEecCCccHHHHHH
Confidence 4678999999998854 355666 999999999998872 11 25998 9999987766555443 3444444
Q ss_pred HHH
Q 016355 149 TAL 151 (391)
Q Consensus 149 ~~~ 151 (391)
.++
T Consensus 180 ~~~ 182 (260)
T PF04641_consen 180 ERM 182 (260)
T ss_pred HHH
Confidence 443
No 107
>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=74.63 E-value=0.62 Score=44.30 Aligned_cols=30 Identities=20% Similarity=0.614 Sum_probs=24.2
Q ss_pred CCCCCccccceeeec-CCCcceEe-cccccee
Q 016355 243 RWRRCQQCRRMIELT-HGCYHMTC-WCGHEFC 272 (391)
Q Consensus 243 ~~k~CP~C~~~IeK~-~GCnhMtC-~C~~~FC 272 (391)
.|.+||+|+..|-+. -.=|.+.| .|||||=
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 589999999988764 45567899 8999864
No 108
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.61 E-value=2.4 Score=45.02 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=7.9
Q ss_pred CCCccccceee
Q 016355 245 RRCQQCRRMIE 255 (391)
Q Consensus 245 k~CP~C~~~Ie 255 (391)
+.||+|++...
T Consensus 42 ~fC~~CG~~~~ 52 (645)
T PRK14559 42 AHCPNCGAETG 52 (645)
T ss_pred ccccccCCccc
Confidence 77888877654
No 109
>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=74.21 E-value=2.8 Score=39.33 Aligned_cols=52 Identities=23% Similarity=0.696 Sum_probs=36.3
Q ss_pred cccccccccC-CCCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHH
Q 016355 77 NCSICCEDKP-YPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK 136 (391)
Q Consensus 77 ~C~IC~e~~~-~~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~ 136 (391)
.|++|-.+.- .+.++.+ .|+|..|-+|+-.-+.. |. -.||. |...+....++
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g~--~~Cpe--C~~iLRk~nfr 56 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----GP--AQCPE--CMVILRKNNFR 56 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----CC--CCCCc--ccchhhhcccc
Confidence 4889987643 3444444 99999999999888752 33 37984 98877554443
No 110
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=73.69 E-value=0.59 Score=44.46 Aligned_cols=31 Identities=19% Similarity=0.478 Sum_probs=24.5
Q ss_pred CCCCCccccceeeec-CCCcceEe-ccccceec
Q 016355 243 RWRRCQQCRRMIELT-HGCYHMTC-WCGHEFCY 273 (391)
Q Consensus 243 ~~k~CP~C~~~IeK~-~GCnhMtC-~C~~~FCw 273 (391)
.|.+||+|+..|-+. -.=|.+.| .|+|||=-
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 489999999988654 45678899 89998743
No 111
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.26 E-value=3.6 Score=40.34 Aligned_cols=59 Identities=15% Similarity=0.301 Sum_probs=41.3
Q ss_pred CCcccccccccccCCC-CeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHh
Q 016355 73 KSPENCSICCEDKPYP-MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 137 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~-~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~ 137 (391)
...|.|+|=-+....+ .-..+.|||+++++=+.+... +|...++||- |......+..++
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC--CCcccCHHhccc
Confidence 4578999965544322 235669999999997776654 5666789998 888766655443
No 112
>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=73.15 E-value=3 Score=27.35 Aligned_cols=22 Identities=27% Similarity=0.822 Sum_probs=17.4
Q ss_pred CCCccccceeee-cCCCcceEe-ccc
Q 016355 245 RRCQQCRRMIEL-THGCYHMTC-WCG 268 (391)
Q Consensus 245 k~CP~C~~~IeK-~~GCnhMtC-~C~ 268 (391)
..||.|++|..+ .+| .+.| .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 799999999988 555 5777 664
No 113
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.10 E-value=4.7 Score=30.86 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=23.2
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||.|+....|..+=---.| +||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 799999999999988888888 777765
No 114
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.01 E-value=2.5 Score=45.35 Aligned_cols=34 Identities=29% Similarity=0.872 Sum_probs=31.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccc-----eecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE-----FCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~-----FCw~C~~~ 278 (391)
-.||+|..+..-..+=|.|.| .||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 589999999988887899999 99986 99999998
No 115
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=72.79 E-value=1.9 Score=46.79 Aligned_cols=26 Identities=35% Similarity=1.005 Sum_probs=23.3
Q ss_pred CCCccccceeeecCCCcceEe-cccccee
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEFC 272 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~FC 272 (391)
..||.|+..++..+||. +| .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999998 99 9999766
No 116
>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=72.74 E-value=3.2 Score=26.11 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=16.1
Q ss_pred CCCccccceeee-cCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIEL-THGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK-~~GCnhMtC-~C~~~F 271 (391)
+-||+|+.+..- .++=.+..| .|+|++
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 579999976543 333333389 898864
No 117
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=72.61 E-value=3.6 Score=39.29 Aligned_cols=43 Identities=23% Similarity=0.641 Sum_probs=32.9
Q ss_pred ccccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccC
Q 016355 76 ENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 127 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~ 127 (391)
..|-.|+++......+.+ .|.+.||.+|= .++...+. .||. |.
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCD-v~iHesLh------~Cpg--Ce 374 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCD-VFIHESLH------NCPG--CE 374 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccch-HHHHhhhh------cCCC--cC
Confidence 349999888888888888 99999999994 45544443 5877 65
No 118
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=72.59 E-value=1.2 Score=41.64 Aligned_cols=34 Identities=26% Similarity=0.637 Sum_probs=27.6
Q ss_pred ccCCCCCccccceeee-cCCCcceEe-ccccceecc
Q 016355 241 NKRWRRCQQCRRMIEL-THGCYHMTC-WCGHEFCYS 274 (391)
Q Consensus 241 ~~~~k~CP~C~~~IeK-~~GCnhMtC-~C~~~FCw~ 274 (391)
...|.+||.|+..+-+ .=+=|.+.| +|+|||=-.
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccccC
Confidence 5678999999988865 458888999 899998543
No 119
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.21 E-value=2.8 Score=45.47 Aligned_cols=50 Identities=26% Similarity=0.681 Sum_probs=36.5
Q ss_pred CcccccccccccC-----CCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 74 SPENCSICCEDKP-----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 74 ~~~~C~IC~e~~~-----~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
...+|+||+.-.. .+. -++ .|.|.|...|+.+|+.+.-+ -+||- |...|+
T Consensus 1468 G~eECaICYsvL~~vdr~lPs-krC~TCknKFH~~CLyKWf~Ss~~-----s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPS-KRCATCKNKFHTRCLYKWFASSAR-----SNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCc-cccchhhhhhhHHHHHHHHHhcCC-----CCCCc--cccccc
Confidence 4668999997543 121 234 79999999999999986432 28998 887664
No 120
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.07 E-value=1.1 Score=40.67 Aligned_cols=19 Identities=32% Similarity=0.933 Sum_probs=15.6
Q ss_pred ccccceeccccccccCCCC
Q 016355 266 WCGHEFCYSCGAEYRDGQQ 284 (391)
Q Consensus 266 ~C~~~FCw~C~~~~~~~~~ 284 (391)
-|||-|||-|+-.|.....
T Consensus 64 lCGHLFCWpClyqWl~~~~ 82 (230)
T KOG0823|consen 64 LCGHLFCWPCLYQWLQTRP 82 (230)
T ss_pred ecccceehHHHHHHHhhcC
Confidence 3899999999999975443
No 121
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=71.51 E-value=1.3 Score=47.57 Aligned_cols=33 Identities=33% Similarity=0.810 Sum_probs=0.0
Q ss_pred CCCCccccceeeecCCCcceEe-ccccc-----eeccccccccCC
Q 016355 244 WRRCQQCRRMIELTHGCYHMTC-WCGHE-----FCYSCGAEYRDG 282 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC-~C~~~-----FCw~C~~~~~~~ 282 (391)
.++||+|+.... .-+| .||.+ +|..|+......
T Consensus 655 ~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 655 RRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ---------------------------------------------
T ss_pred cccCcccCCcch------hhcCcccCCccccceeccccccccCcc
Confidence 489999998763 4689 79976 999999988754
No 122
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.27 E-value=2.8 Score=33.87 Aligned_cols=23 Identities=39% Similarity=0.847 Sum_probs=19.5
Q ss_pred CeeeCCCCCcccccccccCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSS 214 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~ 214 (391)
....|++|+..||..|..-+|+.
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred cceeCCCCCCccccccchhhhhh
Confidence 45679999999999999888854
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.05 E-value=3 Score=46.79 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=10.0
Q ss_pred CCCCCccchhhhhcc
Q 016355 355 PRCTDSYGDAMKDLH 369 (391)
Q Consensus 355 ~~~~~~~~~~~~~~~ 369 (391)
|+.-+.+|+++++||
T Consensus 799 p~Eigvs~eklreLG 813 (1337)
T PRK14714 799 PREIGVSVEKLRELG 813 (1337)
T ss_pred HHHcCCCHHHHHHcC
Confidence 455556677888875
No 124
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.90 E-value=3.5 Score=37.82 Aligned_cols=54 Identities=9% Similarity=0.150 Sum_probs=39.4
Q ss_pred CCcccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHH
Q 016355 73 KSPENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 135 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~-~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i 135 (391)
...+-|++|-++.... ....| +|||+||.+|+...+.. ...||. |+..+...+|
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-------D~v~pv--~d~plkdrdi 274 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-------DMVDPV--TDKPLKDRDI 274 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-------cccccC--CCCcCcccce
Confidence 3668899999987643 34555 99999999999999853 234666 7777665544
No 125
>PF12773 DZR: Double zinc ribbon
Probab=70.49 E-value=2.9 Score=28.33 Aligned_cols=11 Identities=18% Similarity=0.673 Sum_probs=6.1
Q ss_pred CCCccccceee
Q 016355 245 RRCQQCRRMIE 255 (391)
Q Consensus 245 k~CP~C~~~Ie 255 (391)
+.||.|++++.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 45555555554
No 126
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=69.86 E-value=2.5 Score=42.21 Aligned_cols=36 Identities=25% Similarity=0.693 Sum_probs=29.5
Q ss_pred CCcccccccccccCCCCeee-ccCCCcccHHHHHHHHHH
Q 016355 73 KSPENCSICCEDKPYPMMIT-MKCSHKFCSHCMRTYIDG 110 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~-l~C~H~fC~~Cl~~~i~~ 110 (391)
.....|++|......+ +. ..|||.||..|+..+...
T Consensus 19 ~~~l~C~~C~~vl~~p--~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDP--VQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred cccccCccccccccCC--CCCCCCCCcccccccchhhcc
Confidence 4568899999987655 44 599999999999988865
No 127
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.54 E-value=1.6 Score=41.00 Aligned_cols=46 Identities=28% Similarity=0.559 Sum_probs=33.8
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
-.|-|.||-.++..+ +...|+|.||..|....+.- .-+|+. |...+
T Consensus 240 ~Pf~c~icr~~f~~p--Vvt~c~h~fc~~ca~~~~qk-------~~~c~v--C~~~t 285 (313)
T KOG1813|consen 240 LPFKCFICRKYFYRP--VVTKCGHYFCEVCALKPYQK-------GEKCYV--CSQQT 285 (313)
T ss_pred CCccccccccccccc--hhhcCCceeehhhhcccccc-------CCccee--ccccc
Confidence 357799999998766 55699999999998766531 236776 76643
No 128
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=69.48 E-value=1.4 Score=46.56 Aligned_cols=13 Identities=31% Similarity=0.787 Sum_probs=10.9
Q ss_pred CCCcccccccccC
Q 016355 198 VCERFICVECGVP 210 (391)
Q Consensus 198 ~C~~~fC~~C~~~ 210 (391)
.|++.||..|-.+
T Consensus 660 kC~H~FC~~Cvq~ 672 (698)
T KOG0978|consen 660 KCGHVFCEECVQT 672 (698)
T ss_pred hcchHHHHHHHHH
Confidence 7999999999643
No 129
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.40 E-value=2.1 Score=37.26 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=10.3
Q ss_pred CCCccccccccc
Q 016355 198 VCERFICVECGV 209 (391)
Q Consensus 198 ~C~~~fC~~C~~ 209 (391)
+||+.||..|-+
T Consensus 150 kCGHvFC~~Cik 161 (187)
T KOG0320|consen 150 KCGHVFCSQCIK 161 (187)
T ss_pred ccchhHHHHHHH
Confidence 899999998853
No 130
>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=68.93 E-value=4 Score=30.00 Aligned_cols=33 Identities=30% Similarity=0.871 Sum_probs=22.9
Q ss_pred CCccccceeeecCCCcceEe-ccccc-----eecccccccc
Q 016355 246 RCQQCRRMIELTHGCYHMTC-WCGHE-----FCYSCGAEYR 280 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC-~C~~~-----FCw~C~~~~~ 280 (391)
.||.|+.+++..+ .+.+| .|+.. +|-.|+.++.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHH
Confidence 6999999999988 79999 99864 7999999885
No 131
>PF14149 YhfH: YhfH-like protein
Probab=68.59 E-value=0.55 Score=29.86 Aligned_cols=29 Identities=31% Similarity=0.747 Sum_probs=23.8
Q ss_pred HhccCCCCCccccceeeecCCCcceEe-cc
Q 016355 239 AQNKRWRRCQQCRRMIELTHGCYHMTC-WC 267 (391)
Q Consensus 239 ~~~~~~k~CP~C~~~IeK~~GCnhMtC-~C 267 (391)
-.+...|.||.|+..|+--.-|..++| +|
T Consensus 8 frnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 8 FRNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 345566999999999998888888888 76
No 132
>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=68.45 E-value=3.1 Score=28.08 Aligned_cols=25 Identities=20% Similarity=0.529 Sum_probs=20.0
Q ss_pred CCCc--cccceeeecCCCcceEe-cccc
Q 016355 245 RRCQ--QCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 245 k~CP--~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
+.|| +|+.-+.-..--+..+| +||+
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCcccCCceEeeecCCCccCCCccc
Confidence 8999 99998877777789999 9986
No 133
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=68.15 E-value=4.2 Score=25.47 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=13.6
Q ss_pred CCCccccceeeec----CCCcceEe-cccc
Q 016355 245 RRCQQCRRMIELT----HGCYHMTC-WCGH 269 (391)
Q Consensus 245 k~CP~C~~~IeK~----~GCnhMtC-~C~~ 269 (391)
|-||.|+.+++.. ++=..+.| .||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4699999998874 45556788 8875
No 134
>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=67.79 E-value=3.1 Score=33.03 Aligned_cols=24 Identities=29% Similarity=0.818 Sum_probs=18.5
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
+-||+|+.++...+| .+.| .||+.
T Consensus 1 ~fC~~Cg~~l~~~~~--~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKNG--VYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCCC--eEECcCCCCc
Confidence 369999999976653 7888 77775
No 135
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.77 E-value=2.8 Score=40.86 Aligned_cols=47 Identities=26% Similarity=0.794 Sum_probs=33.2
Q ss_pred cccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccC
Q 016355 75 PENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 127 (391)
Q Consensus 75 ~~~C~IC~e~~~~~-~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~ 127 (391)
...|.||-+-++.. ++-.+ .|||.|-..|+.+|++..-.. =.||. |.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~----R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN----RGCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc----CCCCc--ee
Confidence 45799996655544 34445 599999999999999754332 35776 65
No 136
>PRK00420 hypothetical protein; Validated
Probab=66.99 E-value=3.7 Score=33.22 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=20.5
Q ss_pred CCCccccceeee-cCCCcceEeccccceecccccccc
Q 016355 245 RRCQQCRRMIEL-THGCYHMTCWCGHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK-~~GCnhMtC~C~~~FCw~C~~~~~ 280 (391)
..||.|+.++.+ .+ |..||-.||..+.
T Consensus 24 ~~CP~Cg~pLf~lk~---------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKD---------GEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCC---------CceECCCCCCeee
Confidence 899999999986 44 4567777777654
No 137
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=65.91 E-value=4.2 Score=34.66 Aligned_cols=33 Identities=27% Similarity=0.699 Sum_probs=20.9
Q ss_pred CCCccccceeeecCCCcceEecc-------ccceecccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWC-------GHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C-------~~~FCw~C~~~~~ 280 (391)
..||+|+++|.-. .|.-=.. --.||+.||++|.
T Consensus 40 ~~Cp~C~~~IrG~---y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGD---YHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCc---eecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 6899999999743 1110011 3367888888763
No 138
>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=65.36 E-value=4.3 Score=29.53 Aligned_cols=26 Identities=27% Similarity=0.621 Sum_probs=20.4
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
+.||.|+....+...=..++| .||+.
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCE
Confidence 899999999988555557778 67765
No 139
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=64.95 E-value=4.3 Score=40.44 Aligned_cols=47 Identities=28% Similarity=0.752 Sum_probs=34.5
Q ss_pred CCcccccccccccCCC--CeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKPYP--MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~--~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
...-||+||++-...+ -+++..|.|.|--.|+..|.. ..||. |....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---------~scpv--cR~~q 221 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---------SSCPV--CRYCQ 221 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhccc---------CcChh--hhhhc
Confidence 4567999999976543 234459999999999998873 47887 65443
No 140
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=64.69 E-value=4.4 Score=31.69 Aligned_cols=29 Identities=31% Similarity=0.692 Sum_probs=21.9
Q ss_pred CCcccccee--eecCCCcceEe-ccccceecc
Q 016355 246 RCQQCRRMI--ELTHGCYHMTC-WCGHEFCYS 274 (391)
Q Consensus 246 ~CP~C~~~I--eK~~GCnhMtC-~C~~~FCw~ 274 (391)
-||.|+.++ ++.+-||...| .|+|.|=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 599999654 44455999999 899987443
No 141
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.46 E-value=8.2 Score=41.79 Aligned_cols=39 Identities=15% Similarity=0.392 Sum_probs=32.6
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHH
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGK 111 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~ 111 (391)
.+.-+|.+|.-..-...++.++|||.|..+|+...+..-
T Consensus 815 ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred cCccchHHhcchhhcCcceeeeccchHHHHHHHHHHHcc
Confidence 446789999988877777777999999999999988643
No 142
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.77 E-value=1.6 Score=32.50 Aligned_cols=48 Identities=23% Similarity=0.570 Sum_probs=32.9
Q ss_pred cccccccccCC---------CCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 77 NCSICCEDKPY---------PMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 77 ~C~IC~e~~~~---------~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
+|+||--.|.. .+..-+ .|.|.|-..|+.+++.+.-++| .||. |...+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~----~CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG----QCPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc----cCCc--chhee
Confidence 78888766543 232223 6889999999999997655443 6887 76654
No 143
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.75 E-value=4.4 Score=33.65 Aligned_cols=24 Identities=29% Similarity=0.786 Sum_probs=18.9
Q ss_pred CCCccccceeeecCCCcceEeccccceeccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGA 277 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~ 277 (391)
+.||.|++|..+-. |.-||-+|+.
T Consensus 29 ~hCp~Cg~PLF~Kd---------G~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKD---------GEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeC---------CeEECCCCCc
Confidence 89999999997755 4667777773
No 144
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=63.04 E-value=3.6 Score=29.71 Aligned_cols=29 Identities=34% Similarity=0.823 Sum_probs=13.1
Q ss_pred CCCccccceeeec---CCCcceEeccccceecccccccc
Q 016355 245 RRCQQCRRMIELT---HGCYHMTCWCGHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~---~GCnhMtC~C~~~FCw~C~~~~~ 280 (391)
-+|++|....... +||.|+ ||+.|-++.-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~-------fCs~Ci~~~~ 39 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHI-------FCSSCIRDCI 39 (65)
T ss_dssp TS-SSS-S--SS-B---SSS---------B-TTTGGGGT
T ss_pred cCCcHHHHHhcCCceeccCccH-------HHHHHhHHhc
Confidence 5899999876543 555554 6666666543
No 145
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.00 E-value=3.7 Score=29.01 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=10.0
Q ss_pred CCCcccc-ceeeecCCC
Q 016355 245 RRCQQCR-RMIELTHGC 260 (391)
Q Consensus 245 k~CP~C~-~~IeK~~GC 260 (391)
-.||+|+ ..|-+-.-|
T Consensus 28 F~CPnCGe~~I~Rc~~C 44 (61)
T COG2888 28 FPCPNCGEVEIYRCAKC 44 (61)
T ss_pred eeCCCCCceeeehhhhH
Confidence 4777777 666554444
No 146
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=62.95 E-value=1.5 Score=38.91 Aligned_cols=32 Identities=25% Similarity=0.667 Sum_probs=24.3
Q ss_pred CCCCccccceeeecCCCcceEeccccceecccccccc
Q 016355 244 WRRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYR 280 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~ 280 (391)
.-.||-|.-.+.. -+.=.|||.|||.|...|.
T Consensus 18 ~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 3689999887631 1223899999999999984
No 147
>PRK04023 DNA polymerase II large subunit; Validated
Probab=62.89 E-value=4.9 Score=44.16 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=10.1
Q ss_pred CCCCCccchhhhhcc
Q 016355 355 PRCTDSYGDAMKDLH 369 (391)
Q Consensus 355 ~~~~~~~~~~~~~~~ 369 (391)
|+.-+.+++++++||
T Consensus 752 p~EigvsveklreLG 766 (1121)
T PRK04023 752 PREIGVSVEKLRELG 766 (1121)
T ss_pred HHHcCCCHHHHHHcC
Confidence 445556677888885
No 148
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=62.60 E-value=9 Score=36.70 Aligned_cols=49 Identities=20% Similarity=0.537 Sum_probs=35.1
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCc
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 129 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~ 129 (391)
.....|++|......+-... .=|-+||..|+-+|+.+ .| +||..+|...
T Consensus 298 ~~~~~CpvClk~r~Nptvl~-vSGyVfCY~Ci~~Yv~~---~~----~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLE-VSGYVFCYPCIFSYVVN---YG----HCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCCCceEE-ecceEEeHHHHHHHHHh---cC----CCCccCCcch
Confidence 44678999998876553222 44899999999999973 22 7888666554
No 149
>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=62.42 E-value=7 Score=27.27 Aligned_cols=28 Identities=32% Similarity=0.583 Sum_probs=20.5
Q ss_pred CCCccccceeeecCCC--cceEe-cccccee
Q 016355 245 RRCQQCRRMIELTHGC--YHMTC-WCGHEFC 272 (391)
Q Consensus 245 k~CP~C~~~IeK~~GC--nhMtC-~C~~~FC 272 (391)
-.||.|+..|+..+.= -.+.| .||..+=
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 4799999999886532 35778 7887653
No 150
>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=62.25 E-value=10 Score=36.32 Aligned_cols=35 Identities=26% Similarity=0.534 Sum_probs=21.5
Q ss_pred CCCccccceeeecCCCcceEeccccceeccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEY 279 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~ 279 (391)
..||.|++..-.+..=.-|.=.|||.||-.|...+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l 38 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL 38 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHH
Confidence 57999999655443211121157777777777774
No 151
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.99 E-value=5.6 Score=31.49 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=18.7
Q ss_pred CCCcccccee---eecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMI---ELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~I---eK~~GCnhMtC-~C~~~F 271 (391)
-.||+|+... .+..|=-|..| .||+.+
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 6899999432 33446678888 888763
No 152
>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=61.42 E-value=4.3 Score=33.44 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=19.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
|.||+|++.+---.- +-++| +||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 789999988754332 77888 777763
No 153
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=60.81 E-value=4.6 Score=30.22 Aligned_cols=45 Identities=24% Similarity=0.562 Sum_probs=16.3
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcc
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYH 262 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnh 262 (391)
....+.|..|++..|..|. +|. .+.+.+.||+|+++..+..|+-.
T Consensus 25 Ge~FVAC~eC~fPvCr~Cy----------EYE------------------rkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 25 GEVFVACHECAFPVCRPCY----------EYE------------------RKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SSB--S-SSS-----HHHH----------HHH------------------HHTS-SB-TTT--B----TT---
T ss_pred CCEEEEEcccCCccchhHH----------HHH------------------hhcCcccccccCCCcccccCCCC
Confidence 3456779899988887663 332 12233899999999988777654
No 154
>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=60.18 E-value=8.7 Score=22.85 Aligned_cols=20 Identities=20% Similarity=0.571 Sum_probs=13.3
Q ss_pred CCccccceeeecCCCcceEe
Q 016355 246 RCQQCRRMIELTHGCYHMTC 265 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC 265 (391)
.||.|+..+.+..|=-...|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999988777777
No 155
>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=60.17 E-value=7 Score=26.72 Aligned_cols=47 Identities=17% Similarity=0.600 Sum_probs=23.6
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 76 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
..|++-+.....+ .....|.|.-|++ +..|++.....+. -+||. |+.
T Consensus 3 L~CPls~~~i~~P-~Rg~~C~H~~CFD-l~~fl~~~~~~~~--W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP-VRGKNCKHLQCFD-LESFLESNQRTPK--WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE-EEETT--SS--EE-HHHHHHHHHHS-----B-TT--T--
T ss_pred eeCCCCCCEEEeC-ccCCcCcccceEC-HHHHHHHhhccCC--eECcC--CcC
Confidence 4577777665433 2333999998876 7788877766555 48998 764
No 156
>PF14353 CpXC: CpXC protein
Probab=59.77 E-value=7.2 Score=32.22 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=4.5
Q ss_pred CCCcccccee
Q 016355 245 RRCQQCRRMI 254 (391)
Q Consensus 245 k~CP~C~~~I 254 (391)
-.||+|+..+
T Consensus 39 ~~CP~Cg~~~ 48 (128)
T PF14353_consen 39 FTCPSCGHKF 48 (128)
T ss_pred EECCCCCCce
Confidence 3444444444
No 157
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.68 E-value=2.7 Score=39.45 Aligned_cols=29 Identities=24% Similarity=0.709 Sum_probs=22.6
Q ss_pred cccccccccccCCCCeeeccCCCc-ccHHHHH
Q 016355 75 PENCSICCEDKPYPMMITMKCSHK-FCSHCMR 105 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~ 105 (391)
..-|.||||. .-+.+-|.|||. .|..|-+
T Consensus 300 ~~LC~ICmDa--P~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcC--CcceEEeecCcEEeehhhcc
Confidence 5679999984 346677799996 7999843
No 158
>PHA02929 N1R/p28-like protein; Provisional
Probab=59.56 E-value=5 Score=37.06 Aligned_cols=43 Identities=21% Similarity=0.476 Sum_probs=31.2
Q ss_pred CCCCccccceeeecCCCc---ceEeccccceeccccccccCCCCcc
Q 016355 244 WRRCQQCRRMIELTHGCY---HMTCWCGHEFCYSCGAEYRDGQQTC 286 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCn---hMtC~C~~~FCw~C~~~~~~~~~~c 286 (391)
-..||-|...+.....-+ -+.-.|+|.||..|...|......|
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tC 219 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTC 219 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCC
Confidence 378999999876554322 1334899999999999998765544
No 159
>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=58.93 E-value=9.6 Score=24.99 Aligned_cols=24 Identities=25% Similarity=0.652 Sum_probs=13.7
Q ss_pred CCccccce-eeecCCCcceEe-cccc
Q 016355 246 RCQQCRRM-IELTHGCYHMTC-WCGH 269 (391)
Q Consensus 246 ~CP~C~~~-IeK~~GCnhMtC-~C~~ 269 (391)
.||.|+.. |.-+..=.-+.| .||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 58888875 344444445566 5654
No 160
>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=58.88 E-value=12 Score=34.68 Aligned_cols=45 Identities=27% Similarity=0.547 Sum_probs=25.8
Q ss_pred CCCccccCCCCCeeecCccccccccCC--CCCCCCCeeeCCCCCccc
Q 016355 159 SDRIYCPFPNCSVLLDPRECLSARASS--SSQSDNSCVECPVCERFI 203 (391)
Q Consensus 159 ~~~~~CP~p~C~~~~~~~~~~~~~~~~--~~~~~~~~v~C~~C~~~f 203 (391)
..++-||+|+|+.++........+.+. ...+....+.|.+|+..|
T Consensus 121 S~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred cccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 577899999999998764432111110 012233446676666554
No 161
>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=57.74 E-value=7.9 Score=26.71 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=15.8
Q ss_pred CCCccccceee------ecCCCcceE-e-ccccc
Q 016355 245 RRCQQCRRMIE------LTHGCYHMT-C-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~Ie------K~~GCnhMt-C-~C~~~ 270 (391)
|+||.|+-.-+ .+.+..++. | .||+.
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 79999996554 223455553 5 45554
No 162
>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=56.18 E-value=7.8 Score=26.68 Aligned_cols=26 Identities=31% Similarity=0.692 Sum_probs=13.1
Q ss_pred ccccccccCCC-------Ceeec-cCCCcccHHH
Q 016355 78 CSICCEDKPYP-------MMITM-KCSHKFCSHC 103 (391)
Q Consensus 78 C~IC~e~~~~~-------~~~~l-~C~H~fC~~C 103 (391)
|.-|...++.. ..+.. .|++.||.+|
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC 35 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC 35 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHH
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCc
Confidence 44555555543 34556 8999999999
No 163
>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=55.88 E-value=8 Score=30.89 Aligned_cols=25 Identities=24% Similarity=0.576 Sum_probs=18.1
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
-.||+|+.-..=..|=+ +.| -|+|+
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYE 28 (109)
T ss_pred CcCCcCCCcceEecCCe-eECcccccc
Confidence 47999998887777754 666 56655
No 164
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.59 E-value=12 Score=40.33 Aligned_cols=40 Identities=28% Similarity=0.842 Sum_probs=30.6
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 76 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
..|..|--+...+ ++.+.|||.|...|+. ++. -.||. |..
T Consensus 841 skCs~C~~~LdlP-~VhF~CgHsyHqhC~e--------~~~--~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLP-FVHFLCGHSYHQHCLE--------DKE--DKCPK--CLP 880 (933)
T ss_pred eeecccCCccccc-eeeeecccHHHHHhhc--------cCc--ccCCc--cch
Confidence 5799998776554 4566999999999997 222 37988 876
No 165
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=55.25 E-value=9.2 Score=31.06 Aligned_cols=27 Identities=26% Similarity=0.567 Sum_probs=19.6
Q ss_pred CCCccccceeeec--CCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC-~C~~~F 271 (391)
+-||+|+.++.-. ++=+.+.| .||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 6899999887652 23338899 898864
No 166
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=54.17 E-value=3.9 Score=38.35 Aligned_cols=41 Identities=37% Similarity=0.767 Sum_probs=29.7
Q ss_pred CCCccccceeeecCCCcceEe--ccccceeccccccccCCCCcccccCCCCC
Q 016355 245 RRCQQCRRMIELTHGCYHMTC--WCGHEFCYSCGAEYRDGQQTCQCAFWDED 294 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC--~C~~~FCw~C~~~~~~~~~~c~C~~~~~~ 294 (391)
-+|--|.-.| .+-| .|||-||++|-+.+-+.+.+| +.-.++
T Consensus 26 lrC~IC~~~i-------~ip~~TtCgHtFCslCIR~hL~~qp~C--P~Cr~~ 68 (391)
T COG5432 26 LRCRICDCRI-------SIPCETTCGHTFCSLCIRRHLGTQPFC--PVCRED 68 (391)
T ss_pred HHhhhhhhee-------ecceecccccchhHHHHHHHhcCCCCC--cccccc
Confidence 4677777666 3778 899999999999887766554 543333
No 167
>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=54.16 E-value=9.9 Score=24.99 Aligned_cols=25 Identities=20% Similarity=0.646 Sum_probs=15.1
Q ss_pred eeeCCCCCcccccccccCCCCCCCchh
Q 016355 193 CVECPVCERFICVECGVPWHSSLSCEE 219 (391)
Q Consensus 193 ~v~C~~C~~~fC~~C~~~~H~~~sC~e 219 (391)
.+.|+.|+..||...+.+. .+.|..
T Consensus 13 ~~~C~~C~~~FC~~Hr~~e--~H~C~~ 37 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHRLPE--DHNCSK 37 (43)
T ss_dssp HEE-TTTS-EE-TTTHSTT--TCT-SS
T ss_pred CeECCCCCcccCccccCcc--ccCCcc
Confidence 4679999999999998752 335643
No 168
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=53.96 E-value=13 Score=34.43 Aligned_cols=62 Identities=21% Similarity=0.309 Sum_probs=39.9
Q ss_pred HHHHhhCChhHHHHHHHHHHHH-hcC--CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcc
Q 016355 133 VECKSFLPLSSYESLETALAEA-NIL--HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERF 202 (391)
Q Consensus 133 ~~i~~~l~~~~~e~~~~~~~~~-~i~--~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~ 202 (391)
..+..-++++++..|.+..... .+. .-....|- +|...++......... ....++||.||+.
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~------~d~iv~CP~CgRI 230 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRK------KDEIVFCPYCGRI 230 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhc------CCCCccCCccchH
Confidence 4566778999999999887655 222 23344676 6888887743332111 3456889999863
No 169
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=53.11 E-value=15 Score=32.99 Aligned_cols=22 Identities=36% Similarity=0.792 Sum_probs=17.1
Q ss_pred CCCCccccCCCCCeeecCcccc
Q 016355 158 HSDRIYCPFPNCSVLLDPRECL 179 (391)
Q Consensus 158 ~~~~~~CP~p~C~~~~~~~~~~ 179 (391)
.+.++-||+|+|..++..+...
T Consensus 135 sSqRIACPRpnCkRiInL~p~~ 156 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDPLI 156 (275)
T ss_pred ccceeccCCCCcceeeecCCCC
Confidence 3567899999999998775443
No 170
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=52.75 E-value=12 Score=26.96 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=17.7
Q ss_pred CCCCCccccceeee---cCCCcceEe-cccc
Q 016355 243 RWRRCQQCRRMIEL---THGCYHMTC-WCGH 269 (391)
Q Consensus 243 ~~k~CP~C~~~IeK---~~GCnhMtC-~C~~ 269 (391)
.+|+||-|+..+.+ .+|=-...| .|+.
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 35999999976654 455444555 5655
No 171
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=52.10 E-value=5 Score=39.24 Aligned_cols=48 Identities=23% Similarity=0.659 Sum_probs=36.0
Q ss_pred CcccccccccccC--CCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 74 SPENCSICCEDKP--YPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 74 ~~~~C~IC~e~~~--~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
....|..|-+.+. .+..-.++|.|.|...|+..|+.. ++ +-.||. |..
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~--~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG--TRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC--CCCCcc--HHH
Confidence 4678999999874 344556699999999999999942 23 347987 763
No 172
>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=51.83 E-value=10 Score=39.19 Aligned_cols=34 Identities=26% Similarity=0.744 Sum_probs=27.9
Q ss_pred CCCccccceeeecCCCcceEe-ccccc-----eecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE-----FCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~-----FCw~C~~~ 278 (391)
-+||+|..+..-...=|.+.| .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 479999988876555669999 99986 69999875
No 173
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=51.20 E-value=25 Score=26.41 Aligned_cols=50 Identities=24% Similarity=0.596 Sum_probs=20.2
Q ss_pred CCcccccccccccCC----CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKPY----PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~----~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
.....|.||-+++.. +.++.+ .|+-..|+.|+.-- .++|.. .||. |+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE----rkeg~q--~Cpq--Ckt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE----RKEGNQ--VCPQ--CKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH----HHTS-S--B-TT--T--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH----hhcCcc--cccc--cCCCc
Confidence 346789999998742 333444 89999999997543 445655 6888 77543
No 174
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.10 E-value=17 Score=33.01 Aligned_cols=56 Identities=20% Similarity=0.403 Sum_probs=42.7
Q ss_pred CCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhC-CCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQS-SQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~-g~~~i~CP~~~C~~~i 130 (391)
.-.-.|..|-.+....+.+.+.|-|.|--.|+......--.+ ...-.+||. |...|
T Consensus 48 DY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 345679999999998899999999999999999887543221 122368987 88764
No 175
>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=51.03 E-value=11 Score=22.59 Aligned_cols=23 Identities=30% Similarity=0.757 Sum_probs=12.4
Q ss_pred CCCccccceeeec--CCCcceEe-cc
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC-WC 267 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC-~C 267 (391)
++||+|+..|++. +|=+...| +|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CcCccCCCcceEeEecCCCCeECcCC
Confidence 5899999998764 44444555 55
No 176
>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=50.53 E-value=5.9 Score=27.12 Aligned_cols=25 Identities=20% Similarity=0.703 Sum_probs=14.3
Q ss_pred CCCccccceeeecCCCc--ceEe-cccc
Q 016355 245 RRCQQCRRMIELTHGCY--HMTC-WCGH 269 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCn--hMtC-~C~~ 269 (391)
.+|++|+...-+.++=. .+.| +||+
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 46666666666643332 4666 6664
No 177
>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=49.88 E-value=14 Score=25.80 Aligned_cols=45 Identities=29% Similarity=0.654 Sum_probs=30.5
Q ss_pred ccccccccccCCCCeeeccC--CCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 76 ENCSICCEDKPYPMMITMKC--SHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C--~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
-.|..|-.+.+....-..-| ...||.+|....+. -.||. |+..+.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---------~~CPN--CgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---------GVCPN--CGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---------CcCcC--CCCccc
Confidence 35888988887654222233 45799999887763 27887 887653
No 178
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=49.86 E-value=12 Score=25.13 Aligned_cols=33 Identities=24% Similarity=0.616 Sum_probs=22.0
Q ss_pred ccccccccCCCC-eeec-cCCC---cccHHHHHHHHHH
Q 016355 78 CSICCEDKPYPM-MITM-KCSH---KFCSHCMRTYIDG 110 (391)
Q Consensus 78 C~IC~e~~~~~~-~~~l-~C~H---~fC~~Cl~~~i~~ 110 (391)
|-||+++...+. ++.- .|.- ....+|+.+|+..
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 679999876555 3322 4443 6788999999987
No 179
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=49.35 E-value=11 Score=24.51 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=17.0
Q ss_pred CCccccceeeecCCCcceEeccccceecccccccc
Q 016355 246 RCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYR 280 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~ 280 (391)
+||+|++.++...- ..+.- .-|-.|++-|-
T Consensus 1 ~CP~C~~~l~~~~~-~~~~i----d~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDVEI----DVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcccceEEE-CCEEE----EECCCCCeEEc
Confidence 59999997775543 22322 22445666554
No 180
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=49.03 E-value=6.3 Score=30.97 Aligned_cols=33 Identities=18% Similarity=0.355 Sum_probs=25.4
Q ss_pred CCCCcccccccccccCCCCeeeccCCCcccHHH
Q 016355 71 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHC 103 (391)
Q Consensus 71 ~~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~C 103 (391)
.....|+|.-||-....+.+-.-.=|+.+|.+|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 456789999999877666554445689999998
No 181
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=48.87 E-value=5 Score=42.68 Aligned_cols=21 Identities=19% Similarity=0.450 Sum_probs=15.8
Q ss_pred cCCCcccHHHHHHHHHHHhhC
Q 016355 94 KCSHKFCSHCMRTYIDGKVQS 114 (391)
Q Consensus 94 ~C~H~fC~~Cl~~~i~~~i~~ 114 (391)
.|+|.+|..||..+....+..
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~~~ 140 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLEES 140 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhhcc
Confidence 588888888888887765543
No 182
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.58 E-value=13 Score=24.68 Aligned_cols=23 Identities=30% Similarity=0.654 Sum_probs=11.7
Q ss_pred CCccccceeeecCCCcceEe-cccc
Q 016355 246 RCQQCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
.|.+|+..++...+ .-+.| .||+
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCc
Confidence 35555555555433 44555 4554
No 183
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.58 E-value=14 Score=34.19 Aligned_cols=56 Identities=21% Similarity=0.495 Sum_probs=39.8
Q ss_pred CCCcccccccccccCCCCeeec--cCC-----CcccHHHHHHHHHHHhh-CCCcccccCCCccCCc
Q 016355 72 DKSPENCSICCEDKPYPMMITM--KCS-----HKFCSHCMRTYIDGKVQ-SSQVPIRCPQLRCKYF 129 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l--~C~-----H~fC~~Cl~~~i~~~i~-~g~~~i~CP~~~C~~~ 129 (391)
....-.|-|||.+...+..-.- +|. |.....|+..|+.++-. +...++.||+ |...
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 4556789999987665543212 553 67899999999988754 3334799999 8764
No 184
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=48.55 E-value=16 Score=22.63 Aligned_cols=27 Identities=22% Similarity=0.627 Sum_probs=16.3
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
+.|+.|+....-+.-=..+.| .||..|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 678888876554333345666 666543
No 185
>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=48.34 E-value=17 Score=25.74 Aligned_cols=27 Identities=19% Similarity=0.403 Sum_probs=20.7
Q ss_pred CCCccccce----eeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRM----IELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~----IeK~~GCnhMtC-~C~~~F 271 (391)
-.||+|+.+ .-+..|=.++.| .|||..
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 479999863 345677799999 999853
No 186
>PRK10220 hypothetical protein; Provisional
Probab=48.17 E-value=13 Score=29.79 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=17.4
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
-.||+|..-..=..|=+ +.| -|+|+
T Consensus 4 P~CP~C~seytY~d~~~-~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICPECAHE 29 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECCcccCc
Confidence 57999998877766643 556 55554
No 187
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.72 E-value=13 Score=27.39 Aligned_cols=44 Identities=27% Similarity=0.618 Sum_probs=30.1
Q ss_pred cccccccccCCCCeeeccC--CCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 77 NCSICCEDKPYPMMITMKC--SHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l~C--~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.|..|-.+.+....-.+-| .|.||.+|...-+. =.||. |+..+.
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~---------g~CPn--CGGelv 52 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLH---------GLCPN--CGGELV 52 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc---------CcCCC--CCchhh
Confidence 5888888877654333333 58899999876553 26887 887664
No 188
>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=47.66 E-value=17 Score=26.88 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=20.3
Q ss_pred CCCccccce----eeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRM----IELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~----IeK~~GCnhMtC-~C~~~ 270 (391)
-.||+|+.+ .-+..|=.++.| .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 479999864 345678889999 99985
No 189
>PLN03086 PRLI-interacting factor K; Provisional
Probab=47.53 E-value=29 Score=36.28 Aligned_cols=27 Identities=26% Similarity=0.758 Sum_probs=24.5
Q ss_pred CCCcc--ccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQ--CRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~--C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||+ |+..+.+...=+|..| .||..|
T Consensus 434 V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 434 VVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred eeCCcccccceeeccccccCccCCCCCCcc
Confidence 78995 9999999999999999 998776
No 190
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=46.89 E-value=17 Score=24.94 Aligned_cols=30 Identities=20% Similarity=0.556 Sum_probs=24.0
Q ss_pred cccccccccCCCCeeeccCCCcccHHHHHHH
Q 016355 77 NCSICCEDKPYPMMITMKCSHKFCSHCMRTY 107 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~ 107 (391)
.|.||-.....-..+.+.-| ..|.+|+...
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 49999998876555667778 8999999876
No 191
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.79 E-value=13 Score=39.90 Aligned_cols=34 Identities=32% Similarity=0.931 Sum_probs=26.6
Q ss_pred CCCccccceeeecCCCcceEe-ccccc----eecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE----FCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~----FCw~C~~~ 278 (391)
-+||+|..+..-..+=+.|.| .||+. .|-.||..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 588999988887666678999 99974 57777765
No 192
>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=46.52 E-value=15 Score=26.62 Aligned_cols=17 Identities=18% Similarity=0.733 Sum_probs=12.7
Q ss_pred ccHHHHHHHHHHHhhCC
Q 016355 99 FCSHCMRTYIDGKVQSS 115 (391)
Q Consensus 99 fC~~Cl~~~i~~~i~~g 115 (391)
||+.|+.+|+..+..+.
T Consensus 12 FCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 12 FCRNCLSKWYREAAEER 28 (68)
T ss_dssp --HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999998887644
No 193
>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=45.82 E-value=18 Score=26.13 Aligned_cols=34 Identities=24% Similarity=0.569 Sum_probs=20.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccceecccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~~~ 280 (391)
..|+.|+..+ +---..-.| .||.-||-.|.....
T Consensus 10 ~~C~~C~~~F--~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 10 SNCMICGKKF--SLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp SB-TTT--B---BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CcCcCcCCcC--CCceeeEccCCCCCEECCchhCCEE
Confidence 7999999999 344667889 999999999987654
No 194
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=45.40 E-value=4.2 Score=27.66 Aligned_cols=34 Identities=21% Similarity=0.552 Sum_probs=29.6
Q ss_pred CcccccccccccCCCCeeec-cCCCcccHHHHHHH
Q 016355 74 SPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTY 107 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~ 107 (391)
..++|-.|-+.++..++..+ -||-.-|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 46889999999998887777 89999999999853
No 195
>PRK11827 hypothetical protein; Provisional
Probab=45.09 E-value=16 Score=26.02 Aligned_cols=25 Identities=12% Similarity=0.266 Sum_probs=19.4
Q ss_pred CCCccccceeeecCCCcceEe-cccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
-.||.|+...+-..+=+...| .||-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 589999999887766677887 6654
No 196
>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=44.49 E-value=13 Score=28.21 Aligned_cols=27 Identities=30% Similarity=0.703 Sum_probs=15.4
Q ss_pred CCCcccc------ceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCR------RMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~------~~IeK~~GCnhMtC-~C~~~F 271 (391)
-.||.|+ +.|.|..|=-+++| .||..|
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 6899999 23455678888888 886665
No 197
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=44.28 E-value=44 Score=22.18 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=15.0
Q ss_pred CCCccccce-eeecCCCcceEe-cccc
Q 016355 245 RRCQQCRRM-IELTHGCYHMTC-WCGH 269 (391)
Q Consensus 245 k~CP~C~~~-IeK~~GCnhMtC-~C~~ 269 (391)
-.||+|+.. +-...+=....| .|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 569999974 333344445556 6654
No 199
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=44.25 E-value=21 Score=33.72 Aligned_cols=27 Identities=33% Similarity=0.726 Sum_probs=24.6
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
|-||+|+++.+-..|=-.|.| .||+.+
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 999999999999999999999 888764
No 200
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.17 E-value=5.9 Score=37.48 Aligned_cols=27 Identities=33% Similarity=0.886 Sum_probs=19.5
Q ss_pred CCCccccceeeecCCCcceEe----ccccceecccccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC----WCGHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC----~C~~~FCw~C~~~~~ 280 (391)
+.|+-|. |.|.| .|+|+|||+|.+--.
T Consensus 8 ~eC~IC~---------nt~n~Pv~l~C~HkFCyiCiKGsy 38 (324)
T KOG0824|consen 8 KECLICY---------NTGNCPVNLYCFHKFCYICIKGSY 38 (324)
T ss_pred Ccceeee---------ccCCcCccccccchhhhhhhcchh
Confidence 6777766 33444 799999999987643
No 201
>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=43.39 E-value=16 Score=20.99 Aligned_cols=7 Identities=29% Similarity=0.876 Sum_probs=3.8
Q ss_pred CCCcccc
Q 016355 245 RRCQQCR 251 (391)
Q Consensus 245 k~CP~C~ 251 (391)
-.||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 3566664
No 202
>PRK05580 primosome assembly protein PriA; Validated
Probab=42.82 E-value=17 Score=39.13 Aligned_cols=34 Identities=26% Similarity=0.745 Sum_probs=27.1
Q ss_pred CCCccccceeeecCCCcceEe-ccccc-----eecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE-----FCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~-----FCw~C~~~ 278 (391)
-+||+|..+..-...=|.++| .||+. .|-.||+.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 369999988875555578999 99986 59999876
No 203
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=42.72 E-value=20 Score=24.30 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=19.3
Q ss_pred CCCCccccceeeecCC--------CcceEeccccc
Q 016355 244 WRRCQQCRRMIELTHG--------CYHMTCWCGHE 270 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~G--------CnhMtC~C~~~ 270 (391)
+-.||+|+.-..-+++ =-+=||+||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 4799999987766643 44567888765
No 204
>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=42.32 E-value=34 Score=27.83 Aligned_cols=35 Identities=26% Similarity=0.620 Sum_probs=27.4
Q ss_pred CCCCCccccceeeecCCCcceEe-ccccceecccccc
Q 016355 243 RWRRCQQCRRMIELTHGCYHMTC-WCGHEFCYSCGAE 278 (391)
Q Consensus 243 ~~k~CP~C~~~IeK~~GCnhMtC-~C~~~FCw~C~~~ 278 (391)
+.+.|..|+.++-.-.+.. ..| .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 4589999999876665555 888 9999999999988
No 205
>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=42.17 E-value=27 Score=22.78 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=7.3
Q ss_pred CCCccccc-eeee
Q 016355 245 RRCQQCRR-MIEL 256 (391)
Q Consensus 245 k~CP~C~~-~IeK 256 (391)
..||.|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 56777776 4443
No 206
>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=41.57 E-value=18 Score=29.46 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=21.4
Q ss_pred CcccccccccccCC--CCeeec-cCCCcccHHHHHH
Q 016355 74 SPENCSICCEDKPY--PMMITM-KCSHKFCSHCMRT 106 (391)
Q Consensus 74 ~~~~C~IC~e~~~~--~~~~~l-~C~H~fC~~Cl~~ 106 (391)
....|.+|..++.. +.-..+ .|+|.+|..|-..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 45689999987642 223444 9999999998543
No 207
>PLN02189 cellulose synthase
Probab=41.09 E-value=16 Score=40.66 Aligned_cols=46 Identities=24% Similarity=0.556 Sum_probs=31.5
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcce
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHM 263 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhM 263 (391)
....+.|..|++..|..|- +|.. +.+.+.||+|++...+-.|++.+
T Consensus 50 g~~fvaC~~C~fpvCr~Cy----------eyer------------------~eg~q~CpqCkt~Y~r~kgs~~v 95 (1040)
T PLN02189 50 GDLFVACNECGFPVCRPCY----------EYER------------------REGTQNCPQCKTRYKRLKGSPRV 95 (1040)
T ss_pred CCEEEeeccCCCccccchh----------hhhh------------------hcCCccCcccCCchhhccCCCCc
Confidence 4467899999999998774 2211 11228999999888766566543
No 208
>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=40.58 E-value=14 Score=23.49 Aligned_cols=12 Identities=17% Similarity=0.556 Sum_probs=6.2
Q ss_pred CCCccccceeee
Q 016355 245 RRCQQCRRMIEL 256 (391)
Q Consensus 245 k~CP~C~~~IeK 256 (391)
..||.|+..++|
T Consensus 27 ~~CP~Cg~~~~r 38 (41)
T smart00834 27 ATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCccee
Confidence 455555554443
No 209
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=40.16 E-value=18 Score=32.08 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=20.9
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
-.||+|+.++.+.+. |+|.| .||+.
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCE
Confidence 379999999988544 99999 99864
No 210
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=39.87 E-value=23 Score=24.91 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=8.9
Q ss_pred CCCCccccceee
Q 016355 244 WRRCQQCRRMIE 255 (391)
Q Consensus 244 ~k~CP~C~~~Ie 255 (391)
.|+||-|+....
T Consensus 3 LkPCPFCG~~~~ 14 (61)
T PF14354_consen 3 LKPCPFCGSADV 14 (61)
T ss_pred CcCCCCCCCcce
Confidence 489999995443
No 211
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.32 E-value=7.4 Score=36.15 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=25.8
Q ss_pred CCccccccccc-ccC-CCCeeec-cCCCcccHHHHHHHHH
Q 016355 73 KSPENCSICCE-DKP-YPMMITM-KCSHKFCSHCMRTYID 109 (391)
Q Consensus 73 ~~~~~C~IC~e-~~~-~~~~~~l-~C~H~fC~~Cl~~~i~ 109 (391)
....++.+++. +.. ..+.-.+ .|+|.||..|-.-++.
T Consensus 93 ~~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~ 132 (271)
T COG5574 93 NREETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSI 132 (271)
T ss_pred ccccccccccCcccccccccceeeecccccchhhhHHHHH
Confidence 35678999887 332 2334445 8999999999776665
No 212
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=38.68 E-value=22 Score=28.22 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=22.8
Q ss_pred CCeeec--cCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 88 PMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 88 ~~~~~l--~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
.+.+.. .|.|.|-..|+.+|+++. -.||-
T Consensus 72 ~EC~VaWG~CNHaFH~hCisrWlktr-------~vCPL 102 (114)
T KOG2930|consen 72 EECTVAWGVCNHAFHFHCISRWLKTR-------NVCPL 102 (114)
T ss_pred CceEEEeeecchHHHHHHHHHHHhhc-------CcCCC
Confidence 344444 899999999999999863 36887
No 213
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.66 E-value=43 Score=23.35 Aligned_cols=32 Identities=13% Similarity=0.441 Sum_probs=26.2
Q ss_pred cccccccccccC-CCCeeec-cCCCcccHHHHHH
Q 016355 75 PENCSICCEDKP-YPMMITM-KCSHKFCSHCMRT 106 (391)
Q Consensus 75 ~~~C~IC~e~~~-~~~~~~l-~C~H~fC~~Cl~~ 106 (391)
..-|.+|-+.+. ..+.+.. .|+-.+-++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 456999999986 5666777 9999999999954
No 214
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=37.44 E-value=27 Score=29.62 Aligned_cols=36 Identities=19% Similarity=0.397 Sum_probs=20.0
Q ss_pred CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCc
Q 016355 158 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCER 201 (391)
Q Consensus 158 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~ 201 (391)
......||+ |+.-+...+... . ... ...+.||.||.
T Consensus 96 ~~~~Y~Cp~--C~~~y~~~ea~~---~--~d~-~~~f~Cp~Cg~ 131 (147)
T smart00531 96 NNAYYKCPN--CQSKYTFLEANQ---L--LDM-DGTFTCPRCGE 131 (147)
T ss_pred CCcEEECcC--CCCEeeHHHHHH---h--cCC-CCcEECCCCCC
Confidence 345678985 876665533221 0 011 23488998885
No 215
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.21 E-value=21 Score=31.60 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=20.5
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
-.|++|+.+.++ .=+.|+| +||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 589999999999 4488999 99864
No 216
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=37.03 E-value=68 Score=31.59 Aligned_cols=75 Identities=16% Similarity=0.403 Sum_probs=41.9
Q ss_pred hHHHHHHhcCCCC-CCC-CCCCcccccccccccCCCCee--------------------eccCCCcccHHHHHHHHHHHh
Q 016355 55 LRLAQIAVGIVSS-PSQ-GDKSPENCSICCEDKPYPMMI--------------------TMKCSHKFCSHCMRTYIDGKV 112 (391)
Q Consensus 55 ~~~~~~ai~~~~~-~~~-~~~~~~~C~IC~e~~~~~~~~--------------------~l~C~H~fC~~Cl~~~i~~~i 112 (391)
.+..++.+..|.. ... ...+...|.-|+..-+.-++. .+-|.-+.|.+|+.+++.++=
T Consensus 249 ~e~F~~~V~~Np~y~~~~~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQ 328 (358)
T PF10272_consen 249 VEAFKEQVEQNPRYSYPESGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQ 328 (358)
T ss_pred HHHHHHHHHhCCccccCCCccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcC
Confidence 3444444554442 122 234556687787754432211 223445679999999998764
Q ss_pred hCCC------cccccCCCccCCccC
Q 016355 113 QSSQ------VPIRCPQLRCKYFIS 131 (391)
Q Consensus 113 ~~g~------~~i~CP~~~C~~~i~ 131 (391)
.+.. ....||. |.+.+-
T Consensus 329 d~~~~~~Wl~~~~~CPt--CRa~FC 351 (358)
T PF10272_consen 329 DQQHPETWLSGKCPCPT--CRAKFC 351 (358)
T ss_pred CCCChhhhhcCCCCCCC--Ccccce
Confidence 3321 1356776 988764
No 217
>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=36.79 E-value=33 Score=29.53 Aligned_cols=26 Identities=15% Similarity=0.505 Sum_probs=19.0
Q ss_pred CCCCccccceeeecCCCcceEe-ccccc
Q 016355 244 WRRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
+..||.|+..+..++. ....| .|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 3899999999987765 55666 66544
No 218
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=36.66 E-value=9.2 Score=35.79 Aligned_cols=110 Identities=19% Similarity=0.408 Sum_probs=59.3
Q ss_pred CCcccccccccccCCCCee----eccC----CC-cccHHHHHHHHHH-----HhhCCCcccccCCCccCCccCHHHHHhh
Q 016355 73 KSPENCSICCEDKPYPMMI----TMKC----SH-KFCSHCMRTYIDG-----KVQSSQVPIRCPQLRCKYFISTVECKSF 138 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~~~----~l~C----~H-~fC~~Cl~~~i~~-----~i~~g~~~i~CP~~~C~~~i~~~~i~~~ 138 (391)
...+.|.-|...+....-. .+.| .+ .-|..|=+.|+.. -|.....+..|+. |+..|+...+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~i--CGKaFSRPWL--- 202 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGI--CGKAFSRPWL--- 202 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCccccc--ccccccchHH---
Confidence 4556777777666432100 0011 11 2466676776643 2344455667777 8877764321
Q ss_pred CChhHHHHHHHHHHHHhcC---CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcccc
Q 016355 139 LPLSSYESLETALAEANIL---HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFIC 204 (391)
Q Consensus 139 l~~~~~e~~~~~~~~~~i~---~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~fC 204 (391)
...-|. ...-+-|| .|+.++-+...+.+-..+ ..+.....|+.|++.|=
T Consensus 203 -------------LQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAHmQT--HS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 203 -------------LQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAHMQT--HSDVKKHQCPRCGKSFA 254 (279)
T ss_pred -------------hhcccccccCCCCccCC--cccchhcchHHHHHHHHh--hcCCccccCcchhhHHH
Confidence 112222 34557788 688777665444332222 23445677888887774
No 219
>PLN02189 cellulose synthase
Probab=36.64 E-value=31 Score=38.44 Aligned_cols=50 Identities=24% Similarity=0.640 Sum_probs=35.4
Q ss_pred CCcccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~----~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
.....|.||-|+.. ++.++.+ .|+-..|+.|+ .|-. ++|.. .||+ |+...
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg~q--~Cpq--Ckt~Y 86 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REGTQ--NCPQ--CKTRY 86 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCCc--cCcc--cCCch
Confidence 34568999999954 3445556 79999999998 4443 35555 6998 87654
No 220
>PLN02436 cellulose synthase A
Probab=35.82 E-value=33 Score=38.44 Aligned_cols=50 Identities=26% Similarity=0.647 Sum_probs=35.2
Q ss_pred CCcccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~----~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
.....|.||-|++. ++.++.+ .|+-..|+.|+ .|-. ++|.. .||+ |+...
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg~~--~Cpq--ckt~Y 88 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REGNQ--ACPQ--CKTRY 88 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCCc--cCcc--cCCch
Confidence 34568999999863 2345555 79999999998 4443 35554 6988 87654
No 221
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.59 E-value=30 Score=33.69 Aligned_cols=45 Identities=24% Similarity=0.690 Sum_probs=28.3
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
......|.||.++... ..-++|||.-| |..-+-. . ..||. |...|
T Consensus 302 ~~~p~lcVVcl~e~~~--~~fvpcGh~cc--ct~cs~~-------l-~~CPv--CR~rI 346 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS--AVFVPCGHVCC--CTLCSKH-------L-PQCPV--CRQRI 346 (355)
T ss_pred cCCCCceEEecCCccc--eeeecCCcEEE--chHHHhh-------C-CCCch--hHHHH
Confidence 4456789999987643 34459999966 4322211 1 35988 76554
No 222
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=35.31 E-value=35 Score=38.23 Aligned_cols=50 Identities=24% Similarity=0.602 Sum_probs=35.7
Q ss_pred CCcccccccccccCC----CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKPY----PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~----~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
.....|.||-|++.. +.++.+ .|+-..|+.|. .|= .++|.. .||+ |+...
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYE---r~eG~q--~CPq--CktrY 69 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYE---RKDGNQ--SCPQ--CKTKY 69 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhh---hhcCCc--cCCc--cCCch
Confidence 345689999999643 345566 89999999998 443 345655 6998 87644
No 223
>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 PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=35.03 E-value=20 Score=40.13 Aligned_cols=46 Identities=26% Similarity=0.611 Sum_probs=30.9
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcce
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHM 263 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhM 263 (391)
....|.|..|++-.|..|- +|.. +.+.+-||+|++...+-.|+..+
T Consensus 33 Ge~FVAC~eC~FPVCrpCY----------EYEr------------------~eG~q~CPqCktrYkr~kgsprv 78 (1079)
T PLN02638 33 GEPFVACDVCAFPVCRPCY----------EYER------------------KDGNQSCPQCKTKYKRHKGSPAI 78 (1079)
T ss_pred CCEEEEeccCCCccccchh----------hhhh------------------hcCCccCCccCCchhhhcCCCCc
Confidence 4467889999999998664 3321 11228899998888765555543
No 225
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.97 E-value=28 Score=32.90 Aligned_cols=24 Identities=29% Similarity=0.649 Sum_probs=19.5
Q ss_pred CCCccccceeeec--CCCcceEe-ccc
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC-WCG 268 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC-~C~ 268 (391)
++|+.|+.+|+|. +|=+-..| .|.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 8999999999985 77777777 664
No 226
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=34.95 E-value=27 Score=37.29 Aligned_cols=50 Identities=20% Similarity=0.407 Sum_probs=36.9
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCC-CccCC
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ-LRCKY 128 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~-~~C~~ 128 (391)
....+.|.||.-.+...-.+-..|+|....+|+..|+++ |. .||. .||.-
T Consensus 1025 ~~~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~----gd---~CpsGCGC~C 1075 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT----GD---VCPSGCGCHC 1075 (1081)
T ss_pred ccceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc----CC---cCCCCCCcCc
Confidence 355678999887777665555599999999999999975 22 6885 34443
No 227
>PHA02926 zinc finger-like protein; Provisional
Probab=34.92 E-value=20 Score=32.67 Aligned_cols=39 Identities=18% Similarity=0.439 Sum_probs=25.5
Q ss_pred CCCCcccccee-eec-CCCcceEe--ccccceeccccccccCC
Q 016355 244 WRRCQQCRRMI-ELT-HGCYHMTC--WCGHEFCYSCGAEYRDG 282 (391)
Q Consensus 244 ~k~CP~C~~~I-eK~-~GCnhMtC--~C~~~FCw~C~~~~~~~ 282 (391)
-+.|+=|-..+ +|. .++...== .|+|.||+.|-..|...
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence 38999999766 442 11111111 78888999999999853
No 228
>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=34.79 E-value=15 Score=22.59 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=5.5
Q ss_pred CCCcccccee
Q 016355 245 RRCQQCRRMI 254 (391)
Q Consensus 245 k~CP~C~~~I 254 (391)
-+||.|+..|
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 229
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=34.63 E-value=25 Score=24.93 Aligned_cols=34 Identities=24% Similarity=0.615 Sum_probs=24.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccc---eecccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE---FCYSCGAE 278 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~---FCw~C~~~ 278 (391)
..|-.|+..|.-.+..-+..| .||.. =|..|++.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 468888888877776788888 78776 45555554
No 230
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.37 E-value=22 Score=28.82 Aligned_cols=44 Identities=25% Similarity=0.677 Sum_probs=29.3
Q ss_pred cccccccccccCCC-----------Ceeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccC
Q 016355 75 PENCSICCEDKPYP-----------MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 127 (391)
Q Consensus 75 ~~~C~IC~e~~~~~-----------~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~ 127 (391)
...|.-|...++.. ..+.. .|.+.||.+| .-|+.+.+. .||. |.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiHe~Lh------~CPG--C~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDC-DVFVHESLH------CCPG--CI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCcccccc-chhhhhhcc------CCcC--CC
Confidence 45699999877642 23456 8999999999 344544443 4776 65
No 231
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=34.20 E-value=19 Score=39.57 Aligned_cols=24 Identities=42% Similarity=1.025 Sum_probs=19.6
Q ss_pred CCCccccc-eeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRR-MIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~-~IeK~~GCnhMtC-~C~~~ 270 (391)
-.||-|+. .|+..|||| || .||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999996 568899999 68 77765
No 232
>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=34.11 E-value=13 Score=26.33 Aligned_cols=36 Identities=22% Similarity=0.550 Sum_probs=27.9
Q ss_pred CCCccccceeee--cCCCcceEe-ccccceecccccccc
Q 016355 245 RRCQQCRRMIEL--THGCYHMTC-WCGHEFCYSCGAEYR 280 (391)
Q Consensus 245 k~CP~C~~~IeK--~~GCnhMtC-~C~~~FCw~C~~~~~ 280 (391)
..||-|++...- .+-=|+=|| .|+..-|-+||=.-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP~ 41 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNPT 41 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCCC
Confidence 579999987722 144589999 999999999995543
No 233
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.98 E-value=21 Score=36.37 Aligned_cols=35 Identities=26% Similarity=0.540 Sum_probs=24.1
Q ss_pred CCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeee
Q 016355 198 VCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIEL 256 (391)
Q Consensus 198 ~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK 256 (391)
.||+.||+.|--.+ ....+-..++.||=|+..|-.
T Consensus 203 ~CGHiFC~~CiLqy------------------------~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQY------------------------WNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHH------------------------HhhhcccCCccCCchhhhccc
Confidence 69999999996431 111134456899999988853
No 234
>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=33.96 E-value=25 Score=21.88 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=20.5
Q ss_pred CeeeCCCCCcccccccccCCCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSSLS 216 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~~s 216 (391)
..+.|..|+...|..|....|.++.
T Consensus 11 ~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 11 LSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred eEEEeCccChhhhhhcChhhcCCCC
Confidence 4678999999999999877687654
No 235
>PLN02436 cellulose synthase A
Probab=33.71 E-value=25 Score=39.27 Aligned_cols=46 Identities=24% Similarity=0.569 Sum_probs=31.4
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcce
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHM 263 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhM 263 (391)
....|.|..|++..|..|- +|.. +.+.+.||+|++...+-.|++.+
T Consensus 52 Ge~FVACn~C~fpvCr~Cy----------eyer------------------~eg~~~Cpqckt~Y~r~kgs~~~ 97 (1094)
T PLN02436 52 GEPFVACNECAFPVCRPCY----------EYER------------------REGNQACPQCKTRYKRIKGSPRV 97 (1094)
T ss_pred CCEEEeeccCCCccccchh----------hhhh------------------hcCCccCcccCCchhhccCCCCc
Confidence 4467899999999998775 2211 11228999999888765565543
No 236
>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=33.41 E-value=11 Score=26.62 Aligned_cols=13 Identities=23% Similarity=0.728 Sum_probs=6.6
Q ss_pred CCCccccceeeec
Q 016355 245 RRCQQCRRMIELT 257 (391)
Q Consensus 245 k~CP~C~~~IeK~ 257 (391)
.+||.|+.+++-.
T Consensus 3 v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 3 VKCPICGKPVEWS 15 (57)
T ss_dssp EE-TTT--EEE-S
T ss_pred ccCCCCCCeeccc
Confidence 5788888888753
No 237
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=33.39 E-value=16 Score=35.24 Aligned_cols=50 Identities=26% Similarity=0.695 Sum_probs=32.4
Q ss_pred CCccccceeeecCCCcceEeccccceeccccccccCC-CCcc-ccc-CCCCCch
Q 016355 246 RCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDG-QQTC-QCA-FWDEDNS 296 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~~~-~~~c-~C~-~~~~~~~ 296 (391)
-||-|-.+|--++ =|..-|.|||..|-.|...+... .+.| .|. .|++++.
T Consensus 16 ~cplcie~mditd-knf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv 68 (480)
T COG5175 16 YCPLCIEPMDITD-KNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENV 68 (480)
T ss_pred cCccccccccccc-CCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccce
Confidence 4999988876444 37788999998777777666532 1223 233 4665543
No 238
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=33.23 E-value=14 Score=39.99 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=0.0
Q ss_pred CCCCCccchhhhhcc
Q 016355 355 PRCTDSYGDAMKDLH 369 (391)
Q Consensus 355 ~~~~~~~~~~~~~~~ 369 (391)
|+.-+.++++|++||
T Consensus 781 P~EIgvsvEkLrELG 795 (900)
T PF03833_consen 781 PREIGVSVEKLRELG 795 (900)
T ss_dssp ---------------
T ss_pred HHhcCCCHHHHHHhC
Confidence 455556677777774
No 239
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.03 E-value=12 Score=39.07 Aligned_cols=35 Identities=23% Similarity=0.668 Sum_probs=26.7
Q ss_pred cccccccccccCCCCe--eeccCCCcccHHHHHHHHH
Q 016355 75 PENCSICCEDKPYPMM--ITMKCSHKFCSHCMRTYID 109 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~--~~l~C~H~fC~~Cl~~~i~ 109 (391)
...|.||+..+....+ +++.|||.+|..|++.-..
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 4569999887754432 5569999999999987664
No 240
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=32.82 E-value=97 Score=27.83 Aligned_cols=23 Identities=13% Similarity=-0.025 Sum_probs=13.4
Q ss_pred CccCHHHHHhhCChhHHHHHHHH
Q 016355 128 YFISTVECKSFLPLSSYESLETA 150 (391)
Q Consensus 128 ~~i~~~~i~~~l~~~~~e~~~~~ 150 (391)
..++..++.++.+..+...++..
T Consensus 112 ~~YSl~DL~~v~~G~L~~~L~~l 134 (202)
T PF13901_consen 112 HLYSLADLVQVKSGQLLPQLEKL 134 (202)
T ss_pred ceEcHHHHHHHhhchHHHHHHHH
Confidence 34566777777665555544443
No 241
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.73 E-value=55 Score=28.63 Aligned_cols=58 Identities=26% Similarity=0.558 Sum_probs=37.7
Q ss_pred CCCcccccccccccCC---CC--eeeccCCCcccHHHHHHHHHHHhhCCC-cc---cccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKPY---PM--MITMKCSHKFCSHCMRTYIDGKVQSSQ-VP---IRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~---~~--~~~l~C~H~fC~~Cl~~~i~~~i~~g~-~~---i~CP~~~C~~~i~ 131 (391)
+.....|.||+..... ++ .-...||..|..-|+..|+..-+...+ +. =.||- |..++.
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 3455678888753221 11 112379999999999999988775543 22 26888 887764
No 242
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=32.61 E-value=42 Score=31.18 Aligned_cols=48 Identities=25% Similarity=0.528 Sum_probs=34.8
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 75 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
...|+|=+-.+..+ +++-.|||+|=++=+..++. +...++||..+|..
T Consensus 176 s~rdPis~~~I~nP-viSkkC~HvydrDsI~~~l~-----~~~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIVNP-VISKKCGHVYDRDSIMQILC-----DEITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhhch-hhhcCcCcchhhhhHHHHhc-----cCceeecccccCCc
Confidence 35688866655433 45569999998887777663 34568999999993
No 243
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=32.49 E-value=35 Score=25.74 Aligned_cols=35 Identities=26% Similarity=0.598 Sum_probs=23.5
Q ss_pred cccccccccc-CCCCeeec--cCCCcccHHHHHHHHHH
Q 016355 76 ENCSICCEDK-PYPMMITM--KCSHKFCSHCMRTYIDG 110 (391)
Q Consensus 76 ~~C~IC~e~~-~~~~~~~l--~C~H~fC~~Cl~~~i~~ 110 (391)
.+|+-|.... +..+.... .|.|.|-..|+.+|+.+
T Consensus 32 ~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh
Confidence 3455554322 23343333 79999999999999987
No 244
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=32.45 E-value=22 Score=33.89 Aligned_cols=31 Identities=35% Similarity=0.789 Sum_probs=20.4
Q ss_pred cccccccccccCCCCeeec-cCCCcccHHHHHHH
Q 016355 75 PENCSICCEDKPYPMMITM-KCSHKFCSHCMRTY 107 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~ 107 (391)
...|--| +++..---.+ +|.|.||.+|.+..
T Consensus 90 VHfCd~C--d~PI~IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRC--DFPIAIYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeeccc--CCcceeeecccccchhhhhhhhhcC
Confidence 4567767 3443322345 99999999997644
No 245
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=32.24 E-value=47 Score=28.58 Aligned_cols=50 Identities=16% Similarity=0.369 Sum_probs=34.4
Q ss_pred CcccccccccccCCCCeeeccCCC---cccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 74 SPENCSICCEDKPYPMMITMKCSH---KFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H---~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
....|-||+++.... ...+.|.. ....+|++.|+... ...+|+. |+..+.
T Consensus 7 ~~~~CRIC~~~~~~~-~~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Cei--C~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEYDVV-TNYCNCKNENKIVHKECLEEWINTS-----KNKSCKI--CNGPYN 59 (162)
T ss_pred CCCeeEecCCCCCCc-cCCcccCCCchHHHHHHHHHHHhcC-----CCCcccc--cCCeEE
Confidence 456899999986422 22235655 46999999999742 3458988 887654
No 246
>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=31.87 E-value=43 Score=21.48 Aligned_cols=20 Identities=25% Similarity=0.765 Sum_probs=13.2
Q ss_pred CCCccccceeeec---CCCcceEe
Q 016355 245 RRCQQCRRMIELT---HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~---~GCnhMtC 265 (391)
+.||.|+..+... .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 5899999665442 45 55666
No 247
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=31.49 E-value=45 Score=31.19 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=22.1
Q ss_pred CCCCccccceeeecCCCcceEe-ccccc
Q 016355 244 WRRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
.+-||+|+.++....|=..+.| .||..
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCE
Confidence 3899999999887666578999 89854
No 248
>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=31.33 E-value=17 Score=23.32 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=20.8
Q ss_pred CeeeCCCCCcccccccccCCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSSL 215 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~~ 215 (391)
..+.|..|+..+|..|...-|.++
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 457899999999999998888875
No 249
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=31.26 E-value=25 Score=27.00 Aligned_cols=43 Identities=23% Similarity=0.509 Sum_probs=32.8
Q ss_pred CCCccccceeeecCCCcceEeccccceeccccccccCCC-CcccccC
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDGQ-QTCQCAF 290 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~~~~-~~c~C~~ 290 (391)
..||.|+.+ .+.|--+...|++.|=..|...|-... ..-.||.
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPm 76 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPM 76 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHccccCCCCCCC
Confidence 468888887 477888888999999999999997643 1235554
No 250
>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=31.11 E-value=48 Score=21.76 Aligned_cols=41 Identities=22% Similarity=0.633 Sum_probs=19.2
Q ss_pred ccccccccCCCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCC
Q 016355 78 CSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 123 (391)
Q Consensus 78 C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~ 123 (391)
|.+|-+-......-.- +|+=.+-..|+..|+...- .+ +||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~----~~-~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS----NP-KCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S----S--B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC----CC-CCcC
Confidence 5667665544421111 4888899999999996432 12 7886
No 251
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.06 E-value=39 Score=26.06 Aligned_cols=16 Identities=19% Similarity=0.810 Sum_probs=14.0
Q ss_pred ccHHHHHHHHHHHhhC
Q 016355 99 FCSHCMRTYIDGKVQS 114 (391)
Q Consensus 99 fC~~Cl~~~i~~~i~~ 114 (391)
||+.|+.+|+..+...
T Consensus 43 FCRNCLs~Wy~eaae~ 58 (104)
T COG3492 43 FCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 9999999999887754
No 252
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=30.93 E-value=15 Score=34.87 Aligned_cols=21 Identities=29% Similarity=0.814 Sum_probs=17.3
Q ss_pred eeeCCCCCcccccccccCCCC
Q 016355 193 CVECPVCERFICVECGVPWHS 213 (391)
Q Consensus 193 ~v~C~~C~~~fC~~C~~~~H~ 213 (391)
.-.|+.|+..||..|..-.|.
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ceechhhhhhhhhhhHHHHHH
Confidence 356999999999999876664
No 253
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.58 E-value=36 Score=32.10 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=15.2
Q ss_pred CCCccccceeeec--CCCcceEe
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC 265 (391)
++||+|+.+|+|. +|=.-..|
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~C 258 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFC 258 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEEC
Confidence 7999999999874 55333444
No 254
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=30.48 E-value=18 Score=35.64 Aligned_cols=37 Identities=22% Similarity=0.573 Sum_probs=29.1
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYI 108 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i 108 (391)
+..+.+|+|||-.++...-.+.-|.-.+|.+|+..+-
T Consensus 71 ~rr~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 71 SRRKTECPICFLYYPSAKNLVRCCSETICGECFAPFG 107 (482)
T ss_pred ccccccCceeeeecccccchhhhhccchhhhheeccc
Confidence 3456899999999987644444899999999997653
No 255
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.34 E-value=44 Score=31.66 Aligned_cols=44 Identities=32% Similarity=0.711 Sum_probs=30.1
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 76 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
.-|+.|-.-.. +.+-+-.|+|.||.+|+..-+. +. ...||. |..
T Consensus 275 LkCplc~~Llr-np~kT~cC~~~fc~eci~~al~----ds--Df~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLR-NPMKTPCCGHTFCDECIGTALL----DS--DFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhh-CcccCccccchHHHHHHhhhhh----hc--cccCCC--ccc
Confidence 78999976443 2233338999999999876553 22 358988 765
No 256
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.24 E-value=37 Score=29.93 Aligned_cols=58 Identities=17% Similarity=0.319 Sum_probs=28.4
Q ss_pred cCHHHHHhhCChhHHHHHHHHHHHHhcC--CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCc
Q 016355 130 ISTVECKSFLPLSSYESLETALAEANIL--HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCER 201 (391)
Q Consensus 130 i~~~~i~~~l~~~~~e~~~~~~~~~~i~--~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~ 201 (391)
++.+.+..++..+.... .+.+.+..-. ......||+ |+.-+...+.. ...+.||.||.
T Consensus 85 l~~~~i~d~ik~~~~~~-~~klk~~l~~e~~~~~Y~Cp~--C~~rytf~eA~-----------~~~F~Cp~Cg~ 144 (178)
T PRK06266 85 PELEKLPEIIKKKKMEE-LKKLKEQLEEEENNMFFFCPN--CHIRFTFDEAM-----------EYGFRCPQCGE 144 (178)
T ss_pred eCHHHHHHHHHHHHHHH-HHHHHHHhhhccCCCEEECCC--CCcEEeHHHHh-----------hcCCcCCCCCC
Confidence 44555555554443222 2222222222 345678985 77555443221 13467888884
No 257
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=30.01 E-value=36 Score=27.41 Aligned_cols=13 Identities=54% Similarity=1.211 Sum_probs=10.8
Q ss_pred cceEeccccceec
Q 016355 261 YHMTCWCGHEFCY 273 (391)
Q Consensus 261 nhMtC~C~~~FCw 273 (391)
..+.|.|||+||-
T Consensus 23 k~vkc~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKCDCGHEFCD 35 (112)
T ss_pred ceeeccCCCeecC
Confidence 3688999999984
No 258
>PLN02400 cellulose synthase
Probab=29.83 E-value=35 Score=38.24 Aligned_cols=46 Identities=26% Similarity=0.582 Sum_probs=29.9
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcce
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHM 263 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnhM 263 (391)
....|.|..|+.-.|..|- +|. +. .+.+.||+|++...+-.|+..+
T Consensus 52 Ge~FVAC~eCaFPVCRpCY----------EYE------Rk------------eGnq~CPQCkTrYkR~KgsprV 97 (1085)
T PLN02400 52 GDVFVACNECAFPVCRPCY----------EYE------RK------------DGTQCCPQCKTRYRRHKGSPRV 97 (1085)
T ss_pred CCEEEEEccCCCccccchh----------hee------cc------------cCCccCcccCCccccccCCCCC
Confidence 4467889999999998775 221 11 1227788888877765555543
No 259
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=29.65 E-value=36 Score=29.31 Aligned_cols=32 Identities=22% Similarity=0.457 Sum_probs=18.9
Q ss_pred CCCCccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCcc
Q 016355 158 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERF 202 (391)
Q Consensus 158 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~ 202 (391)
+.....||+ |..-+...+.. ...+.||.||..
T Consensus 106 ~~~~Y~Cp~--c~~r~tf~eA~-----------~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPN--MCVRFTFNEAM-----------ELNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCC--CCcEeeHHHHH-----------HcCCcCCCCCCE
Confidence 345667985 77555443221 134779988853
No 260
>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=29.64 E-value=37 Score=23.30 Aligned_cols=35 Identities=23% Similarity=0.447 Sum_probs=24.8
Q ss_pred ccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHH
Q 016355 76 ENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDG 110 (391)
Q Consensus 76 ~~C~IC~e~~~~~-~~~~l-~C~H~fC~~Cl~~~i~~ 110 (391)
..|.+|-..+... .-... .||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 3588887766542 22344 89999999999877543
No 261
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=29.31 E-value=49 Score=26.43 Aligned_cols=16 Identities=31% Similarity=0.833 Sum_probs=11.1
Q ss_pred CCccccCCCCCeeecCcc
Q 016355 160 DRIYCPFPNCSVLLDPRE 177 (391)
Q Consensus 160 ~~~~CP~p~C~~~~~~~~ 177 (391)
...+|+ .|++.+.+.+
T Consensus 3 ~~rfC~--eCNNmLYPkE 18 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKE 18 (113)
T ss_pred ccchhh--hhhccccccc
Confidence 346787 6888887743
No 262
>PF15616 TerY-C: TerY-C metal binding domain
Probab=28.93 E-value=34 Score=28.53 Aligned_cols=23 Identities=30% Similarity=0.839 Sum_probs=14.5
Q ss_pred CCCccccceeeecCCCcceEeccccceec
Q 016355 245 RRCQQCRRMIELTHGCYHMTCWCGHEFCY 273 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC~C~~~FCw 273 (391)
--||-|+... ....|.||.-|||
T Consensus 78 PgCP~CGn~~------~fa~C~CGkl~Ci 100 (131)
T PF15616_consen 78 PGCPHCGNQY------AFAVCGCGKLFCI 100 (131)
T ss_pred CCCCCCcChh------cEEEecCCCEEEe
Confidence 7899999875 2233455555554
No 263
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=28.86 E-value=58 Score=36.49 Aligned_cols=52 Identities=19% Similarity=0.558 Sum_probs=36.8
Q ss_pred CCCcccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 72 DKSPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~----~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.-....|.||-|++. ++.++.+ .|+-..|+.|+ .|- .++|.. .||. |+....
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye---~~~g~~--~cp~--c~t~y~ 68 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYE---RSEGNQ--CCPQ--CNTRYK 68 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhh---hhcCCc--cCCc--cCCchh
Confidence 345678999999864 3345566 89999999998 443 345555 6988 876543
No 264
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=28.83 E-value=40 Score=26.90 Aligned_cols=25 Identities=28% Similarity=0.759 Sum_probs=16.3
Q ss_pred CCCccccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
-.||+|+.-..=.+|= .|.| .|+++
T Consensus 4 p~cp~c~sEytYed~~-~~~cpec~~e 29 (112)
T COG2824 4 PPCPKCNSEYTYEDGG-QLICPECAHE 29 (112)
T ss_pred CCCCccCCceEEecCc-eEeCchhccc
Confidence 5899997655544333 7777 66554
No 265
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=28.69 E-value=28 Score=19.99 Aligned_cols=10 Identities=50% Similarity=1.271 Sum_probs=7.5
Q ss_pred eeCCCCCccc
Q 016355 194 VECPVCERFI 203 (391)
Q Consensus 194 v~C~~C~~~f 203 (391)
+.|+.||+.|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 4588888776
No 266
>PF14369 zf-RING_3: zinc-finger
Probab=28.23 E-value=58 Score=20.40 Aligned_cols=29 Identities=28% Similarity=0.628 Sum_probs=16.4
Q ss_pred ccccCCCCCeeecCccccccccCCCCCCCCCeeeCCCCCccc
Q 016355 162 IYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 203 (391)
Q Consensus 162 ~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~v~C~~C~~~f 203 (391)
.||= .|...+.... .....+.||.|+..|
T Consensus 3 ywCh--~C~~~V~~~~-----------~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH--QCNRFVRIAP-----------SPDSDVACPRCHGGF 31 (35)
T ss_pred EeCc--cCCCEeEeCc-----------CCCCCcCCcCCCCcE
Confidence 4666 5877766511 111224699998665
No 267
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.17 E-value=30 Score=33.50 Aligned_cols=34 Identities=29% Similarity=0.789 Sum_probs=25.2
Q ss_pred CCCcccccccccccCCCCeeeccCCCcccHHHHHHH
Q 016355 72 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTY 107 (391)
Q Consensus 72 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~ 107 (391)
+.....|.||-+...-. ..++|+|..|.-|-...
T Consensus 58 DEen~~C~ICA~~~TYs--~~~PC~H~~CH~Ca~Rl 91 (493)
T COG5236 58 DEENMNCQICAGSTTYS--ARYPCGHQICHACAVRL 91 (493)
T ss_pred ccccceeEEecCCceEE--EeccCCchHHHHHHHHH
Confidence 45678999998865422 23399999999997543
No 268
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.09 E-value=31 Score=23.56 Aligned_cols=10 Identities=40% Similarity=0.816 Sum_probs=5.2
Q ss_pred CCCcccccee
Q 016355 245 RRCQQCRRMI 254 (391)
Q Consensus 245 k~CP~C~~~I 254 (391)
-+||.|+..|
T Consensus 25 irCp~Cg~rI 34 (49)
T COG1996 25 IRCPYCGSRI 34 (49)
T ss_pred eeCCCCCcEE
Confidence 4555555444
No 269
>smart00336 BBOX B-Box-type zinc finger.
Probab=27.97 E-value=45 Score=21.01 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=19.8
Q ss_pred CeeeCCCCCcccccccccCCCCCC
Q 016355 192 SCVECPVCERFICVECGVPWHSSL 215 (391)
Q Consensus 192 ~~v~C~~C~~~fC~~C~~~~H~~~ 215 (391)
..+.|..|+...|..|....|.++
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred eEEECCCCCcccccccChhhcCCC
Confidence 357799999999999997777665
No 270
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.89 E-value=32 Score=24.24 Aligned_cols=21 Identities=29% Similarity=0.632 Sum_probs=14.3
Q ss_pred CCCCCccccceeeecCCCcceEe-ccc
Q 016355 243 RWRRCQQCRRMIELTHGCYHMTC-WCG 268 (391)
Q Consensus 243 ~~k~CP~C~~~IeK~~GCnhMtC-~C~ 268 (391)
.+-.||+|+.+.. .|-.| .||
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCPSCG 47 (57)
T ss_pred cceECCCCCCccC-----CeEECCCCC
Confidence 3468999998887 25555 454
No 271
>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=27.69 E-value=60 Score=25.20 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=21.9
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||.|+..-.|..+----.| .|+..|
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 689999998888877777778 777665
No 272
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=27.43 E-value=40 Score=27.17 Aligned_cols=22 Identities=36% Similarity=0.866 Sum_probs=14.1
Q ss_pred CeeeCCCCCccc--------ccccccCCCC
Q 016355 192 SCVECPVCERFI--------CVECGVPWHS 213 (391)
Q Consensus 192 ~~v~C~~C~~~f--------C~~C~~~~H~ 213 (391)
..+.||.|++.+ |-.|+.+-+-
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 345677776544 7888777544
No 273
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=27.39 E-value=34 Score=38.22 Aligned_cols=45 Identities=29% Similarity=0.663 Sum_probs=29.6
Q ss_pred CCCeeeCCCCCcccccccccCCCCCCCchhHhcCcccccChhHHHHHHHHhccCCCCCccccceeeecCCCcc
Q 016355 190 DNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYH 262 (391)
Q Consensus 190 ~~~~v~C~~C~~~fC~~C~~~~H~~~sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~IeK~~GCnh 262 (391)
....|.|..|+...|..|- +|.. +.+.+.||+|++...+-.|++.
T Consensus 31 Ge~FVAC~eC~fpvCr~cy----------eye~------------------~~g~~~cp~c~t~y~~~~~~~~ 75 (1044)
T PLN02915 31 GQPFVACHVCGFPVCKPCY----------EYER------------------SEGNQCCPQCNTRYKRHKGCPR 75 (1044)
T ss_pred CCEEEEeccCCCccccchh----------hhhh------------------hcCCccCCccCCchhhhcCCCC
Confidence 4467899999999998775 2211 1122788888887765555544
No 274
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=27.31 E-value=40 Score=31.85 Aligned_cols=50 Identities=30% Similarity=0.495 Sum_probs=35.8
Q ss_pred CCCCCcccccccccccCC--CCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCC
Q 016355 70 QGDKSPENCSICCEDKPY--PMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 128 (391)
Q Consensus 70 ~~~~~~~~C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~ 128 (391)
.+....+.|+||.+.... +....+.|||..-..|++.++.. | .+||. |..
T Consensus 153 ~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~----~---y~CP~--C~~ 204 (276)
T KOG1940|consen 153 VERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE----G---YTCPI--CSK 204 (276)
T ss_pred hhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc----C---CCCCc--ccc
Confidence 344556679999997643 22333499999999999988842 3 47998 877
No 275
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.92 E-value=89 Score=25.83 Aligned_cols=37 Identities=16% Similarity=0.389 Sum_probs=26.7
Q ss_pred HHHHHHHHhccCCCCCccccc---eeeecCCCcceEe-ccccc
Q 016355 232 DITLHRLAQNKRWRRCQQCRR---MIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 232 ~~~~~~l~~~~~~k~CP~C~~---~IeK~~GCnhMtC-~C~~~ 270 (391)
+..+......- -.||.|+. .+.|.++=..|.| .||+.
T Consensus 83 ~~~L~~fI~~y--VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 83 QDLLDKFIKEY--VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHHHCHH--SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHHHHHE--EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 33444444333 79999995 4677899999999 89974
No 276
>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=26.83 E-value=61 Score=19.79 Aligned_cols=24 Identities=25% Similarity=0.767 Sum_probs=20.7
Q ss_pred CCccccceeeecCCCcceEe-cccc
Q 016355 246 RCQQCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 246 ~CP~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
.|+.|++.+.-..|=.++.| .|.+
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 68999999999999999998 7764
No 277
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.82 E-value=36 Score=40.38 Aligned_cols=27 Identities=33% Similarity=0.892 Sum_probs=23.3
Q ss_pred CCCccccce------eeecCCCcceEe-ccccceec
Q 016355 245 RRCQQCRRM------IELTHGCYHMTC-WCGHEFCY 273 (391)
Q Consensus 245 k~CP~C~~~------IeK~~GCnhMtC-~C~~~FCw 273 (391)
..||.|+.. ++..+||. +| .||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 459999999 88899997 99 99988774
No 278
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.77 E-value=45 Score=31.45 Aligned_cols=21 Identities=29% Similarity=0.611 Sum_probs=15.0
Q ss_pred CCCccccceeeec--CCCcceEe
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC 265 (391)
++||+|+.+|+|. +|=.-..|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~C 268 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFC 268 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEEC
Confidence 7899999999874 55333334
No 279
>PRK12495 hypothetical protein; Provisional
Probab=26.76 E-value=53 Score=29.83 Aligned_cols=30 Identities=27% Similarity=0.582 Sum_probs=23.5
Q ss_pred CCCCccccceeeecCCCcceEeccccceeccccccccCC
Q 016355 244 WRRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDG 282 (391)
Q Consensus 244 ~k~CP~C~~~IeK~~GCnhMtC~C~~~FCw~C~~~~~~~ 282 (391)
.+.||.|+.+|-+-.|+ .||-.|.......
T Consensus 42 a~hC~~CG~PIpa~pG~---------~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ---------EFCPTCQQPVTED 71 (226)
T ss_pred hhhcccccCcccCCCCe---------eECCCCCCccccc
Confidence 38999999999966665 5788888777643
No 280
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=26.24 E-value=17 Score=34.53 Aligned_cols=17 Identities=12% Similarity=0.380 Sum_probs=14.8
Q ss_pred CCCccccceeeecCCCc
Q 016355 245 RRCQQCRRMIELTHGCY 261 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCn 261 (391)
|.||.|.-.|.|.+-|.
T Consensus 124 K~Cp~C~d~VqrIeq~~ 140 (389)
T KOG2932|consen 124 KICPLCDDRVQRIEQIM 140 (389)
T ss_pred ccCcCcccHHHHHHHhc
Confidence 89999999999988773
No 281
>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=26.07 E-value=48 Score=31.30 Aligned_cols=21 Identities=29% Similarity=0.532 Sum_probs=15.1
Q ss_pred CCCccccceeeec--CCCcceEe
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC 265 (391)
++||+|+.+|+|. +|=+-..|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~C 268 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFC 268 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEEC
Confidence 6999999999875 55333334
No 282
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=26.00 E-value=15 Score=39.05 Aligned_cols=56 Identities=29% Similarity=0.602 Sum_probs=40.6
Q ss_pred CcccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCHHHHHh
Q 016355 74 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 137 (391)
Q Consensus 74 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~~~i~~ 137 (391)
...+|+||+..+..+ ..+.|.|.||..|+..-+...-+ ...||. |+..+.-..++.
T Consensus 20 k~lEc~ic~~~~~~p--~~~kc~~~~l~~~~n~~f~~~~~----~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 20 KILECPICLEHVKEP--SLLKCDHIFLKFCLNKLFESKKG----PKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred hhccCCceeEEeecc--chhhhhHHHHhhhhhceeeccCc----cccchh--hhhhhhhhhccc
Confidence 467899999988755 55699999999999877754322 467887 776655444433
No 283
>PLN02400 cellulose synthase
Probab=25.93 E-value=48 Score=37.24 Aligned_cols=50 Identities=26% Similarity=0.626 Sum_probs=35.5
Q ss_pred CCcccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCcc
Q 016355 73 KSPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 130 (391)
Q Consensus 73 ~~~~~C~IC~e~~~----~~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i 130 (391)
.....|.||-|++. ++.++.+ .|+-..|+.|+ .|= .++|.. .||+ |+...
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYE---RkeGnq--~CPQ--CkTrY 88 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYE---RKDGTQ--CCPQ--CKTRY 88 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCCCccccchh-hee---cccCCc--cCcc--cCCcc
Confidence 34568999999964 3345555 99999999998 332 345655 6998 87654
No 284
>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=25.81 E-value=1.5e+02 Score=20.20 Aligned_cols=41 Identities=15% Similarity=0.361 Sum_probs=22.2
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 75 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.|.|+.|...+... =|..++...=......+.||. |...+.
T Consensus 2 ~f~CP~C~~~~~~~--------------~L~~H~~~~H~~~~~~v~CPi--C~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGFSES--------------SLVEHCEDEHRSESKNVVCPI--CSSRVT 42 (54)
T ss_pred CcCCCCCCCccCHH--------------HHHHHHHhHCcCCCCCccCCC--chhhhh
Confidence 57899998743321 123333332222223579998 876544
No 285
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.56 E-value=44 Score=24.30 Aligned_cols=15 Identities=20% Similarity=0.616 Sum_probs=10.7
Q ss_pred CCeeeCCCCCccccc
Q 016355 191 NSCVECPVCERFICV 205 (391)
Q Consensus 191 ~~~v~C~~C~~~fC~ 205 (391)
...++|..||...+.
T Consensus 36 st~V~C~~CG~~l~~ 50 (67)
T COG2051 36 STVVTCLICGTTLAE 50 (67)
T ss_pred ceEEEecccccEEEe
Confidence 356888888876653
No 286
>PLN02195 cellulose synthase A
Probab=25.52 E-value=68 Score=35.70 Aligned_cols=50 Identities=20% Similarity=0.563 Sum_probs=36.5
Q ss_pred CcccccccccccCC----CCeeec-cCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 74 SPENCSICCEDKPY----PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 74 ~~~~C~IC~e~~~~----~~~~~l-~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
....|.||-++... +.++.+ .|+-..|+.|. .|= .++|.. .||+ |+....
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eye---r~eg~q--~Cpq--Ckt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYE---IKEGRK--VCLR--CGGPYD 59 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCCCccccchh-hhh---hhcCCc--cCCc--cCCccc
Confidence 35579999997643 345566 99999999998 443 345655 6998 988765
No 287
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.38 E-value=49 Score=31.22 Aligned_cols=21 Identities=24% Similarity=0.535 Sum_probs=15.0
Q ss_pred CCCccccceeeec--CCCcceEe
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC 265 (391)
++||+|+.+|++. +|=.-..|
T Consensus 245 ~pCprCG~~I~~~~~~gR~t~~C 267 (272)
T PRK14810 245 EPCLNCKTPIRRVVVAGRSSHYC 267 (272)
T ss_pred CcCCCCCCeeEEEEECCCccEEC
Confidence 7999999999874 55333334
No 288
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.36 E-value=48 Score=31.44 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=16.6
Q ss_pred CCCccccceeeec--CCCcceEe-cc
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC-WC 267 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC-~C 267 (391)
++||+|+.+|+|. +|=+-..| .|
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCC
Confidence 7999999999874 66444444 44
No 289
>PRK10445 endonuclease VIII; Provisional
Probab=25.36 E-value=51 Score=30.94 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=15.3
Q ss_pred CCCccccceeeec--CCCcceEe
Q 016355 245 RRCQQCRRMIELT--HGCYHMTC 265 (391)
Q Consensus 245 k~CP~C~~~IeK~--~GCnhMtC 265 (391)
++||+|+..|++. +|=.-..|
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~C 258 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWC 258 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEEC
Confidence 7999999999874 56444444
No 290
>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=25.23 E-value=19 Score=21.79 Aligned_cols=18 Identities=28% Similarity=0.519 Sum_probs=9.3
Q ss_pred ccccCCCccCCccCHHHH
Q 016355 118 PIRCPQLRCKYFISTVEC 135 (391)
Q Consensus 118 ~i~CP~~~C~~~i~~~~i 135 (391)
.++||..+|...+.....
T Consensus 2 ~vrCPvkdC~EEv~lgKY 19 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKY 19 (30)
T ss_dssp EEE--STT---EEEHHHH
T ss_pred ccccccccCcchhhhhhh
Confidence 379999999998866543
No 291
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.17 E-value=61 Score=29.97 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=28.9
Q ss_pred CCCccccceeeecCCCcceEe----ccccceeccccccccCCCC
Q 016355 245 RRCQQCRRMIELTHGCYHMTC----WCGHEFCYSCGAEYRDGQQ 284 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC----~C~~~FCw~C~~~~~~~~~ 284 (391)
-.||-|+..+. |-|.| .||+.||+-|-..+-..+.
T Consensus 222 yiCpvtrd~Lt-----Nt~~ca~Lr~sg~Vv~~ecvEklir~D~ 260 (303)
T KOG3039|consen 222 YICPVTRDTLT-----NTTPCAVLRPSGHVVTKECVEKLIRKDM 260 (303)
T ss_pred eecccchhhhc-----CccceEEeccCCcEeeHHHHHHhccccc
Confidence 47999988775 88999 7999999999988765543
No 292
>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=25.02 E-value=29 Score=24.24 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=9.8
Q ss_pred CCCCCccccceee
Q 016355 243 RWRRCQQCRRMIE 255 (391)
Q Consensus 243 ~~k~CP~C~~~Ie 255 (391)
+...||.|+.+..
T Consensus 25 ~l~~c~~cg~~~~ 37 (56)
T PF01783_consen 25 NLVKCPNCGEPKL 37 (56)
T ss_dssp SEEESSSSSSEES
T ss_pred ceeeeccCCCEec
Confidence 3478999987775
No 293
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.95 E-value=1.6e+02 Score=24.83 Aligned_cols=33 Identities=24% Similarity=0.301 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHHHhcC---CCCCccccCCCCCeeecC
Q 016355 141 LSSYESLETALAEANIL---HSDRIYCPFPNCSVLLDP 175 (391)
Q Consensus 141 ~~~~e~~~~~~~~~~i~---~~~~~~CP~p~C~~~~~~ 175 (391)
.+..+.+.+.+....+. .+.+..||. |+..+..
T Consensus 68 ~~~~~QL~ev~~~~~l~~~~~~~~sRC~~--CN~~L~~ 103 (147)
T PF01927_consen 68 DDPEEQLREVLERFGLKLRLDPIFSRCPK--CNGPLRP 103 (147)
T ss_pred CCHHHHHHHHHHHcCCccccCCCCCccCC--CCcEeee
Confidence 34455566655555544 233678995 7765544
No 294
>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=24.91 E-value=39 Score=23.58 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=10.0
Q ss_pred CCCCCccccceee
Q 016355 243 RWRRCQQCRRMIE 255 (391)
Q Consensus 243 ~~k~CP~C~~~Ie 255 (391)
..-.||+|+.+..
T Consensus 25 ~l~~C~~cG~~~~ 37 (55)
T TIGR01031 25 TLVVCPNCGEFKL 37 (55)
T ss_pred cceECCCCCCccc
Confidence 3467999998876
No 295
>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=24.70 E-value=76 Score=24.68 Aligned_cols=27 Identities=26% Similarity=0.485 Sum_probs=21.3
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||.|+..-.|..+----.| .|+..|
T Consensus 36 y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred ccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 799999988777777777777 777665
No 296
>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=24.08 E-value=1.3e+02 Score=25.87 Aligned_cols=36 Identities=25% Similarity=0.718 Sum_probs=21.4
Q ss_pred cccccccccccCCCCeeec------cCCCccc------HHHHHHHHHHH
Q 016355 75 PENCSICCEDKPYPMMITM------KCSHKFC------SHCMRTYIDGK 111 (391)
Q Consensus 75 ~~~C~IC~e~~~~~~~~~l------~C~H~fC------~~Cl~~~i~~~ 111 (391)
..+|+||+|- |.+-+.-+ +|.-++| ..|+.+|-+..
T Consensus 2 d~~CpICme~-PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~ 49 (162)
T PF07800_consen 2 DVTCPICMEH-PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAY 49 (162)
T ss_pred CccCceeccC-CCceEEEEeccccCCccccccCCccchhHHHHHHHHHh
Confidence 4579999974 44432211 3433344 47888887764
No 297
>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=23.80 E-value=78 Score=18.36 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=18.2
Q ss_pred CccccceeeecCCCcceEe-cccc
Q 016355 247 CQQCRRMIELTHGCYHMTC-WCGH 269 (391)
Q Consensus 247 CP~C~~~IeK~~GCnhMtC-~C~~ 269 (391)
|-+|++++.-..|=.++.| .|.+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 5678888888888888888 7764
No 298
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=23.73 E-value=34 Score=22.88 Aligned_cols=33 Identities=18% Similarity=0.466 Sum_probs=25.6
Q ss_pred cccccccccCCCCeeec-cCCCcccHHHHHHHHH
Q 016355 77 NCSICCEDKPYPMMITM-KCSHKFCSHCMRTYID 109 (391)
Q Consensus 77 ~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~~i~ 109 (391)
.|.||........++.. .|+..|...|+.-...
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 37889887777788888 8998888888776554
No 299
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=23.54 E-value=5.2 Score=39.03 Aligned_cols=46 Identities=22% Similarity=0.491 Sum_probs=21.3
Q ss_pred CCCcccccccccCCCCCC-CchhHhcCcccccChhHHHHHHHHhccCCCCCcccccee
Q 016355 198 VCERFICVECGVPWHSSL-SCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMI 254 (391)
Q Consensus 198 ~C~~~fC~~C~~~~H~~~-sC~e~~~~~~~~~~~~~~~~~~l~~~~~~k~CP~C~~~I 254 (391)
.|...+|..|.+.++.+. .|.... +.+.+....+.+-+|+.|+...
T Consensus 249 k~kav~C~~C~yt~~~~~~~C~~~~-----------H~l~~~~a~KRFFkC~~C~~Rt 295 (344)
T PF09332_consen 249 KCKAVTCKQCKYTAFKPSDRCKEEG-----------HPLKWHDAVKRFFKCKDCGNRT 295 (344)
T ss_dssp EEEEEEETTT--EESS--HHHHHTT-------------EEEEEEE-EEEE-T-TS-EE
T ss_pred EEEEEEcCCCCCcccCcchhHHhcC-----------CceEEeeeeeeeEECCCCCCee
Confidence 478889999988776665 564321 1122222334456788777654
No 300
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.44 E-value=52 Score=21.13 Aligned_cols=18 Identities=28% Similarity=0.756 Sum_probs=15.4
Q ss_pred eeeCCCCCcccccccccC
Q 016355 193 CVECPVCERFICVECGVP 210 (391)
Q Consensus 193 ~v~C~~C~~~fC~~C~~~ 210 (391)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 467999999999988865
No 301
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.12 E-value=83 Score=24.44 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=21.8
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||.|+..-.|..+----.| .|+..|
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 799999988888877777778 777665
No 302
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=23.09 E-value=45 Score=27.72 Aligned_cols=13 Identities=23% Similarity=0.490 Sum_probs=10.0
Q ss_pred CCCccccceeeec
Q 016355 245 RRCQQCRRMIELT 257 (391)
Q Consensus 245 k~CP~C~~~IeK~ 257 (391)
|.||+|++-|--.
T Consensus 111 K~C~~C~tGiYS~ 123 (128)
T PF11682_consen 111 KYCPKCGTGIYSI 123 (128)
T ss_pred EecCCCCCcccce
Confidence 8899999877433
No 303
>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=22.88 E-value=35 Score=24.25 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=7.5
Q ss_pred CCCccccceee
Q 016355 245 RRCQQCRRMIE 255 (391)
Q Consensus 245 k~CP~C~~~Ie 255 (391)
|.||.|+.+|.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 56777777665
No 304
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=22.78 E-value=60 Score=27.27 Aligned_cols=25 Identities=20% Similarity=0.591 Sum_probs=16.8
Q ss_pred CCCc--cccceeeecCCCcceEe-ccccc
Q 016355 245 RRCQ--QCRRMIELTHGCYHMTC-WCGHE 270 (391)
Q Consensus 245 k~CP--~C~~~IeK~~GCnhMtC-~C~~~ 270 (391)
..|| .|+..+..+ |=+.++| .|+..
T Consensus 19 ~aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp EE-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred CCCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 7899 999998888 3356888 77754
No 305
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.51 E-value=84 Score=30.14 Aligned_cols=53 Identities=17% Similarity=0.335 Sum_probs=34.5
Q ss_pred CCcccccccccccCCCC-eeeccCCCcccHHHHHHHHHHHhhCCCcccccCCCccCCccC
Q 016355 73 KSPENCSICCEDKPYPM-MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 131 (391)
Q Consensus 73 ~~~~~C~IC~e~~~~~~-~~~l~C~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~ 131 (391)
.+.|.|++=-+.-..++ -+.+.|||.+=.+=+...- .+|...++||- |...-.
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~~~FKCPY--CP~~~~ 387 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGVLSFKCPY--CPEMSK 387 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCcEEeeCCC--CCcchh
Confidence 45789998554433222 2456999999766554332 46777889998 876543
No 306
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.34 E-value=47 Score=27.42 Aligned_cols=20 Identities=30% Similarity=0.647 Sum_probs=14.3
Q ss_pred ccccccCCCCeeeccCCCcccH
Q 016355 80 ICCEDKPYPMMITMKCSHKFCS 101 (391)
Q Consensus 80 IC~e~~~~~~~~~l~C~H~fC~ 101 (391)
||.+ +...++.+.|||.||-
T Consensus 62 i~qs--~~~rv~rcecghsf~d 81 (165)
T COG4647 62 ICQS--AQKRVIRCECGHSFGD 81 (165)
T ss_pred EEec--ccccEEEEeccccccC
Confidence 4544 3445778899999985
No 307
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.17 E-value=55 Score=35.10 Aligned_cols=43 Identities=23% Similarity=0.575 Sum_probs=30.4
Q ss_pred HHHHHHHHhccCCCCCccccceeeecCC--------Ccce-Ee-ccccceecc
Q 016355 232 DITLHRLAQNKRWRRCQQCRRMIELTHG--------CYHM-TC-WCGHEFCYS 274 (391)
Q Consensus 232 ~~~~~~l~~~~~~k~CP~C~~~IeK~~G--------CnhM-tC-~C~~~FCw~ 274 (391)
...+..++++..|..|-.|+.-....+| =|-+ -| +||+.+|-.
T Consensus 54 l~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~ 106 (877)
T KOG1873|consen 54 LSHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGR 106 (877)
T ss_pred HHHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCC
Confidence 3445555556688999999998877775 2222 38 999988755
No 308
>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=22.13 E-value=49 Score=22.39 Aligned_cols=44 Identities=30% Similarity=0.716 Sum_probs=21.1
Q ss_pred ccccccccccCCCCeeeccC-CCcccHHHHHHHHHHHhhCCCcccccCCCccCCccCH
Q 016355 76 ENCSICCEDKPYPMMITMKC-SHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 132 (391)
Q Consensus 76 ~~C~IC~e~~~~~~~~~l~C-~H~fC~~Cl~~~i~~~i~~g~~~i~CP~~~C~~~i~~ 132 (391)
+.|-.|.-.. ..+ +.| .|..|..|+...+.. .-+||. |+.+++.
T Consensus 3 ~nCKsCWf~~--k~L--i~C~dHYLCl~CLt~ml~~-------s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN--KGL--IKCSDHYLCLNCLTLMLSR-------SDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S----SSE--EE-SS-EEEHHHHHHT-SS-------SSEETT--TTEE---
T ss_pred ccChhhhhcC--CCe--eeecchhHHHHHHHHHhcc-------ccCCCc--ccCcCcc
Confidence 4577776432 222 255 599999999877732 237988 8887763
No 309
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.84 E-value=91 Score=26.09 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=9.6
Q ss_pred CCccccCCCCCeeecC
Q 016355 160 DRIYCPFPNCSVLLDP 175 (391)
Q Consensus 160 ~~~~CP~p~C~~~~~~ 175 (391)
...+|+ +|+.....
T Consensus 69 ~~~~C~--~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCR--NCGNEWSL 82 (135)
T ss_pred eEEECC--CCCCEEec
Confidence 456898 58876655
No 310
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.40 E-value=44 Score=33.06 Aligned_cols=7 Identities=29% Similarity=1.084 Sum_probs=4.9
Q ss_pred CCCcccc
Q 016355 245 RRCQQCR 251 (391)
Q Consensus 245 k~CP~C~ 251 (391)
+-||+|+
T Consensus 2 ~fC~kcG 8 (465)
T COG4640 2 KFCPKCG 8 (465)
T ss_pred Ccccccc
Confidence 5677777
No 311
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.02 E-value=1e+02 Score=23.89 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=21.0
Q ss_pred CCCccccceeeecCCCcceEe-ccccce
Q 016355 245 RRCQQCRRMIELTHGCYHMTC-WCGHEF 271 (391)
Q Consensus 245 k~CP~C~~~IeK~~GCnhMtC-~C~~~F 271 (391)
..||.|+..-.|..+----.| .|+..|
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred ccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 799999888777777777777 776665
No 312
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=20.67 E-value=59 Score=30.08 Aligned_cols=37 Identities=35% Similarity=0.950 Sum_probs=23.7
Q ss_pred CCCcccccee-----eecCCCcceEe-ccccce-----------eccccccccC
Q 016355 245 RRCQQCRRMI-----ELTHGCYHMTC-WCGHEF-----------CYSCGAEYRD 281 (391)
Q Consensus 245 k~CP~C~~~I-----eK~~GCnhMtC-~C~~~F-----------Cw~C~~~~~~ 281 (391)
-+|-+|++.. -|..|=-...| +|++.| ||.|+.+...
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~P 186 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVYP 186 (278)
T ss_pred ccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCccCc
Confidence 4566666543 34466666677 777766 8888877643
No 313
>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=20.01 E-value=53 Score=31.26 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=16.5
Q ss_pred CCCccccce-----eeecC--CCcceEe-ccccce------eccccccc
Q 016355 245 RRCQQCRRM-----IELTH--GCYHMTC-WCGHEF------CYSCGAEY 279 (391)
Q Consensus 245 k~CP~C~~~-----IeK~~--GCnhMtC-~C~~~F------Cw~C~~~~ 279 (391)
..||-|+.. |...+ |=-++.| .|+++| |-.||..=
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 799999975 33334 7889999 898875 77788763
Done!