Query 024715
Match_columns 263
No_of_seqs 176 out of 1451
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 06:49:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024715.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024715hhsearch_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 6.3E-36 1.4E-40 263.9 10.5 198 19-219 144-344 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 2.8E-36 6E-41 257.0 6.6 198 17-219 180-407 (445)
3 KOG1815 Predicted E3 ubiquitin 99.9 9.1E-28 2E-32 217.5 11.5 193 19-218 68-266 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 5.9E-27 1.3E-31 193.6 8.0 196 15-220 215-439 (446)
5 smart00647 IBR In Between Ring 99.2 2.5E-11 5.5E-16 80.5 5.1 63 94-158 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 5.1E-12 1.1E-16 83.8 0.7 63 94-158 1-64 (64)
7 PLN03208 E3 ubiquitin-protein 98.6 4.4E-08 9.6E-13 77.7 5.2 70 15-90 12-89 (193)
8 PF15227 zf-C3HC4_4: zinc fing 98.6 1.1E-08 2.3E-13 61.6 1.0 41 24-72 1-41 (42)
9 PF13445 zf-RING_UBOX: RING-ty 98.6 4.1E-08 9E-13 59.0 2.2 43 24-71 1-43 (43)
10 smart00647 IBR In Between Ring 98.5 1.6E-07 3.6E-12 61.9 5.1 42 179-220 16-62 (64)
11 PF00097 zf-C3HC4: Zinc finger 98.5 1.1E-07 2.3E-12 57.0 2.9 40 24-72 1-40 (41)
12 PF01485 IBR: IBR domain; Int 98.4 7.6E-08 1.6E-12 63.5 1.4 42 179-220 16-62 (64)
13 PF13923 zf-C3HC4_2: Zinc fing 98.4 1.5E-07 3.3E-12 55.7 2.4 38 24-72 1-38 (39)
14 PF13639 zf-RING_2: Ring finge 98.4 1E-07 2.2E-12 58.1 0.9 41 23-72 2-42 (44)
15 KOG0320 Predicted E3 ubiquitin 98.3 3.9E-07 8.4E-12 70.7 3.3 57 18-86 128-184 (187)
16 PF14634 zf-RING_5: zinc-RING 98.3 6.5E-07 1.4E-11 54.4 2.8 44 23-77 1-44 (44)
17 PF13920 zf-C3HC4_3: Zinc fing 98.1 1.6E-06 3.4E-11 54.3 2.5 46 21-80 2-48 (50)
18 cd00162 RING RING-finger (Real 98.1 2.9E-06 6.2E-11 51.3 3.3 44 23-78 1-44 (45)
19 PHA02926 zinc finger-like prot 98.0 4.6E-06 1E-10 67.2 4.0 59 18-80 167-230 (242)
20 KOG0823 Predicted E3 ubiquitin 98.0 7.3E-06 1.6E-10 66.5 3.8 60 18-88 44-103 (230)
21 PHA02929 N1R/p28-like protein; 97.9 9.2E-06 2E-10 67.4 3.9 52 19-80 172-227 (238)
22 KOG2177 Predicted E3 ubiquitin 97.9 8E-06 1.7E-10 70.6 3.0 109 18-158 10-122 (386)
23 KOG2164 Predicted E3 ubiquitin 97.9 8.3E-06 1.8E-10 73.2 2.8 60 21-89 186-245 (513)
24 smart00504 Ubox Modified RING 97.8 2.9E-05 6.4E-10 50.9 4.0 51 22-86 2-52 (63)
25 KOG0317 Predicted E3 ubiquitin 97.8 1.9E-05 4.2E-10 66.0 3.7 52 19-84 237-288 (293)
26 smart00184 RING Ring finger. E 97.8 2.4E-05 5.2E-10 45.4 3.1 38 24-72 1-38 (39)
27 COG5540 RING-finger-containing 97.6 3.6E-05 7.7E-10 64.7 2.9 54 18-81 320-373 (374)
28 TIGR00599 rad18 DNA repair pro 97.6 0.0001 2.2E-09 65.6 5.1 67 19-99 24-91 (397)
29 TIGR00570 cdk7 CDK-activating 97.5 0.00023 5E-09 61.0 6.3 53 22-84 4-58 (309)
30 KOG0287 Postreplication repair 97.5 4.8E-05 1E-09 64.9 1.5 66 19-98 21-87 (442)
31 KOG4628 Predicted E3 ubiquitin 97.4 9.4E-05 2E-09 64.3 3.0 50 20-79 228-277 (348)
32 PF11789 zf-Nse: Zinc-finger o 97.4 0.00017 3.7E-09 46.2 2.7 50 18-76 8-57 (57)
33 KOG1002 Nucleotide excision re 97.2 0.0004 8.8E-09 62.7 4.0 66 15-89 530-595 (791)
34 PF12678 zf-rbx1: RING-H2 zinc 97.0 0.00057 1.2E-08 46.2 2.3 45 22-76 20-73 (73)
35 KOG0978 E3 ubiquitin ligase in 96.9 0.00045 9.8E-09 65.1 2.3 56 19-87 641-696 (698)
36 COG5574 PEX10 RING-finger-cont 96.9 0.00085 1.8E-08 55.6 3.6 52 21-84 215-266 (271)
37 PF11793 FANCL_C: FANCL C-term 96.9 0.00045 9.7E-09 46.3 1.6 59 21-81 2-67 (70)
38 KOG4367 Predicted Zn-finger pr 96.6 0.0012 2.5E-08 58.4 2.4 81 132-219 174-256 (699)
39 PF04564 U-box: U-box domain; 96.3 0.0039 8.4E-08 42.2 2.7 52 20-84 3-54 (73)
40 PF14835 zf-RING_6: zf-RING of 96.1 0.00079 1.7E-08 43.6 -1.2 50 20-84 6-55 (65)
41 COG5432 RAD18 RING-finger-cont 96.1 0.004 8.6E-08 52.3 2.4 66 19-98 23-89 (391)
42 PF14570 zf-RING_4: RING/Ubox 96.1 0.0058 1.2E-07 37.4 2.5 47 24-79 1-47 (48)
43 KOG0006 E3 ubiquitin-protein l 96.0 0.0063 1.4E-07 51.8 3.1 93 42-154 341-437 (446)
44 KOG2660 Locus-specific chromos 95.8 0.0056 1.2E-07 52.5 2.2 53 18-83 12-64 (331)
45 COG5243 HRD1 HRD ubiquitin lig 95.4 0.014 3E-07 50.8 3.3 54 18-81 284-346 (491)
46 KOG1814 Predicted E3 ubiquitin 95.3 0.017 3.7E-07 51.0 3.5 114 19-153 271-405 (445)
47 KOG1039 Predicted E3 ubiquitin 95.1 0.019 4.2E-07 50.3 3.1 95 18-115 158-264 (344)
48 KOG0824 Predicted E3 ubiquitin 94.2 0.037 8.1E-07 47.0 2.7 52 19-83 5-56 (324)
49 PF10571 UPF0547: Uncharacteri 94.2 0.02 4.4E-07 30.3 0.8 23 182-208 1-24 (26)
50 smart00744 RINGv The RING-vari 94.0 0.077 1.7E-06 32.8 3.2 42 23-72 1-47 (49)
51 COG5220 TFB3 Cdk activating ki 93.7 0.021 4.5E-07 46.8 0.3 53 20-79 9-63 (314)
52 KOG4185 Predicted E3 ubiquitin 93.7 0.12 2.6E-06 44.7 5.0 51 20-79 2-54 (296)
53 KOG0828 Predicted E3 ubiquitin 93.6 0.051 1.1E-06 49.1 2.6 54 19-81 569-635 (636)
54 KOG1952 Transcription factor N 93.6 0.036 7.9E-07 53.2 1.7 56 18-76 188-243 (950)
55 PF12861 zf-Apc11: Anaphase-pr 93.6 0.076 1.6E-06 36.7 2.8 54 21-81 21-83 (85)
56 KOG0802 E3 ubiquitin ligase [P 93.5 0.046 1E-06 51.5 2.3 51 18-78 288-339 (543)
57 PF04641 Rtf2: Rtf2 RING-finge 93.1 0.2 4.4E-06 42.5 5.4 72 18-100 110-182 (260)
58 KOG1940 Zn-finger protein [Gen 93.1 0.17 3.6E-06 43.0 4.8 49 19-77 156-204 (276)
59 KOG3039 Uncharacterized conser 93.0 0.07 1.5E-06 44.0 2.2 59 19-87 219-277 (303)
60 KOG1734 Predicted RING-contain 92.6 0.03 6.5E-07 46.7 -0.4 57 19-84 222-285 (328)
61 KOG3800 Predicted E3 ubiquitin 92.5 0.24 5.3E-06 41.9 4.9 51 23-82 2-53 (300)
62 COG5152 Uncharacterized conser 92.4 0.079 1.7E-06 42.2 1.8 46 19-78 194-239 (259)
63 KOG2879 Predicted E3 ubiquitin 92.4 0.13 2.9E-06 43.1 3.1 52 18-80 236-287 (298)
64 KOG0804 Cytoplasmic Zn-finger 92.1 0.062 1.3E-06 48.1 0.9 52 18-81 172-223 (493)
65 COG5175 MOT2 Transcriptional r 92.1 0.19 4.1E-06 43.5 3.8 58 20-86 13-70 (480)
66 KOG4159 Predicted E3 ubiquitin 91.9 0.16 3.4E-06 45.7 3.3 50 18-81 81-130 (398)
67 KOG3053 Uncharacterized conser 91.8 0.38 8.2E-06 40.0 5.2 63 16-80 15-82 (293)
68 KOG0827 Predicted E3 ubiquitin 91.8 0.13 2.8E-06 45.3 2.5 53 21-80 4-56 (465)
69 KOG1645 RING-finger-containing 91.7 0.098 2.1E-06 46.3 1.8 56 21-84 4-60 (463)
70 KOG1812 Predicted E3 ubiquitin 91.4 0.16 3.4E-06 45.7 2.8 42 108-156 304-345 (384)
71 KOG4739 Uncharacterized protei 91.1 0.078 1.7E-06 43.8 0.5 56 21-90 3-58 (233)
72 KOG0311 Predicted E3 ubiquitin 91.0 0.036 7.7E-07 48.1 -1.6 49 19-79 41-89 (381)
73 KOG4172 Predicted E3 ubiquitin 91.0 0.12 2.6E-06 32.2 1.1 47 21-80 7-54 (62)
74 KOG4265 Predicted E3 ubiquitin 91.0 0.24 5.1E-06 43.3 3.3 49 18-80 287-336 (349)
75 smart00661 RPOL9 RNA polymeras 90.9 0.21 4.5E-06 31.0 2.2 27 182-208 1-30 (52)
76 PF13719 zinc_ribbon_5: zinc-r 90.9 0.17 3.7E-06 29.2 1.7 32 111-144 3-35 (37)
77 PF13248 zf-ribbon_3: zinc-rib 90.5 0.15 3.1E-06 26.9 1.1 12 182-193 3-14 (26)
78 PF13240 zinc_ribbon_2: zinc-r 90.4 0.15 3.2E-06 26.1 1.0 11 183-193 1-11 (23)
79 KOG0297 TNF receptor-associate 90.3 0.49 1.1E-05 42.7 4.9 51 18-81 18-68 (391)
80 PHA03096 p28-like protein; Pro 90.2 0.2 4.3E-06 43.0 2.2 54 22-79 179-236 (284)
81 KOG1815 Predicted E3 ubiquitin 90.1 0.22 4.8E-06 45.7 2.6 40 181-220 158-200 (444)
82 PHA00626 hypothetical protein 90.0 0.24 5.2E-06 31.1 1.8 27 183-209 2-34 (59)
83 PF13717 zinc_ribbon_4: zinc-r 89.6 0.28 6E-06 28.1 1.8 32 111-144 3-35 (36)
84 PF05883 Baculo_RING: Baculovi 88.6 0.19 4.2E-06 37.7 0.9 38 19-57 24-67 (134)
85 KOG4445 Uncharacterized conser 88.3 0.34 7.4E-06 41.2 2.2 65 15-82 109-188 (368)
86 KOG1785 Tyrosine kinase negati 87.9 0.26 5.6E-06 43.6 1.3 48 19-78 367-414 (563)
87 PRK00398 rpoP DNA-directed RNA 87.6 0.56 1.2E-05 28.4 2.3 29 182-210 4-33 (46)
88 PRK00432 30S ribosomal protein 87.4 0.44 9.5E-06 29.5 1.8 26 181-208 20-47 (50)
89 PF14447 Prok-RING_4: Prokaryo 87.0 0.35 7.7E-06 30.4 1.2 48 20-83 6-53 (55)
90 KOG2817 Predicted E3 ubiquitin 86.8 0.66 1.4E-05 41.1 3.2 60 19-86 332-391 (394)
91 KOG1428 Inhibitor of type V ad 86.7 0.67 1.5E-05 47.7 3.5 185 17-216 3482-3684(3738)
92 PLN03086 PRLI-interacting fact 86.6 0.94 2E-05 42.6 4.3 59 65-144 405-463 (567)
93 KOG3002 Zn finger protein [Gen 86.5 0.79 1.7E-05 39.7 3.5 47 18-80 45-91 (299)
94 PF07975 C1_4: TFIIH C1-like d 86.5 0.22 4.7E-06 31.0 0.1 39 117-155 4-42 (51)
95 COG5236 Uncharacterized conser 86.0 0.67 1.5E-05 40.3 2.8 67 18-96 58-124 (493)
96 KOG0825 PHD Zn-finger protein 85.2 0.59 1.3E-05 45.0 2.2 42 20-61 95-139 (1134)
97 COG1998 RPS31 Ribosomal protei 85.0 0.66 1.4E-05 28.3 1.6 26 181-206 19-45 (51)
98 PF14803 Nudix_N_2: Nudix N-te 84.8 0.64 1.4E-05 26.2 1.4 31 111-143 1-31 (34)
99 PF14952 zf-tcix: Putative tre 84.5 0.51 1.1E-05 28.0 1.0 26 179-208 9-37 (44)
100 KOG2906 RNA polymerase III sub 84.4 0.76 1.6E-05 32.4 1.9 29 183-211 3-34 (105)
101 TIGR02098 MJ0042_CXXC MJ0042 f 83.2 0.9 2E-05 26.1 1.7 32 111-144 3-35 (38)
102 COG5219 Uncharacterized conser 82.5 0.73 1.6E-05 45.3 1.7 54 20-81 1468-1524(1525)
103 KOG4692 Predicted E3 ubiquitin 82.2 0.91 2E-05 39.6 2.0 50 18-81 419-468 (489)
104 KOG1813 Predicted E3 ubiquitin 82.2 0.51 1.1E-05 40.2 0.5 45 21-79 241-285 (313)
105 KOG1941 Acetylcholine receptor 82.0 0.59 1.3E-05 41.3 0.8 53 19-79 363-415 (518)
106 PF09297 zf-NADH-PPase: NADH p 81.1 2 4.3E-05 23.7 2.5 27 181-207 3-30 (32)
107 smart00661 RPOL9 RNA polymeras 80.9 1.4 3E-05 27.2 2.0 28 112-143 2-29 (52)
108 PF01599 Ribosomal_S27: Riboso 80.8 1.2 2.5E-05 27.2 1.6 29 110-142 18-46 (47)
109 PF09538 FYDLN_acid: Protein o 80.7 0.9 2E-05 33.1 1.3 27 182-209 10-37 (108)
110 PF02150 RNA_POL_M_15KD: RNA p 78.4 1.3 2.9E-05 25.1 1.2 28 111-143 2-29 (35)
111 PF14569 zf-UDP: Zinc-binding 77.9 2.8 6E-05 28.3 2.8 44 132-199 26-69 (80)
112 KOG2034 Vacuolar sorting prote 77.9 1.3 2.8E-05 43.3 1.7 42 19-62 815-856 (911)
113 PF12906 RINGv: RING-variant d 76.7 1.3 2.7E-05 27.0 0.9 33 24-58 1-38 (47)
114 PRK05654 acetyl-CoA carboxylas 76.0 0.57 1.2E-05 40.5 -1.1 30 179-208 25-56 (292)
115 KOG3268 Predicted E3 ubiquitin 75.8 4.6 9.9E-05 31.9 3.9 62 18-81 162-229 (234)
116 PF05290 Baculo_IE-1: Baculovi 75.4 4.2 9.2E-05 30.5 3.5 53 19-79 78-131 (140)
117 KOG1701 Focal adhesion adaptor 74.9 2.5 5.5E-05 37.9 2.6 69 132-206 380-460 (468)
118 PF09889 DUF2116: Uncharacteri 74.4 0.39 8.4E-06 30.8 -1.9 27 182-219 4-31 (59)
119 PF06677 Auto_anti-p27: Sjogre 73.8 2.9 6.3E-05 24.7 1.9 22 182-205 18-41 (41)
120 PRK14559 putative protein seri 73.5 2.2 4.7E-05 41.1 2.0 10 206-215 41-50 (645)
121 PHA02825 LAP/PHD finger-like p 73.3 6.7 0.00014 30.5 4.2 54 19-83 6-62 (162)
122 CHL00174 accD acetyl-CoA carbo 72.9 0.7 1.5E-05 39.8 -1.3 30 180-209 37-68 (296)
123 KOG2807 RNA polymerase II tran 72.6 0.74 1.6E-05 39.7 -1.2 24 132-155 343-366 (378)
124 PF14446 Prok-RING_1: Prokaryo 72.6 3.9 8.4E-05 25.7 2.3 37 19-55 3-39 (54)
125 TIGR00515 accD acetyl-CoA carb 72.2 0.77 1.7E-05 39.5 -1.2 30 179-208 24-55 (285)
126 PF03119 DNA_ligase_ZBD: NAD-d 72.0 4.1 8.8E-05 21.8 2.0 20 183-202 1-20 (28)
127 COG5222 Uncharacterized conser 71.5 6.1 0.00013 33.8 4.0 44 22-77 275-318 (427)
128 KOG1001 Helicase-like transcri 70.6 1.4 2.9E-05 42.7 -0.1 48 22-82 455-502 (674)
129 PF07191 zinc-ribbons_6: zinc- 70.1 3.3 7.2E-05 27.5 1.7 33 183-217 3-41 (70)
130 PF08746 zf-RING-like: RING-li 70.0 4.3 9.2E-05 24.2 2.0 42 24-72 1-42 (43)
131 KOG3161 Predicted E3 ubiquitin 70.0 1.7 3.6E-05 41.0 0.4 39 19-57 9-47 (861)
132 PF14149 YhfH: YhfH-like prote 68.2 0.49 1.1E-05 27.1 -2.2 30 173-202 5-34 (37)
133 COG0777 AccD Acetyl-CoA carbox 67.7 2 4.3E-05 36.4 0.4 33 178-210 25-59 (294)
134 PF12773 DZR: Double zinc ribb 67.6 3.7 8.1E-05 25.0 1.5 27 108-141 10-36 (50)
135 TIGR01384 TFS_arch transcripti 67.6 3.8 8.1E-05 29.4 1.8 23 183-207 2-25 (104)
136 PRK14892 putative transcriptio 67.4 4.7 0.0001 28.8 2.2 29 180-208 20-52 (99)
137 PF07282 OrfB_Zn_ribbon: Putat 66.9 4.5 9.9E-05 26.5 1.9 28 181-208 28-56 (69)
138 PF10122 Mu-like_Com: Mu-like 66.9 2.4 5.3E-05 26.1 0.5 25 182-206 5-32 (51)
139 PRK14714 DNA polymerase II lar 66.6 5.6 0.00012 40.8 3.2 9 111-121 668-676 (1337)
140 COG1645 Uncharacterized Zn-fin 66.5 3.4 7.4E-05 31.0 1.3 24 181-213 28-51 (131)
141 PRK08665 ribonucleotide-diphos 66.1 3.4 7.3E-05 40.7 1.6 26 182-209 725-751 (752)
142 smart00064 FYVE Protein presen 65.1 5.7 0.00012 25.9 2.1 39 20-58 9-47 (68)
143 PRK00420 hypothetical protein; 63.1 5.5 0.00012 29.2 1.9 29 180-217 22-51 (112)
144 COG2888 Predicted Zn-ribbon RN 63.0 6.8 0.00015 25.0 2.0 30 111-146 10-39 (61)
145 PF06844 DUF1244: Protein of u 62.9 6.3 0.00014 25.7 1.9 17 46-62 11-27 (68)
146 PF07503 zf-HYPF: HypF finger; 62.7 4.5 9.8E-05 23.0 1.1 32 47-80 1-32 (35)
147 COG5194 APC11 Component of SCF 62.5 8.2 0.00018 26.2 2.5 31 41-81 52-82 (88)
148 PF01363 FYVE: FYVE zinc finge 62.4 1.6 3.4E-05 28.7 -1.0 37 18-54 6-42 (69)
149 PHA02862 5L protein; Provision 62.2 10 0.00022 29.0 3.1 48 22-82 3-55 (156)
150 KOG0825 PHD Zn-finger protein 61.8 8.2 0.00018 37.6 3.2 53 21-84 123-175 (1134)
151 PF01428 zf-AN1: AN1-like Zinc 61.5 7 0.00015 23.2 1.8 19 133-151 12-30 (43)
152 TIGR02300 FYDLN_acid conserved 60.9 5 0.00011 29.9 1.3 26 182-208 10-36 (129)
153 PRK14890 putative Zn-ribbon RN 60.5 5.6 0.00012 25.4 1.3 12 182-193 26-38 (59)
154 cd00065 FYVE FYVE domain; Zinc 60.5 6.2 0.00014 24.6 1.6 37 22-58 3-39 (57)
155 COG1198 PriA Primosomal protei 60.4 7.1 0.00015 38.1 2.7 34 182-215 445-484 (730)
156 PRK09710 lar restriction allev 60.2 7.4 0.00016 25.3 1.9 28 180-207 5-36 (64)
157 KOG2691 RNA polymerase II subu 60.1 12 0.00026 26.9 3.1 34 109-144 3-36 (113)
158 PF14569 zf-UDP: Zinc-binding 59.9 19 0.0004 24.4 3.8 52 19-79 7-61 (80)
159 PF14353 CpXC: CpXC protein 59.6 6.2 0.00013 29.4 1.7 16 67-84 1-16 (128)
160 KOG3970 Predicted E3 ubiquitin 59.4 10 0.00022 31.1 3.0 59 18-80 47-105 (299)
161 PF10367 Vps39_2: Vacuolar sor 58.7 3 6.4E-05 29.8 -0.2 33 19-53 76-108 (109)
162 PF06827 zf-FPG_IleRS: Zinc fi 58.3 6.1 0.00013 21.3 1.1 24 182-205 2-28 (30)
163 PF08274 PhnA_Zn_Ribbon: PhnA 58.0 5.6 0.00012 21.7 0.9 26 112-144 4-29 (30)
164 PF12760 Zn_Tnp_IS1595: Transp 58.0 24 0.00052 21.1 3.8 34 173-206 7-45 (46)
165 PRK14559 putative protein seri 57.6 9.1 0.0002 37.0 2.8 12 181-192 41-52 (645)
166 PLN00209 ribosomal protein S27 57.1 13 0.00029 25.6 2.8 31 111-146 37-67 (86)
167 TIGR03655 anti_R_Lar restricti 56.7 11 0.00024 23.4 2.3 28 182-209 2-37 (53)
168 PLN02189 cellulose synthase 54.5 12 0.00026 37.8 3.2 64 109-201 33-96 (1040)
169 TIGR00686 phnA alkylphosphonat 54.2 8.5 0.00018 27.8 1.6 27 112-145 4-30 (109)
170 KOG0317 Predicted E3 ubiquitin 53.9 2 4.3E-05 36.6 -1.9 20 199-218 251-271 (293)
171 KOG2930 SCF ubiquitin ligase, 53.7 13 0.00028 26.6 2.4 31 41-81 79-109 (114)
172 PF06906 DUF1272: Protein of u 53.3 15 0.00031 23.2 2.3 47 22-82 6-54 (57)
173 PF15616 TerY-C: TerY-C metal 53.3 10 0.00022 28.6 1.9 26 180-211 76-101 (131)
174 COG1997 RPL43A Ribosomal prote 53.0 22 0.00048 24.7 3.3 29 180-208 34-63 (89)
175 cd00021 BBOX B-Box-type zinc f 52.7 8.7 0.00019 21.7 1.2 26 132-157 10-35 (39)
176 PTZ00083 40S ribosomal protein 52.2 15 0.00033 25.3 2.4 31 111-146 36-66 (85)
177 PLN03208 E3 ubiquitin-protein 51.9 2.9 6.3E-05 33.7 -1.2 37 176-217 13-49 (193)
178 PF00643 zf-B_box: B-box zinc 51.8 4.9 0.00011 23.4 0.0 25 133-157 14-38 (42)
179 KOG4362 Transcriptional regula 51.8 2.1 4.6E-05 40.9 -2.3 58 18-86 18-75 (684)
180 PRK04023 DNA polymerase II lar 51.3 14 0.0003 37.2 2.9 33 108-152 624-661 (1121)
181 KOG3039 Uncharacterized conser 50.8 16 0.00034 30.6 2.8 40 19-62 41-80 (303)
182 COG2051 RPS27A Ribosomal prote 50.7 10 0.00022 24.8 1.3 31 111-146 20-50 (67)
183 KOG0978 E3 ubiquitin ligase in 50.5 6.9 0.00015 37.8 0.8 12 180-191 677-688 (698)
184 PF13453 zf-TFIIB: Transcripti 50.4 11 0.00023 22.0 1.3 12 183-194 1-12 (41)
185 PF02591 DUF164: Putative zinc 49.9 14 0.00031 23.1 1.9 22 170-191 35-56 (56)
186 PF07754 DUF1610: Domain of un 49.7 15 0.00032 19.0 1.6 22 117-142 3-24 (24)
187 PRK10220 hypothetical protein; 49.4 12 0.00027 27.0 1.7 28 111-145 4-31 (111)
188 TIGR02443 conserved hypothetic 49.3 20 0.00042 23.0 2.5 27 182-208 10-41 (59)
189 COG1594 RPB9 DNA-directed RNA 49.3 13 0.00028 27.3 1.9 31 110-144 2-32 (113)
190 KOG0826 Predicted E3 ubiquitin 49.1 15 0.00033 32.0 2.6 49 19-78 298-346 (357)
191 PF09526 DUF2387: Probable met 48.8 18 0.00039 24.1 2.4 26 183-208 10-40 (71)
192 PF03854 zf-P11: P-11 zinc fin 48.2 6.2 0.00013 24.0 0.1 44 22-81 3-47 (50)
193 COG5151 SSL1 RNA polymerase II 47.9 5.5 0.00012 34.3 -0.2 44 109-154 361-408 (421)
194 smart00336 BBOX B-Box-type zin 47.8 16 0.00034 20.9 1.8 26 132-157 13-38 (42)
195 KOG2906 RNA polymerase III sub 47.6 13 0.00028 26.3 1.6 29 111-143 2-30 (105)
196 KOG0823 Predicted E3 ubiquitin 47.2 5.6 0.00012 32.8 -0.3 17 203-219 64-80 (230)
197 PF14354 Lar_restr_allev: Rest 46.5 18 0.00039 22.9 2.1 13 180-192 2-14 (61)
198 TIGR00570 cdk7 CDK-activating 45.6 20 0.00043 31.2 2.8 54 111-195 4-57 (309)
199 COG1645 Uncharacterized Zn-fin 45.3 14 0.00029 27.9 1.5 24 111-142 29-52 (131)
200 TIGR01206 lysW lysine biosynth 44.5 21 0.00046 22.4 2.1 31 111-145 3-33 (54)
201 PLN02638 cellulose synthase A 44.2 21 0.00045 36.4 3.0 61 111-200 18-78 (1079)
202 COG3492 Uncharacterized protei 43.9 23 0.0005 24.7 2.3 17 46-62 42-58 (104)
203 KOG3579 Predicted E3 ubiquitin 43.5 23 0.00049 30.3 2.7 52 18-76 265-321 (352)
204 smart00834 CxxC_CXXC_SSSS Puta 43.0 19 0.00042 20.5 1.7 29 111-142 6-34 (41)
205 PF14445 Prok-RING_2: Prokaryo 43.0 4.9 0.00011 24.7 -0.9 37 19-56 5-41 (57)
206 PF05129 Elf1: Transcription e 42.9 18 0.00038 24.8 1.7 30 180-209 21-57 (81)
207 PF05605 zf-Di19: Drought indu 42.6 22 0.00048 22.0 2.0 39 21-78 2-40 (54)
208 PF02318 FYVE_2: FYVE-type zin 42.0 51 0.0011 24.2 4.2 36 109-151 53-88 (118)
209 TIGR01053 LSD1 zinc finger dom 41.9 27 0.0006 19.1 2.0 26 112-143 3-28 (31)
210 PRK13130 H/ACA RNA-protein com 41.3 43 0.00094 21.2 3.1 37 67-105 17-53 (56)
211 PLN02436 cellulose synthase A 41.1 27 0.00058 35.6 3.2 63 110-201 36-98 (1094)
212 PF07800 DUF1644: Protein of u 41.1 46 0.00099 25.9 3.8 90 21-126 2-123 (162)
213 PF09723 Zn-ribbon_8: Zinc rib 40.6 22 0.00047 20.9 1.6 28 112-142 7-34 (42)
214 TIGR00622 ssl1 transcription f 40.5 14 0.0003 27.0 0.9 43 111-155 56-102 (112)
215 TIGR00595 priA primosomal prot 40.2 22 0.00048 33.3 2.4 33 183-215 224-262 (505)
216 KOG2979 Protein involved in DN 40.1 32 0.00069 29.0 3.1 51 19-78 174-224 (262)
217 KOG1493 Anaphase-promoting com 39.6 6.9 0.00015 26.4 -0.7 52 23-81 22-82 (84)
218 PF14471 DUF4428: Domain of un 39.0 30 0.00065 21.4 2.1 30 23-55 1-30 (51)
219 PRK00415 rps27e 30S ribosomal 39.0 24 0.00052 22.6 1.7 30 111-145 12-41 (59)
220 PF08792 A2L_zn_ribbon: A2L zi 38.5 33 0.00071 19.1 2.0 28 110-143 3-30 (33)
221 PRK04023 DNA polymerase II lar 38.4 24 0.00052 35.6 2.4 32 180-217 625-662 (1121)
222 smart00659 RPOLCX RNA polymera 38.1 31 0.00066 20.6 2.0 13 180-192 18-30 (44)
223 PF10083 DUF2321: Uncharacteri 38.0 19 0.00041 27.9 1.3 38 180-217 38-79 (158)
224 PRK11827 hypothetical protein; 38.0 29 0.00062 22.3 2.0 29 180-208 7-36 (60)
225 PRK14714 DNA polymerase II lar 37.6 23 0.00051 36.6 2.2 30 182-217 668-703 (1337)
226 COG0266 Nei Formamidopyrimidin 37.3 24 0.00051 30.2 2.0 24 182-205 246-272 (273)
227 COG5220 TFB3 Cdk activating ki 35.7 39 0.00085 28.2 2.9 54 68-124 11-65 (314)
228 smart00154 ZnF_AN1 AN1-like Zi 35.0 28 0.00061 20.1 1.5 18 134-151 12-29 (39)
229 PLN02436 cellulose synthase A 34.8 37 0.0008 34.7 3.1 52 19-79 34-88 (1094)
230 smart00531 TFIIE Transcription 34.8 21 0.00045 27.4 1.2 33 108-142 97-131 (147)
231 smart00734 ZnF_Rad18 Rad18-lik 34.6 8.8 0.00019 20.1 -0.7 20 68-89 2-21 (26)
232 PRK14873 primosome assembly pr 34.5 29 0.00062 33.8 2.3 34 182-215 393-431 (665)
233 PF09788 Tmemb_55A: Transmembr 34.3 38 0.00083 28.5 2.7 38 107-144 120-167 (256)
234 smart00249 PHD PHD zinc finger 34.2 19 0.00042 20.7 0.7 34 23-57 1-34 (47)
235 PRK14811 formamidopyrimidine-D 34.2 28 0.00061 29.7 2.0 25 182-206 236-263 (269)
236 KOG0309 Conserved WD40 repeat- 34.1 39 0.00084 33.1 2.9 47 19-76 1026-1072(1081)
237 PLN02915 cellulose synthase A 34.0 46 0.001 33.9 3.6 43 132-198 32-74 (1044)
238 PF02891 zf-MIZ: MIZ/SP-RING z 33.7 29 0.00063 21.3 1.5 47 22-77 3-49 (50)
239 PF01667 Ribosomal_S27e: Ribos 33.6 31 0.00067 21.8 1.6 31 111-146 8-38 (55)
240 PF03604 DNA_RNApol_7kD: DNA d 33.4 30 0.00065 19.1 1.3 22 117-143 5-26 (32)
241 KOG2807 RNA polymerase II tran 32.8 21 0.00045 31.2 0.9 46 20-76 329-374 (378)
242 PF02748 PyrI_C: Aspartate car 32.8 39 0.00084 21.0 1.9 34 109-143 5-44 (52)
243 KOG1571 Predicted E3 ubiquitin 32.7 28 0.00061 30.8 1.7 45 18-79 302-346 (355)
244 PF08271 TF_Zn_Ribbon: TFIIB z 32.6 37 0.00081 19.9 1.8 26 112-142 2-27 (43)
245 PRK10445 endonuclease VIII; Pr 32.3 33 0.00072 29.2 2.1 24 182-205 236-262 (263)
246 PRK14810 formamidopyrimidine-D 31.9 33 0.00073 29.3 2.1 24 182-205 245-271 (272)
247 PF10426 zf-RAG1: Recombinatio 31.6 17 0.00036 19.8 0.1 15 67-81 2-16 (30)
248 PRK01103 formamidopyrimidine/5 31.6 35 0.00076 29.2 2.1 24 182-205 246-272 (274)
249 PF13913 zf-C2HC_2: zinc-finge 31.3 23 0.00051 18.2 0.6 10 135-144 3-12 (25)
250 COG0068 HypF Hydrogenase matur 31.1 29 0.00062 33.7 1.6 59 19-79 99-183 (750)
251 TIGR00373 conserved hypothetic 31.0 25 0.00054 27.4 1.1 30 108-142 107-136 (158)
252 PF09788 Tmemb_55A: Transmembr 30.7 2E+02 0.0042 24.4 6.2 33 182-214 124-173 (256)
253 TIGR03826 YvyF flagellar opero 30.5 54 0.0012 25.0 2.7 14 109-124 2-15 (137)
254 PRK12286 rpmF 50S ribosomal pr 30.4 45 0.00098 21.2 2.0 26 106-142 23-48 (57)
255 PRK05580 primosome assembly pr 30.3 38 0.00083 33.1 2.4 33 183-215 392-430 (679)
256 PHA02929 N1R/p28-like protein; 30.2 25 0.00053 29.5 0.9 41 179-219 172-215 (238)
257 PF13834 DUF4193: Domain of un 30.2 25 0.00054 25.0 0.8 35 15-51 64-98 (99)
258 TIGR00577 fpg formamidopyrimid 30.1 37 0.00079 29.0 2.0 23 182-204 246-271 (272)
259 PF10497 zf-4CXXC_R1: Zinc-fin 30.0 94 0.002 22.4 3.8 57 19-77 5-69 (105)
260 PLN02400 cellulose synthase 30.0 39 0.00085 34.5 2.4 61 111-200 37-97 (1085)
261 KOG4275 Predicted E3 ubiquitin 30.0 17 0.00037 31.2 -0.0 31 21-55 300-331 (350)
262 PRK06266 transcription initiat 29.7 28 0.0006 27.8 1.1 30 108-142 115-144 (178)
263 PRK09521 exosome complex RNA-b 29.4 40 0.00088 27.0 2.1 25 183-208 151-176 (189)
264 COG5109 Uncharacterized conser 29.3 47 0.001 28.9 2.4 55 19-81 334-388 (396)
265 KOG2164 Predicted E3 ubiquitin 29.0 46 0.00099 30.9 2.5 35 139-193 203-237 (513)
266 PRK13945 formamidopyrimidine-D 28.9 38 0.00082 29.1 1.9 24 182-205 255-281 (282)
267 COG3024 Uncharacterized protei 28.9 21 0.00046 23.1 0.3 14 180-193 6-19 (65)
268 PF04216 FdhE: Protein involve 28.8 30 0.00065 29.8 1.3 35 182-216 173-221 (290)
269 PF11023 DUF2614: Protein of u 28.4 38 0.00082 24.7 1.5 23 131-153 66-96 (114)
270 PRK03681 hypA hydrogenase nick 28.0 60 0.0013 23.8 2.6 27 109-142 69-95 (114)
271 TIGR03037 anthran_nbaC 3-hydro 28.0 26 0.00056 27.4 0.6 21 169-189 139-159 (159)
272 PRK13264 3-hydroxyanthranilate 28.0 25 0.00054 28.0 0.6 49 142-193 120-169 (177)
273 KOG2932 E3 ubiquitin ligase in 27.9 36 0.00079 29.5 1.6 32 21-55 90-121 (389)
274 PRK12495 hypothetical protein; 27.9 60 0.0013 26.7 2.7 29 180-217 41-69 (226)
275 COG2260 Predicted Zn-ribbon RN 27.7 1.2E+02 0.0025 19.4 3.4 35 69-105 19-53 (59)
276 KOG4684 Uncharacterized conser 27.7 49 0.0011 27.1 2.2 36 108-143 136-179 (275)
277 PF09680 Tiny_TM_bacill: Prote 27.3 68 0.0015 16.4 1.9 12 237-248 9-20 (24)
278 TIGR01732 tiny_TM_bacill conse 27.3 73 0.0016 16.7 2.0 14 236-249 10-23 (26)
279 COG1198 PriA Primosomal protei 27.1 47 0.001 32.7 2.3 35 111-151 445-484 (730)
280 PF01194 RNA_pol_N: RNA polyme 26.2 81 0.0018 20.3 2.6 14 66-81 3-16 (60)
281 PLN02915 cellulose synthase A 26.0 64 0.0014 32.9 3.1 55 17-80 11-68 (1044)
282 PF03833 PolC_DP2: DNA polymer 25.9 23 0.00049 35.1 0.0 34 180-219 654-693 (900)
283 PF10764 Gin: Inhibitor of sig 25.8 39 0.00084 20.4 1.0 35 23-62 1-35 (46)
284 PLN03086 PRLI-interacting fact 25.3 41 0.00089 31.9 1.6 29 180-208 432-463 (567)
285 PRK00241 nudC NADH pyrophospha 25.1 55 0.0012 27.7 2.2 28 180-207 98-126 (256)
286 TIGR01031 rpmF_bact ribosomal 25.1 60 0.0013 20.4 1.8 25 107-142 23-47 (55)
287 COG3677 Transposase and inacti 24.8 1.2E+02 0.0027 22.7 3.8 37 108-146 28-65 (129)
288 TIGR00100 hypA hydrogenase nic 24.7 78 0.0017 23.2 2.7 24 110-141 70-93 (115)
289 PF01214 CK_II_beta: Casein ki 24.7 1.1E+02 0.0025 24.4 3.8 35 108-142 97-135 (184)
290 COG2816 NPY1 NTP pyrophosphohy 24.7 1E+02 0.0022 26.5 3.7 30 108-143 109-138 (279)
291 PF06943 zf-LSD1: LSD1 zinc fi 24.1 97 0.0021 16.1 2.2 23 184-206 1-24 (25)
292 PLN02638 cellulose synthase A 24.1 80 0.0017 32.4 3.4 52 18-78 14-68 (1079)
293 KOG2114 Vacuolar assembly/sort 24.1 41 0.0009 33.3 1.4 43 19-77 838-880 (933)
294 PLN02189 cellulose synthase 23.8 60 0.0013 33.1 2.4 52 19-79 32-86 (1040)
295 PRK12380 hydrogenase nickel in 23.6 83 0.0018 23.0 2.6 24 110-141 70-93 (113)
296 PF09332 Mcm10: Mcm10 replicat 23.6 20 0.00043 31.8 -0.8 60 139-205 249-310 (344)
297 PF14787 zf-CCHC_5: GAG-polypr 23.3 53 0.0011 18.7 1.2 20 143-162 3-22 (36)
298 PF01927 Mut7-C: Mut7-C RNAse 23.2 1.4E+02 0.0031 22.7 4.0 36 89-126 67-105 (147)
299 PF01783 Ribosomal_L32p: Ribos 23.1 72 0.0016 20.0 1.9 25 107-142 23-47 (56)
300 PF08209 Sgf11: Sgf11 (transcr 23.1 45 0.00098 18.6 0.9 14 181-194 4-17 (33)
301 PRK05978 hypothetical protein; 22.9 46 0.001 25.7 1.2 33 180-219 32-65 (148)
302 COG3813 Uncharacterized protei 22.9 71 0.0015 21.3 1.9 59 23-98 7-67 (84)
303 PF10272 Tmpp129: Putative tra 22.9 78 0.0017 28.3 2.8 66 17-84 267-355 (358)
304 PRK03824 hypA hydrogenase nick 22.8 83 0.0018 23.8 2.6 15 109-125 69-83 (135)
305 TIGR00595 priA primosomal prot 22.8 66 0.0014 30.2 2.4 34 112-151 224-262 (505)
306 COG1096 Predicted RNA-binding 22.8 59 0.0013 26.1 1.8 24 182-207 150-174 (188)
307 PF14205 Cys_rich_KTR: Cystein 22.5 61 0.0013 20.4 1.4 32 110-143 4-37 (55)
308 PF00098 zf-CCHC: Zinc knuckle 22.4 58 0.0013 15.3 1.1 16 144-159 2-17 (18)
309 PRK00241 nudC NADH pyrophospha 22.3 1.4E+02 0.0031 25.2 4.2 31 108-144 97-127 (256)
310 PRK02935 hypothetical protein; 22.2 62 0.0013 23.3 1.6 23 131-153 67-97 (110)
311 COG1656 Uncharacterized conser 22.2 1E+02 0.0022 24.2 2.9 17 108-126 95-111 (165)
312 PF14369 zf-RING_3: zinc-finge 22.2 77 0.0017 17.8 1.7 29 111-144 3-31 (35)
313 PF03884 DUF329: Domain of unk 22.2 40 0.00086 21.5 0.6 12 182-193 3-14 (57)
314 PF08882 Acetone_carb_G: Aceto 22.2 42 0.00091 24.4 0.8 14 198-211 23-36 (112)
315 PF00096 zf-C2H2: Zinc finger, 21.8 38 0.00083 16.4 0.4 8 136-143 2-9 (23)
316 PLN02195 cellulose synthase A 21.7 87 0.0019 31.8 3.1 56 107-191 3-58 (977)
317 PF01530 zf-C2HC: Zinc finger, 21.5 53 0.0011 18.1 0.9 11 68-78 2-12 (31)
318 PF09151 DUF1936: Domain of un 21.4 45 0.00099 18.2 0.6 9 183-191 3-11 (36)
319 TIGR02605 CxxC_CxxC_SSSS putat 21.4 70 0.0015 19.4 1.6 28 112-142 7-34 (52)
320 PF13465 zf-H2C2_2: Zinc-finge 21.3 54 0.0012 16.8 0.9 13 132-144 12-24 (26)
321 PF03615 GCM: GCM motif protei 21.3 52 0.0011 24.8 1.1 23 179-207 80-106 (143)
322 PF11781 RRN7: RNA polymerase 20.8 82 0.0018 17.8 1.7 24 182-207 9-34 (36)
323 COG5183 SSM4 Protein involved 20.7 1.2E+02 0.0025 30.3 3.5 60 15-82 6-68 (1175)
324 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.5 64 0.0014 25.1 1.6 26 181-207 34-60 (166)
325 PF04981 NMD3: NMD3 family ; 20.4 62 0.0013 26.9 1.6 9 182-190 36-44 (236)
326 PHA02325 hypothetical protein 20.3 58 0.0013 21.1 1.0 12 180-191 2-13 (72)
327 PF01396 zf-C4_Topoisom: Topoi 20.1 58 0.0013 18.8 1.0 20 182-202 2-24 (39)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.3e-36 Score=263.88 Aligned_cols=198 Identities=30% Similarity=0.727 Sum_probs=168.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCChhhHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCD 98 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~ 98 (263)
....+|.||+.+....+.++....|+|.||.+|+++|++.+. .....++||..+|...++.+....+|++.+.++|..
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~--~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKL--LSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhh--ccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 357899999966555544444788999999999999999994 357889999999999999999999999999999999
Q ss_pred HHHHHhhcCCCcccCCccccccceecccccc-CCCCceeCCccccccccccccCCCCCCCchhHHhcccc--chHHHHHH
Q 024715 99 VLCEDYVLGFERSYCPNTNCMALVVNECERS-GKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQ--NDIVFGQL 175 (263)
Q Consensus 99 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~--~~~~~~~~ 175 (263)
.+.+.++...+.+|||+++|...+......+ .+.....|..|+..||.+|+.+||++.+|++++++... .+....+.
T Consensus 222 ~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~ 301 (384)
T KOG1812|consen 222 RLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKY 301 (384)
T ss_pred HHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHH
Confidence 9999999766666999999998887665321 23567789999999999999999999999999998754 33344444
Q ss_pred HhcCCcccCCCCCceeecCCCCceeEeecCCceecccCcccCCC
Q 024715 176 VERMKWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKISSG 219 (263)
Q Consensus 176 ~~~~~~k~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~ 219 (263)
+. ..||+||+|+..|++.+|||||+|+||++|||.|+..|..+
T Consensus 302 la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 302 LA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred HH-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhC
Confidence 44 78999999999999999999999999999999999998654
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-36 Score=257.00 Aligned_cols=198 Identities=26% Similarity=0.637 Sum_probs=165.8
Q ss_pred CCCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCChhhHHHH
Q 024715 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKW 96 (263)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 96 (263)
.....+.|.||+++......| ..++|+|.||+.|++.|++..++++....++||.++|+...+...++.+|+.+++++|
T Consensus 180 F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arY 258 (445)
T KOG1814|consen 180 FVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARY 258 (445)
T ss_pred HHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHH
Confidence 356789999999999654554 5799999999999999999999998899999999999999999999999999999999
Q ss_pred HHHHHHHhh-cCCCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHH--------hcccc
Q 024715 97 CDVLCEDYV-LGFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESR--------NLRDQ 167 (263)
Q Consensus 97 ~~~~~~~~~-~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~--------~~~~~ 167 (263)
++++.+..+ .+.+.+|||++.|..+...+++ ...+.|..|++.||+.|+..||++..|.--. +|.+.
T Consensus 259 e~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~----~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~ 334 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCPRACCQLPVKQDPG----RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEA 334 (445)
T ss_pred HHHHHHHHHHhhcccccCChhhccCccccCch----hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhc
Confidence 999999888 6788999999999999855555 6799999999999999999999998887421 11111
Q ss_pred chH------------HHHHH--------HhcCCcccCCCCCceeecCCCCceeEe-ecCCceecccCcccCCC
Q 024715 168 NDI------------VFGQL--------VERMKWARCPACGHCVERKDGCSVVMC-RCNTRFCYECGRKISSG 219 (263)
Q Consensus 168 ~~~------------~~~~~--------~~~~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~ 219 (263)
+.+ .+.++ ....+.|+||+|++.|+|++|||+|+| .|++.|||+|+.....+
T Consensus 335 d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~ 407 (445)
T KOG1814|consen 335 DEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPE 407 (445)
T ss_pred CHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCC
Confidence 000 00111 112355999999999999999999999 69999999999987755
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=9.1e-28 Score=217.51 Aligned_cols=193 Identities=24% Similarity=0.539 Sum_probs=162.2
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCCh-hhHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA-SLFSKWC 97 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~ 97 (263)
....+|.||++.... ....+.|+|.||..||..|+...|.++....|+||.++|.+.+....+..++++ +..++|.
T Consensus 68 ~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 456899999999954 224689999999999999999999976555599999999999999999999998 4899999
Q ss_pred HHHHHHhhcC-CCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHH-
Q 024715 98 DVLCEDYVLG-FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQL- 175 (263)
Q Consensus 98 ~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~- 175 (263)
+.+...++.. ....|||+|+|+..+..... ....+.|. |+..||+.|..+||.+.+|.....|..........+
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~~---~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~ 220 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGSL---ESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN 220 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccCC---CccceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh
Confidence 9999999965 44799999999998886421 26789995 777999999999999999999998876532222221
Q ss_pred HhcCCcccCCCCCceeecCCCCceeEe-e--cCCceecccCcccCC
Q 024715 176 VERMKWARCPACGHCVERKDGCSVVMC-R--CNTRFCYECGRKISS 218 (263)
Q Consensus 176 ~~~~~~k~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~ 218 (263)
....++++||+|.++|+|++|||||+| . |+++|||+|++.|..
T Consensus 221 wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~ 266 (444)
T KOG1815|consen 221 WILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSD 266 (444)
T ss_pred hhhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccc
Confidence 235678999999999999999999999 4 999999999888764
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=5.9e-27 Score=193.61 Aligned_cols=196 Identities=22% Similarity=0.553 Sum_probs=153.5
Q ss_pred cCCCCCccccccccccccccccccccCCCC--CccHHHHHHHHHHHHhhCCC-------CcccccCCCCCCC-ccCcccc
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCT--HPFCQDCIARYIQVKVQDDN-------TAKIDCPGLDCKH-NLDPFAC 84 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~-------~~~i~CP~~~C~~-~l~~~~i 84 (263)
...+..+.+|..|.+.-+.. + .++|. |..|.+|++.|..+.+.++. .+.+.||. +|.. .|..-..
T Consensus 215 i~~N~~ni~C~~Ctdv~~~v--l--vf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HH 289 (446)
T KOG0006|consen 215 IATNSRNITCITCTDVRSPV--L--VFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHH 289 (446)
T ss_pred hhcccccceeEEecCCccce--E--EEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhh
Confidence 34567889999999887432 2 36776 99999999999999997542 45688886 6664 4444456
Q ss_pred ccCCChhhHHHHHHHHHHHhhcCCCcccCCccccccceeccccccCCCCceeCCc-cccccccccccCCCCCCCchhHHh
Q 024715 85 EPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNECERSGKVKKTQCPN-CKQWFCFQCKLKWHAGYRCEESRN 163 (263)
Q Consensus 85 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~ 163 (263)
.++|..+.|++|+++..+.++...+.+.||+|+|+..+..++. ..+++|+. |++.||..|...||.+. |.+.-.
T Consensus 290 F~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD----~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~ 364 (446)
T KOG0006|consen 290 FRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD----QRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFE 364 (446)
T ss_pred heecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC----CCcccCCCCchhHhHHHHHhhhcccc-ceeeec
Confidence 7799999999999999999998888999999999999998886 68999996 99999999999999875 442111
Q ss_pred cc----------c--cchHHH---HHHHhcCCcccCCCCCceeecCCCCceeEe-e--cCCceecccCcccCCCC
Q 024715 164 LR----------D--QNDIVF---GQLVERMKWARCPACGHCVERKDGCSVVMC-R--CNTRFCYECGRKISSGC 220 (263)
Q Consensus 164 ~~----------~--~~~~~~---~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~ 220 (263)
.. + .+++.. .....+..+|+||+|.++.||+|||.||.| + ||.+|||.|+-.|+.-|
T Consensus 365 as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~C 439 (446)
T KOG0006|consen 365 ASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVC 439 (446)
T ss_pred cccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhh
Confidence 00 0 011111 112223467999999999999999999999 6 99999999999999755
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.20 E-value=2.5e-11 Score=80.46 Aligned_cols=63 Identities=33% Similarity=0.836 Sum_probs=53.9
Q ss_pred HHHHHHHHHHhhcC-CCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCc
Q 024715 94 SKWCDVLCEDYVLG-FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRC 158 (263)
Q Consensus 94 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 158 (263)
++|++++.+.+++. ++.+|||+++|..++...+. .....+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~--~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE--EGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC--CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47888999998854 68899999999999988641 12679999999999999999999999887
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=99.17 E-value=5.1e-12 Score=83.81 Aligned_cols=63 Identities=29% Similarity=0.755 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhhc-CCCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCc
Q 024715 94 SKWCDVLCEDYVL-GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRC 158 (263)
Q Consensus 94 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 158 (263)
++|++++.+.+++ ..+.++||+++|+.++...+... ...+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~--~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCN--SPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTT--S--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCC--CCeeECCCCCCcCccccCcccCCCCCC
Confidence 4677877787774 45678999999999999887732 124999999999999999999999876
No 7
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.64 E-value=4.4e-08 Score=77.74 Aligned_cols=70 Identities=26% Similarity=0.626 Sum_probs=51.7
Q ss_pred cCCCCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhh--------CCCCcccccCCCCCCCccCcccccc
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQ--------DDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~--------~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
..+..+.++|+||++.+.++ ..++|||.||..|+..|+...-. ........||. |+..++...+..
T Consensus 12 ~~~~~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvP 85 (193)
T PLN03208 12 LVDSGGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVP 85 (193)
T ss_pred eccCCCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEE
Confidence 33345679999999998655 24789999999999999764321 01234679999 999998877776
Q ss_pred CCCh
Q 024715 87 VIPA 90 (263)
Q Consensus 87 ~l~~ 90 (263)
+...
T Consensus 86 iygr 89 (193)
T PLN03208 86 IYGR 89 (193)
T ss_pred eecc
Confidence 6553
No 8
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.62 E-value=1.1e-08 Score=61.56 Aligned_cols=41 Identities=27% Similarity=0.772 Sum_probs=28.7
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
|+||++.+.++. .++|||+||..|+.+++...- ...+.||.
T Consensus 1 CpiC~~~~~~Pv----~l~CGH~FC~~Cl~~~~~~~~----~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDPV----SLPCGHSFCRSCLERLWKEPS----GSGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSEE----E-SSSSEEEHHHHHHHHCCSS----SST---SS
T ss_pred CCccchhhCCcc----ccCCcCHHHHHHHHHHHHccC----CcCCCCcC
Confidence 899999998774 489999999999999986432 22388987
No 9
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.55 E-value=4.1e-08 Score=59.04 Aligned_cols=43 Identities=28% Similarity=0.726 Sum_probs=24.8
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCP 71 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP 71 (263)
|+||.+ +...++....++|||+||++|+.+++.... ...++||
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 766556556789999999999999998543 3467887
No 10
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.54 E-value=1.6e-07 Score=61.93 Aligned_cols=42 Identities=29% Similarity=0.801 Sum_probs=38.0
Q ss_pred CCcccCC--CCCceeecCC--CCceeEe-ecCCceecccCcccCCCC
Q 024715 179 MKWARCP--ACGHCVERKD--GCSVVMC-RCNTRFCYECGRKISSGC 220 (263)
Q Consensus 179 ~~~k~CP--~C~~~i~k~~--GCnhm~C-~C~~~FC~~C~~~~~~~~ 220 (263)
..++.|| +|...|+..+ +..+|+| .|++.|||.|+..||.+.
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPV 62 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCC
Confidence 5788999 9999999975 9999999 799999999999998764
No 11
>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=98.49 E-value=1.1e-07 Score=57.01 Aligned_cols=40 Identities=33% Similarity=0.957 Sum_probs=33.3
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
|+||++.+..+. ..++|+|.||.+|+.+|++. ...++||.
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 799999996654 25999999999999999997 34567887
No 12
>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=98.44 E-value=7.6e-08 Score=63.54 Aligned_cols=42 Identities=38% Similarity=1.022 Sum_probs=31.1
Q ss_pred CCcccCCC--CCceeecCCCCce--eEee-cCCceecccCcccCCCC
Q 024715 179 MKWARCPA--CGHCVERKDGCSV--VMCR-CNTRFCYECGRKISSGC 220 (263)
Q Consensus 179 ~~~k~CP~--C~~~i~k~~GCnh--m~C~-C~~~FC~~C~~~~~~~~ 220 (263)
...+.||+ |...+.+..+.++ |+|. |++.|||.|+.+||.+.
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV 62 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence 35589988 9999999999999 9995 99999999999998763
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=98.43 E-value=1.5e-07 Score=55.69 Aligned_cols=38 Identities=32% Similarity=0.954 Sum_probs=29.3
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
|+||++.+.++. ..++|||.||.+|+.+|++. ..+||.
T Consensus 1 C~iC~~~~~~~~---~~~~CGH~fC~~C~~~~~~~--------~~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRDPV---VVTPCGHSFCKECIEKYLEK--------NPKCPV 38 (39)
T ss_dssp ETTTTSB-SSEE---EECTTSEEEEHHHHHHHHHC--------TSB-TT
T ss_pred CCCCCCcccCcC---EECCCCCchhHHHHHHHHHC--------cCCCcC
Confidence 899999986642 25999999999999999883 267886
No 14
>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=98.38 E-value=1e-07 Score=58.09 Aligned_cols=41 Identities=29% Similarity=0.754 Sum_probs=32.5
Q ss_pred ccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
+|+||++++.+.+.+. .++|+|.||.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~-~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVV-KLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEE-EETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeEE-EccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 6999999997655543 57799999999999999752 28987
No 15
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.33 E-value=3.9e-07 Score=70.67 Aligned_cols=57 Identities=21% Similarity=0.662 Sum_probs=44.9
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
..+.+.|+||++.+..... ....|||.||..|++..+. ...+||. |+..|+..++..
T Consensus 128 ~~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk--------~~~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALK--------NTNKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhhccc--cccccchhHHHHHHHHHHH--------hCCCCCC--cccccchhhhee
Confidence 3566999999999965433 4689999999999998886 3457999 888888766544
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.28 E-value=6.5e-07 Score=54.45 Aligned_cols=44 Identities=27% Similarity=0.868 Sum_probs=34.6
Q ss_pred ccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCC
Q 024715 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (263)
.|+||++.+.+... +.+++|||.||.+|+.... ...+.||. |+.
T Consensus 1 ~C~~C~~~~~~~~~-~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERR-PRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CRK 44 (44)
T ss_pred CCcCcCccccCCCC-eEEcccCCHHHHHHHHhhc--------CCCCCCcC--CCC
Confidence 48999999943333 3579999999999999888 34678998 763
No 17
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.14 E-value=1.6e-06 Score=54.29 Aligned_cols=46 Identities=30% Similarity=0.761 Sum_probs=36.2
Q ss_pred ccccccccccccccccccccCCCCCc-cHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
...|.||++...+. .+.+|+|. ||.+|+.+++. ...+||. |++.++
T Consensus 2 ~~~C~iC~~~~~~~----~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDV----VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSE----EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCce----EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 46899999987432 35899999 99999999998 3468999 998875
No 18
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.12 E-value=2.9e-06 Score=51.30 Aligned_cols=44 Identities=32% Similarity=0.856 Sum_probs=33.6
Q ss_pred ccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
+|+||++.+... + ...+|+|.||.+|+..|++. ....||. |+..
T Consensus 1 ~C~iC~~~~~~~--~-~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFREP--V-VLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhhCc--e-EecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 589999998322 1 24669999999999999874 3457998 8764
No 19
>PHA02926 zinc finger-like protein; Provisional
Probab=98.05 E-value=4.6e-06 Score=67.19 Aligned_cols=59 Identities=25% Similarity=0.592 Sum_probs=43.3
Q ss_pred CCCcccccccccccccc-----ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 18 GGSSFTCEICIEPMAAS-----KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~-----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
.++..+|+||+|..-.. ..|-.+.+|+|.||..|+..|...... ....-.||. |+..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE--TGASDNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc--cCcCCcCCC--Ccceee
Confidence 45678999999986321 234445789999999999999986532 234567999 997654
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=7.3e-06 Score=66.46 Aligned_cols=60 Identities=28% Similarity=0.725 Sum_probs=49.3
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVI 88 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l 88 (263)
+...++|.||+|.-.++. +..|||.||=.||.+|+..+... -.||. |+..++.+.+-.+.
T Consensus 44 ~~~~FdCNICLd~akdPV----vTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPV----VTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCCE----EeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeee
Confidence 577899999999987663 48899999999999999977643 45799 99998887765554
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.93 E-value=9.2e-06 Score=67.35 Aligned_cols=52 Identities=29% Similarity=0.670 Sum_probs=39.3
Q ss_pred CCccccccccccccccc----cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 19 GSSFTCEICIEPMAASK----KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
.+..+|+||++++.+.. .+..+.+|+|.||.+|+..|+.. ...||. |+..+.
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 45689999999875432 12245789999999999999752 247999 998765
No 22
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=8e-06 Score=70.64 Aligned_cols=109 Identities=22% Similarity=0.481 Sum_probs=69.9
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCChhhHHHHH
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWC 97 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 97 (263)
..+...|+||++.+..+ .+++|+|.||..|+...+. ..+.||. |.. ... .+...-.+....
T Consensus 10 ~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~ 70 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSR----NLRPNVLLANLV 70 (386)
T ss_pred ccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chh----ccCccHHHHHHH
Confidence 45789999999999777 3699999999999999998 4589999 884 222 222222333333
Q ss_pred HHHHHHhhcCC---CcccCCccccccceeccccccCCCCceeCCccccccccccc-cCCCCCCCc
Q 024715 98 DVLCEDYVLGF---ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCK-LKWHAGYRC 158 (263)
Q Consensus 98 ~~~~~~~~~~~---~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C 158 (263)
........... ....|+... ....+.|..|....|..|. ...|.++.-
T Consensus 71 ~~~~~~~~~~~~~~~~~~c~~~~-------------~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 71 ERLRQLRLSRPLGSKEELCEKHG-------------EELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred HHHHhcCCcccccccchhhhhcC-------------CcceEEecccccccCCCCCCcccccCCcc
Confidence 33222211100 011233111 0257889999999999998 667777653
No 23
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=8.3e-06 Score=73.20 Aligned_cols=60 Identities=30% Similarity=0.676 Sum_probs=48.6
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCC
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIP 89 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 89 (263)
...|+||+++..-+ ..+.|||.||-.||.+||.... ...+..||. |...|...++..+.-
T Consensus 186 ~~~CPICL~~~~~p----~~t~CGHiFC~~CiLqy~~~s~---~~~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVP----VRTNCGHIFCGPCILQYWNYSA---IKGPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCcc----cccccCceeeHHHHHHHHhhhc---ccCCccCCc--hhhhccccceeeeee
Confidence 78999999998544 3467999999999999999883 245678999 999998877766543
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=97.80 E-value=2.9e-05 Score=50.85 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=40.9
Q ss_pred cccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc
Q 024715 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
+.|+||.+.+.++ ..++|||.||+.|+.+|+.. ...||. |+..++.+++..
T Consensus 2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhcee
Confidence 5799999999765 24789999999999999974 247999 888886655443
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=1.9e-05 Score=65.98 Aligned_cols=52 Identities=27% Similarity=0.754 Sum_probs=42.9
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
.....|.+|+|...++ +.++|||.||-.|+..|....- .||. |...+.+..+
T Consensus 237 ~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 3458999999998666 3699999999999999997443 3999 9999888665
No 26
>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=97.79 E-value=2.4e-05 Score=45.41 Aligned_cols=38 Identities=32% Similarity=0.903 Sum_probs=28.5
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
|+||++..... ..++|+|.||.+|+..|+. .....||.
T Consensus 1 C~iC~~~~~~~----~~~~C~H~~c~~C~~~~~~-------~~~~~CP~ 38 (39)
T smart00184 1 CPICLEELKDP----VVLPCGHTFCRSCIRKWLK-------SGNNTCPI 38 (39)
T ss_pred CCcCccCCCCc----EEecCCChHHHHHHHHHHH-------hCcCCCCC
Confidence 78999884322 3588999999999999987 12356876
No 27
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.64 E-value=3.6e-05 Score=64.70 Aligned_cols=54 Identities=20% Similarity=0.656 Sum_probs=45.8
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
.....+|.||++.|...+.+ ..++|.|.|...|+.+|+. .+..+||. |+.++++
T Consensus 320 a~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 45568999999999777665 4799999999999999997 56788999 9988765
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.58 E-value=0.0001 Score=65.61 Aligned_cols=67 Identities=21% Similarity=0.533 Sum_probs=48.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccc-cCCChhhHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACE-PVIPASLFSKWC 97 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~ 97 (263)
...+.|+||.+.+..+. .++|+|.||..|+..|+.. ...||. |+..+....++ ..+-.++++.|.
T Consensus 24 e~~l~C~IC~d~~~~Pv----itpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPV----LTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred ccccCCCcCchhhhCcc----CCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHHH
Confidence 45689999999996552 4899999999999999862 137999 99987765443 233345666666
Q ss_pred HH
Q 024715 98 DV 99 (263)
Q Consensus 98 ~~ 99 (263)
.+
T Consensus 90 ~~ 91 (397)
T TIGR00599 90 NL 91 (397)
T ss_pred Hh
Confidence 43
No 29
>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=97.52 E-value=0.00023 Score=60.96 Aligned_cols=53 Identities=23% Similarity=0.541 Sum_probs=37.5
Q ss_pred cccccccccccc-cc-cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 22 FTCEICIEPMAA-SK-KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 22 ~~C~IC~~~~~~-~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
..|++|..+.-. +. .+.+ .+|||.||..|+...+. ..+..||. |+..+....+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i-~~CGH~~C~sCv~~l~~-------~~~~~CP~--C~~~lrk~~f 58 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMV-NVCGHTLCESCVDLLFV-------RGSGSCPE--CDTPLRKNNF 58 (309)
T ss_pred CCCCcCCCCCccCccccccc-CCCCCcccHHHHHHHhc-------CCCCCCCC--CCCccchhhc
Confidence 579999985322 22 2222 37999999999999984 23458998 9987766543
No 30
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.46 E-value=4.8e-05 Score=64.85 Aligned_cols=66 Identities=23% Similarity=0.498 Sum_probs=50.2
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc-CCChhhHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP-VIPASLFSKWC 97 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~ 97 (263)
+....|.||++.|..+ .+.+|+|.||.-|++.|+. +...||. |..++...+++. .+-+++++.|.
T Consensus 21 D~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~--------~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLS--------YKPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhc--------cCCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 5678999999999644 3588999999999999996 5567999 999888877664 22335555554
Q ss_pred H
Q 024715 98 D 98 (263)
Q Consensus 98 ~ 98 (263)
-
T Consensus 87 ~ 87 (442)
T KOG0287|consen 87 F 87 (442)
T ss_pred H
Confidence 3
No 31
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=9.4e-05 Score=64.32 Aligned_cols=50 Identities=30% Similarity=0.747 Sum_probs=41.5
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
+..+|.||+|++...+.++ .++|.|.|...|+..|+... .-.||. |+..+
T Consensus 228 ~~~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di 277 (348)
T KOG4628|consen 228 ATDTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDI 277 (348)
T ss_pred CCceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-------CccCCC--CCCcC
Confidence 3479999999998888775 59999999999999999844 235999 88743
No 32
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.35 E-value=0.00017 Score=46.17 Aligned_cols=50 Identities=32% Similarity=0.709 Sum_probs=33.9
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (263)
..-.+.|+|-...+.++.. ...|+|.|-++-+..|+. ....+.||..||+
T Consensus 8 ~~~~~~CPiT~~~~~~PV~---s~~C~H~fek~aI~~~i~------~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVK---SKKCGHTFEKEAILQYIQ------RNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSEEE---ESSS--EEEHHHHHHHCT------TTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCCcC---cCCCCCeecHHHHHHHHH------hcCCCCCCCCCCC
Confidence 5567899999999977643 578999999999999992 4678999999985
No 33
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.17 E-value=0.0004 Score=62.67 Aligned_cols=66 Identities=24% Similarity=0.640 Sum_probs=50.9
Q ss_pred cCCCCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCC
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIP 89 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 89 (263)
..++.+...|.+|-++-.+. ....|.|.||+-|++.|+.....+ ..++||. |...++.+.-+..+.
T Consensus 530 ~~enk~~~~C~lc~d~aed~----i~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP~--C~i~LsiDlse~ale 595 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDY----IESSCHHKFCRLCIKEYVESFMEN---NNVTCPV--CHIGLSIDLSEPALE 595 (791)
T ss_pred CccccCceeecccCChhhhh----HhhhhhHHHHHHHHHHHHHhhhcc---cCCCCcc--ccccccccccchhhh
Confidence 34456789999999887543 248899999999999999988865 3399999 998877665444444
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=96.95 E-value=0.00057 Score=46.22 Aligned_cols=45 Identities=29% Similarity=0.643 Sum_probs=31.1
Q ss_pred cccccccccccccc---------cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCC
Q 024715 22 FTCEICIEPMAASK---------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (263)
Q Consensus 22 ~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (263)
-.|.||++++.+.. ..+....|+|.|...||.+|++.+ -.||. |+
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~--CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL--CR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT--SS
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC--CC
Confidence 34999999994331 122346799999999999999521 28998 64
No 35
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.00045 Score=65.15 Aligned_cols=56 Identities=18% Similarity=0.585 Sum_probs=45.0
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPV 87 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~ 87 (263)
.+...|++|.+-..+ . .+..|+|.||.+|++..+.+.-+ +||. |+..|...++..+
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 KELLKCSVCNTRWKD--A--VITKCGHVFCEECVQTRYETRQR-------KCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCchhh--H--HHHhcchHHHHHHHHHHHHHhcC-------CCCC--CCCCCCccccccc
Confidence 456899999965533 2 25889999999999999986553 6999 9999999888764
No 36
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.00085 Score=55.64 Aligned_cols=52 Identities=23% Similarity=0.561 Sum_probs=39.7
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
.+.|.||++....+ ...+|||.||..|+...++. ...-.||. |.+...+..+
T Consensus 215 d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~------~k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTK------KKYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCc----ccccccchhhHHHHHHHHHh------hccccCch--hhhhccchhh
Confidence 56699999988554 35899999999999996542 22345999 9988777655
No 37
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.92 E-value=0.00045 Score=46.32 Aligned_cols=59 Identities=15% Similarity=0.351 Sum_probs=28.7
Q ss_pred ccccccccccccccccc--ccc--CCCCCccHHHHHHHHHHHHhhCCCCc-c--cccCCCCCCCccCc
Q 024715 21 SFTCEICIEPMAASKKF--KNR--NLCTHPFCQDCIARYIQVKVQDDNTA-K--IDCPGLDCKHNLDP 81 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~--~~~--~~C~H~fC~~Cl~~~~~~~i~~~~~~-~--i~CP~~~C~~~l~~ 81 (263)
..+|.||++...+.... ... ..|+..|...||.+|+...-+.+... + -+||. |+.+|..
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 46899999987522221 112 36889999999999998877653322 2 37999 9988754
No 38
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.65 E-value=0.0012 Score=58.45 Aligned_cols=81 Identities=17% Similarity=0.430 Sum_probs=46.9
Q ss_pred CCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCceeecCCCCce-eEe-ecCCcee
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGCSV-VMC-RCNTRFC 209 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GCnh-m~C-~C~~~FC 209 (263)
...+.|..|...+|.-|+..-|++..=-.-.++...++-.+.....-...-+|- -.+|=|| |+| .|+.-.|
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct-------~h~~e~~smyc~~ck~pvc 246 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCT-------DHELENHSMYCVQCKMPVC 246 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhcc-------CCCCCCceEEEEecCChHH
Confidence 467999999999999999999986432111111111111110000001112222 1234455 999 7999999
Q ss_pred cccCcccCCC
Q 024715 210 YECGRKISSG 219 (263)
Q Consensus 210 ~~C~~~~~~~ 219 (263)
|.|++...+.
T Consensus 247 ~~clee~khs 256 (699)
T KOG4367|consen 247 YQCLEEGKHS 256 (699)
T ss_pred HHHHHhhccc
Confidence 9999986544
No 39
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.26 E-value=0.0039 Score=42.15 Aligned_cols=52 Identities=19% Similarity=0.212 Sum_probs=38.1
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
+.+.|+|+.+-+.++. .+++||+|.+.++..|+.. ....||. ++..++..++
T Consensus 3 ~~f~CpIt~~lM~dPV----i~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMRDPV----ILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-SSEE----EETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHhhCce----eCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 4689999999998774 3788999999999999973 4567998 7888877544
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.11 E-value=0.00079 Score=43.59 Aligned_cols=50 Identities=26% Similarity=0.574 Sum_probs=23.8
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
+...|++|.+.+..+.. +..|.|.||..|+...+. -.||. |..+--..++
T Consensus 6 ~lLrCs~C~~~l~~pv~---l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~ 55 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVC---LGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDI 55 (65)
T ss_dssp HTTS-SSS-S--SS-B------SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS-
T ss_pred HhcCCcHHHHHhcCCce---eccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHH
Confidence 45789999999865533 578999999999976332 24999 9876544443
No 41
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.09 E-value=0.004 Score=52.34 Aligned_cols=66 Identities=21% Similarity=0.421 Sum_probs=46.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc-CCChhhHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP-VIPASLFSKWC 97 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~ 97 (263)
+....|.||-+.+..+ ...+|||.||.-|++.|+. ....||. |....-...++. .+..++.+.|.
T Consensus 23 Ds~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~--------~qp~CP~--Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 23 DSMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLG--------TQPFCPV--CREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hhHHHhhhhhheeecc----eecccccchhHHHHHHHhc--------CCCCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence 5567899999998544 3589999999999999985 4456999 987655544332 33445555554
Q ss_pred H
Q 024715 98 D 98 (263)
Q Consensus 98 ~ 98 (263)
.
T Consensus 89 ~ 89 (391)
T COG5432 89 R 89 (391)
T ss_pred h
Confidence 4
No 42
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.09 E-value=0.0058 Score=37.38 Aligned_cols=47 Identities=23% Similarity=0.601 Sum_probs=22.8
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
|++|.++++..+.-+..-+|+..+|+.|+.+..+ ...=+||. |+.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~-------~~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE-------NEGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT-------SS-SB-TT--T--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh-------ccCCCCCC--CCCCC
Confidence 7899999855443223467899999999988775 12346998 88754
No 43
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.97 E-value=0.0063 Score=51.80 Aligned_cols=93 Identities=19% Similarity=0.520 Sum_probs=59.2
Q ss_pred CCCCccHHHHHHHHHHHHhhCC--CCcccccCCCCCCCccCccccccCCChhhHHHHHHHHHHHhhcCCCcccCCccccc
Q 024715 42 LCTHPFCQDCIARYIQVKVQDD--NTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCM 119 (263)
Q Consensus 42 ~C~H~fC~~Cl~~~~~~~i~~~--~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~ 119 (263)
.|+-.||++|+..|-.-.-... .... ..|...++.+. ....+|+.+..+- + ....+.|| +|.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t-----~tc~y~vde~~-------a~~arwd~as~~T-I-k~tTkpCP--kCh 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGT-----TTCAYRVDERA-------AEQARWDAASKET-I-KKTTKPCP--KCH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccc-----cceeeecChhh-------hhhhhhhhhhhhh-h-hhccCCCC--Ccc
Confidence 4899999999998865222110 0001 11333333321 3446777664332 2 24557788 898
Q ss_pred cceeccccccCCCCceeCCc--cccccccccccCCCC
Q 024715 120 ALVVNECERSGKVKKTQCPN--CKQWFCFQCKLKWHA 154 (263)
Q Consensus 120 ~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 154 (263)
........ ...+.|+. |+..||+.|+.+|..
T Consensus 405 vptErnGG----CmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 405 VPTERNGG----CMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred CccccCCc----eEEeecCCCCCCceeEeccCChhhh
Confidence 87766655 78899976 999999999999954
No 44
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.81 E-value=0.0056 Score=52.48 Aligned_cols=53 Identities=25% Similarity=0.640 Sum_probs=42.8
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (263)
-...++|.+|--.+.+... +..|-|+||+.||.+|++. ...||. |+..+....
T Consensus 12 ~n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih~t~ 64 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIHKTH 64 (331)
T ss_pred cccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHH--------hccCCc--cceeccCcc
Confidence 3567899999999977754 4789999999999999995 347999 987665543
No 45
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.014 Score=50.81 Aligned_cols=54 Identities=24% Similarity=0.540 Sum_probs=40.0
Q ss_pred CCCccccccccccccccc---------cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASK---------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
......|.||+|+.-.++ .-+.-++|||.+...|++.|++.+ -+||. |+.++-.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~if 346 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVIF 346 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCcccc
Confidence 355679999999943433 112358999999999999999833 37999 9987543
No 46
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.33 E-value=0.017 Score=50.98 Aligned_cols=114 Identities=20% Similarity=0.477 Sum_probs=70.6
Q ss_pred CCcccccc--ccccc-cc-cccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCC-----C
Q 024715 19 GSSFTCEI--CIEPM-AA-SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVI-----P 89 (263)
Q Consensus 19 ~~~~~C~I--C~~~~-~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l-----~ 89 (263)
+....||- |..+. .+ ...+.....|.-+||..|...|-- + .+ |+.+... .++-.+ +
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG--~-------s~-----Ck~~~~~-~~~l~~~~~~~d 335 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG--V-------SP-----CKVKAEK-LIELYLEYLEAD 335 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC--C-------Cc-----ccCchHH-HHHHHHHHhhcC
Confidence 34567776 55442 11 223334566889999999998864 1 12 5544321 111111 1
Q ss_pred ----hhhHHHHHHHHHHHhhc--------CCCcccCCccccccceeccccccCCCCceeCCccccccccccccCCC
Q 024715 90 ----ASLFSKWCDVLCEDYVL--------GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWH 153 (263)
Q Consensus 90 ----~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H 153 (263)
.++..+|-+.+.+..+. ..+...|| .|...+...++ .+++.|..|++.||+.|....-
T Consensus 336 ~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG----CnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 336 EARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG----CNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC----ccceeeccccccceeehhhhcC
Confidence 12344555333332221 35678999 89999988776 7999999999999999998654
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.06 E-value=0.019 Score=50.32 Aligned_cols=95 Identities=20% Similarity=0.412 Sum_probs=58.5
Q ss_pred CCCccccccccccccccc----cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc---cc---cccC
Q 024715 18 GGSSFTCEICIEPMAASK----KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP---FA---CEPV 87 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~---~~---i~~~ 87 (263)
..+...|.||++...... .|-++.+|.|.||..|++.|-...-. +....-.||. |...... .. ...-
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~ 234 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCccccccccceeeeecc
Confidence 466889999999986543 13344679999999999999754433 2455678999 8754322 11 1111
Q ss_pred CChhhHHHHHHHHHHHhh--cCCCcccCCc
Q 024715 88 IPASLFSKWCDVLCEDYV--LGFERSYCPN 115 (263)
Q Consensus 88 l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~ 115 (263)
-...+.+.|.+.+..... -....-.||.
T Consensus 235 ~k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 235 EKQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred cccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 223456677766544322 2245567886
No 48
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.23 E-value=0.037 Score=46.96 Aligned_cols=52 Identities=25% Similarity=0.520 Sum_probs=40.7
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (263)
...-+|.||+.+-..+ +.+.|+|.||.-|++.-+. .....|+. |..+|+...
T Consensus 5 ~~~~eC~IC~nt~n~P----v~l~C~HkFCyiCiKGsy~-------ndk~~Cav--CR~pids~i 56 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP----VNLYCFHKFCYICIKGSYK-------NDKKTCAV--CRFPIDSTI 56 (324)
T ss_pred ccCCcceeeeccCCcC----ccccccchhhhhhhcchhh-------cCCCCCce--ecCCCCcch
Confidence 4567899999988555 3599999999999998776 33455999 998877653
No 49
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.22 E-value=0.02 Score=30.29 Aligned_cols=23 Identities=35% Similarity=0.941 Sum_probs=14.9
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCce
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
|.||.|+..|... -..| .||+.|
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 5788888887532 2456 377665
No 50
>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=93.99 E-value=0.077 Score=32.76 Aligned_cols=42 Identities=21% Similarity=0.499 Sum_probs=29.5
Q ss_pred ccccccccccccccccccCCCC-----CccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 23 TCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
.|-||++...+.+.+ ..+|. |.+..+||.+|+...- ...||.
T Consensus 1 ~CrIC~~~~~~~~~l--~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPL--VSPCRCKGSLKYVHQECLERWINESG------NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCee--EeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence 488999844334444 36774 7899999999998554 247887
No 51
>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=93.71 E-value=0.021 Score=46.82 Aligned_cols=53 Identities=23% Similarity=0.505 Sum_probs=38.0
Q ss_pred Ccccccccccccc-ccccccccCC-CCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 20 SSFTCEICIEPMA-ASKKFKNRNL-CTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 20 ~~~~C~IC~~~~~-~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
..--|+||..+.- .++..+-+.+ |-|.+|.+|+.+.++ ..|-.||.++|+..|
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHHH
Confidence 3457999975543 3333222234 999999999999986 667889999998643
No 52
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.66 E-value=0.12 Score=44.75 Aligned_cols=51 Identities=29% Similarity=0.688 Sum_probs=40.5
Q ss_pred Ccccccccccccccc--ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 20 SSFTCEICIEPMAAS--KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
....|.||-++++.. +..+..+.|||.+|..|+...+. ...+.||. |..+.
T Consensus 2 ~~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-------~~~i~cpf--cR~~~ 54 (296)
T KOG4185|consen 2 SFPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-------NSRILCPF--CRETT 54 (296)
T ss_pred CCCceeecCccccccCcccCCcccccCceehHhHHHHHhc-------CceeeccC--CCCcc
Confidence 357899999999765 33445688999999999999886 56677888 98874
No 53
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.64 E-value=0.051 Score=49.11 Aligned_cols=54 Identities=28% Similarity=0.695 Sum_probs=40.8
Q ss_pred CCcccccccccccccccc----c---------cccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 19 GSSFTCEICIEPMAASKK----F---------KNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~----~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
.....|.||+.+++.-.. . ....+|.|.|...||.+|+. ...+.||. |..++++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd-------~ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD-------TYKLICPV--CRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 456799999988853211 0 13469999999999999997 56688999 9887754
No 54
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.58 E-value=0.036 Score=53.19 Aligned_cols=56 Identities=21% Similarity=0.594 Sum_probs=46.4
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (263)
....++|.||++.+.....+++..+|-|.|...|+++|..+.-++ ....-+||. |.
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~-~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKT-GQDGWRCPA--CQ 243 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhc-cCccccCCc--cc
Confidence 467899999999998888888788899999999999999983333 456678987 66
No 55
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.56 E-value=0.076 Score=36.66 Aligned_cols=54 Identities=26% Similarity=0.606 Sum_probs=37.1
Q ss_pred cccccccccccccc--cc-c------cccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 21 SFTCEICIEPMAAS--KK-F------KNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 21 ~~~C~IC~~~~~~~--~~-~------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
.-.|.||...|+.. +- + .....|+|.|...|+.+|++++-. .-.||. |.+++..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWKF 83 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeeee
Confidence 45688887777521 00 1 023579999999999999997522 237999 9987654
No 56
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.50 E-value=0.046 Score=51.49 Aligned_cols=51 Identities=25% Similarity=0.619 Sum_probs=38.7
Q ss_pred CCCcccccccccccccccc-ccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 18 GGSSFTCEICIEPMAASKK-FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
......|.||.|+...... -...++|+|.|+..|++.|++. .-.||. |...
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~--CR~~ 339 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPT--CRTV 339 (543)
T ss_pred hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCc--chhh
Confidence 3457899999999966321 0135899999999999999996 236998 7763
No 57
>PF04641 Rtf2: Rtf2 RING-finger
Probab=93.13 E-value=0.2 Score=42.55 Aligned_cols=72 Identities=17% Similarity=0.357 Sum_probs=54.6
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCCh-hhHHHH
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA-SLFSKW 96 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~ 96 (263)
....+.|||-..++.....|..+.+|||+|....++..- .+ -.||. |+.++...+|-.+-+. +.++..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l 178 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNPPEEELEKL 178 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecCCccHHHHH
Confidence 467899999999997666777788999999999999882 11 24999 9999998887776654 344444
Q ss_pred HHHH
Q 024715 97 CDVL 100 (263)
Q Consensus 97 ~~~~ 100 (263)
.+.+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4443
No 58
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=93.11 E-value=0.17 Score=43.05 Aligned_cols=49 Identities=29% Similarity=0.526 Sum_probs=39.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (263)
.....|+||.+.+.........++|+|..-..|++.+.. .. .+||. |..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~-------~~-y~CP~--C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC-------EG-YTCPI--CSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc-------cC-CCCCc--ccc
Confidence 344559999999877766666799999999999999986 23 88999 988
No 59
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.97 E-value=0.07 Score=44.01 Aligned_cols=59 Identities=10% Similarity=0.241 Sum_probs=47.7
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPV 87 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~ 87 (263)
+..+.|+||-+.+.+......+.+|||.+|.+|..+++. ..+.||. |+.++.+++|-.+
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir--------~D~v~pv--~d~plkdrdiI~L 277 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR--------KDMVDPV--TDKPLKDRDIIGL 277 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc--------ccccccC--CCCcCcccceEee
Confidence 478999999999977665556788999999999999986 3456788 8898888776543
No 60
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.57 E-value=0.03 Score=46.74 Aligned_cols=57 Identities=26% Similarity=0.459 Sum_probs=43.9
Q ss_pred CCccccccccccccccc-------cccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 19 GSSFTCEICIEPMAASK-------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
.+...|.||-..+.... +. ..++|+|.|...|++.|.. -...-+||- |++.++...+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvient-y~LsCnHvFHEfCIrGWci------vGKkqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENT-YKLSCNHVFHEFCIRGWCI------VGKKQTCPY--CKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhh-eeeecccchHHHhhhhhee------ecCCCCCch--HHHHhhHhhh
Confidence 45678999988876543 22 3589999999999999987 345568999 9998876543
No 61
>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=92.48 E-value=0.24 Score=41.92 Aligned_cols=51 Identities=24% Similarity=0.518 Sum_probs=36.3
Q ss_pred cccccccc-ccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcc
Q 024715 23 TCEICIEP-MAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (263)
Q Consensus 23 ~C~IC~~~-~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (263)
.|++|-.+ +..++.+..+.+|+|..|.+|+...+. ..+-.||. |..++-..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cpe--C~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCPE--CMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCCc--ccchhhhc
Confidence 48888543 334444444568999999999999886 55667996 99876443
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.44 E-value=0.079 Score=42.24 Aligned_cols=46 Identities=28% Similarity=0.608 Sum_probs=34.0
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
.-.+.|.||-+++..+. ...|||.||..|...-+. ....|-. |+..
T Consensus 194 ~IPF~C~iCKkdy~spv----vt~CGH~FC~~Cai~~y~--------kg~~C~~--Cgk~ 239 (259)
T COG5152 194 KIPFLCGICKKDYESPV----VTECGHSFCSLCAIRKYQ--------KGDECGV--CGKA 239 (259)
T ss_pred CCceeehhchhhccchh----hhhcchhHHHHHHHHHhc--------cCCccee--cchh
Confidence 44689999999996652 489999999999876554 2345665 6654
No 63
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.35 E-value=0.13 Score=43.12 Aligned_cols=52 Identities=33% Similarity=0.654 Sum_probs=39.0
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
.....+|++|-+.=..+ + ....|+|.||--|+..-... ...++||. |+....
T Consensus 236 ~t~~~~C~~Cg~~PtiP--~-~~~~C~HiyCY~Ci~ts~~~------~asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP--H-VIGKCGHIYCYYCIATSRLW------DASFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCC--e-eeccccceeehhhhhhhhcc------hhhcccCc--cCCCCc
Confidence 35568999999875333 2 25779999999999987762 34579999 997655
No 64
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=92.07 E-value=0.062 Score=48.07 Aligned_cols=52 Identities=29% Similarity=0.600 Sum_probs=40.3
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
-.+.-+|+||+|-.++....+....|.|+|--.|+..|+. ..||. |.....+
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~~q~p 223 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRYCQSP 223 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhhhcCc
Confidence 3577899999999976655544577999999999998875 56888 7765443
No 65
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.07 E-value=0.19 Score=43.46 Aligned_cols=58 Identities=28% Similarity=0.508 Sum_probs=41.6
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
+.-.|++|+|+++-.+.-+...+||-.+|+-||...-+ .++ =+||. |....+++-++-
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq-~ln------grcpa--crr~y~denv~~ 70 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQ-NLN------GRCPA--CRRKYDDENVRY 70 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHh-hcc------CCChH--hhhhccccceeE
Confidence 34449999999965544333578999999999975433 343 37999 999888776653
No 66
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.92 E-value=0.16 Score=45.66 Aligned_cols=50 Identities=28% Similarity=0.756 Sum_probs=38.1
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
....+.|.||+..+.++. .++|||.||..|+.+ .+. ....||. |...+..
T Consensus 81 ~~sef~c~vc~~~l~~pv----~tpcghs~c~~Cl~r----~ld----~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYPPV----VTPCGHSFCLECLDR----SLD----QETECPL--CRDELVE 130 (398)
T ss_pred ccchhhhhhhHhhcCCCc----cccccccccHHHHHH----Hhc----cCCCCcc--ccccccc
Confidence 367899999999986653 479999999999777 222 3456888 8877653
No 67
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.84 E-value=0.38 Score=40.05 Aligned_cols=63 Identities=19% Similarity=0.406 Sum_probs=45.9
Q ss_pred CCCCCccccccccccccccccccccCCCC-----CccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 16 GGGGSSFTCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
.++...-.|-||+..-.+...--=.-+|. |.....||..|+..+-..+...++.||. |..+..
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTEYi 82 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTEYI 82 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcchhe
Confidence 34456679999998775543210124553 6799999999999888766678999999 986543
No 68
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.79 E-value=0.13 Score=45.25 Aligned_cols=53 Identities=23% Similarity=0.600 Sum_probs=38.0
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
...|.||-+-++....+-.+..|||.|...|+..|++..-.. -.||. |.-.+.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ik~~ 56 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQIKLQ 56 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eeeccc
Confidence 468999966665555555556699999999999999844432 36888 774333
No 69
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.74 E-value=0.098 Score=46.29 Aligned_cols=56 Identities=23% Similarity=0.573 Sum_probs=42.4
Q ss_pred cccccccccccccc-ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 21 SFTCEICIEPMAAS-KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 21 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
..+|+||++.+.-+ +....++.|+|.|=.+|+++|+- ......||. |+.+-..+++
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~katkr~i 60 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGKATKRQI 60 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCChhHHHHH
Confidence 57899999988644 33335688999999999999993 246688999 9876544443
No 70
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.40 E-value=0.16 Score=45.70 Aligned_cols=42 Identities=21% Similarity=0.641 Sum_probs=35.0
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCC
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGY 156 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~ 156 (263)
...+.|| .|...+....+ .+.++|. |+..||+.|...|..+.
T Consensus 304 ~~wr~Cp--kC~~~ie~~~G----Cnhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELSEG----CNHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCc--ccceeeeecCC----cceEEee-ccccchhhcCcchhhCC
Confidence 5568899 89998866655 7899998 99999999999986543
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.06 E-value=0.078 Score=43.75 Aligned_cols=56 Identities=23% Similarity=0.556 Sum_probs=38.4
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCCh
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA 90 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 90 (263)
-+.|..|+.--+ ...|+ ++.|.|.||..|.+.-. +-.||. |+..+....+..-|+.
T Consensus 3 ~VhCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~~----------~~~C~l--Ckk~ir~i~l~~slp~ 58 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFF-LTACRHVFCEPCLKASS----------PDVCPL--CKKSIRIIQLNRSLPT 58 (233)
T ss_pred eEEeccccccCC-CCcee-eeechhhhhhhhcccCC----------cccccc--ccceeeeeecccccch
Confidence 457888886664 55664 78999999999986432 228999 9987655444444443
No 72
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.99 E-value=0.036 Score=48.09 Aligned_cols=49 Identities=29% Similarity=0.809 Sum_probs=36.0
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
...+.|+||++-+... + +...|.|.||.+|+..-+.. ..-.||. |+..+
T Consensus 41 ~~~v~c~icl~llk~t--m-ttkeClhrfc~~ci~~a~r~-------gn~ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLKKT--M-TTKECLHRFCFDCIWKALRS-------GNNECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHHh-------cCCCCch--HHhhc
Confidence 4568999999988533 2 34679999999999887762 2335888 87543
No 73
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.98 E-value=0.12 Score=32.22 Aligned_cols=47 Identities=30% Similarity=0.540 Sum_probs=35.3
Q ss_pred ccccccccccccccccccccCCCCCc-cHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
..+|.||+|.-.++ .+-.|||. +|-+|-.+.++. ..-.||. |.+++.
T Consensus 7 ~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~-------~~g~CPi--CRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKA-------LHGCCPI--CRAPIK 54 (62)
T ss_pred ccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHc-------cCCcCcc--hhhHHH
Confidence 37899999876444 24689996 899999888873 3346998 888763
No 74
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.97 E-value=0.24 Score=43.27 Aligned_cols=49 Identities=22% Similarity=0.577 Sum_probs=37.0
Q ss_pred CCCccccccccccccccccccccCCCCCc-cHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
+.+..+|.||+++-.+. .+++|.|. .|.+|.+..-- ..=.||. |++.+.
T Consensus 287 ~~~gkeCVIClse~rdt----~vLPCRHLCLCs~Ca~~Lr~--------q~n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESRDT----VVLPCRHLCLCSGCAKSLRY--------QTNNCPI--CRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCcce----EEecchhhehhHhHHHHHHH--------hhcCCCc--cccchH
Confidence 35678999999987543 35999996 99999887651 1235999 998764
No 75
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.94 E-value=0.21 Score=31.01 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=20.1
Q ss_pred ccCCCCCceeecCCC--CceeEe-ecCCce
Q 024715 182 ARCPACGHCVERKDG--CSVVMC-RCNTRF 208 (263)
Q Consensus 182 k~CP~C~~~i~k~~G--Cnhm~C-~C~~~F 208 (263)
+-||.|+.++...++ -++..| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 369999998876643 468889 599764
No 76
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.88 E-value=0.17 Score=29.20 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=24.0
Q ss_pred ccCCccccccceeccccc-cCCCCceeCCcccccc
Q 024715 111 SYCPNTNCMALVVNECER-SGKVKKTQCPNCKQWF 144 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 144 (263)
+.|| .|+..+...+.. ......++|+.|+..|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 5799 799988877652 1236799999998765
No 77
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.52 E-value=0.15 Score=26.95 Aligned_cols=12 Identities=33% Similarity=0.946 Sum_probs=8.7
Q ss_pred ccCCCCCceeec
Q 024715 182 ARCPACGHCVER 193 (263)
Q Consensus 182 k~CP~C~~~i~k 193 (263)
+.||+|+..+..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 578888886654
No 78
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.44 E-value=0.15 Score=26.13 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=8.1
Q ss_pred cCCCCCceeec
Q 024715 183 RCPACGHCVER 193 (263)
Q Consensus 183 ~CP~C~~~i~k 193 (263)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 47888888864
No 79
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=90.30 E-value=0.49 Score=42.72 Aligned_cols=51 Identities=24% Similarity=0.702 Sum_probs=39.2
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
-.+...|++|...+.++.. ...|+|.||..|+..+.+. ...||. |...+..
T Consensus 18 ~~~~l~C~~C~~vl~~p~~---~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~~~ 68 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQ---TTTCGHRFCAGCLLESLSN--------HQKCPV--CRQELTQ 68 (391)
T ss_pred CcccccCccccccccCCCC---CCCCCCcccccccchhhcc--------CcCCcc--cccccch
Confidence 4677999999999976632 2589999999999999874 456887 6554433
No 80
>PHA03096 p28-like protein; Provisional
Probab=90.19 E-value=0.2 Score=43.03 Aligned_cols=54 Identities=20% Similarity=0.354 Sum_probs=36.8
Q ss_pred ccccccccccccc---ccccc-cCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 22 FTCEICIEPMAAS---KKFKN-RNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 22 ~~C~IC~~~~~~~---~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
..|.||++..... +.++. +..|.|.||..|++.|....... ...-.||. |...+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~--e~~~~c~~--~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYK--ETEPENRR--LNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhc--ccCccccc--hhhHH
Confidence 7899999887532 33333 45699999999999999987643 33334444 54443
No 81
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.14 E-value=0.22 Score=45.72 Aligned_cols=40 Identities=33% Similarity=0.769 Sum_probs=34.7
Q ss_pred cccCC--CCCceeec-CCCCceeEeecCCceecccCcccCCCC
Q 024715 181 WARCP--ACGHCVER-KDGCSVVMCRCNTRFCYECGRKISSGC 220 (263)
Q Consensus 181 ~k~CP--~C~~~i~k-~~GCnhm~C~C~~~FC~~C~~~~~~~~ 220 (263)
.+-|| .|+..+.- .+...-+.|.|++.|||.|+.+||.+.
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~ 200 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPV 200 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCC
Confidence 46666 69999887 788999999999999999999999875
No 82
>PHA00626 hypothetical protein
Probab=90.00 E-value=0.24 Score=31.07 Aligned_cols=27 Identities=22% Similarity=0.669 Sum_probs=19.9
Q ss_pred cCCCCCc-eeecCCCCce----eEe-ecCCcee
Q 024715 183 RCPACGH-CVERKDGCSV----VMC-RCNTRFC 209 (263)
Q Consensus 183 ~CP~C~~-~i~k~~GCnh----m~C-~C~~~FC 209 (263)
.||+|+. -|.|.+-|+. ..| .||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5999999 4878777654 668 4887773
No 83
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.64 E-value=0.28 Score=28.11 Aligned_cols=32 Identities=34% Similarity=0.675 Sum_probs=23.6
Q ss_pred ccCCccccccceeccccc-cCCCCceeCCcccccc
Q 024715 111 SYCPNTNCMALVVNECER-SGKVKKTQCPNCKQWF 144 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 144 (263)
+.|| .|+..+..++.. ......++|+.|+..|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 5788 799888776652 2336789999998765
No 84
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=88.61 E-value=0.19 Score=37.73 Aligned_cols=38 Identities=21% Similarity=0.523 Sum_probs=28.3
Q ss_pred CCccccccccccccccccccccCCCC------CccHHHHHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCT------HPFCQDCIARYIQ 57 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~~ 57 (263)
....+|.||++.+...+.++ ..+|+ |.||.+|+++|-.
T Consensus 24 ~~~~EC~IC~~~I~~~~GvV-~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 24 RCTVECQICFDRIDNNDGVV-YVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred ccCeeehhhhhhhhcCCCEE-EEecCCeehHHHHHHHHHHHHHHh
Confidence 45789999999997723332 35564 7899999999943
No 85
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=88.27 E-value=0.34 Score=41.25 Aligned_cols=65 Identities=23% Similarity=0.498 Sum_probs=48.4
Q ss_pred cCCCCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhC---------------CCCcccccCCCCCCCcc
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD---------------DNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~---------------~~~~~i~CP~~~C~~~l 79 (263)
..++.+...|.||+--|.+.+.| +...|.|+|...||.+|++..+.+ .....-.||. |...|
T Consensus 109 T~nn~p~gqCvICLygfa~~~~f-t~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i 185 (368)
T KOG4445|consen 109 TENNHPNGQCVICLYGFASSPAF-TVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERI 185 (368)
T ss_pred ccCCCCCCceEEEEEeecCCCce-eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhc
Confidence 44567889999999999877766 468999999999999999876531 0122335999 98766
Q ss_pred Ccc
Q 024715 80 DPF 82 (263)
Q Consensus 80 ~~~ 82 (263)
.++
T Consensus 186 ~~e 188 (368)
T KOG4445|consen 186 KIE 188 (368)
T ss_pred ccc
Confidence 543
No 86
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=87.91 E-value=0.26 Score=43.59 Aligned_cols=48 Identities=25% Similarity=0.610 Sum_probs=35.2
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
+...-|.||-|.-.+. .+.+|||..|..||..|-.+. ..-.||. |..+
T Consensus 367 sTFeLCKICaendKdv----kIEPCGHLlCt~CLa~WQ~sd------~gq~CPF--CRcE 414 (563)
T KOG1785|consen 367 STFELCKICAENDKDV----KIEPCGHLLCTSCLAAWQDSD------EGQTCPF--CRCE 414 (563)
T ss_pred chHHHHHHhhccCCCc----ccccccchHHHHHHHhhcccC------CCCCCCc--eeeE
Confidence 4556799999876443 358999999999999986422 2347999 7643
No 87
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.58 E-value=0.56 Score=28.37 Aligned_cols=29 Identities=31% Similarity=0.670 Sum_probs=19.1
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCceec
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRFCY 210 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~FC~ 210 (263)
-+||+|+..++.+..=..++| .||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 368888887766654446777 47776543
No 88
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=87.35 E-value=0.44 Score=29.52 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=19.2
Q ss_pred cccCCCCCc-eeecCCCCceeEe-ecCCce
Q 024715 181 WARCPACGH-CVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 181 ~k~CP~C~~-~i~k~~GCnhm~C-~C~~~F 208 (263)
.+.||+|+. ...... +.++| +||+.+
T Consensus 20 ~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 468999998 444434 68999 699865
No 89
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=86.96 E-value=0.35 Score=30.36 Aligned_cols=48 Identities=19% Similarity=0.369 Sum_probs=33.0
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccc
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (263)
..+.|..|...-... ..++|+|.+|..||-.. ..-.||. |+..++..+
T Consensus 6 ~~~~~~~~~~~~~~~----~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKG----TVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFDD 53 (55)
T ss_pred cceeEEEcccccccc----ccccccceeeccccChh----------hccCCCC--CCCcccCCC
Confidence 445666666554222 35999999999998632 2235999 999887654
No 90
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.78 E-value=0.66 Score=41.13 Aligned_cols=60 Identities=18% Similarity=0.370 Sum_probs=42.4
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
-+.|.|||=-+.-. .++-+..+.|||.++++=+.+..+ ++...++||. |...-...+.++
T Consensus 332 HSvF~CPVlKeqts-deNPPm~L~CGHVISkdAlnrLS~-----ng~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTS-DENPPMMLICGHVISKDALNRLSK-----NGSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhcc-CCCCCeeeeccceecHHHHHHHhh-----CCCeeeeCCC--CCcccCHHhccc
Confidence 46789999765553 223334699999999998877665 3445799999 987766655544
No 91
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=86.66 E-value=0.67 Score=47.67 Aligned_cols=185 Identities=19% Similarity=0.386 Sum_probs=99.0
Q ss_pred CCCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCC--CcccccCCCCCCCccCccccccCCChhhHH
Q 024715 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDN--TAKIDCPGLDCKHNLDPFACEPVIPASLFS 94 (263)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~ 94 (263)
.++..--|.||+.+-...... .-+.|+|.|...|.+..++.+-.... ..-|.||. |..+|+.-.++.+|++ +.+
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP-iKe 3557 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP-IKE 3557 (3738)
T ss_pred hcccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH-HHH
Confidence 345567899999776443222 24899999999999999987765422 23589999 9999988888888874 223
Q ss_pred HHHHHHHHHhh--c-----CCCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCC-CCchhHHhccc
Q 024715 95 KWCDVLCEDYV--L-----GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAG-YRCEESRNLRD 166 (263)
Q Consensus 95 ~~~~~~~~~~~--~-----~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~-~~C~~~~~~~~ 166 (263)
-|++...++.. + ....+.=|. .-+..++. +.... .=-++.|.+|++.|-+| ..|+.... .+
T Consensus 3558 l~edV~~KA~MRLEYeGL~ks~AiT~P~----~~FYNdPa--~YAmn----RY~Y~vC~KCrKAYFGGEaRCdAe~~-~d 3626 (3738)
T KOG1428|consen 3558 LYEDVRRKALMRLEYEGLHKSEAITTPG----VRFYNDPA--GYAMN----RYAYYVCYKCRKAYFGGEARCDAEAG-GD 3626 (3738)
T ss_pred HHHHHHHHHhhhhhhccccccccccCCC----ceeccChh--hhhhh----hhhhhhhhhhhhhhcCchhhcchhcC-CC
Confidence 33332222211 1 122233331 11111111 00000 11356778888887665 45876544 22
Q ss_pred cch--HHHHHHHh-cCCcccCCCCCceee--cCCCCce---eEeecCCceecccCccc
Q 024715 167 QND--IVFGQLVE-RMKWARCPACGHCVE--RKDGCSV---VMCRCNTRFCYECGRKI 216 (263)
Q Consensus 167 ~~~--~~~~~~~~-~~~~k~CP~C~~~i~--k~~GCnh---m~C~C~~~FC~~C~~~~ 216 (263)
+.+ +++-.... ......||+-+.-.- |-.=|-. ..|-=-+|||-.|-..+
T Consensus 3627 dydP~ELiCG~CSDvS~aQmCPkHGtdfLEYKCRyCCSvAVfFCFGTTHFCn~CHDDF 3684 (3738)
T KOG1428|consen 3627 DYDPRELICGACSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDF 3684 (3738)
T ss_pred CCCHHHhhhccccccccceecccccchhhhhhhheeeeEeEEEEcccccccchhhhHH
Confidence 212 11111111 234577888766432 1111111 12222478888887764
No 92
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.59 E-value=0.94 Score=42.59 Aligned_cols=59 Identities=20% Similarity=0.446 Sum_probs=37.5
Q ss_pred CcccccCCCCCCCccCccccccCCChhhHHHHHHHHHHHhhcCCCcccCCccccccceeccccccCCCCceeCCcccccc
Q 024715 65 TAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 65 ~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
...+.||+ |+..++...+...+. .=....+.||+.+|+..+..... ...+.|+.|+..|
T Consensus 405 ~~~V~C~N--C~~~i~l~~l~lHe~---------------~C~r~~V~Cp~~~Cg~v~~r~el----~~H~~C~~Cgk~f 463 (567)
T PLN03086 405 VDTVECRN--CKHYIPSRSIALHEA---------------YCSRHNVVCPHDGCGIVLRVEEA----KNHVHCEKCGQAF 463 (567)
T ss_pred CCeEECCC--CCCccchhHHHHHHh---------------hCCCcceeCCcccccceeecccc----ccCccCCCCCCcc
Confidence 45678988 888776533221100 00134577997779998876655 4667899888766
No 93
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=86.53 E-value=0.79 Score=39.68 Aligned_cols=47 Identities=21% Similarity=0.636 Sum_probs=33.8
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
....++|+||++.+..+ .|. .+=||..|.+|-.+ ..-+||. |..++.
T Consensus 45 ~~~lleCPvC~~~l~~P-i~Q--C~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP-IFQ--CDNGHLACSSCRTK-----------VSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCccc-cee--cCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence 46678999999999654 321 33389999999862 2346887 887776
No 94
>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=86.49 E-value=0.22 Score=30.96 Aligned_cols=39 Identities=26% Similarity=0.702 Sum_probs=19.0
Q ss_pred ccccceeccccccCCCCceeCCccccccccccccCCCCC
Q 024715 117 NCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAG 155 (263)
Q Consensus 117 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~ 155 (263)
.|...+.............+|+.|+..||..|-.-.|..
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 455555443321112468999999999999998877754
No 95
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.98 E-value=0.67 Score=40.30 Aligned_cols=67 Identities=21% Similarity=0.587 Sum_probs=43.4
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCChhhHHHH
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKW 96 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 96 (263)
+.+...|.||.+... +...++|+|.+|.-|-.+.-.. ...-.||. |+.....-.+..-.+.++-+++
T Consensus 58 DEen~~C~ICA~~~T----Ys~~~PC~H~~CH~Ca~RlRAL------Y~~K~C~~--CrTE~e~V~fT~~~~~DI~D~~ 124 (493)
T COG5236 58 DEENMNCQICAGSTT----YSARYPCGHQICHACAVRLRAL------YMQKGCPL--CRTETEAVVFTASSPADITDRR 124 (493)
T ss_pred ccccceeEEecCCce----EEEeccCCchHHHHHHHHHHHH------HhccCCCc--cccccceEEEecCCCCcchhHh
Confidence 456789999998873 4456999999999998765432 23346888 8876544433333333333333
No 96
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=85.15 E-value=0.59 Score=44.97 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=21.3
Q ss_pred CccccccccccccccccccccC---CCCCccHHHHHHHHHHHHhh
Q 024715 20 SSFTCEICIEPMAASKKFKNRN---LCTHPFCQDCIARYIQVKVQ 61 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~---~C~H~fC~~Cl~~~~~~~i~ 61 (263)
+..+|.+|..++.+.+.-+..+ .|+|.+|..||..|....+.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 3445555555554422111122 26666666666666665554
No 97
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=85.03 E-value=0.66 Score=28.33 Aligned_cols=26 Identities=31% Similarity=0.557 Sum_probs=19.5
Q ss_pred cccCCCCCceeecCCCCceeEe-ecCC
Q 024715 181 WARCPACGHCVERKDGCSVVMC-RCNT 206 (263)
Q Consensus 181 ~k~CP~C~~~i~k~~GCnhm~C-~C~~ 206 (263)
-+.||+|+.-+.....=+...| +||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 4789999976665555557889 7886
No 98
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.77 E-value=0.64 Score=26.25 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=15.9
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
.+|| .|+..+...-...+...+.+|+.|+..
T Consensus 1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 4788 798887654332233689999999864
No 99
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=84.47 E-value=0.51 Score=28.00 Aligned_cols=26 Identities=31% Similarity=0.822 Sum_probs=19.6
Q ss_pred CCcccCCCCCceeecCCCCceeEee---cCCce
Q 024715 179 MKWARCPACGHCVERKDGCSVVMCR---CNTRF 208 (263)
Q Consensus 179 ~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~F 208 (263)
.+.|+||+|+..- |..-+.|+ |++.|
T Consensus 9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hccccCCcCcCcc----CcccccccCCccchhh
Confidence 4679999999876 66667773 76655
No 100
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=84.38 E-value=0.76 Score=32.40 Aligned_cols=29 Identities=34% Similarity=0.890 Sum_probs=22.2
Q ss_pred cCCCCCcee--ecCCCCceeEee-cCCceecc
Q 024715 183 RCPACGHCV--ERKDGCSVVMCR-CNTRFCYE 211 (263)
Q Consensus 183 ~CP~C~~~i--~k~~GCnhm~C~-C~~~FC~~ 211 (263)
-||.|+..+ ++.+.||...|+ |.|.|=-.
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 599999855 445559999995 99987543
No 101
>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=83.23 E-value=0.9 Score=26.10 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=21.7
Q ss_pred ccCCccccccceecccccc-CCCCceeCCcccccc
Q 024715 111 SYCPNTNCMALVVNECERS-GKVKKTQCPNCKQWF 144 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~ 144 (263)
+.|| .|+..+...+... .....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5688 7998777665422 123479999998754
No 102
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.47 E-value=0.73 Score=45.33 Aligned_cols=54 Identities=19% Similarity=0.569 Sum_probs=38.6
Q ss_pred Cccccccccccccccc-ccc--ccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 20 SSFTCEICIEPMAASK-KFK--NRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~-~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
..-+|.||+......+ .++ ....|.|.|...|+-+|+.+ ...-+||. |+..++.
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~S------s~~s~CPl--CRseitf 1524 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFAS------SARSNCPL--CRSEITF 1524 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHh------cCCCCCCc--ccccccc
Confidence 4468999998774211 111 23568999999999999984 44457999 9977653
No 103
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.22 E-value=0.91 Score=39.64 Aligned_cols=50 Identities=22% Similarity=0.393 Sum_probs=35.9
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
+++...|+||+-.-.. . ...+|+|.-|.+|+.+++-+ .-.|-. |+..+..
T Consensus 419 ~sEd~lCpICyA~pi~--A--vf~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPIN--A--VFAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVID 468 (489)
T ss_pred CcccccCcceecccch--h--hccCCCCchHHHHHHHHHhc--------CCeeeE--ecceeee
Confidence 4677899999965422 2 24899999999999999862 234666 7766543
No 104
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.21 E-value=0.51 Score=40.16 Aligned_cols=45 Identities=27% Similarity=0.560 Sum_probs=34.9
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
.+-|.||-.+|..+. ...|+|+||..|....+. ..-+|+. |++..
T Consensus 241 Pf~c~icr~~f~~pV----vt~c~h~fc~~ca~~~~q--------k~~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPV----VTKCGHYFCEVCALKPYQ--------KGEKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccccch----hhcCCceeehhhhccccc--------cCCccee--ccccc
Confidence 467999999996652 489999999999877664 2346777 88654
No 105
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=81.98 E-value=0.59 Score=41.33 Aligned_cols=53 Identities=21% Similarity=0.563 Sum_probs=40.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
.....|..|-+.+.....-...++|.|.|...|+..|++ ...+-.||. |+...
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~------~n~~rsCP~--Crklr 415 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE------NNGTRSCPN--CRKLR 415 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH------hCCCCCCcc--HHHHH
Confidence 345789999988865444335799999999999999995 355668998 88543
No 106
>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=81.12 E-value=2 Score=23.70 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=15.7
Q ss_pred cccCCCCCceeecCCCCceeEe-ecCCc
Q 024715 181 WARCPACGHCVERKDGCSVVMC-RCNTR 207 (263)
Q Consensus 181 ~k~CP~C~~~i~k~~GCnhm~C-~C~~~ 207 (263)
.+-||.|+.+.....+=--+.| .|+..
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4678888888888877677888 57764
No 107
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=80.90 E-value=1.4 Score=27.18 Aligned_cols=28 Identities=18% Similarity=0.662 Sum_probs=19.4
Q ss_pred cCCccccccceeccccccCCCCceeCCccccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
+|| .|+..+....... ...+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~~--~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKE--KRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCC--CCEEECCcCCCe
Confidence 688 8999776664421 247889988854
No 108
>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=80.77 E-value=1.2 Score=27.17 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=20.5
Q ss_pred cccCCccccccceeccccccCCCCceeCCcccc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
...||++.|+..+..+.. ..+..|..|+.
T Consensus 18 rk~CP~~~CG~GvFMA~H----~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEH----KDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-----SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeec----CCCccCCCccc
Confidence 578999999987665555 45788888775
No 109
>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=80.73 E-value=0.9 Score=33.06 Aligned_cols=27 Identities=30% Similarity=0.818 Sum_probs=20.3
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCcee
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRFC 209 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~FC 209 (263)
|.||+||....-..- +-++| .||+.|=
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCccC
Confidence 679999987765544 77888 5888763
No 110
>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=78.36 E-value=1.3 Score=25.12 Aligned_cols=28 Identities=25% Similarity=0.731 Sum_probs=18.8
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
++|| .|++.+....... ..+.|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~---~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKE---KRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETT---TTEEESSSS-E
T ss_pred eeCC--CCCccceEcCCCc---cCcCCCCCCCc
Confidence 5788 8999998877643 23378877754
No 111
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=77.91 E-value=2.8 Score=28.32 Aligned_cols=44 Identities=23% Similarity=0.429 Sum_probs=17.3
Q ss_pred CCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCceeecCCCCce
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGCSV 199 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GCnh 199 (263)
...+.|..|++..|..| .++ -.+.+.+.||.|+.+..+.-|+..
T Consensus 26 e~FVAC~eC~fPvCr~C----------yEY--------------Erkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 26 EVFVACHECAFPVCRPC----------YEY--------------ERKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SB--S-SSS-----HHH----------HHH--------------HHHTS-SB-TTT--B----TT---
T ss_pred CEEEEEcccCCccchhH----------HHH--------------HhhcCcccccccCCCcccccCCCC
Confidence 57889999999888754 333 234577899999999988777643
No 112
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=77.89 E-value=1.3 Score=43.30 Aligned_cols=42 Identities=26% Similarity=0.546 Sum_probs=33.0
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD 62 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 62 (263)
.+.-+|.+|...+. ...| ...+|||.|..+|+.+........
T Consensus 815 ep~d~C~~C~~~ll-~~pF-~vf~CgH~FH~~Cl~~~v~~~~~~ 856 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLL-IKPF-YVFPCGHCFHRDCLIRHVLSLLSE 856 (911)
T ss_pred cCccchHHhcchhh-cCcc-eeeeccchHHHHHHHHHHHccccH
Confidence 35568999999984 4445 368999999999999988766653
No 113
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=76.66 E-value=1.3 Score=27.04 Aligned_cols=33 Identities=24% Similarity=0.648 Sum_probs=22.3
Q ss_pred cccccccccccccccccCCCC--C---ccHHHHHHHHHHH
Q 024715 24 CEICIEPMAASKKFKNRNLCT--H---PFCQDCIARYIQV 58 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~ 58 (263)
|-||+++......++ .+|. - .+..+||.+|+..
T Consensus 1 CrIC~~~~~~~~~li--~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLI--SPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE---SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCcee--cccccCCCcchhHHHHHHHHHHh
Confidence 678998876554343 5553 3 6889999999997
No 114
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=75.99 E-value=0.57 Score=40.47 Aligned_cols=30 Identities=30% Similarity=0.935 Sum_probs=23.8
Q ss_pred CCcccCCCCCceeecC-CCCceeEe-ecCCce
Q 024715 179 MKWARCPACGHCVERK-DGCSVVMC-RCNTRF 208 (263)
Q Consensus 179 ~~~k~CP~C~~~i~k~-~GCnhm~C-~C~~~F 208 (263)
..|.+||+|+..+.+. -.=|...| +|++||
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3599999999988654 44567899 699998
No 115
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.76 E-value=4.6 Score=31.87 Aligned_cols=62 Identities=19% Similarity=0.460 Sum_probs=41.4
Q ss_pred CCCcccccccccccccc---ccccccCCCCCccHHHHHHHHHHHHhhCCCCccc---ccCCCCCCCccCc
Q 024715 18 GGSSFTCEICIEPMAAS---KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKI---DCPGLDCKHNLDP 81 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i---~CP~~~C~~~l~~ 81 (263)
+++...|.||+-.-.+. +..-.-..|+..|..-||..|++.-+..+..+.| .||. |+.++..
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 45567788887544332 1111135699999999999999987765433333 7998 9988764
No 116
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=75.43 E-value=4.2 Score=30.53 Aligned_cols=53 Identities=28% Similarity=0.604 Sum_probs=40.1
Q ss_pred CCccccccccccccccccccccC-CCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRN-LCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
....+|.||-|...+. .|...- -||=.+|..|....|+..- ....||. |+..+
T Consensus 78 ~~lYeCnIC~etS~ee-~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSAEE-RFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSF 131 (140)
T ss_pred CCceeccCcccccchh-hcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--ccccc
Confidence 4788999999998544 443333 3899999999999998654 4568999 98654
No 117
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=74.95 E-value=2.5 Score=37.91 Aligned_cols=69 Identities=19% Similarity=0.422 Sum_probs=37.1
Q ss_pred CCceeCCccc----cccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCceee-cCCC--C----cee
Q 024715 132 VKKTQCPNCK----QWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVE-RKDG--C----SVV 200 (263)
Q Consensus 132 ~~~~~C~~C~----~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~-k~~G--C----nhm 200 (263)
.+.+.|-.+- .--|..|..++-....+++..+.... |..+ -.+--+|-.|+..+. +.+| | ||+
T Consensus 380 ~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvam-dr~f-----Hv~CY~CEDCg~~LS~e~e~qgCyPld~Hl 453 (468)
T KOG1701|consen 380 QNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAM-DRDF-----HVNCYKCEDCGLLLSSEEEGQGCYPLDGHL 453 (468)
T ss_pred CCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEc-cccc-----cccceehhhcCccccccCCCCcceeccCce
Confidence 5678886553 22377777776554444432221110 0000 112346778888886 4433 4 888
Q ss_pred Eee-cCC
Q 024715 201 MCR-CNT 206 (263)
Q Consensus 201 ~C~-C~~ 206 (263)
.|+ |+.
T Consensus 454 lCk~Ch~ 460 (468)
T KOG1701|consen 454 LCKTCHL 460 (468)
T ss_pred eechhhh
Confidence 884 864
No 118
>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=74.45 E-value=0.39 Score=30.83 Aligned_cols=27 Identities=26% Similarity=0.823 Sum_probs=19.6
Q ss_pred ccCCCCCceeecCCCCceeEeecCCceec-ccCcccCCC
Q 024715 182 ARCPACGHCVERKDGCSVVMCRCNTRFCY-ECGRKISSG 219 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C~C~~~FC~-~C~~~~~~~ 219 (263)
|-||.||.+|.. ...||. .|++.|...
T Consensus 4 kHC~~CG~~Ip~-----------~~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 4 KHCPVCGKPIPP-----------DESFCSPKCREEYRKR 31 (59)
T ss_pred CcCCcCCCcCCc-----------chhhhCHHHHHHHHHH
Confidence 679999999874 257884 788777643
No 119
>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=73.79 E-value=2.9 Score=24.69 Aligned_cols=22 Identities=45% Similarity=1.173 Sum_probs=16.4
Q ss_pred ccCCCCCceeec-CCCCceeEe-ecC
Q 024715 182 ARCPACGHCVER-KDGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k-~~GCnhm~C-~C~ 205 (263)
..||.|+.++.+ ..| .++| .|+
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 689999999988 455 4666 453
No 120
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=73.51 E-value=2.2 Score=41.09 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=7.8
Q ss_pred CceecccCcc
Q 024715 206 TRFCYECGRK 215 (263)
Q Consensus 206 ~~FC~~C~~~ 215 (263)
..||-.||.+
T Consensus 41 ~~fC~~CG~~ 50 (645)
T PRK14559 41 EAHCPNCGAE 50 (645)
T ss_pred cccccccCCc
Confidence 4588888887
No 121
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=73.35 E-value=6.7 Score=30.48 Aligned_cols=54 Identities=17% Similarity=0.354 Sum_probs=37.8
Q ss_pred CCccccccccccccccccccccCCCCC---ccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTH---PFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (263)
.....|-||.++.. ... ....|.. ...++|+++|+.. .....|+. |+.++....
T Consensus 6 ~~~~~CRIC~~~~~-~~~--~PC~CkGs~k~VH~sCL~rWi~~------s~~~~Cei--C~~~Y~i~~ 62 (162)
T PHA02825 6 LMDKCCWICKDEYD-VVT--NYCNCKNENKIVHKECLEEWINT------SKNKSCKI--CNGPYNIKK 62 (162)
T ss_pred CCCCeeEecCCCCC-Ccc--CCcccCCCchHHHHHHHHHHHhc------CCCCcccc--cCCeEEEEE
Confidence 45678999998863 221 2233444 5799999999983 35678999 998776553
No 122
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=72.85 E-value=0.7 Score=39.84 Aligned_cols=30 Identities=20% Similarity=0.554 Sum_probs=22.8
Q ss_pred CcccCCCCCceeecC-CCCceeEe-ecCCcee
Q 024715 180 KWARCPACGHCVERK-DGCSVVMC-RCNTRFC 209 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~-~GCnhm~C-~C~~~FC 209 (263)
.|.+||+|+..+.+. -.=|...| .|++||=
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 589999999988655 34567888 5988763
No 123
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=72.61 E-value=0.74 Score=39.73 Aligned_cols=24 Identities=29% Similarity=0.852 Sum_probs=20.3
Q ss_pred CCceeCCccccccccccccCCCCC
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAG 155 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~ 155 (263)
...++|..|+..||..|..-.|..
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCcEEchhccceeeccchHHHHhh
Confidence 568999999999999998876643
No 124
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.56 E-value=3.9 Score=25.69 Aligned_cols=37 Identities=16% Similarity=0.438 Sum_probs=30.0
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARY 55 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 55 (263)
...--|.+|-+.|.+.+.+++...|+-.+.++||...
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3556799999999767666667889999999999654
No 125
>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=72.18 E-value=0.77 Score=39.51 Aligned_cols=30 Identities=27% Similarity=0.862 Sum_probs=23.3
Q ss_pred CCcccCCCCCceeecC-CCCceeEe-ecCCce
Q 024715 179 MKWARCPACGHCVERK-DGCSVVMC-RCNTRF 208 (263)
Q Consensus 179 ~~~k~CP~C~~~i~k~-~GCnhm~C-~C~~~F 208 (263)
..|.+||+|+..+.+. -.=|...| .|++||
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 3589999999988765 44566889 599986
No 126
>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=72.00 E-value=4.1 Score=21.82 Aligned_cols=20 Identities=35% Similarity=0.919 Sum_probs=12.9
Q ss_pred cCCCCCceeecCCCCceeEe
Q 024715 183 RCPACGHCVERKDGCSVVMC 202 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C 202 (263)
.||.|+..+.+..|=-.+.|
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 49999999999888666666
No 127
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=71.52 E-value=6.1 Score=33.85 Aligned_cols=44 Identities=27% Similarity=0.830 Sum_probs=32.8
Q ss_pred cccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCC
Q 024715 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (263)
.-|+.|-.-...+.. ...|+|.||.+|+..-+. ...+.||. |..
T Consensus 275 LkCplc~~Llrnp~k---T~cC~~~fc~eci~~al~-------dsDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMK---TPCCGHTFCDECIGTALL-------DSDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhhCccc---CccccchHHHHHHhhhhh-------hccccCCC--ccc
Confidence 789999876644421 256999999999987665 34578999 875
No 128
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=70.55 E-value=1.4 Score=42.68 Aligned_cols=48 Identities=31% Similarity=0.701 Sum_probs=34.9
Q ss_pred cccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcc
Q 024715 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (263)
+.|.||.+ . +. . ....|+|.||.+|+..++...- .-.||. |...+...
T Consensus 455 ~~c~ic~~-~-~~-~--~it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD-L-DS-F--FITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKEK 502 (674)
T ss_pred cccccccc-c-cc-c--eeecccchHHHHHHHhcccccc------CCCCcH--HHHHHHHH
Confidence 89999999 2 21 2 2589999999999999997332 226777 88665443
No 129
>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=70.11 E-value=3.3 Score=27.47 Aligned_cols=33 Identities=30% Similarity=0.925 Sum_probs=21.4
Q ss_pred cCCCCCceeecCCCCceeEe-ecCCc-----eecccCcccC
Q 024715 183 RCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRKIS 217 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~ 217 (263)
.||.|...++..+ .+.+| .|+.+ +|-.|+++..
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 5999999999888 68899 58755 6888888843
No 130
>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=70.03 E-value=4.3 Score=24.17 Aligned_cols=42 Identities=24% Similarity=0.686 Sum_probs=20.0
Q ss_pred cccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
|.+|-+-+.....- ....|+=.+...|+..|++..- ..+||.
T Consensus 1 C~~C~~iv~~G~~C-~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRC-SNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE--SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccC-CCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 56777666433221 1235888999999999998332 237886
No 131
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.01 E-value=1.7 Score=41.04 Aligned_cols=39 Identities=18% Similarity=0.479 Sum_probs=31.2
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQ 57 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 57 (263)
.....|.||+..|.........+.|||++|..|+.....
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 345789999988866655556789999999999987765
No 132
>PF14149 YhfH: YhfH-like protein
Probab=68.21 E-value=0.49 Score=27.14 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=22.3
Q ss_pred HHHHhcCCcccCCCCCceeecCCCCceeEe
Q 024715 173 GQLVERMKWARCPACGHCVERKDGCSVVMC 202 (263)
Q Consensus 173 ~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C 202 (263)
.+..+....|.|+.||..|+-..-|-..+|
T Consensus 5 ~eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 5 VEFFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 455667788999999999876655555555
No 133
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=67.68 E-value=2 Score=36.40 Aligned_cols=33 Identities=27% Similarity=0.809 Sum_probs=25.9
Q ss_pred cCCcccCCCCCceeecC-CCCceeEe-ecCCceec
Q 024715 178 RMKWARCPACGHCVERK-DGCSVVMC-RCNTRFCY 210 (263)
Q Consensus 178 ~~~~k~CP~C~~~i~k~-~GCnhm~C-~C~~~FC~ 210 (263)
+..|.+||.|+..+.+. -+=|...| +|++||=-
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccccc
Confidence 56799999999988755 55677888 69998743
No 134
>PF12773 DZR: Double zinc ribbon
Probab=67.63 E-value=3.7 Score=25.01 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=15.0
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCccc
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (263)
.+..+|| .|+..+.... ...+.|+.|+
T Consensus 10 ~~~~fC~--~CG~~l~~~~-----~~~~~C~~Cg 36 (50)
T PF12773_consen 10 DDAKFCP--HCGTPLPPPD-----QSKKICPNCG 36 (50)
T ss_pred ccccCCh--hhcCChhhcc-----CCCCCCcCCc
Confidence 3456777 6776665111 3456676665
No 135
>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=67.58 E-value=3.8 Score=29.42 Aligned_cols=23 Identities=39% Similarity=1.015 Sum_probs=18.0
Q ss_pred cCCCCCceeecCCCCceeEe-ecCCc
Q 024715 183 RCPACGHCVERKDGCSVVMC-RCNTR 207 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C-~C~~~ 207 (263)
.||.|+.++...++ .+.| .|++.
T Consensus 2 fC~~Cg~~l~~~~~--~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNG--VYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCC--eEECcCCCCc
Confidence 59999999977653 7888 48876
No 136
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=67.45 E-value=4.7 Score=28.84 Aligned_cols=29 Identities=28% Similarity=0.720 Sum_probs=19.8
Q ss_pred CcccCCCCCcee---ecCCCCceeEe-ecCCce
Q 024715 180 KWARCPACGHCV---ERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 180 ~~k~CP~C~~~i---~k~~GCnhm~C-~C~~~F 208 (263)
..-.||+|+... .+..|=-|+.| .||+.+
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 446799999432 23346678999 598874
No 137
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=66.92 E-value=4.5 Score=26.50 Aligned_cols=28 Identities=29% Similarity=0.764 Sum_probs=20.7
Q ss_pred cccCCCCCceeecCCCCceeEee-cCCce
Q 024715 181 WARCPACGHCVERKDGCSVVMCR-CNTRF 208 (263)
Q Consensus 181 ~k~CP~C~~~i~k~~GCnhm~C~-C~~~F 208 (263)
.+.||.|+....+...=..++|. ||..+
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCEE
Confidence 47899999999885555567784 87653
No 138
>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=66.88 E-value=2.4 Score=26.14 Aligned_cols=25 Identities=28% Similarity=0.752 Sum_probs=13.8
Q ss_pred ccCCCCCceeecCCCCc--eeEe-ecCC
Q 024715 182 ARCPACGHCVERKDGCS--VVMC-RCNT 206 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCn--hm~C-~C~~ 206 (263)
.+|++|+.++-+.++=. .|.| +|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 45666666666643333 4556 4654
No 139
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=66.60 E-value=5.6 Score=40.79 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=5.1
Q ss_pred ccCCccccccc
Q 024715 111 SYCPNTNCMAL 121 (263)
Q Consensus 111 ~~Cp~~~C~~~ 121 (263)
+.|| .|+..
T Consensus 668 rkCP--kCG~~ 676 (1337)
T PRK14714 668 RRCP--SCGTE 676 (1337)
T ss_pred EECC--CCCCc
Confidence 5566 56553
No 140
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=66.45 E-value=3.4 Score=31.03 Aligned_cols=24 Identities=50% Similarity=1.063 Sum_probs=19.7
Q ss_pred cccCCCCCceeecCCCCceeEeecCCceecccC
Q 024715 181 WARCPACGHCVERKDGCSVVMCRCNTRFCYECG 213 (263)
Q Consensus 181 ~k~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~ 213 (263)
.+-||.||.++++..| .-||-+|+
T Consensus 28 ~~hCp~Cg~PLF~KdG---------~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDG---------EVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCC---------eEECCCCC
Confidence 4789999999988666 67777777
No 141
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=66.11 E-value=3.4 Score=40.66 Aligned_cols=26 Identities=38% Similarity=1.200 Sum_probs=22.6
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCcee
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRFC 209 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~FC 209 (263)
..||.|+..+...+||. +| .||+.=|
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 35999999999999997 99 4998766
No 142
>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 PRK00420 hypothetical protein; Validated
Probab=63.11 E-value=5.5 Score=29.16 Aligned_cols=29 Identities=31% Similarity=0.555 Sum_probs=21.7
Q ss_pred CcccCCCCCceeec-CCCCceeEeecCCceecccCcccC
Q 024715 180 KWARCPACGHCVER-KDGCSVVMCRCNTRFCYECGRKIS 217 (263)
Q Consensus 180 ~~k~CP~C~~~i~k-~~GCnhm~C~C~~~FC~~C~~~~~ 217 (263)
....||.|+.++.+ ..| ..||-.||..+.
T Consensus 22 l~~~CP~Cg~pLf~lk~g---------~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG---------EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCCC---------ceECCCCCCeee
Confidence 34799999999987 555 667777777644
No 144
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.00 E-value=6.8 Score=25.03 Aligned_cols=30 Identities=23% Similarity=0.517 Sum_probs=19.2
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (263)
-.|- .|+..+..... ...+.||.||...=.
T Consensus 10 ~~Ct--SCg~~i~p~e~----~v~F~CPnCGe~~I~ 39 (61)
T COG2888 10 PVCT--SCGREIAPGET----AVKFPCPNCGEVEIY 39 (61)
T ss_pred ceec--cCCCEeccCCc----eeEeeCCCCCceeee
Confidence 3455 57777655444 578899988854433
No 145
>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=62.92 E-value=6.3 Score=25.71 Aligned_cols=17 Identities=18% Similarity=0.897 Sum_probs=13.0
Q ss_pred ccHHHHHHHHHHHHhhC
Q 024715 46 PFCQDCIARYIQVKVQD 62 (263)
Q Consensus 46 ~fC~~Cl~~~~~~~i~~ 62 (263)
-||++||.+|+...-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999988775
No 146
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=62.73 E-value=4.5 Score=22.95 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=17.1
Q ss_pred cHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 47 FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 47 fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
+|.+|++.|....-..-....+.|+. |+-.+.
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCEE
Confidence 48889998865443322356789988 886554
No 147
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=62.54 E-value=8.2 Score=26.23 Aligned_cols=31 Identities=29% Similarity=0.636 Sum_probs=24.1
Q ss_pred CCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 41 NLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 41 ~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
..|.|.|..-|+.+|+.+ .-.||. +++++..
T Consensus 52 G~CnHaFH~HCI~rWL~T--------k~~CPl--d~q~w~~ 82 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDT--------KGVCPL--DRQTWVL 82 (88)
T ss_pred EecchHHHHHHHHHHHhh--------CCCCCC--CCceeEE
Confidence 458999999999999986 225888 7766544
No 148
>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=62.36 E-value=1.6 Score=28.74 Aligned_cols=37 Identities=16% Similarity=0.471 Sum_probs=18.9
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHH
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIAR 54 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~ 54 (263)
+.+...|.+|...|.....-...-.||+.||.+|...
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 3567899999999954433334567999999888753
No 149
>PHA02862 5L protein; Provisional
Probab=62.23 E-value=10 Score=29.03 Aligned_cols=48 Identities=23% Similarity=0.477 Sum_probs=35.4
Q ss_pred cccccccccccccccccccCCCC-----CccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcc
Q 024715 22 FTCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (263)
..|=||.++..+. ..+|. ....++||.+|+. ...+..||. |+.+....
T Consensus 3 diCWIC~~~~~e~-----~~PC~C~GS~K~VHq~CL~~WIn------~S~k~~CeL--CkteY~Ik 55 (156)
T PHA02862 3 DICWICNDVCDER-----NNFCGCNEEYKVVHIKCMQLWIN------YSKKKECNL--CKTKYNIK 55 (156)
T ss_pred CEEEEecCcCCCC-----cccccccCcchhHHHHHHHHHHh------cCCCcCccC--CCCeEEEE
Confidence 4689999986432 24554 4699999999995 356789999 99877543
No 150
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=61.76 E-value=8.2 Score=37.58 Aligned_cols=53 Identities=15% Similarity=0.496 Sum_probs=36.9
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccc
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (263)
...|++|+..+.+... ..-..|+|.||..|+..|-... -+||. |..++..-.+
T Consensus 123 ~~~CP~Ci~s~~DqL~-~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~~v~V 175 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLE-ESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFGEVKV 175 (1134)
T ss_pred hhhhhHHHHHHHHHhh-ccccccccccHHHHhhhhhhhc--------ccCch--hhhhhheeee
Confidence 4567888877755433 2346799999999999998632 36888 8766554333
No 151
>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=61.52 E-value=7 Score=23.15 Aligned_cols=19 Identities=26% Similarity=0.773 Sum_probs=13.7
Q ss_pred CceeCCccccccccccccC
Q 024715 133 KKTQCPNCKQWFCFQCKLK 151 (263)
Q Consensus 133 ~~~~C~~C~~~~C~~C~~~ 151 (263)
..+.|+.|+..||...+.+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 4689999999999988875
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=60.90 E-value=5 Score=29.93 Aligned_cols=26 Identities=15% Similarity=0.276 Sum_probs=19.1
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCce
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
+.||+|+....-..- +-++| .||+.|
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 679999987764444 77888 588774
No 153
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.54 E-value=5.6 Score=25.39 Aligned_cols=12 Identities=42% Similarity=1.052 Sum_probs=7.2
Q ss_pred ccCCCCCce-eec
Q 024715 182 ARCPACGHC-VER 193 (263)
Q Consensus 182 k~CP~C~~~-i~k 193 (263)
-.||+|+.. |-+
T Consensus 26 F~CPnCG~~~I~R 38 (59)
T PRK14890 26 FLCPNCGEVIIYR 38 (59)
T ss_pred eeCCCCCCeeEee
Confidence 357777766 444
No 154
>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=60.53 E-value=6.2 Score=24.61 Aligned_cols=37 Identities=22% Similarity=0.573 Sum_probs=26.8
Q ss_pred cccccccccccccccccccCCCCCccHHHHHHHHHHH
Q 024715 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQV 58 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 58 (263)
..|.+|-..|.....-.....||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 4688998888654333345679999999999877553
No 155
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.40 E-value=7.1 Score=38.14 Aligned_cols=34 Identities=29% Similarity=0.774 Sum_probs=28.9
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCc-----eecccCcc
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (263)
-.||+|..+..-...=+.|.| .||++ .|-.||+.
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 379999998876666699999 59987 89999998
No 156
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=60.25 E-value=7.4 Score=25.30 Aligned_cols=28 Identities=29% Similarity=0.628 Sum_probs=19.0
Q ss_pred CcccCCCCCceeec---CCCCceeEe-ecCCc
Q 024715 180 KWARCPACGHCVER---KDGCSVVMC-RCNTR 207 (263)
Q Consensus 180 ~~k~CP~C~~~i~k---~~GCnhm~C-~C~~~ 207 (263)
..|+||.|+..+.+ .+|=-.+.| .|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 57999999986543 355445667 47764
No 157
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=60.09 E-value=12 Score=26.94 Aligned_cols=34 Identities=15% Similarity=0.462 Sum_probs=23.6
Q ss_pred CcccCCccccccceeccccccCCCCceeCCcccccc
Q 024715 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
..++|+ .|++.+....+.+++.....|..|.+.+
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYVE 36 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcceE
Confidence 457888 8999888776655556667777665443
No 158
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=59.88 E-value=19 Score=24.42 Aligned_cols=52 Identities=23% Similarity=0.593 Sum_probs=21.5
Q ss_pred CCcccccccccccccc---ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAAS---KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
.....|.||-+++... +.|.....|+-.+|+.|+.--.+ + ..-.||. |+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErk----e---g~q~Cpq--Ckt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERK----E---GNQVCPQ--CKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHH----T---S-SB-TT--T--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhh----c---Ccccccc--cCCCc
Confidence 4567899999988643 44666677999999999875544 2 2345888 88543
No 159
>PF14353 CpXC: CpXC protein
Probab=59.58 E-value=6.2 Score=29.45 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.9
Q ss_pred ccccCCCCCCCccCcccc
Q 024715 67 KIDCPGLDCKHNLDPFAC 84 (263)
Q Consensus 67 ~i~CP~~~C~~~l~~~~i 84 (263)
.|+||. |+..+..+..
T Consensus 1 ~itCP~--C~~~~~~~v~ 16 (128)
T PF14353_consen 1 EITCPH--CGHEFEFEVW 16 (128)
T ss_pred CcCCCC--CCCeeEEEEE
Confidence 378999 9988766544
No 160
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.40 E-value=10 Score=31.13 Aligned_cols=59 Identities=22% Similarity=0.511 Sum_probs=45.1
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
++=.--|..|-.++...+.. -+.|-|.|.-+||..+...--....-....||. |+.+|-
T Consensus 47 sDY~pNC~LC~t~La~gdt~--RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiF 105 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPLASGDTT--RLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIF 105 (299)
T ss_pred cCCCCCCceeCCccccCcce--eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccC
Confidence 44456799999998777764 489999999999999887655543445578998 987653
No 161
>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=58.66 E-value=3 Score=29.84 Aligned_cols=33 Identities=27% Similarity=0.565 Sum_probs=25.6
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIA 53 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~ 53 (263)
.+...|.+|...+.. ..| ...+|+|.|...|++
T Consensus 76 ~~~~~C~vC~k~l~~-~~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceE-EEeCCCeEEeccccc
Confidence 345679999999965 344 468999999999875
No 162
>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=58.26 E-value=6.1 Score=21.27 Aligned_cols=24 Identities=38% Similarity=1.007 Sum_probs=12.7
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
++||.|+..|++. +|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 4799999988654 45555556 453
No 163
>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=58.01 E-value=5.6 Score=21.71 Aligned_cols=26 Identities=27% Similarity=0.540 Sum_probs=12.5
Q ss_pred cCCccccccceeccccccCCCCceeCCcccccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
.|| .|+.-....+ ...+.|+.|+..|
T Consensus 4 ~Cp--~C~se~~y~D-----~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCP--LCGSEYTYED-----GELLVCPECGHEW 29 (30)
T ss_dssp --T--TT-----EE------SSSEEETTTTEEE
T ss_pred CCC--CCCCcceecc-----CCEEeCCcccccC
Confidence 366 6766665544 3678898887653
No 164
>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=57.96 E-value=24 Score=21.10 Aligned_cols=34 Identities=26% Similarity=0.694 Sum_probs=18.6
Q ss_pred HHHHhcCCc---ccCCCCCce-eecCCCCceeEe-ecCC
Q 024715 173 GQLVERMKW---ARCPACGHC-VERKDGCSVVMC-RCNT 206 (263)
Q Consensus 173 ~~~~~~~~~---k~CP~C~~~-i~k~~GCnhm~C-~C~~ 206 (263)
.+++....| -.||.|+.. +.+..+=....| .|++
T Consensus 7 ~~~l~~~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 7 REYLEEIRWPDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred HHHHHHhcCCCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 344444444 469999984 333344344556 3654
No 165
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.60 E-value=9.1 Score=36.96 Aligned_cols=12 Identities=42% Similarity=0.861 Sum_probs=6.4
Q ss_pred cccCCCCCceee
Q 024715 181 WARCPACGHCVE 192 (263)
Q Consensus 181 ~k~CP~C~~~i~ 192 (263)
.+.||+||..+.
T Consensus 41 ~~fC~~CG~~~~ 52 (645)
T PRK14559 41 EAHCPNCGAETG 52 (645)
T ss_pred cccccccCCccc
Confidence 455666655543
No 166
>PLN00209 ribosomal protein S27; Provisional
Probab=57.13 E-value=13 Score=25.63 Aligned_cols=31 Identities=16% Similarity=0.494 Sum_probs=23.5
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (263)
+.|| +|...-..-+.. ...|.|..|+...|.
T Consensus 37 VkCp--~C~n~q~VFShA---~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSHS---QTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEecC---ceEEEccccCCEeec
Confidence 6799 898876665543 578999999887774
No 167
>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=56.73 E-value=11 Score=23.38 Aligned_cols=28 Identities=25% Similarity=0.448 Sum_probs=16.6
Q ss_pred ccCCCCCceee------cCCCCceeE-e-ecCCcee
Q 024715 182 ARCPACGHCVE------RKDGCSVVM-C-RCNTRFC 209 (263)
Q Consensus 182 k~CP~C~~~i~------k~~GCnhm~-C-~C~~~FC 209 (263)
|+||.|+-.-+ .+.+..++. | .|+...-
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 78999998655 123445544 6 3665543
No 168
>PLN02189 cellulose synthase
Probab=54.51 E-value=12 Score=37.77 Aligned_cols=64 Identities=22% Similarity=0.381 Sum_probs=43.2
Q ss_pred CcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCC
Q 024715 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACG 188 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~ 188 (263)
+...|. -|+..+-..... ...+.|..|++-.|..|. ++. ++.+.+.||.|+
T Consensus 33 ~~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr~Cy----------eye--------------r~eg~q~CpqCk 83 (1040)
T PLN02189 33 DGQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCRPCY----------EYE--------------RREGTQNCPQCK 83 (1040)
T ss_pred cCcccc--ccccccCcCCCC---CEEEeeccCCCccccchh----------hhh--------------hhcCCccCcccC
Confidence 345666 677666543331 578999999999997653 332 234668899999
Q ss_pred ceeecCCCCceeE
Q 024715 189 HCVERKDGCSVVM 201 (263)
Q Consensus 189 ~~i~k~~GCnhm~ 201 (263)
....+.-|++.+.
T Consensus 84 t~Y~r~kgs~~v~ 96 (1040)
T PLN02189 84 TRYKRLKGSPRVE 96 (1040)
T ss_pred CchhhccCCCCcC
Confidence 9998766665543
No 169
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=54.25 E-value=8.5 Score=27.80 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=19.2
Q ss_pred cCCccccccceeccccccCCCCceeCCccccccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQWFC 145 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 145 (263)
.|| .|+.-+.+++. ..+.||.|++.|=
T Consensus 4 ~CP--~C~seytY~dg-----~~~iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG-----TQLICPSCLYEWN 30 (109)
T ss_pred cCC--cCCCcceEecC-----CeeECcccccccc
Confidence 477 78887777765 5688888776553
No 170
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=53.86 E-value=2 Score=36.55 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=16.9
Q ss_pred eeEe-ecCCceecccCcccCC
Q 024715 199 VVMC-RCNTRFCYECGRKISS 218 (263)
Q Consensus 199 hm~C-~C~~~FC~~C~~~~~~ 218 (263)
|-+| .||+-|||.|...|-.
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred CCCcCcCcchHHHHHHHHHHc
Confidence 5678 5999999999999864
No 171
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=53.75 E-value=13 Score=26.63 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=23.9
Q ss_pred CCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 41 NLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 41 ~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
..|.|.|..-|+.+|+++. -.||. +.....+
T Consensus 79 G~CNHaFH~hCisrWlktr--------~vCPL--dn~eW~~ 109 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR--------NVCPL--DNKEWVF 109 (114)
T ss_pred eecchHHHHHHHHHHHhhc--------CcCCC--cCcceeE
Confidence 4689999999999999843 36898 6665543
No 172
>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=53.30 E-value=15 Score=23.24 Aligned_cols=47 Identities=26% Similarity=0.650 Sum_probs=31.4
Q ss_pred cccccccccccccccccccCCCC--CccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcc
Q 024715 22 FTCEICIEPMAASKKFKNRNLCT--HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (263)
-.|..|-.+++.... ...-|. .+||.+|....+. -.||+ |+..|..+
T Consensus 6 pnCE~C~~dLp~~s~--~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv~R 54 (57)
T PF06906_consen 6 PNCECCDKDLPPDSP--EAYICSFECTFCADCAETMLN----------GVCPN--CGGELVRR 54 (57)
T ss_pred CCccccCCCCCCCCC--cceEEeEeCcccHHHHHHHhc----------CcCcC--CCCccccC
Confidence 357888888854431 123354 5899999987763 25999 99877554
No 173
>PF15616 TerY-C: TerY-C metal binding domain
Probab=53.27 E-value=10 Score=28.57 Aligned_cols=26 Identities=31% Similarity=0.913 Sum_probs=18.5
Q ss_pred CcccCCCCCceeecCCCCceeEeecCCceecc
Q 024715 180 KWARCPACGHCVERKDGCSVVMCRCNTRFCYE 211 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C~C~~~FC~~ 211 (263)
+.--||.|+...- .+.|.||.-|||.
T Consensus 76 g~PgCP~CGn~~~------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 76 GAPGCPHCGNQYA------FAVCGCGKLFCID 101 (131)
T ss_pred CCCCCCCCcChhc------EEEecCCCEEEeC
Confidence 3468999999853 3556777777764
No 174
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.03 E-value=22 Score=24.66 Aligned_cols=29 Identities=24% Similarity=0.735 Sum_probs=20.8
Q ss_pred CcccCCCCCceeecCCCCceeEe-ecCCce
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
....||.|+...-|..+=---.| +||+.|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 34689999999887766555566 476665
No 175
>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=52.65 E-value=8.7 Score=21.66 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=21.7
Q ss_pred CCceeCCccccccccccccCCCCCCC
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAGYR 157 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (263)
...+.|..|+...|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 45889999999999999887677653
No 176
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=52.19 E-value=15 Score=25.29 Aligned_cols=31 Identities=19% Similarity=0.522 Sum_probs=23.6
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (263)
+.|| +|...-..-+.. ...|.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFShA---~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSHA---QTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEecC---ceEEEccccCCEeec
Confidence 6799 898876665543 578999999988774
No 177
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=51.92 E-value=2.9 Score=33.66 Aligned_cols=37 Identities=27% Similarity=0.491 Sum_probs=25.9
Q ss_pred HhcCCcccCCCCCceeecCCCCceeEeecCCceecccCcccC
Q 024715 176 VERMKWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKIS 217 (263)
Q Consensus 176 ~~~~~~k~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~ 217 (263)
....+.-.||-|.-.+.. -+.=.||+.|||.|...|.
T Consensus 13 ~~~~~~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCCccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 333445689999886642 1222699999999998874
No 178
>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=51.82 E-value=4.9 Score=23.39 Aligned_cols=25 Identities=24% Similarity=0.679 Sum_probs=22.2
Q ss_pred CceeCCccccccccccccCCCCCCC
Q 024715 133 KKTQCPNCKQWFCFQCKLKWHAGYR 157 (263)
Q Consensus 133 ~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (263)
..+.|..|+..+|..|....|.++.
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred eEEEecCCCCccCccCCCCCCCCCE
Confidence 6899999999999999998888753
No 179
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=51.77 E-value=2.1 Score=40.91 Aligned_cols=58 Identities=21% Similarity=0.484 Sum_probs=44.2
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcccccc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (263)
.....+|+||++.+..+ +.+.|.|.||..|+..-+...- ....||. |+..++....+.
T Consensus 18 ~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKK-----GPKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccC-----ccccchh--hhhhhhhhhccc
Confidence 35678999999998655 3689999999999988776433 2678888 887776665554
No 180
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.31 E-value=14 Score=37.22 Aligned_cols=33 Identities=27% Similarity=0.723 Sum_probs=20.4
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCcccc-----ccccccccCC
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ-----WFCFQCKLKW 152 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~~ 152 (263)
.....|| .|+... ..+.|+.||. .+|..|+...
T Consensus 624 Vg~RfCp--sCG~~t----------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 624 IGRRKCP--SCGKET----------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred ccCccCC--CCCCcC----------CcccCCCCCCCCCcceeCccccCcC
Confidence 3456787 676653 3467777774 4677775543
No 181
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.81 E-value=16 Score=30.60 Aligned_cols=40 Identities=15% Similarity=0.231 Sum_probs=32.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD 62 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 62 (263)
.+.-.|.+|+.++.++. +.+=||.||++|+..||..+-++
T Consensus 41 K~FdcCsLtLqPc~dPv----it~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDPV----ITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred CCcceeeeecccccCCc----cCCCCeeeeHHHHHHHHHHHHHH
Confidence 44568999999997663 47789999999999999987764
No 182
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=50.65 E-value=10 Score=24.83 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=23.1
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (263)
+.|| +|++....-... ...+.|..|+...+.
T Consensus 20 VkCp--dC~N~q~vFsha---st~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP--DCGNEQVVFSHA---STVVTCLICGTTLAE 50 (67)
T ss_pred EECC--CCCCEEEEeccC---ceEEEecccccEEEe
Confidence 6799 898877665543 578999999877663
No 183
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=50.52 E-value=6.9 Score=37.77 Aligned_cols=12 Identities=25% Similarity=0.902 Sum_probs=9.8
Q ss_pred CcccCCCCCcee
Q 024715 180 KWARCPACGHCV 191 (263)
Q Consensus 180 ~~k~CP~C~~~i 191 (263)
..++||+|+...
T Consensus 677 RqRKCP~Cn~aF 688 (698)
T KOG0978|consen 677 RQRKCPKCNAAF 688 (698)
T ss_pred hcCCCCCCCCCC
Confidence 468999999865
No 184
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=50.45 E-value=11 Score=22.04 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=8.2
Q ss_pred cCCCCCceeecC
Q 024715 183 RCPACGHCVERK 194 (263)
Q Consensus 183 ~CP~C~~~i~k~ 194 (263)
+||+|+...+..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 488888866544
No 185
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=49.91 E-value=14 Score=23.15 Aligned_cols=22 Identities=18% Similarity=0.498 Sum_probs=15.7
Q ss_pred HHHHHHHhcCCcccCCCCCcee
Q 024715 170 IVFGQLVERMKWARCPACGHCV 191 (263)
Q Consensus 170 ~~~~~~~~~~~~k~CP~C~~~i 191 (263)
..+.++........||+|+..+
T Consensus 35 ~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 35 QELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHHHcCCCeEECcCCCccC
Confidence 4455666666788999999753
No 186
>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=49.72 E-value=15 Score=18.98 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=13.0
Q ss_pred ccccceeccccccCCCCceeCCcccc
Q 024715 117 NCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 117 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.|+..+..... ...+.||.||.
T Consensus 3 sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCccc----CceEeCCCCCC
Confidence 35444443332 57888888873
No 187
>PRK10220 hypothetical protein; Provisional
Probab=49.40 E-value=12 Score=27.02 Aligned_cols=28 Identities=25% Similarity=0.572 Sum_probs=19.5
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFC 145 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 145 (263)
-.|| .|+.-+.+++. ..+.||.|+..|=
T Consensus 4 P~CP--~C~seytY~d~-----~~~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCP--KCNSEYTYEDN-----GMYICPECAHEWN 31 (111)
T ss_pred CcCC--CCCCcceEcCC-----CeEECCcccCcCC
Confidence 3577 78887777665 5688887776553
No 188
>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=49.33 E-value=20 Score=22.96 Aligned_cols=27 Identities=30% Similarity=0.694 Sum_probs=19.6
Q ss_pred ccCCCCCce----eecCCCCceeEe-ecCCce
Q 024715 182 ARCPACGHC----VERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 182 k~CP~C~~~----i~k~~GCnhm~C-~C~~~F 208 (263)
-.||+|+.. .-+..|=.++.| .||+.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 369999873 345577788999 699753
No 189
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=49.27 E-value=13 Score=27.26 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=22.3
Q ss_pred cccCCccccccceeccccccCCCCceeCCcccccc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
.++|| .|++.+....... ...+.|+.|++..
T Consensus 2 m~FCp--~Cgsll~p~~~~~--~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDE--GGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCC--CcEEECCCCCcch
Confidence 36899 8999998865433 3588888887643
No 190
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=49.11 E-value=15 Score=31.97 Aligned_cols=49 Identities=18% Similarity=0.448 Sum_probs=35.2
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
.....|+||+....++... ..=|-.||-.|+.+|+. ..=+||..++...
T Consensus 298 ~~~~~CpvClk~r~Nptvl---~vSGyVfCY~Ci~~Yv~--------~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVL---EVSGYVFCYPCIFSYVV--------NYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCCCceE---EecceEEeHHHHHHHHH--------hcCCCCccCCcch
Confidence 3456899999888655332 33488999999999997 1236998666544
No 191
>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=48.79 E-value=18 Score=24.13 Aligned_cols=26 Identities=31% Similarity=0.716 Sum_probs=19.4
Q ss_pred cCCCCCce----eecCCCCceeEe-ecCCce
Q 024715 183 RCPACGHC----VERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 183 ~CP~C~~~----i~k~~GCnhm~C-~C~~~F 208 (263)
.||.|+.. .-+..|=.++.| .||+..
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 69999873 335577888999 699753
No 192
>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=48.25 E-value=6.2 Score=23.99 Aligned_cols=44 Identities=23% Similarity=0.612 Sum_probs=22.0
Q ss_pred cccccccccccccccccccCCC-CCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 22 FTCEICIEPMAASKKFKNRNLC-THPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
+-|.-|+-... .+..| .|+.|..|+..++. ..-.||. |+.+++.
T Consensus 3 ~nCKsCWf~~k------~Li~C~dHYLCl~CLt~ml~--------~s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFANK------GLIKCSDHYLCLNCLTLMLS--------RSDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S--S------SEEE-SS-EEEHHHHHHT-S--------SSSEETT--TTEE---
T ss_pred ccChhhhhcCC------CeeeecchhHHHHHHHHHhc--------cccCCCc--ccCcCcc
Confidence 34566654432 13456 59999999988774 3346998 9988764
No 193
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=47.94 E-value=5.5 Score=34.31 Aligned_cols=44 Identities=25% Similarity=0.465 Sum_probs=30.6
Q ss_pred CcccCCccccccceeccccc----cCCCCceeCCccccccccccccCCCC
Q 024715 109 ERSYCPNTNCMALVVNECER----SGKVKKTQCPNCKQWFCFQCKLKWHA 154 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~ 154 (263)
....|- .|+..+...+.. +......+|+.|+..||..|..-.|.
T Consensus 361 ks~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 361 KSTHCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred CCccce--eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 345677 688777654331 12256899999999999999776653
No 194
>smart00336 BBOX B-Box-type zinc finger.
Probab=47.84 E-value=16 Score=20.93 Aligned_cols=26 Identities=23% Similarity=0.514 Sum_probs=21.5
Q ss_pred CCceeCCccccccccccccCCCCCCC
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAGYR 157 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (263)
...+.|..|....|..|....|.++.
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred ceEEECCCCCcccccccChhhcCCCc
Confidence 45889999999999999987776653
No 195
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=47.64 E-value=13 Score=26.32 Aligned_cols=29 Identities=24% Similarity=0.695 Sum_probs=20.5
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
.+|| .|++.++++.+.+ ...+.|..|.+.
T Consensus 2 ~FCP--~Cgn~Live~g~~--~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGES--CNRFSCRTCPYV 30 (105)
T ss_pred cccC--CCCCEEEEecCCe--EeeEEcCCCCce
Confidence 4789 8999998877643 456677666543
No 196
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.18 E-value=5.6 Score=32.83 Aligned_cols=17 Identities=24% Similarity=0.614 Sum_probs=14.0
Q ss_pred ecCCceecccCcccCCC
Q 024715 203 RCNTRFCYECGRKISSG 219 (263)
Q Consensus 203 ~C~~~FC~~C~~~~~~~ 219 (263)
-||+-|||-|+-.|.+-
T Consensus 64 lCGHLFCWpClyqWl~~ 80 (230)
T KOG0823|consen 64 LCGHLFCWPCLYQWLQT 80 (230)
T ss_pred ecccceehHHHHHHHhh
Confidence 38999999999988643
No 197
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=46.46 E-value=18 Score=22.90 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=9.6
Q ss_pred CcccCCCCCceee
Q 024715 180 KWARCPACGHCVE 192 (263)
Q Consensus 180 ~~k~CP~C~~~i~ 192 (263)
..|+||-||....
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 4689999996443
No 198
>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=45.59 E-value=20 Score=31.18 Aligned_cols=54 Identities=17% Similarity=0.372 Sum_probs=31.8
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCce
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 190 (263)
..|| .|..-....+.. ...+. .||..||..|-... . ..+...||.|+..
T Consensus 4 ~~CP--~Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~~l-----------------------~-~~~~~~CP~C~~~ 52 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSL---KLMVN--VCGHTLCESCVDLL-----------------------F-VRGSGSCPECDTP 52 (309)
T ss_pred CCCC--cCCCCCccCccc---ccccC--CCCCcccHHHHHHH-----------------------h-cCCCCCCCCCCCc
Confidence 4588 677644333320 12233 68999998775421 1 1133489999998
Q ss_pred eecCC
Q 024715 191 VERKD 195 (263)
Q Consensus 191 i~k~~ 195 (263)
+.|..
T Consensus 53 lrk~~ 57 (309)
T TIGR00570 53 LRKNN 57 (309)
T ss_pred cchhh
Confidence 87753
No 199
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.33 E-value=14 Score=27.87 Aligned_cols=24 Identities=25% Similarity=0.658 Sum_probs=18.5
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.+|| .|+..++..+ -.++||.|++
T Consensus 29 ~hCp--~Cg~PLF~Kd------G~v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFRKD------GEVFCPVCGY 52 (131)
T ss_pred hhCc--ccCCcceeeC------CeEECCCCCc
Confidence 7899 8999888743 3788888775
No 200
>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=44.53 E-value=21 Score=22.40 Aligned_cols=31 Identities=23% Similarity=0.342 Sum_probs=21.9
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFC 145 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 145 (263)
+.|| .|+.-+...+... ...+.|+.|+..+=
T Consensus 3 ~~CP--~CG~~iev~~~~~--GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECP--DCGAEIELENPEL--GELVICDECGAELE 33 (54)
T ss_pred cCCC--CCCCEEecCCCcc--CCEEeCCCCCCEEE
Confidence 4688 8999887755432 46789998886553
No 201
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=44.24 E-value=21 Score=36.37 Aligned_cols=61 Identities=21% Similarity=0.423 Sum_probs=40.4
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCce
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 190 (263)
..|- -|+.-+-.... ....|.|..|++-.|..| -+|+ ++.+.+.||+|+..
T Consensus 18 qiCq--ICGD~vg~~~~---Ge~FVAC~eC~FPVCrpC----------YEYE--------------r~eG~q~CPqCktr 68 (1079)
T PLN02638 18 QVCQ--ICGDNVGKTVD---GEPFVACDVCAFPVCRPC----------YEYE--------------RKDGNQSCPQCKTK 68 (1079)
T ss_pred ceee--ecccccCcCCC---CCEEEEeccCCCccccch----------hhhh--------------hhcCCccCCccCCc
Confidence 3454 56655544332 157899999999999755 3333 23466889999999
Q ss_pred eecCCCCcee
Q 024715 191 VERKDGCSVV 200 (263)
Q Consensus 191 i~k~~GCnhm 200 (263)
..+.-|+..+
T Consensus 69 Ykr~kgsprv 78 (1079)
T PLN02638 69 YKRHKGSPAI 78 (1079)
T ss_pred hhhhcCCCCc
Confidence 8866665544
No 202
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.91 E-value=23 Score=24.70 Aligned_cols=17 Identities=18% Similarity=0.792 Sum_probs=15.1
Q ss_pred ccHHHHHHHHHHHHhhC
Q 024715 46 PFCQDCIARYIQVKVQD 62 (263)
Q Consensus 46 ~fC~~Cl~~~~~~~i~~ 62 (263)
-||++||..|+..+-+.
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 59999999999988875
No 203
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.53 E-value=23 Score=30.32 Aligned_cols=52 Identities=25% Similarity=0.692 Sum_probs=38.7
Q ss_pred CCCccccccccccccccccccccCCC----CCccHHHHHHHHHHHHhhCCCCcccccCCC-CCC
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLC----THPFCQDCIARYIQVKVQDDNTAKIDCPGL-DCK 76 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C----~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~-~C~ 76 (263)
......|.+|-|-+.+. .| ..| .|.||..|-+..|+.+-.. ..+.||.. +|-
T Consensus 265 ~~apLcCTLC~ERLEDT-HF---VQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSGdkCP 321 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDT-HF---VQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSGDKCP 321 (352)
T ss_pred CCCceeehhhhhhhccC-ce---eecCCCcccceecccCHHHHHhhcCC---CceeCCCCCcCc
Confidence 45669999999998654 33 344 6999999999999977654 36778863 443
No 204
>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=43.00 E-value=19 Score=20.54 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=18.4
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
..|+ .|+..+......+. ...+.||.|+.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 3577 78886654433221 46778988875
No 205
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=43.00 E-value=4.9 Score=24.67 Aligned_cols=37 Identities=22% Similarity=0.528 Sum_probs=29.1
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHH
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYI 56 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 56 (263)
...++|..|-+.++.. .++...-||-.-|..||+.-+
T Consensus 5 Fsry~CDLCn~~~p~~-~LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 5 FSRYSCDLCNSSHPIS-ELRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred HhhHhHHhhcccCcHH-HHHHHhhhchhhhhhhhhhhH
Confidence 4678999999999544 445567899999999998544
No 206
>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=42.93 E-value=18 Score=24.84 Aligned_cols=30 Identities=33% Similarity=0.882 Sum_probs=15.7
Q ss_pred CcccCCCCCc------eeecCCCCceeEe-ecCCcee
Q 024715 180 KWARCPACGH------CVERKDGCSVVMC-RCNTRFC 209 (263)
Q Consensus 180 ~~k~CP~C~~------~i~k~~GCnhm~C-~C~~~FC 209 (263)
..-.||.|+. -|.+..|=-++.| .||..|=
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 3458999992 3456677788999 4887763
No 207
>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=42.63 E-value=22 Score=22.02 Aligned_cols=39 Identities=21% Similarity=0.522 Sum_probs=23.3
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
.+.|+.|.+.++ .. =|..++...=.. ....+.||. |...
T Consensus 2 ~f~CP~C~~~~~-~~---------------~L~~H~~~~H~~-~~~~v~CPi--C~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ES---------------SLVEHCEDEHRS-ESKNVVCPI--CSSR 40 (54)
T ss_pred CcCCCCCCCccC-HH---------------HHHHHHHhHCcC-CCCCccCCC--chhh
Confidence 578999988553 21 233444433222 244799999 9864
No 208
>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=41.97 E-value=51 Score=24.19 Aligned_cols=36 Identities=19% Similarity=0.450 Sum_probs=24.9
Q ss_pred CcccCCccccccceeccccccCCCCceeCCccccccccccccC
Q 024715 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLK 151 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 151 (263)
+...|. .|...+.... +....|..|+..+|..|...
T Consensus 53 ~~~~C~--~C~~~fg~l~-----~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCA--RCGKPFGFLF-----NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-T--TTS-BCSCTS-----TTCEEETTTTEEEETTSEEE
T ss_pred CCcchh--hhCCcccccC-----CCCCcCCcCCccccCccCCc
Confidence 346787 6776543322 34689999999999999986
No 209
>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=41.88 E-value=27 Score=19.14 Aligned_cols=26 Identities=19% Similarity=0.553 Sum_probs=20.0
Q ss_pred cCCccccccceeccccccCCCCceeCCccccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
.|. .|+..+..... ...++|..|+..
T Consensus 3 ~C~--~C~t~L~yP~g----A~~vrCs~C~~v 28 (31)
T TIGR01053 3 VCG--GCRTLLMYPRG----ASSVRCALCQTV 28 (31)
T ss_pred CcC--CCCcEeecCCC----CCeEECCCCCeE
Confidence 566 78888887776 679999988653
No 210
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=41.29 E-value=43 Score=21.20 Aligned_cols=37 Identities=19% Similarity=0.225 Sum_probs=28.2
Q ss_pred ccccCCCCCCCccCccccccCCChhhHHHHHHHHHHHhh
Q 024715 67 KIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYV 105 (263)
Q Consensus 67 ~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~ 105 (263)
...||. |+.......-..+-.+|-+.+|...+.+...
T Consensus 17 k~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 17 KEICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred cccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 346888 9988777777777777889999988776543
No 211
>PLN02436 cellulose synthase A
Probab=41.10 E-value=27 Score=35.59 Aligned_cols=63 Identities=22% Similarity=0.389 Sum_probs=41.3
Q ss_pred cccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGH 189 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 189 (263)
...|. -|+.-+-.... ....|.|..|++..|..|. ++. ++.+.+.||.|+.
T Consensus 36 ~~iCq--ICGD~Vg~t~d---Ge~FVACn~C~fpvCr~Cy----------eye--------------r~eg~~~Cpqckt 86 (1094)
T PLN02436 36 GQTCQ--ICGDEIELTVD---GEPFVACNECAFPVCRPCY----------EYE--------------RREGNQACPQCKT 86 (1094)
T ss_pred Ccccc--ccccccCcCCC---CCEEEeeccCCCccccchh----------hhh--------------hhcCCccCcccCC
Confidence 34555 56655543322 1578999999999997653 322 2346688999999
Q ss_pred eeecCCCCceeE
Q 024715 190 CVERKDGCSVVM 201 (263)
Q Consensus 190 ~i~k~~GCnhm~ 201 (263)
...+.-|++.+.
T Consensus 87 ~Y~r~kgs~~~~ 98 (1094)
T PLN02436 87 RYKRIKGSPRVE 98 (1094)
T ss_pred chhhccCCCCcC
Confidence 988666655443
No 212
>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=41.06 E-value=46 Score=25.94 Aligned_cols=90 Identities=13% Similarity=0.374 Sum_probs=48.0
Q ss_pred ccccccccccccccccccc---cCCCCCcc------HHHHHHHHHHHHhhCC-----------------------CCccc
Q 024715 21 SFTCEICIEPMAASKKFKN---RNLCTHPF------CQDCIARYIQVKVQDD-----------------------NTAKI 68 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~---~~~C~H~f------C~~Cl~~~~~~~i~~~-----------------------~~~~i 68 (263)
..+|+||+|.=-+...+.- ...|.-++ -.+||.+|-....+.. ....+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L 81 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL 81 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence 4689999987433221110 01132223 3578888877765422 12367
Q ss_pred ccCCCCCCCccCccccccCCChhhHHHHHHHHHHHhhcCCCcccCCccccccceeccc
Q 024715 69 DCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNEC 126 (263)
Q Consensus 69 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 126 (263)
.||. |...+..-.+. +.. +.++ ....+.|+..+|.+.....+
T Consensus 82 ~CPL--CRG~V~GWtvv-----e~A--------R~~L-N~K~RsC~~e~C~F~GtY~e 123 (162)
T PF07800_consen 82 ACPL--CRGEVKGWTVV-----EPA--------RRFL-NAKKRSCSQESCSFSGTYSE 123 (162)
T ss_pred cCcc--ccCceeceEEc-----hHH--------HHHh-ccCCccCcccccccccCHHH
Confidence 8988 88765432211 111 1122 24557788888877665544
No 213
>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=40.56 E-value=22 Score=20.89 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=18.3
Q ss_pred cCCccccccceeccccccCCCCceeCCcccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.|+ +|+..+......++ ...+.||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCE--ECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeC--CCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 477 78866655443333 56888988875
No 214
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.53 E-value=14 Score=27.05 Aligned_cols=43 Identities=21% Similarity=0.524 Sum_probs=29.6
Q ss_pred ccCCccccccceeccccc----cCCCCceeCCccccccccccccCCCCC
Q 024715 111 SYCPNTNCMALVVNECER----SGKVKKTQCPNCKQWFCFQCKLKWHAG 155 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~~ 155 (263)
..|- .|+..+...... ........|+.|+..||..|..-+|..
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 4577 788777543210 011457899999999999998877753
No 215
>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=40.23 E-value=22 Score=33.34 Aligned_cols=33 Identities=24% Similarity=0.709 Sum_probs=25.7
Q ss_pred cCCCCCceeecCCCCceeEe-ecCCc-----eecccCcc
Q 024715 183 RCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (263)
+||+|..+..-...=|.+.| .||+. .|-.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 69999988875545568999 59976 69999875
No 216
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=40.13 E-value=32 Score=28.98 Aligned_cols=51 Identities=24% Similarity=0.406 Sum_probs=37.8
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
.=...|+|=+.++..+. ....|+|.|=++=+..++. ....+.||..+|..+
T Consensus 174 ~fs~rdPis~~~I~nPv---iSkkC~HvydrDsI~~~l~------~~~~i~CPv~gC~~~ 224 (262)
T KOG2979|consen 174 VFSNRDPISKKPIVNPV---ISKKCGHVYDRDSIMQILC------DEITIRCPVLGCENP 224 (262)
T ss_pred hhcccCchhhhhhhchh---hhcCcCcchhhhhHHHHhc------cCceeecccccCCcc
Confidence 33467887776665543 2578999998888888876 456799999999943
No 217
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=39.57 E-value=6.9 Score=26.36 Aligned_cols=52 Identities=25% Similarity=0.653 Sum_probs=35.5
Q ss_pred cccccccccccc--------cccc-ccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 23 TCEICIEPMAAS--------KKFK-NRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 23 ~C~IC~~~~~~~--------~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
+|.||-.+|+.. +.-+ ....|.|.|-.-|+.+|+.+..++ -.||. |++.+..
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~~~ 82 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTWQF 82 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chheeEe
Confidence 899998888532 1110 112478999999999999866654 46998 8877643
No 218
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=39.02 E-value=30 Score=21.37 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=21.8
Q ss_pred ccccccccccccccccccCCCCCccHHHHHHHH
Q 024715 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARY 55 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 55 (263)
.|.||-.+......+ -+.=| .+|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~--k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF--KIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce--eccCc-cchHHHHHHh
Confidence 489999888544332 25556 8999999876
No 219
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=38.99 E-value=24 Score=22.58 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=21.3
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFC 145 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 145 (263)
+.|| +|......-+.. ...+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsha---~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHA---STVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEecC---CcEEECcccCCCcc
Confidence 6788 888776655443 46888888887665
No 220
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=38.46 E-value=33 Score=19.11 Aligned_cols=28 Identities=18% Similarity=0.243 Sum_probs=17.3
Q ss_pred cccCCccccccceeccccccCCCCceeCCccccc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
...|+ .|++..+.... ....+|..|+..
T Consensus 3 ~~~C~--~C~~~~i~~~~----~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNKE----DDYEVCIFCGSS 30 (33)
T ss_pred ceEcC--CCCCCeEEEec----CCeEEcccCCcE
Confidence 35577 68777766333 346677777654
No 221
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.37 E-value=24 Score=35.61 Aligned_cols=32 Identities=31% Similarity=0.775 Sum_probs=25.4
Q ss_pred CcccCCCCCceeecCCCCceeEe-ecCC-----ceecccCcccC
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-RCNT-----RFCYECGRKIS 217 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~C~~-----~FC~~C~~~~~ 217 (263)
..+.||.|+... ....| .||. .||-.|+....
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC
Confidence 448999999985 45789 5985 49999988855
No 222
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=38.11 E-value=31 Score=20.63 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=8.7
Q ss_pred CcccCCCCCceee
Q 024715 180 KWARCPACGHCVE 192 (263)
Q Consensus 180 ~~k~CP~C~~~i~ 192 (263)
...+||.|+..|.
T Consensus 18 ~~irC~~CG~rIl 30 (44)
T smart00659 18 DVVRCRECGYRIL 30 (44)
T ss_pred CceECCCCCceEE
Confidence 4467888877663
No 223
>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=38.02 E-value=19 Score=27.91 Aligned_cols=38 Identities=18% Similarity=0.488 Sum_probs=22.2
Q ss_pred CcccCCCCCceeecCCCCceeEe-e---cCCceecccCcccC
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-R---CNTRFCYECGRKIS 217 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~---C~~~FC~~C~~~~~ 217 (263)
.+..||+|+.+|.-..-..-+.= . =--.||..||++|.
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 45689999999974411111100 0 13468888888853
No 224
>PRK11827 hypothetical protein; Provisional
Probab=37.97 E-value=29 Score=22.35 Aligned_cols=29 Identities=21% Similarity=0.418 Sum_probs=20.4
Q ss_pred CcccCCCCCceeecCCCCceeEe-ecCCce
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
.+-.||.|+-.++-+.+=+.+.| .|+-.|
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeec
Confidence 34579999998887665567777 476543
No 225
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.63 E-value=23 Score=36.59 Aligned_cols=30 Identities=37% Similarity=1.001 Sum_probs=22.6
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCce-----ecccCcccC
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTRF-----CYECGRKIS 217 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~F-----C~~C~~~~~ 217 (263)
++||+|+..+.. -.| .||.+. |-.||....
T Consensus 668 rkCPkCG~~t~~------~fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCcccc------ccCcccCCcCCCceeCccCCCccC
Confidence 799999998753 288 488663 888888754
No 226
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.33 E-value=24 Score=30.22 Aligned_cols=24 Identities=33% Similarity=0.825 Sum_probs=20.1
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
.+|+.|+.+|+|. +|=+-.+| .|.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 6899999999977 88887888 475
No 227
>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=35.68 E-value=39 Score=28.18 Aligned_cols=54 Identities=17% Similarity=0.396 Sum_probs=38.0
Q ss_pred cccCCCCCCCc-cCccccccCCChhhHHHHHHHHHHHhhcCCCcccCCccccccceec
Q 024715 68 IDCPGLDCKHN-LDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVN 124 (263)
Q Consensus 68 i~CP~~~C~~~-l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 124 (263)
-+||. |+.- ....++.-+++++-+-+.-+.-..+.+. .+-..||.++|+.++..
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIFs-~GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIFS-RGPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHhc-CCCCCCCCccHHHHHHH
Confidence 37999 9864 3345788888888777666654444432 56688999999987644
No 228
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=34.98 E-value=28 Score=20.14 Aligned_cols=18 Identities=28% Similarity=0.744 Sum_probs=16.0
Q ss_pred ceeCCccccccccccccC
Q 024715 134 KTQCPNCKQWFCFQCKLK 151 (263)
Q Consensus 134 ~~~C~~C~~~~C~~C~~~ 151 (263)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 688999999999988876
No 229
>PLN02436 cellulose synthase A
Probab=34.85 E-value=37 Score=34.66 Aligned_cols=52 Identities=31% Similarity=0.729 Sum_probs=36.2
Q ss_pred CCccccccccccccc---cccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAA---SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
.....|.||-+++.. .+.|+..-.|+-.+|+.|. +|-. + ...-.||. |+...
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~---eg~~~Cpq--ckt~Y 88 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---R---EGNQACPQ--CKTRY 88 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---h---cCCccCcc--cCCch
Confidence 445699999999743 3456666679999999999 4433 2 23346998 88643
No 230
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=34.75 E-value=21 Score=27.40 Aligned_cols=33 Identities=21% Similarity=0.386 Sum_probs=19.6
Q ss_pred CCcccCCccccccceecccccc--CCCCceeCCcccc
Q 024715 108 FERSYCPNTNCMALVVNECERS--GKVKKTQCPNCKQ 142 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~ 142 (263)
.....|| .|+..+...+... +....+.||.||.
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 4467899 6887666433211 1123488988774
No 231
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=34.56 E-value=8.8 Score=20.10 Aligned_cols=20 Identities=15% Similarity=0.436 Sum_probs=13.7
Q ss_pred cccCCCCCCCccCccccccCCC
Q 024715 68 IDCPGLDCKHNLDPFACEPVIP 89 (263)
Q Consensus 68 i~CP~~~C~~~l~~~~i~~~l~ 89 (263)
+.||. |...+....+...|+
T Consensus 2 v~CPi--C~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLD 21 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHH
Confidence 57998 988876655555444
No 232
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.51 E-value=29 Score=33.79 Aligned_cols=34 Identities=26% Similarity=0.607 Sum_probs=25.1
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCc----eecccCcc
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTR----FCYECGRK 215 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~----FC~~C~~~ 215 (263)
-+||+|..+..-..+=+.+.| .||+. .|-.|+..
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 379999988876555578999 59864 57777665
No 233
>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=34.25 E-value=38 Score=28.48 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=24.7
Q ss_pred CCCcccCCccccccceecccccc----------CCCCceeCCcccccc
Q 024715 107 GFERSYCPNTNCMALVVNECERS----------GKVKKTQCPNCKQWF 144 (263)
Q Consensus 107 ~~~~~~Cp~~~C~~~~~~~~~~~----------~~~~~~~C~~C~~~~ 144 (263)
...++.||.++|+.++....... ....++.|.+|...|
T Consensus 120 sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 120 SSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred ccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 35678999999999997655411 113456776665443
No 234
>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 PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.24 E-value=28 Score=29.68 Aligned_cols=25 Identities=32% Similarity=0.922 Sum_probs=18.4
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecCC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCNT 206 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~~ 206 (263)
++||.|+..|++. +|=.-.+| .|..
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 6899999999865 66655666 4643
No 236
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=34.07 E-value=39 Score=33.08 Aligned_cols=47 Identities=26% Similarity=0.603 Sum_probs=33.9
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (263)
...+.|.||--.+..... ....|+|....+|...|++..- .||. ||+
T Consensus 1026 ~~~~~C~~C~l~V~gss~--~Cg~C~Hv~H~sc~~eWf~~gd--------~Cps-GCG 1072 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRGSSN--FCGTCGHVGHTSCMMEWFRTGD--------VCPS-GCG 1072 (1081)
T ss_pred cceeeeeeEeeEeeccch--hhccccccccHHHHHHHHhcCC--------cCCC-CCC
Confidence 456778888766644433 2688999999999999998322 6886 344
No 237
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=34.03 E-value=46 Score=33.90 Aligned_cols=43 Identities=26% Similarity=0.534 Sum_probs=29.9
Q ss_pred CCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCceeecCCCCc
Q 024715 132 VKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGCS 198 (263)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GCn 198 (263)
...|.|..|++..|..|. ++. .+.+.+.||.|+....+.-|.+
T Consensus 32 e~FVAC~eC~fpvCr~cy----------eye--------------~~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 32 QPFVACHVCGFPVCKPCY----------EYE--------------RSEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred CEEEEeccCCCccccchh----------hhh--------------hhcCCccCCccCCchhhhcCCC
Confidence 578999999999998663 222 2345677888888887544443
No 238
>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=33.66 E-value=29 Score=21.26 Aligned_cols=47 Identities=17% Similarity=0.546 Sum_probs=23.7
Q ss_pred cccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCC
Q 024715 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (263)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (263)
..|+|-+..+..+.. ...|.|.-|- =+..|+....+. ..-.||. |++
T Consensus 3 L~CPls~~~i~~P~R---g~~C~H~~CF-Dl~~fl~~~~~~---~~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVR---GKNCKHLQCF-DLESFLESNQRT---PKWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSEEE---ETT--SS--E-EHHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeCcc---CCcCcccceE-CHHHHHHHhhcc---CCeECcC--CcC
Confidence 467777777754432 4789999763 366778777764 3378998 875
No 239
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=33.63 E-value=31 Score=21.78 Aligned_cols=31 Identities=16% Similarity=0.389 Sum_probs=19.1
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (263)
+.|| +|...-..-+.. ...+.|..|+...|.
T Consensus 8 VkCp--~C~~~q~vFSha---~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSHA---QTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT----SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEecC---CeEEEcccCCCEecC
Confidence 5788 888776655442 578999999887774
No 240
>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=33.43 E-value=30 Score=19.15 Aligned_cols=22 Identities=27% Similarity=0.495 Sum_probs=12.4
Q ss_pred ccccceeccccccCCCCceeCCccccc
Q 024715 117 NCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 117 ~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
+|+..+.... ...++|+.||..
T Consensus 5 ~Cg~~~~~~~-----~~~irC~~CG~R 26 (32)
T PF03604_consen 5 ECGAEVELKP-----GDPIRCPECGHR 26 (32)
T ss_dssp SSSSSE-BST-----SSTSSBSSSS-S
T ss_pred cCCCeeEcCC-----CCcEECCcCCCe
Confidence 5666665333 346788888753
No 241
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.78 E-value=21 Score=31.15 Aligned_cols=46 Identities=30% Similarity=0.821 Sum_probs=31.2
Q ss_pred CccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCC
Q 024715 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (263)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (263)
....|..|.++..+...+ ....|.+.||.+|=. ++-..+. .||. |.
T Consensus 329 ~~~~Cf~C~~~~~~~~~y-~C~~Ck~~FCldCDv-~iHesLh-------~Cpg--Ce 374 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRY-RCESCKNVFCLDCDV-FIHESLH-------NCPG--CE 374 (378)
T ss_pred CCcceeeeccccCCCCcE-EchhccceeeccchH-HHHhhhh-------cCCC--cC
Confidence 334499998777655554 468899999999954 3333443 3776 65
No 242
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=32.76 E-value=39 Score=21.00 Aligned_cols=34 Identities=29% Similarity=0.510 Sum_probs=18.1
Q ss_pred CcccCCccccccceecccc------ccCCCCceeCCccccc
Q 024715 109 ERSYCPNTNCMALVVNECE------RSGKVKKTQCPNCKQW 143 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~------~~~~~~~~~C~~C~~~ 143 (263)
+.+.||||.|-.- ..++. .+.....++|..|...
T Consensus 5 gvl~C~Np~CITn-~~E~v~~~F~v~~~~~~~~rC~YCe~~ 44 (52)
T PF02748_consen 5 GVLKCPNPNCITN-SNEPVESRFYVIDKEPIKLRCHYCERI 44 (52)
T ss_dssp SSSE-SSTTBTTT--TSSS--EEEEEETTTCEEEETTT--E
T ss_pred eEEEcCCCCcccC-CCCCCCceEEEEeCCCCEEEeeCCCCE
Confidence 4578999999765 11111 1122567888877653
No 243
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.71 E-value=28 Score=30.76 Aligned_cols=45 Identities=20% Similarity=0.490 Sum_probs=29.6
Q ss_pred CCCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
......|.||.++..+. ...+|||.-| |..-+- ....||. |.+.|
T Consensus 302 ~~~p~lcVVcl~e~~~~----~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSA----VFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred cCCCCceEEecCCccce----eeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 34567899999988553 2489999866 433221 2234998 87654
No 244
>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=32.56 E-value=37 Score=19.87 Aligned_cols=26 Identities=31% Similarity=0.598 Sum_probs=14.1
Q ss_pred cCCccccccceeccccccCCCCceeCCcccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.|| .|+......+.. ...+.|+.||.
T Consensus 2 ~Cp--~Cg~~~~~~D~~---~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPE---RGELVCPNCGL 27 (43)
T ss_dssp SBT--TTSSSEEEEETT---TTEEEETTT-B
T ss_pred CCc--CCcCCceEEcCC---CCeEECCCCCC
Confidence 477 677755333321 35667776664
No 245
>PRK10445 endonuclease VIII; Provisional
Probab=32.29 E-value=33 Score=29.15 Aligned_cols=24 Identities=25% Similarity=0.760 Sum_probs=18.3
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
++||.|+..|++. +|=.-.+| .|.
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 6899999999865 77666666 464
No 246
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.86 E-value=33 Score=29.28 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=18.0
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
++||.|+..|++. +|=.-.+| .|.
T Consensus 245 ~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 245 EPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CcCCCCCCeeEEEEECCCccEECcCCc
Confidence 6999999999865 66655666 454
No 247
>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=31.61 E-value=17 Score=19.83 Aligned_cols=15 Identities=27% Similarity=0.729 Sum_probs=7.4
Q ss_pred ccccCCCCCCCccCc
Q 024715 67 KIDCPGLDCKHNLDP 81 (263)
Q Consensus 67 ~i~CP~~~C~~~l~~ 81 (263)
.++||..+|...+..
T Consensus 2 ~vrCPvkdC~EEv~l 16 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSL 16 (30)
T ss_dssp EEE--STT---EEEH
T ss_pred ccccccccCcchhhh
Confidence 478999999987754
No 248
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=31.56 E-value=35 Score=29.16 Aligned_cols=24 Identities=38% Similarity=0.942 Sum_probs=18.2
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
++||.|+..|+|. +|=.-.+| .|.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 6899999999866 66666666 464
No 249
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.34 E-value=23 Score=18.19 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=6.3
Q ss_pred eeCCcccccc
Q 024715 135 TQCPNCKQWF 144 (263)
Q Consensus 135 ~~C~~C~~~~ 144 (263)
+.|+.|+..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5666666655
No 250
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=31.05 E-value=29 Score=33.69 Aligned_cols=59 Identities=29% Similarity=0.576 Sum_probs=40.1
Q ss_pred CCcccccccccccccccc------ccccCCCCC--------------------ccHHHHHHHHHHHHhhCCCCcccccCC
Q 024715 19 GSSFTCEICIEPMAASKK------FKNRNLCTH--------------------PFCQDCIARYIQVKVQDDNTAKIDCPG 72 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~------~~~~~~C~H--------------------~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (263)
....+|.-|++++.++.. |...+.||- ..|.+|.+.|-.-.-+.=...++.||.
T Consensus 99 pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aCp~ 178 (750)
T COG0068 99 PDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIACPK 178 (750)
T ss_pred CchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccCcc
Confidence 456799999998877654 334455653 269999998865433322456899999
Q ss_pred CCCCCcc
Q 024715 73 LDCKHNL 79 (263)
Q Consensus 73 ~~C~~~l 79 (263)
|+-.+
T Consensus 179 --CGP~~ 183 (750)
T COG0068 179 --CGPHL 183 (750)
T ss_pred --cCCCe
Confidence 88543
No 251
>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=31.00 E-value=25 Score=27.39 Aligned_cols=30 Identities=20% Similarity=0.275 Sum_probs=19.9
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
+....|| .|..-+...+.. ...+.||.||.
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~---~~~F~Cp~Cg~ 136 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAM---ELNFTCPRCGA 136 (158)
T ss_pred CCeEECC--CCCcEeeHHHHH---HcCCcCCCCCC
Confidence 4567798 587666554442 35789988874
No 252
>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=30.71 E-value=2e+02 Score=24.38 Aligned_cols=33 Identities=24% Similarity=0.696 Sum_probs=22.8
Q ss_pred ccCCC--CCceeecC--------------CCCceeEe-ecCCceecccCc
Q 024715 182 ARCPA--CGHCVERK--------------DGCSVVMC-RCNTRFCYECGR 214 (263)
Q Consensus 182 k~CP~--C~~~i~k~--------------~GCnhm~C-~C~~~FC~~C~~ 214 (263)
..||. |+..|... .|--.++| .|...|=|.=..
T Consensus 124 IaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~ 173 (256)
T PF09788_consen 124 IACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLT 173 (256)
T ss_pred ccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCC
Confidence 45775 88877532 23334899 799999998655
No 253
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=30.53 E-value=54 Score=24.95 Aligned_cols=14 Identities=43% Similarity=0.873 Sum_probs=9.8
Q ss_pred CcccCCccccccceec
Q 024715 109 ERSYCPNTNCMALVVN 124 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~ 124 (263)
+...|| .|+..+..
T Consensus 2 ~l~nC~--~CgklF~~ 15 (137)
T TIGR03826 2 ELANCP--KCGRLFVK 15 (137)
T ss_pred CCcccc--ccchhhhh
Confidence 345688 78887766
No 254
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=30.36 E-value=45 Score=21.15 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=16.2
Q ss_pred cCCCcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 106 LGFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 106 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
..+.+..|| .|+.+. .....|+.||+
T Consensus 23 ~~~~l~~C~--~CG~~~---------~~H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECP--NCGEPK---------LPHRVCPSCGY 48 (57)
T ss_pred cCCcceECC--CCCCcc---------CCeEECCCCCc
Confidence 346667787 677665 33556777764
No 255
>PRK05580 primosome assembly protein PriA; Validated
Probab=30.26 E-value=38 Score=33.06 Aligned_cols=33 Identities=27% Similarity=0.717 Sum_probs=25.6
Q ss_pred cCCCCCceeecCCCCceeEe-ecCCc-----eecccCcc
Q 024715 183 RCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (263)
+||+|..+..-...=+.+.| .||+. .|-.|++.
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 69999988764444578999 59976 58999776
No 256
>PHA02929 N1R/p28-like protein; Provisional
Probab=30.23 E-value=25 Score=29.49 Aligned_cols=41 Identities=27% Similarity=0.430 Sum_probs=27.2
Q ss_pred CCcccCCCCCceeecCCCCc---eeEeecCCceecccCcccCCC
Q 024715 179 MKWARCPACGHCVERKDGCS---VVMCRCNTRFCYECGRKISSG 219 (263)
Q Consensus 179 ~~~k~CP~C~~~i~k~~GCn---hm~C~C~~~FC~~C~~~~~~~ 219 (263)
.....||-|.-.+.....-+ -+.-.|++.||..|...|...
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~ 215 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE 215 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc
Confidence 34578999998876543221 133358888888888888643
No 257
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=30.19 E-value=25 Score=25.05 Aligned_cols=35 Identities=29% Similarity=0.605 Sum_probs=23.3
Q ss_pred cCCCCCccccccccccccccccccccCCCCCccHHHH
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDC 51 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~C 51 (263)
...+...|+|.-||-..-.+ .+- ...=|+.+|.+|
T Consensus 64 iP~q~DEFTCssCFLV~HRS-qLa-~~~~g~~iC~DC 98 (99)
T PF13834_consen 64 IPKQADEFTCSSCFLVHHRS-QLA-REKDGQPICRDC 98 (99)
T ss_pred ecCCCCceeeeeeeeEechh-hhc-cccCCCEecccc
Confidence 55567889999999666333 221 233478888887
No 258
>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=30.10 E-value=37 Score=29.04 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=17.5
Q ss_pred ccCCCCCceeecC--CCCceeEe-ec
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RC 204 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C 204 (263)
++||.|+..|.+. +|=.-.+| .|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCC
Confidence 6899999999876 66555666 35
No 259
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=30.03 E-value=94 Score=22.40 Aligned_cols=57 Identities=21% Similarity=0.507 Sum_probs=33.9
Q ss_pred CCcccccccccccccccccc----ccCCC---CCccHHHHHHHHHHHHhhCC-CCcccccCCCCCCC
Q 024715 19 GSSFTCEICIEPMAASKKFK----NRNLC---THPFCQDCIARYIQVKVQDD-NTAKIDCPGLDCKH 77 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~----~~~~C---~H~fC~~Cl~~~~~~~i~~~-~~~~i~CP~~~C~~ 77 (263)
....+|..|.....+....- ....| .-.||..||...+...+.+. ....-.||. |..
T Consensus 5 ~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--Crg 69 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRG 69 (105)
T ss_pred CCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCC--CCC
Confidence 34456777766443222110 12456 67899999998887666431 134578987 665
No 260
>PLN02400 cellulose synthase
Probab=30.01 E-value=39 Score=34.52 Aligned_cols=61 Identities=23% Similarity=0.358 Sum_probs=39.0
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCce
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 190 (263)
..|- -|+.-+-.... ....|.|..|++-.|..|. ++++ +.+.+.||+|+..
T Consensus 37 qiCq--ICGD~VG~t~d---Ge~FVAC~eCaFPVCRpCY----------EYER--------------keGnq~CPQCkTr 87 (1085)
T PLN02400 37 QICQ--ICGDDVGVTET---GDVFVACNECAFPVCRPCY----------EYER--------------KDGTQCCPQCKTR 87 (1085)
T ss_pred ceee--ecccccCcCCC---CCEEEEEccCCCccccchh----------heec--------------ccCCccCcccCCc
Confidence 4455 56655544332 2578999999999998664 3222 3456778888888
Q ss_pred eecCCCCcee
Q 024715 191 VERKDGCSVV 200 (263)
Q Consensus 191 i~k~~GCnhm 200 (263)
..+.-|+..+
T Consensus 88 YkR~KgsprV 97 (1085)
T PLN02400 88 YRRHKGSPRV 97 (1085)
T ss_pred cccccCCCCC
Confidence 8766555444
No 261
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.99 E-value=17 Score=31.17 Aligned_cols=31 Identities=26% Similarity=0.526 Sum_probs=22.6
Q ss_pred ccccccccccccccccccccCCCCCc-cHHHHHHHH
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARY 55 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 55 (263)
...|.||++.- .+-| +++|||. -|..|-+.+
T Consensus 300 ~~LC~ICmDaP--~DCv--fLeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCV--FLECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHHhcCC--cceE--EeecCcEEeehhhcccc
Confidence 67899999875 3444 4999995 677775543
No 262
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.68 E-value=28 Score=27.77 Aligned_cols=30 Identities=23% Similarity=0.503 Sum_probs=19.5
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
+....|| .|+.-+...+.. ...+.||.||.
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~---~~~F~Cp~Cg~ 144 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM---EYGFRCPQCGE 144 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh---hcCCcCCCCCC
Confidence 4567798 587666554432 35788887763
No 263
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=29.39 E-value=40 Score=26.98 Aligned_cols=25 Identities=20% Similarity=0.522 Sum_probs=20.4
Q ss_pred cCCCCCceeecCCCCceeEe-ecCCce
Q 024715 183 RCPACGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 183 ~CP~C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
.|+.|+.+..+... |.|.| .|++..
T Consensus 151 ~~~~~g~~~~~~~~-~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKGE-NELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECCC-CEEECCCCCCEE
Confidence 69999999988555 99999 698653
No 264
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.29 E-value=47 Score=28.93 Aligned_cols=55 Identities=16% Similarity=0.321 Sum_probs=35.3
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCc
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (263)
.+.+.||+=-+.-. .++-+.++.|||.+=++=+.. +..++...++||. |...-..
T Consensus 334 Hs~FiCPVlKe~~t-~ENpP~ml~CgHVIskeal~~-----LS~nG~~~FKCPY--CP~~~~~ 388 (396)
T COG5109 334 HSLFICPVLKELCT-DENPPVMLECGHVISKEALSV-----LSQNGVLSFKCPY--CPEMSKY 388 (396)
T ss_pred cceeeccccHhhhc-ccCCCeeeeccceeeHHHHHH-----HhhcCcEEeeCCC--CCcchhh
Confidence 45688988554442 223345699999997765544 3334566899998 8764333
No 265
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.00 E-value=46 Score=30.92 Aligned_cols=35 Identities=26% Similarity=0.579 Sum_probs=24.6
Q ss_pred ccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCCCCceeec
Q 024715 139 NCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVER 193 (263)
Q Consensus 139 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 193 (263)
.||..||+.|...+ ..+.+...++.||-|+..|..
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 48999999886642 111134578999999998865
No 266
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.95 E-value=38 Score=29.11 Aligned_cols=24 Identities=38% Similarity=0.836 Sum_probs=18.7
Q ss_pred ccCCCCCceeecC--CCCceeEe-ecC
Q 024715 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (263)
Q Consensus 182 k~CP~C~~~i~k~--~GCnhm~C-~C~ 205 (263)
++||.|+..|.|. +|=.-.+| .|.
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 6999999999865 77666667 464
No 267
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.85 E-value=21 Score=23.14 Aligned_cols=14 Identities=36% Similarity=0.686 Sum_probs=10.9
Q ss_pred CcccCCCCCceeec
Q 024715 180 KWARCPACGHCVER 193 (263)
Q Consensus 180 ~~k~CP~C~~~i~k 193 (263)
.+.+||.|+.++..
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 45789998888874
No 268
>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=28.85 E-value=30 Score=29.80 Aligned_cols=35 Identities=31% Similarity=0.824 Sum_probs=16.6
Q ss_pred ccCCCCCce-----eecCC--CCceeEe-ecCCce------ecccCccc
Q 024715 182 ARCPACGHC-----VERKD--GCSVVMC-RCNTRF------CYECGRKI 216 (263)
Q Consensus 182 k~CP~C~~~-----i~k~~--GCnhm~C-~C~~~F------C~~C~~~~ 216 (263)
..||-||.. |...+ |=.+++| .|+++| |-.||..-
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 689999985 33334 7899999 599886 77888873
No 269
>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=28.37 E-value=38 Score=24.73 Aligned_cols=23 Identities=35% Similarity=0.859 Sum_probs=14.9
Q ss_pred CCCceeCCcccccc--------ccccccCCC
Q 024715 131 KVKKTQCPNCKQWF--------CFQCKLKWH 153 (263)
Q Consensus 131 ~~~~~~C~~C~~~~--------C~~C~~~~H 153 (263)
+...+.||.|++.+ |..|+.+.+
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 35677788776443 777777654
No 270
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.02 E-value=60 Score=23.76 Aligned_cols=27 Identities=22% Similarity=0.721 Sum_probs=15.9
Q ss_pred CcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
...+|+ +|+..+..... ..+.||.||.
T Consensus 69 ~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCE--TCQQYVTLLTQ-----RVRRCPQCHG 95 (114)
T ss_pred cEEEcc--cCCCeeecCCc-----cCCcCcCcCC
Confidence 347788 78866554322 2356777763
No 271
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=28.02 E-value=26 Score=27.41 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=15.4
Q ss_pred hHHHHHHHhcCCcccCCCCCc
Q 024715 169 DIVFGQLVERMKWARCPACGH 189 (263)
Q Consensus 169 ~~~~~~~~~~~~~k~CP~C~~ 189 (263)
...+.+...+...|.|++||.
T Consensus 139 ~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 139 PPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred HHHHHHHhCChhhccCCccCC
Confidence 345566666778899999984
No 272
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=27.96 E-value=25 Score=27.99 Aligned_cols=49 Identities=22% Similarity=0.518 Sum_probs=27.7
Q ss_pred cccccccccCCCC-CCCchhHHhccccchHHHHHHHhcCCcccCCCCCceeec
Q 024715 142 QWFCFQCKLKWHA-GYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVER 193 (263)
Q Consensus 142 ~~~C~~C~~~~H~-~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 193 (263)
..+|..|....|. -..|.+... +-...+.+...+...|.|++||..-..
T Consensus 120 ~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 120 QWYCDECNHKVHEVEVQLTDIET---DLPPVFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred EEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhcCHhhccCCcCCcccCc
Confidence 3444455555543 122433322 123455666667788999999987653
No 273
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.94 E-value=36 Score=29.51 Aligned_cols=32 Identities=28% Similarity=0.653 Sum_probs=22.9
Q ss_pred ccccccccccccccccccccCCCCCccHHHHHHHH
Q 024715 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARY 55 (263)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 55 (263)
...|.-|--.+. .+-.+.+|.|.||.+|.+..
T Consensus 90 VHfCd~Cd~PI~---IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIA---IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcce---eeecccccchhhhhhhhhcC
Confidence 567888866653 22235899999999998643
No 274
>PRK12495 hypothetical protein; Provisional
Probab=27.88 E-value=60 Score=26.74 Aligned_cols=29 Identities=34% Similarity=0.841 Sum_probs=22.1
Q ss_pred CcccCCCCCceeecCCCCceeEeecCCceecccCcccC
Q 024715 180 KWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKIS 217 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~ 217 (263)
..+-||.|+.+|.+..| ..||-.|...+.
T Consensus 41 sa~hC~~CG~PIpa~pG---------~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG---------QEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCcccCCCC---------eeECCCCCCccc
Confidence 34789999999997777 467777776654
No 275
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=27.73 E-value=1.2e+02 Score=19.44 Aligned_cols=35 Identities=17% Similarity=0.262 Sum_probs=25.1
Q ss_pred ccCCCCCCCccCccccccCCChhhHHHHHHHHHHHhh
Q 024715 69 DCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYV 105 (263)
Q Consensus 69 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~ 105 (263)
+||. |+.......-..+-..|-+.+|...+.+...
T Consensus 19 ~Cp~--CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~ 53 (59)
T COG2260 19 KCPV--CGGDTKVPHPPRFSPEDKYGKYRRELKKRLG 53 (59)
T ss_pred cCCC--CCCccccCCCCCCCccchHHHHHHHHHHHhc
Confidence 5998 9876655555556666788899888776543
No 276
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=27.72 E-value=49 Score=27.12 Aligned_cols=36 Identities=19% Similarity=0.431 Sum_probs=23.0
Q ss_pred CCcccCCccccccceeccccccC--------CCCceeCCccccc
Q 024715 108 FERSYCPNTNCMALVVNECERSG--------KVKKTQCPNCKQW 143 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~--------~~~~~~C~~C~~~ 143 (263)
..++-||.|.|..++......+. ..-+|.|.+|+..
T Consensus 136 SqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~t 179 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNET 179 (275)
T ss_pred cceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCccce
Confidence 56788999999998876543221 1235667665533
No 277
>PF09680 Tiny_TM_bacill: Protein of unknown function (Tiny_TM_bacill); InterPro: IPR010070 This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=27.31 E-value=68 Score=16.43 Aligned_cols=12 Identities=25% Similarity=0.897 Sum_probs=8.1
Q ss_pred HHHHHHHHHhhh
Q 024715 237 MMVIFHVIVLAG 248 (263)
Q Consensus 237 ~~~~~~~~~~~~ 248 (263)
+.++|+++++.|
T Consensus 9 ivVLFILLiIvG 20 (24)
T PF09680_consen 9 IVVLFILLIIVG 20 (24)
T ss_pred HHHHHHHHHHhc
Confidence 456777777766
No 278
>TIGR01732 tiny_TM_bacill conserved hypothetical tiny transmembrane protein. This model represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=27.26 E-value=73 Score=16.68 Aligned_cols=14 Identities=29% Similarity=0.731 Sum_probs=9.2
Q ss_pred HHHHHHHHHHhhhh
Q 024715 236 AMMVIFHVIVLAGM 249 (263)
Q Consensus 236 ~~~~~~~~~~~~~~ 249 (263)
++.++|+++++.|-
T Consensus 10 livVLFILLIIiga 23 (26)
T TIGR01732 10 LIVVLFILLVIVGA 23 (26)
T ss_pred HHHHHHHHHHHhhe
Confidence 45567777777663
No 279
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.15 E-value=47 Score=32.70 Aligned_cols=35 Identities=23% Similarity=0.541 Sum_probs=26.3
Q ss_pred ccCCccccccceeccccccCCCCceeCCccccc-----cccccccC
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW-----FCFQCKLK 151 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 151 (263)
..|| .|..++..... .....|+.||+. .|..|+..
T Consensus 445 ~~Cp--~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECP--NCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCC--CCCcceEEecC----CCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4466 67777766655 578999999876 68888887
No 280
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=26.24 E-value=81 Score=20.28 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=10.1
Q ss_pred cccccCCCCCCCccCc
Q 024715 66 AKIDCPGLDCKHNLDP 81 (263)
Q Consensus 66 ~~i~CP~~~C~~~l~~ 81 (263)
.|++|+. |+.++..
T Consensus 3 iPVRCFT--CGkvi~~ 16 (60)
T PF01194_consen 3 IPVRCFT--CGKVIGN 16 (60)
T ss_dssp -SSS-ST--TTSBTCG
T ss_pred CceecCC--CCCChhH
Confidence 5899998 9998863
No 281
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=26.04 E-value=64 Score=32.94 Aligned_cols=55 Identities=22% Similarity=0.679 Sum_probs=38.0
Q ss_pred CCCCcccccccccccccc---ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccC
Q 024715 17 GGGSSFTCEICIEPMAAS---KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (263)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (263)
.......|.||-+++... +.|+..-.|+-.+|+.|. +|-. ++ ..-.||. |+....
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~---~~---g~~~cp~--c~t~y~ 68 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYER---SE---GNQCCPQ--CNTRYK 68 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhhh---hc---CCccCCc--cCCchh
Confidence 344677899999997543 446666779999999999 4432 22 3346998 886543
No 282
>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=25.87 E-value=23 Score=35.07 Aligned_cols=34 Identities=29% Similarity=0.821 Sum_probs=0.0
Q ss_pred CcccCCCCCceeecCCCCceeEe-ecCCc-----eecccCcccCCC
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRKISSG 219 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~~~ 219 (263)
..++||+|+..... .+| .||.+ +|..|+......
T Consensus 654 ~~r~Cp~Cg~~t~~------~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 654 GRRRCPKCGKETFY------NRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ----------------------------------------------
T ss_pred ecccCcccCCcchh------hcCcccCCccccceeccccccccCcc
Confidence 45899999998753 678 59876 899998886543
No 283
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=25.85 E-value=39 Score=20.43 Aligned_cols=35 Identities=20% Similarity=0.501 Sum_probs=26.4
Q ss_pred ccccccccccccccccccCCCCCccHHHHHHHHHHHHhhC
Q 024715 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD 62 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 62 (263)
.|.||-++..+. +.--+..+|.+|-+..++....+
T Consensus 1 ~CiiC~~~~~~G-----I~I~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEEG-----IHIYGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCCC-----EEEECeEehHHHHHHhccCCCCC
Confidence 488898887543 23358899999999999877765
No 284
>PLN03086 PRLI-interacting factor K; Provisional
Probab=25.30 E-value=41 Score=31.94 Aligned_cols=29 Identities=28% Similarity=0.743 Sum_probs=24.5
Q ss_pred CcccCCC--CCceeecCCCCceeEe-ecCCce
Q 024715 180 KWARCPA--CGHCVERKDGCSVVMC-RCNTRF 208 (263)
Q Consensus 180 ~~k~CP~--C~~~i~k~~GCnhm~C-~C~~~F 208 (263)
+...||+ |+..+.+...=+|..| .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 4578995 9999999999999999 598765
No 285
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.13 E-value=55 Score=27.73 Aligned_cols=28 Identities=25% Similarity=0.613 Sum_probs=21.2
Q ss_pred CcccCCCCCceeecCCCCceeEe-ecCCc
Q 024715 180 KWARCPACGHCVERKDGCSVVMC-RCNTR 207 (263)
Q Consensus 180 ~~k~CP~C~~~i~k~~GCnhm~C-~C~~~ 207 (263)
..+-||.||..+....+=..+.| .|+..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 35899999999877655567888 58743
No 286
>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=25.12 E-value=60 Score=20.41 Aligned_cols=25 Identities=28% Similarity=0.697 Sum_probs=15.1
Q ss_pred CCCcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 107 GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 107 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.+.+..|| .|+.+. .....|+.||+
T Consensus 23 ~p~l~~C~--~cG~~~---------~~H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCP--NCGEFK---------LPHRVCPSCGY 47 (55)
T ss_pred CCcceECC--CCCCcc---------cCeeECCccCe
Confidence 35566777 676655 33556766664
No 287
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.82 E-value=1.2e+02 Score=22.68 Aligned_cols=37 Identities=19% Similarity=0.449 Sum_probs=22.3
Q ss_pred CCcccCCccccccceecc-ccccCCCCceeCCcccccccc
Q 024715 108 FERSYCPNTNCMALVVNE-CERSGKVKKTQCPNCKQWFCF 146 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~-~~~~~~~~~~~C~~C~~~~C~ 146 (263)
....+|| -|....... ...........|+.|++.|=.
T Consensus 28 ~~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 28 ITKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cccCcCC--CCCccceeeECCccccccccccCCcCcceee
Confidence 4458899 787766222 221122568889888776643
No 288
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.75 E-value=78 Score=23.15 Aligned_cols=24 Identities=29% Similarity=0.726 Sum_probs=13.3
Q ss_pred cccCCccccccceeccccccCCCCceeCCccc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (263)
..+|+ +|+..+.... ..+.||.|+
T Consensus 70 ~~~C~--~Cg~~~~~~~------~~~~CP~Cg 93 (115)
T TIGR00100 70 ECECE--DCSEEVSPEI------DLYRCPKCH 93 (115)
T ss_pred EEEcc--cCCCEEecCC------cCccCcCCc
Confidence 46677 6775554432 235566665
No 289
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=24.70 E-value=1.1e+02 Score=24.43 Aligned_cols=35 Identities=26% Similarity=0.444 Sum_probs=16.6
Q ss_pred CCcccCCccccccceecccccc----CCCCceeCCcccc
Q 024715 108 FERSYCPNTNCMALVVNECERS----GKVKKTQCPNCKQ 142 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~----~~~~~~~C~~C~~ 142 (263)
.++-.||+-.|++.-...-+.+ ....++.||.|+.
T Consensus 97 g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~d 135 (184)
T PF01214_consen 97 GDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKD 135 (184)
T ss_dssp TTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTE
T ss_pred CcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCcc
Confidence 5667899999987432221111 1145566665543
No 290
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.69 E-value=1e+02 Score=26.45 Aligned_cols=30 Identities=17% Similarity=0.358 Sum_probs=23.3
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCccccc
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (263)
...++|+ .|+........ .....|+.|+..
T Consensus 109 ~~~RFCg--~CG~~~~~~~~----g~~~~C~~cg~~ 138 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREG----GWARVCPKCGHE 138 (279)
T ss_pred hhCcCCC--CCCCcCccccC----ceeeeCCCCCCc
Confidence 4568999 89988877666 578899998744
No 291
>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=24.15 E-value=97 Score=16.10 Aligned_cols=23 Identities=30% Similarity=0.732 Sum_probs=16.4
Q ss_pred CCCCCceeecCCCCceeEee-cCC
Q 024715 184 CPACGHCVERKDGCSVVMCR-CNT 206 (263)
Q Consensus 184 CP~C~~~i~k~~GCnhm~C~-C~~ 206 (263)
|-+|+.++.--.|=.++.|. |++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 45677777777777778883 654
No 292
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=24.13 E-value=80 Score=32.39 Aligned_cols=52 Identities=29% Similarity=0.828 Sum_probs=36.3
Q ss_pred CCCcccccccccccccc---ccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCc
Q 024715 18 GGSSFTCEICIEPMAAS---KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (263)
Q Consensus 18 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (263)
+.....|.||-+++... +.|+..-.|+-..|+.|. +|-. ++ ..-.||. |+..
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr---~e---G~q~CPq--Cktr 68 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER---KD---GNQSCPQ--CKTK 68 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh---hc---CCccCCc--cCCc
Confidence 34556999999997543 456666779999999999 4433 22 3346998 8854
No 293
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.08 E-value=41 Score=33.26 Aligned_cols=43 Identities=26% Similarity=0.582 Sum_probs=32.5
Q ss_pred CCccccccccccccccccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCC
Q 024715 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (263)
.+...|..|--+...+.. -..|+|.|.+.|+. + ..-.||. |..
T Consensus 838 ~q~skCs~C~~~LdlP~V---hF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 838 FQVSKCSACEGTLDLPFV---HFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeeeeecccCCcccccee---eeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 344689999988865543 37899999999998 1 2357998 876
No 294
>PLN02189 cellulose synthase
Probab=23.80 E-value=60 Score=33.11 Aligned_cols=52 Identities=29% Similarity=0.704 Sum_probs=35.8
Q ss_pred CCccccccccccccc---cccccccCCCCCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCcc
Q 024715 19 GSSFTCEICIEPMAA---SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (263)
Q Consensus 19 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (263)
.....|.||-+++.. .+.|+..-.|+-.+|+.|. +|-. + ...-.||. |+...
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~---eg~q~Cpq--Ckt~Y 86 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---R---EGTQNCPQ--CKTRY 86 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---h---cCCccCcc--cCCch
Confidence 445699999999753 3446555669999999999 4433 2 23346998 88643
No 295
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.63 E-value=83 Score=22.96 Aligned_cols=24 Identities=29% Similarity=0.841 Sum_probs=13.1
Q ss_pred cccCCccccccceeccccccCCCCceeCCccc
Q 024715 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (263)
..+|+ +|+..+.... ..+.||.|+
T Consensus 70 ~~~C~--~Cg~~~~~~~------~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCW--DCSQVVEIHQ------HDAQCPHCH 93 (113)
T ss_pred EEEcc--cCCCEEecCC------cCccCcCCC
Confidence 46677 6775554432 234466665
No 296
>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=23.62 E-value=20 Score=31.78 Aligned_cols=60 Identities=25% Similarity=0.522 Sum_probs=24.8
Q ss_pred ccccccccccccCCCCC-CCchhHHhccccchHHHHHHHhcCCcccCCCCCceeecCCCCceeEe-ecC
Q 024715 139 NCKQWFCFQCKLKWHAG-YRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGCSVVMC-RCN 205 (263)
Q Consensus 139 ~C~~~~C~~C~~~~H~~-~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C-~C~ 205 (263)
.|...+|..|+..+... ..|.+........+ ....+-+|++|+....-.+--..-.| .||
T Consensus 249 k~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~-------a~KRFFkC~~C~~Rt~sl~r~P~~~C~~Cg 310 (344)
T PF09332_consen 249 KCKAVTCKQCKYTAFKPSDRCKEEGHPLKWHD-------AVKRFFKCKDCGNRTISLERLPKKHCSNCG 310 (344)
T ss_dssp EEEEEEETTT--EESS--HHHHHTT--EEEEE-------EE-EEEE-T-TS-EEEESSSS--S--TTT-
T ss_pred EEEEEEcCCCCCcccCcchhHHhcCCceEEee-------eeeeeEECCCCCCeeeecccCCCCCCCcCC
Confidence 36788888898765543 34765432111101 12345689999986543322233445 355
No 297
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.26 E-value=53 Score=18.72 Aligned_cols=20 Identities=20% Similarity=0.524 Sum_probs=11.2
Q ss_pred ccccccccCCCCCCCchhHH
Q 024715 143 WFCFQCKLKWHAGYRCEESR 162 (263)
Q Consensus 143 ~~C~~C~~~~H~~~~C~~~~ 162 (263)
..|.+|++..|....|..-.
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 35888999999988887533
No 298
>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=23.22 E-value=1.4e+02 Score=22.75 Aligned_cols=36 Identities=17% Similarity=0.069 Sum_probs=21.4
Q ss_pred ChhhHHHHHHHHHHHhhc---CCCcccCCccccccceeccc
Q 024715 89 PASLFSKWCDVLCEDYVL---GFERSYCPNTNCMALVVNEC 126 (263)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~---~~~~~~Cp~~~C~~~~~~~~ 126 (263)
+.+..+++.+.+....+. .+....|+ .|++.+...+
T Consensus 67 ~~~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~ 105 (147)
T PF01927_consen 67 SDDPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVS 105 (147)
T ss_pred CCCHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeech
Confidence 335556666665544332 23367899 8998775543
No 299
>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=23.14 E-value=72 Score=20.03 Aligned_cols=25 Identities=28% Similarity=0.640 Sum_probs=14.4
Q ss_pred CCCcccCCccccccceeccccccCCCCceeCCcccc
Q 024715 107 GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 107 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
..+...|| .|+.+. .....|+.||+
T Consensus 23 ~~~l~~c~--~cg~~~---------~~H~vc~~cG~ 47 (56)
T PF01783_consen 23 APNLVKCP--NCGEPK---------LPHRVCPSCGY 47 (56)
T ss_dssp TTSEEESS--SSSSEE---------STTSBCTTTBB
T ss_pred ccceeeec--cCCCEe---------cccEeeCCCCe
Confidence 34566777 566544 23456666653
No 300
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=23.08 E-value=45 Score=18.61 Aligned_cols=14 Identities=36% Similarity=0.997 Sum_probs=9.7
Q ss_pred cccCCCCCceeecC
Q 024715 181 WARCPACGHCVERK 194 (263)
Q Consensus 181 ~k~CP~C~~~i~k~ 194 (263)
+-.||+|+..|.-+
T Consensus 4 ~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 4 YVECPNCGRPVAAS 17 (33)
T ss_dssp EEE-TTTSSEEEGG
T ss_pred eEECCCCcCCcchh
Confidence 45799999988643
No 301
>PRK05978 hypothetical protein; Provisional
Probab=22.94 E-value=46 Score=25.69 Aligned_cols=33 Identities=30% Similarity=0.610 Sum_probs=19.5
Q ss_pred CcccCCCCCcee-ecCCCCceeEeecCCceecccCcccCCC
Q 024715 180 KWARCPACGHCV-ERKDGCSVVMCRCNTRFCYECGRKISSG 219 (263)
Q Consensus 180 ~~k~CP~C~~~i-~k~~GCnhm~C~C~~~FC~~C~~~~~~~ 219 (263)
-.-+||+|+.-= .+ |-..| ..-|-.||..+++.
T Consensus 32 l~grCP~CG~G~LF~--g~Lkv-----~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFR--AFLKP-----VDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccc--ccccc-----CCCccccCCccccC
Confidence 346899999732 21 11112 45677788887654
No 302
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.88 E-value=71 Score=21.28 Aligned_cols=59 Identities=24% Similarity=0.629 Sum_probs=35.5
Q ss_pred ccccccccccccccccccCCC--CCccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCccccccCCChhhHHHHHH
Q 024715 23 TCEICIEPMAASKKFKNRNLC--THPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCD 98 (263)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~ 98 (263)
.|..|-.++++... ..+-| .|+||.+|...-+. =.||+ |+..+.-.-++ +...+.+|-.
T Consensus 7 nCECCDrDLpp~s~--dA~ICtfEcTFCadCae~~l~----------g~CPn--CGGelv~RP~R---Paa~L~r~PA 67 (84)
T COG3813 7 NCECCDRDLPPDST--DARICTFECTFCADCAENRLH----------GLCPN--CGGELVARPIR---PAAKLARYPA 67 (84)
T ss_pred CCcccCCCCCCCCC--ceeEEEEeeehhHhHHHHhhc----------CcCCC--CCchhhcCcCC---hHHHHhhCch
Confidence 47777777754322 12445 58999999875443 35998 99877554443 3344444443
No 303
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=22.86 E-value=78 Score=28.27 Aligned_cols=66 Identities=18% Similarity=0.514 Sum_probs=40.8
Q ss_pred CCCCcccccccccccccccccccc-------------CCC-----CCccHHHHHHHHHHHHhhCCC-----CcccccCCC
Q 024715 17 GGGSSFTCEICIEPMAASKKFKNR-------------NLC-----THPFCQDCIARYIQVKVQDDN-----TAKIDCPGL 73 (263)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~-------------~~C-----~H~fC~~Cl~~~~~~~i~~~~-----~~~i~CP~~ 73 (263)
...+.-.|.-|+..-++.+..... .+| .-.-|.+|+.+|+.++-++.. .....||.
T Consensus 267 ~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt- 345 (358)
T PF10272_consen 267 SGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPT- 345 (358)
T ss_pred CccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC-
Confidence 345667888888766443221110 123 234699999999998876432 23467777
Q ss_pred CCCCccCcccc
Q 024715 74 DCKHNLDPFAC 84 (263)
Q Consensus 74 ~C~~~l~~~~i 84 (263)
|.+.+-..++
T Consensus 346 -CRa~FCilDV 355 (358)
T PF10272_consen 346 -CRAKFCILDV 355 (358)
T ss_pred -Ccccceeeee
Confidence 9988765443
No 304
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.84 E-value=83 Score=23.78 Aligned_cols=15 Identities=20% Similarity=0.173 Sum_probs=10.7
Q ss_pred CcccCCccccccceecc
Q 024715 109 ERSYCPNTNCMALVVNE 125 (263)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~ 125 (263)
...+|+ +|+..+...
T Consensus 69 ~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCR--NCGNEWSLK 83 (135)
T ss_pred eEEECC--CCCCEEecc
Confidence 457888 788777654
No 305
>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=22.84 E-value=66 Score=30.21 Aligned_cols=34 Identities=29% Similarity=0.600 Sum_probs=25.2
Q ss_pred cCCccccccceeccccccCCCCceeCCccccc-----cccccccC
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQW-----FCFQCKLK 151 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 151 (263)
.|| .|...+..... .....|+.||+. .|..|+..
T Consensus 224 ~C~--~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCP--NCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCC--CCCCceEEecC----CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 366 67777766554 568899999866 59999875
No 306
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.83 E-value=59 Score=26.07 Aligned_cols=24 Identities=25% Similarity=0.714 Sum_probs=18.6
Q ss_pred ccCCCCCceeecCCCCceeEe-ecCCc
Q 024715 182 ARCPACGHCVERKDGCSVVMC-RCNTR 207 (263)
Q Consensus 182 k~CP~C~~~i~k~~GCnhm~C-~C~~~ 207 (263)
-.|++|+...++ .=+.|+| .||..
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 479999999999 4467888 58753
No 307
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=22.48 E-value=61 Score=20.36 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=15.8
Q ss_pred cccCCccccccceeccccc--cCCCCceeCCccccc
Q 024715 110 RSYCPNTNCMALVVNECER--SGKVKKTQCPNCKQW 143 (263)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 143 (263)
.+.|| .|++--...-.. .-++..+.||.|++.
T Consensus 4 Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 4 WILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EEECC--CCCCccceeeecCceeccccccCCCCCce
Confidence 35677 677543222111 112456677766543
No 308
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=22.36 E-value=58 Score=15.27 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=11.4
Q ss_pred cccccccCCCCCCCch
Q 024715 144 FCFQCKLKWHAGYRCE 159 (263)
Q Consensus 144 ~C~~C~~~~H~~~~C~ 159 (263)
.|++|+..-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4788888877766553
No 309
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.27 E-value=1.4e+02 Score=25.15 Aligned_cols=31 Identities=16% Similarity=0.470 Sum_probs=22.6
Q ss_pred CCcccCCccccccceeccccccCCCCceeCCcccccc
Q 024715 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
...++|| .|+........ .....|+.|+...
T Consensus 97 ~~~~fC~--~CG~~~~~~~~----~~~~~C~~c~~~~ 127 (256)
T PRK00241 97 RSHRFCG--YCGHPMHPSKT----EWAMLCPHCRERY 127 (256)
T ss_pred hcCcccc--ccCCCCeecCC----ceeEECCCCCCEE
Confidence 5679999 89988765543 4678899887543
No 310
>PRK02935 hypothetical protein; Provisional
Probab=22.25 E-value=62 Score=23.32 Aligned_cols=23 Identities=26% Similarity=0.743 Sum_probs=13.1
Q ss_pred CCCceeCCcccc--------ccccccccCCC
Q 024715 131 KVKKTQCPNCKQ--------WFCFQCKLKWH 153 (263)
Q Consensus 131 ~~~~~~C~~C~~--------~~C~~C~~~~H 153 (263)
+...+.||.|++ ..|..|+.|.+
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 356677777653 33566665543
No 311
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.23 E-value=1e+02 Score=24.24 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=12.9
Q ss_pred CCcccCCccccccceeccc
Q 024715 108 FERSYCPNTNCMALVVNEC 126 (263)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~ 126 (263)
++...|| .|++.+....
T Consensus 95 ~e~~RCp--~CN~~L~~vs 111 (165)
T COG1656 95 PEFSRCP--ECNGELEKVS 111 (165)
T ss_pred cccccCc--ccCCEeccCc
Confidence 5578899 8999886543
No 312
>PF14369 zf-RING_3: zinc-finger
Probab=22.20 E-value=77 Score=17.81 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=16.2
Q ss_pred ccCCccccccceeccccccCCCCceeCCcccccc
Q 024715 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (263)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (263)
.||= .|+..+...... ...+.||.|+..|
T Consensus 3 ywCh--~C~~~V~~~~~~---~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH--QCNRFVRIAPSP---DSDVACPRCHGGF 31 (35)
T ss_pred EeCc--cCCCEeEeCcCC---CCCcCCcCCCCcE
Confidence 3565 677777654331 1234688776543
No 313
>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=22.17 E-value=40 Score=21.46 Aligned_cols=12 Identities=50% Similarity=1.168 Sum_probs=5.8
Q ss_pred ccCCCCCceeec
Q 024715 182 ARCPACGHCVER 193 (263)
Q Consensus 182 k~CP~C~~~i~k 193 (263)
.+||.|+..++-
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 567888777764
No 314
>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=22.15 E-value=42 Score=24.44 Aligned_cols=14 Identities=43% Similarity=1.056 Sum_probs=11.4
Q ss_pred ceeEeecCCceecc
Q 024715 198 SVVMCRCNTRFCYE 211 (263)
Q Consensus 198 nhm~C~C~~~FC~~ 211 (263)
.-+.|.||+.||-.
T Consensus 23 k~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 23 KVVKCDCGHEFCDA 36 (112)
T ss_pred ceeeccCCCeecCh
Confidence 46889999999853
No 315
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.83 E-value=38 Score=16.37 Aligned_cols=8 Identities=38% Similarity=1.098 Sum_probs=3.7
Q ss_pred eCCccccc
Q 024715 136 QCPNCKQW 143 (263)
Q Consensus 136 ~C~~C~~~ 143 (263)
.|+.|+..
T Consensus 2 ~C~~C~~~ 9 (23)
T PF00096_consen 2 KCPICGKS 9 (23)
T ss_dssp EETTTTEE
T ss_pred CCCCCCCc
Confidence 35555443
No 316
>PLN02195 cellulose synthase A
Probab=21.70 E-value=87 Score=31.79 Aligned_cols=56 Identities=18% Similarity=0.323 Sum_probs=0.0
Q ss_pred CCCcccCCccccccceeccccccCCCCceeCCccccccccccccCCCCCCCchhHHhccccchHHHHHHHhcCCcccCCC
Q 024715 107 GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPA 186 (263)
Q Consensus 107 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~ 186 (263)
..+...|- -|+..+-..... ...|.|..|++..|..| -++-++.+.+.||+
T Consensus 3 ~~~~~~c~--~cgd~~~~~~~g---~~fvaC~eC~~pvCrpC------------------------yeyer~eg~q~Cpq 53 (977)
T PLN02195 3 ESGAPICA--TCGEEVGVDSNG---EAFVACHECSYPLCKAC------------------------LEYEIKEGRKVCLR 53 (977)
T ss_pred cCCCccce--ecccccCcCCCC---CeEEEeccCCCccccch------------------------hhhhhhcCCccCCc
Q ss_pred CCcee
Q 024715 187 CGHCV 191 (263)
Q Consensus 187 C~~~i 191 (263)
|+...
T Consensus 54 Ckt~Y 58 (977)
T PLN02195 54 CGGPY 58 (977)
T ss_pred cCCcc
No 317
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=21.55 E-value=53 Score=18.08 Aligned_cols=11 Identities=27% Similarity=0.927 Sum_probs=6.9
Q ss_pred cccCCCCCCCc
Q 024715 68 IDCPGLDCKHN 78 (263)
Q Consensus 68 i~CP~~~C~~~ 78 (263)
.+||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 57999999853
No 318
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=21.42 E-value=45 Score=18.18 Aligned_cols=9 Identities=56% Similarity=1.257 Sum_probs=6.3
Q ss_pred cCCCCCcee
Q 024715 183 RCPACGHCV 191 (263)
Q Consensus 183 ~CP~C~~~i 191 (263)
-||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999855
No 319
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=21.38 E-value=70 Score=19.38 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=16.0
Q ss_pred cCCccccccceeccccccCCCCceeCCcccc
Q 024715 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (263)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (263)
.|+ +|+..+......++ ...+.||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCT--ACGHRFEVLQKMSD-DPLATCPECGG 34 (52)
T ss_pred EeC--CCCCEeEEEEecCC-CCCCCCCCCCC
Confidence 476 78875554322111 35567888875
No 320
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.28 E-value=54 Score=16.82 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=9.1
Q ss_pred CCceeCCcccccc
Q 024715 132 VKKTQCPNCKQWF 144 (263)
Q Consensus 132 ~~~~~C~~C~~~~ 144 (263)
...+.|+.|++.|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 4567888887665
No 321
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=21.27 E-value=52 Score=24.79 Aligned_cols=23 Identities=30% Similarity=0.782 Sum_probs=12.4
Q ss_pred CCcccCCC--CCceeecCCCCceeEee--cCCc
Q 024715 179 MKWARCPA--CGHCVERKDGCSVVMCR--CNTR 207 (263)
Q Consensus 179 ~~~k~CP~--C~~~i~k~~GCnhm~C~--C~~~ 207 (263)
+..|.||+ |.-.++ ++-|+ |||-
T Consensus 80 Qq~k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 80 QQGKPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp HHHSB-SS--S--BEE------EE---TBTTB-
T ss_pred hcCCCCCccccCCcee------EEeccCcCCCc
Confidence 34689999 998888 68884 8753
No 322
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.79 E-value=82 Score=17.84 Aligned_cols=24 Identities=38% Similarity=0.910 Sum_probs=15.2
Q ss_pred ccCCCCCceeec-CCCCceeEe-ecCCc
Q 024715 182 ARCPACGHCVER-KDGCSVVMC-RCNTR 207 (263)
Q Consensus 182 k~CP~C~~~i~k-~~GCnhm~C-~C~~~ 207 (263)
.+|+.|+..... ++| ..+| +||+.
T Consensus 9 ~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 459999887433 244 5667 57653
No 323
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=20.74 E-value=1.2e+02 Score=30.28 Aligned_cols=60 Identities=12% Similarity=0.306 Sum_probs=39.5
Q ss_pred cCCCCCccccccccccccccccccccCCCC---CccHHHHHHHHHHHHhhCCCCcccccCCCCCCCccCcc
Q 024715 15 KGGGGSSFTCEICIEPMAASKKFKNRNLCT---HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (263)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~---H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (263)
+..+.+.-+|-||-.+-...+.++....|. ..+.++||-+|+. .....+|-. |..++...
T Consensus 6 ~~mN~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~------~s~~~kCdi--Chy~~~Fk 68 (1175)
T COG5183 6 TPMNEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWME------CSGTKKCDI--CHYEYKFK 68 (1175)
T ss_pred CCCCccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHh------cCCCcceee--ecceeeee
Confidence 344455689999975554444443233343 2589999999998 456678877 88766544
No 324
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.49 E-value=64 Score=25.05 Aligned_cols=26 Identities=27% Similarity=0.816 Sum_probs=17.8
Q ss_pred cccCCCCCceeecCCCCceeEe-ecCCc
Q 024715 181 WARCPACGHCVERKDGCSVVMC-RCNTR 207 (263)
Q Consensus 181 ~k~CP~C~~~i~k~~GCnhm~C-~C~~~ 207 (263)
+..||.|+..+...+. ....| +|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4789999999887654 34555 35544
No 325
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=20.43 E-value=62 Score=26.94 Aligned_cols=9 Identities=44% Similarity=1.298 Sum_probs=3.8
Q ss_pred ccCCCCCce
Q 024715 182 ARCPACGHC 190 (263)
Q Consensus 182 k~CP~C~~~ 190 (263)
..||.|+..
T Consensus 36 ~~C~~Cg~~ 44 (236)
T PF04981_consen 36 TICPKCGRY 44 (236)
T ss_pred eECCCCCCE
Confidence 344444443
No 326
>PHA02325 hypothetical protein
Probab=20.30 E-value=58 Score=21.13 Aligned_cols=12 Identities=33% Similarity=0.706 Sum_probs=8.3
Q ss_pred CcccCCCCCcee
Q 024715 180 KWARCPACGHCV 191 (263)
Q Consensus 180 ~~k~CP~C~~~i 191 (263)
..|.||+|++.-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 357788888754
No 327
>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=20.11 E-value=58 Score=18.76 Aligned_cols=20 Identities=30% Similarity=0.874 Sum_probs=12.7
Q ss_pred ccCCCCCceeecC---CCCceeEe
Q 024715 182 ARCPACGHCVERK---DGCSVVMC 202 (263)
Q Consensus 182 k~CP~C~~~i~k~---~GCnhm~C 202 (263)
+.||.|+..+... .| ..+.|
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 5799999765433 33 55555
Done!