Query 035729
Match_columns 208
No_of_seqs 143 out of 1306
Neff 9.5
Searched_HMMs 46136
Date Fri Mar 29 05:52:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035729hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814 Predicted E3 ubiquitin 100.0 7.4E-36 1.6E-40 238.1 5.7 186 17-207 178-392 (445)
2 KOG1812 Predicted E3 ubiquitin 100.0 5.9E-34 1.3E-38 234.5 9.3 182 21-206 144-329 (384)
3 KOG1815 Predicted E3 ubiquitin 99.9 1.7E-26 3.8E-31 194.9 9.6 179 20-205 67-248 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 9.1E-24 2E-28 164.0 6.1 180 17-206 215-420 (446)
5 smart00647 IBR In Between Ring 99.3 1E-12 2.2E-17 81.8 3.6 63 96-160 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 2.2E-13 4.8E-18 84.8 -0.3 63 96-160 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.8 7.4E-10 1.6E-14 62.5 0.1 41 26-74 1-41 (42)
8 PLN03208 E3 ubiquitin-protein 98.8 9.3E-09 2E-13 76.4 5.0 66 21-92 16-89 (193)
9 KOG0320 Predicted E3 ubiquitin 98.7 1.8E-08 4E-13 73.1 4.5 59 18-88 126-184 (187)
10 PF13445 zf-RING_UBOX: RING-ty 98.7 6.9E-09 1.5E-13 58.6 1.7 43 26-73 1-43 (43)
11 PF13639 zf-RING_2: Ring finge 98.7 4.5E-09 9.7E-14 60.2 0.1 41 25-74 2-42 (44)
12 PF13923 zf-C3HC4_2: Zinc fing 98.6 9.8E-09 2.1E-13 57.1 0.9 38 26-74 1-38 (39)
13 PF00097 zf-C3HC4: Zinc finger 98.6 2.3E-08 4.9E-13 56.3 2.2 40 26-74 1-40 (41)
14 PF14634 zf-RING_5: zinc-RING 98.6 7.6E-08 1.6E-12 55.0 3.2 44 25-79 1-44 (44)
15 KOG0823 Predicted E3 ubiquitin 98.5 1.4E-07 2.9E-12 71.6 3.5 61 20-91 44-104 (230)
16 cd00162 RING RING-finger (Real 98.4 5E-07 1.1E-11 51.3 3.4 44 25-80 1-44 (45)
17 PHA02926 zinc finger-like prot 98.4 5.4E-07 1.2E-11 67.9 4.3 59 20-82 167-230 (242)
18 PF13920 zf-C3HC4_3: Zinc fing 98.3 2.8E-07 6.1E-12 54.1 1.3 46 23-82 2-48 (50)
19 KOG2177 Predicted E3 ubiquitin 98.2 1.1E-06 2.3E-11 71.1 3.8 112 18-161 8-123 (386)
20 PHA02929 N1R/p28-like protein; 98.2 1.6E-06 3.4E-11 67.2 3.2 52 21-82 172-227 (238)
21 smart00184 RING Ring finger. E 98.1 3.6E-06 7.8E-11 46.0 3.3 30 26-59 1-30 (39)
22 KOG2164 Predicted E3 ubiquitin 98.1 1.6E-06 3.4E-11 72.8 2.6 60 23-91 186-245 (513)
23 smart00504 Ubox Modified RING 98.1 3.8E-06 8.2E-11 51.7 3.6 51 24-88 2-52 (63)
24 TIGR00599 rad18 DNA repair pro 98.0 1E-05 2.3E-10 67.2 5.0 68 19-100 22-90 (397)
25 KOG4628 Predicted E3 ubiquitin 97.9 4.1E-06 9E-11 68.0 1.9 48 24-81 230-277 (348)
26 KOG0317 Predicted E3 ubiquitin 97.9 1.2E-05 2.5E-10 63.0 4.1 53 21-87 237-289 (293)
27 COG5540 RING-finger-containing 97.9 7.5E-06 1.6E-10 64.4 2.7 55 19-83 319-373 (374)
28 KOG0287 Postreplication repair 97.9 7.3E-06 1.6E-10 65.4 2.3 66 20-99 20-86 (442)
29 TIGR00570 cdk7 CDK-activating 97.9 4.3E-05 9.3E-10 61.2 6.6 55 24-88 4-60 (309)
30 KOG0978 E3 ubiquitin ligase in 97.5 6.5E-05 1.4E-09 66.2 2.6 58 19-89 639-696 (698)
31 KOG1002 Nucleotide excision re 97.5 0.00013 2.8E-09 61.8 4.1 66 17-91 530-595 (791)
32 PF12678 zf-rbx1: RING-H2 zinc 97.3 8.6E-05 1.9E-09 47.1 0.9 46 23-78 19-73 (73)
33 PF11789 zf-Nse: Zinc-finger o 97.1 0.00023 5E-09 42.8 1.5 50 20-78 8-57 (57)
34 COG5432 RAD18 RING-finger-cont 97.1 0.00039 8.5E-09 54.7 2.8 68 17-98 19-87 (391)
35 PF11793 FANCL_C: FANCL C-term 97.1 0.00016 3.5E-09 45.4 0.4 59 23-83 2-67 (70)
36 COG5574 PEX10 RING-finger-cont 97.1 0.00046 1E-08 53.6 2.8 52 23-86 215-266 (271)
37 PF14835 zf-RING_6: zf-RING of 97.0 6E-05 1.3E-09 45.7 -1.8 50 23-87 7-56 (65)
38 KOG1039 Predicted E3 ubiquitin 97.0 0.0014 3.1E-08 53.6 5.1 95 20-117 158-264 (344)
39 PF04564 U-box: U-box domain; 96.7 0.001 2.2E-08 42.2 2.1 53 22-87 3-55 (73)
40 COG5243 HRD1 HRD ubiquitin lig 96.5 0.0024 5.1E-08 52.1 3.0 52 20-81 284-344 (491)
41 KOG0802 E3 ubiquitin ligase [P 96.3 0.0027 5.9E-08 55.7 2.6 51 19-79 287-338 (543)
42 KOG4185 Predicted E3 ubiquitin 96.2 0.01 2.2E-07 48.0 5.5 124 22-158 2-131 (296)
43 KOG2660 Locus-specific chromos 96.2 0.0038 8.2E-08 50.2 2.9 53 20-85 12-64 (331)
44 KOG4159 Predicted E3 ubiquitin 96.0 0.0059 1.3E-07 51.1 3.2 50 20-83 81-130 (398)
45 COG5175 MOT2 Transcriptional r 95.8 0.023 4.9E-07 46.0 5.3 62 23-93 14-76 (480)
46 PF14570 zf-RING_4: RING/Ubox 95.8 0.012 2.6E-07 33.8 2.7 47 26-81 1-47 (48)
47 smart00744 RINGv The RING-vari 95.7 0.016 3.5E-07 33.6 3.1 42 25-74 1-47 (49)
48 KOG0828 Predicted E3 ubiquitin 95.5 0.012 2.5E-07 49.9 3.0 55 19-83 567-635 (636)
49 KOG0824 Predicted E3 ubiquitin 95.5 0.014 2.9E-07 46.5 3.0 53 21-86 5-57 (324)
50 KOG4739 Uncharacterized protei 95.4 0.011 2.5E-07 45.5 2.5 56 22-91 2-57 (233)
51 COG5152 Uncharacterized conser 95.3 0.013 2.7E-07 43.8 2.2 36 19-58 192-227 (259)
52 PF12861 zf-Apc11: Anaphase-pr 95.2 0.025 5.5E-07 36.6 3.0 53 23-82 21-82 (85)
53 KOG2879 Predicted E3 ubiquitin 95.1 0.018 4E-07 45.2 2.7 52 20-82 236-287 (298)
54 COG5220 TFB3 Cdk activating ki 95.1 0.0071 1.5E-07 46.5 0.4 52 23-81 10-63 (314)
55 PF04641 Rtf2: Rtf2 RING-finge 95.0 0.039 8.5E-07 43.8 4.5 72 20-102 110-182 (260)
56 KOG4172 Predicted E3 ubiquitin 94.7 0.0093 2E-07 34.8 0.2 45 24-81 8-53 (62)
57 KOG1814 Predicted E3 ubiquitin 94.6 0.017 3.7E-07 47.8 1.5 111 23-154 273-404 (445)
58 KOG0006 E3 ubiquitin-protein l 94.6 0.037 8E-07 44.4 3.2 91 44-157 341-438 (446)
59 smart00647 IBR In Between Ring 94.1 0.095 2.1E-06 31.8 3.8 32 174-205 8-44 (64)
60 KOG1812 Predicted E3 ubiquitin 94.1 0.032 7E-07 46.8 2.1 42 110-158 304-345 (384)
61 KOG3002 Zn finger protein [Gen 94.0 0.028 6E-07 45.5 1.4 47 18-82 43-91 (299)
62 KOG4367 Predicted Zn-finger pr 93.9 0.051 1.1E-06 45.5 2.9 34 22-59 3-36 (699)
63 PF05883 Baculo_RING: Baculovi 93.8 0.029 6.3E-07 39.5 1.1 79 20-101 23-115 (134)
64 KOG0297 TNF receptor-associate 93.6 0.084 1.8E-06 44.5 3.7 51 20-83 18-68 (391)
65 KOG3039 Uncharacterized conser 93.5 0.054 1.2E-06 41.9 2.2 58 21-88 219-276 (303)
66 KOG1428 Inhibitor of type V ad 93.5 0.056 1.2E-06 51.7 2.6 71 19-92 3482-3554(3738)
67 KOG1645 RING-finger-containing 93.4 0.043 9.3E-07 45.5 1.7 56 23-86 4-60 (463)
68 KOG1734 Predicted RING-contain 93.2 0.016 3.6E-07 45.3 -1.0 56 22-86 223-285 (328)
69 KOG0311 Predicted E3 ubiquitin 92.8 0.018 3.8E-07 46.8 -1.3 50 20-81 40-89 (381)
70 PF07975 C1_4: TFIIH C1-like d 92.6 0.031 6.6E-07 32.6 -0.2 43 119-161 4-47 (51)
71 KOG3053 Uncharacterized conser 92.5 0.41 8.8E-06 37.5 5.7 59 21-81 18-81 (293)
72 KOG0827 Predicted E3 ubiquitin 92.4 0.13 2.8E-06 42.5 3.0 50 23-79 4-53 (465)
73 KOG4265 Predicted E3 ubiquitin 92.2 0.18 3.9E-06 41.2 3.6 49 19-81 286-335 (349)
74 PF14447 Prok-RING_4: Prokaryo 91.6 0.091 2E-06 31.0 1.0 47 24-86 8-54 (55)
75 PHA03096 p28-like protein; Pro 91.6 0.14 3.1E-06 41.1 2.4 53 24-80 179-235 (284)
76 PF03119 DNA_ligase_ZBD: NAD-d 91.5 0.21 4.6E-06 25.2 2.2 23 185-207 1-23 (28)
77 KOG0804 Cytoplasmic Zn-finger 91.4 0.13 2.7E-06 43.4 1.9 52 18-81 170-221 (493)
78 KOG1952 Transcription factor N 91.1 0.18 3.9E-06 45.7 2.8 59 18-79 186-244 (950)
79 KOG0825 PHD Zn-finger protein 90.9 0.14 3.1E-06 46.0 1.9 20 134-153 228-248 (1134)
80 KOG4445 Uncharacterized conser 90.9 0.21 4.5E-06 39.9 2.6 64 17-83 109-187 (368)
81 KOG1940 Zn-finger protein [Gen 90.7 0.6 1.3E-05 37.2 5.1 50 20-79 155-204 (276)
82 PF01485 IBR: IBR domain; Int 89.8 0.14 3.1E-06 30.9 0.7 25 181-205 16-44 (64)
83 KOG1785 Tyrosine kinase negati 89.6 0.14 3E-06 42.5 0.8 46 22-79 368-413 (563)
84 PF10571 UPF0547: Uncharacteri 89.4 0.2 4.4E-06 24.8 1.0 23 114-146 2-24 (26)
85 PF13719 zinc_ribbon_5: zinc-r 89.3 0.2 4.4E-06 27.1 1.1 33 112-146 2-35 (37)
86 KOG4692 Predicted E3 ubiquitin 89.3 0.29 6.2E-06 40.1 2.3 49 20-82 419-467 (489)
87 PF05290 Baculo_IE-1: Baculovi 89.2 0.82 1.8E-05 32.1 4.2 53 21-81 78-131 (140)
88 COG5236 Uncharacterized conser 89.0 0.89 1.9E-05 37.2 4.9 54 19-84 57-110 (493)
89 KOG3800 Predicted E3 ubiquitin 89.0 0.9 2E-05 36.2 4.8 52 25-85 2-54 (300)
90 TIGR00622 ssl1 transcription f 87.7 0.71 1.5E-05 31.6 3.1 43 113-157 56-102 (112)
91 PF13717 zinc_ribbon_4: zinc-r 87.6 0.32 6.9E-06 26.1 1.1 33 112-146 2-35 (36)
92 KOG1813 Predicted E3 ubiquitin 86.8 0.25 5.5E-06 39.4 0.6 48 20-81 238-285 (313)
93 KOG1815 Predicted E3 ubiquitin 86.5 0.71 1.5E-05 39.7 3.2 47 111-163 225-278 (444)
94 KOG3268 Predicted E3 ubiquitin 86.0 2.2 4.9E-05 31.5 5.1 63 19-83 161-229 (234)
95 COG5194 APC11 Component of SCF 85.7 1 2.3E-05 28.6 2.8 30 43-82 52-81 (88)
96 KOG2817 Predicted E3 ubiquitin 85.5 0.7 1.5E-05 38.5 2.5 60 22-89 333-392 (394)
97 COG5222 Uncharacterized conser 85.3 1.5 3.3E-05 35.2 4.2 44 24-79 275-318 (427)
98 COG5219 Uncharacterized conser 84.8 0.54 1.2E-05 43.5 1.7 54 21-82 1467-1523(1525)
99 PF14803 Nudix_N_2: Nudix N-te 84.7 0.44 9.6E-06 25.2 0.7 30 114-145 2-31 (34)
100 smart00661 RPOL9 RNA polymeras 84.7 0.59 1.3E-05 27.1 1.3 28 114-145 2-29 (52)
101 PF10367 Vps39_2: Vacuolar sor 83.8 0.26 5.6E-06 33.3 -0.6 32 22-55 77-108 (109)
102 PF02150 RNA_POL_M_15KD: RNA p 83.3 0.35 7.5E-06 25.8 -0.1 28 113-145 2-29 (35)
103 KOG2034 Vacuolar sorting prote 83.0 0.76 1.7E-05 42.1 1.9 41 21-63 815-855 (911)
104 KOG1941 Acetylcholine receptor 82.8 0.54 1.2E-05 39.0 0.8 50 23-80 365-414 (518)
105 KOG1001 Helicase-like transcri 82.0 0.32 7E-06 43.9 -0.8 48 24-84 455-502 (674)
106 TIGR02098 MJ0042_CXXC MJ0042 f 81.9 0.8 1.7E-05 24.6 1.1 32 113-146 3-35 (38)
107 PF08746 zf-RING-like: RING-li 81.3 0.7 1.5E-05 25.9 0.7 42 26-74 1-42 (43)
108 PF01599 Ribosomal_S27: Riboso 81.3 0.63 1.4E-05 26.6 0.5 29 112-144 18-46 (47)
109 KOG3579 Predicted E3 ubiquitin 79.1 1.5 3.2E-05 35.0 2.0 49 20-75 265-317 (352)
110 KOG2930 SCF ubiquitin ligase, 79.0 2.6 5.6E-05 28.3 2.9 29 43-81 79-107 (114)
111 KOG3161 Predicted E3 ubiquitin 78.9 0.83 1.8E-05 40.4 0.7 37 23-59 11-47 (861)
112 PF14446 Prok-RING_1: Prokaryo 78.8 2.3 5E-05 25.0 2.3 36 21-56 3-38 (54)
113 PRK14559 putative protein seri 77.7 1.4 3.1E-05 39.6 1.8 15 181-195 39-53 (645)
114 PF12906 RINGv: RING-variant d 77.7 1.1 2.4E-05 25.6 0.8 34 26-61 1-39 (47)
115 PF06844 DUF1244: Protein of u 77.7 2 4.4E-05 26.2 1.9 17 48-64 11-27 (68)
116 PRK14714 DNA polymerase II lar 75.9 2 4.3E-05 41.2 2.3 12 183-194 709-720 (1337)
117 PF13240 zinc_ribbon_2: zinc-r 75.7 1.3 2.9E-05 21.1 0.6 12 185-196 1-12 (23)
118 PF06677 Auto_anti-p27: Sjogre 75.6 3.3 7.2E-05 22.9 2.3 22 183-206 17-39 (41)
119 cd00021 BBOX B-Box-type zinc f 75.2 1.6 3.5E-05 23.3 1.0 26 134-159 10-35 (39)
120 PF13248 zf-ribbon_3: zinc-rib 75.0 1.5 3.2E-05 21.6 0.7 11 182-192 15-25 (26)
121 KOG2807 RNA polymerase II tran 74.7 1.2 2.7E-05 36.1 0.6 73 68-158 289-367 (378)
122 KOG4275 Predicted E3 ubiquitin 74.0 0.47 1E-05 37.8 -1.9 40 23-80 300-340 (350)
123 PRK00398 rpoP DNA-directed RNA 73.2 1.7 3.7E-05 24.5 0.8 29 113-147 4-32 (46)
124 PF07503 zf-HYPF: HypF finger; 72.7 1.8 3.9E-05 23.1 0.7 32 49-82 1-32 (35)
125 KOG3970 Predicted E3 ubiquitin 72.4 8.9 0.00019 29.6 4.6 55 23-81 50-104 (299)
126 PRK00432 30S ribosomal protein 72.3 2.3 5E-05 24.7 1.2 27 112-146 20-47 (50)
127 PF00643 zf-B_box: B-box zinc 71.7 0.83 1.8E-05 25.1 -0.8 26 134-159 13-38 (42)
128 PHA02825 LAP/PHD finger-like p 70.8 7.1 0.00015 28.5 3.6 51 21-84 6-61 (162)
129 PHA02926 zinc finger-like prot 70.5 1 2.2E-05 34.7 -0.8 37 140-195 195-231 (242)
130 PF14952 zf-tcix: Putative tre 70.5 2.3 4.9E-05 23.8 0.8 13 181-193 9-21 (44)
131 PF06906 DUF1272: Protein of u 69.0 4.4 9.5E-05 24.0 1.8 47 24-84 6-54 (57)
132 COG2888 Predicted Zn-ribbon RN 68.9 3.1 6.8E-05 24.9 1.3 35 112-152 9-43 (61)
133 PF12773 DZR: Double zinc ribb 68.8 3.6 7.8E-05 23.5 1.5 28 110-144 10-37 (50)
134 PF14569 zf-UDP: Zinc-binding 68.4 3.8 8.3E-05 26.0 1.6 61 112-201 9-69 (80)
135 KOG0823 Predicted E3 ubiquitin 67.6 1.7 3.7E-05 33.6 -0.0 38 134-195 59-96 (230)
136 PF09297 zf-NADH-PPase: NADH p 66.1 8.9 0.00019 19.7 2.6 23 183-205 3-25 (32)
137 smart00336 BBOX B-Box-type zin 65.7 4.2 9.1E-05 21.9 1.4 26 134-159 13-38 (42)
138 smart00064 FYVE Protein presen 64.6 5.8 0.00012 24.2 1.9 38 23-60 10-47 (68)
139 KOG3039 Uncharacterized conser 64.3 7.3 0.00016 30.5 2.8 40 21-64 41-80 (303)
140 KOG2979 Protein involved in DN 63.1 14 0.00031 29.2 4.2 48 23-79 176-223 (262)
141 COG3813 Uncharacterized protei 62.1 6.3 0.00014 24.6 1.7 59 25-100 7-67 (84)
142 PHA00626 hypothetical protein 62.1 4.6 9.9E-05 23.9 1.0 15 134-148 21-35 (59)
143 COG5151 SSL1 RNA polymerase II 61.9 1.8 3.8E-05 35.0 -0.9 79 68-157 321-409 (421)
144 KOG1493 Anaphase-promoting com 61.5 2.6 5.6E-05 26.6 -0.0 51 25-82 22-81 (84)
145 PRK00420 hypothetical protein; 61.5 13 0.00028 25.6 3.3 42 94-144 7-48 (112)
146 COG3492 Uncharacterized protei 60.9 10 0.00022 24.8 2.5 17 48-64 42-58 (104)
147 KOG0826 Predicted E3 ubiquitin 60.6 6.2 0.00013 32.2 1.9 63 5-78 281-344 (357)
148 KOG0825 PHD Zn-finger protein 60.2 15 0.00033 33.8 4.4 18 45-62 121-138 (1134)
149 cd00065 FYVE FYVE domain; Zinc 60.0 5.6 0.00012 23.2 1.3 36 24-59 3-38 (57)
150 PF00098 zf-CCHC: Zinc knuckle 59.9 6.7 0.00014 17.4 1.2 16 146-161 2-17 (18)
151 COG5220 TFB3 Cdk activating ki 59.4 11 0.00023 29.5 2.9 56 70-128 11-67 (314)
152 COG1594 RPB9 DNA-directed RNA 58.5 4.8 0.0001 27.7 0.9 31 112-146 2-32 (113)
153 PF06827 zf-FPG_IleRS: Zinc fi 58.4 4.9 0.00011 20.3 0.7 13 184-196 2-14 (30)
154 PLN00209 ribosomal protein S27 58.1 8.3 0.00018 25.0 1.8 31 113-148 37-67 (86)
155 PF02591 DUF164: Putative zinc 57.8 8.5 0.00018 22.6 1.8 21 172-192 35-55 (56)
156 PF06524 NOA36: NOA36 protein; 57.3 5.4 0.00012 31.5 1.0 50 134-195 169-221 (314)
157 PF07754 DUF1610: Domain of un 56.9 7.4 0.00016 18.8 1.1 11 134-144 14-24 (24)
158 KOG2906 RNA polymerase III sub 56.3 4.4 9.6E-05 26.9 0.4 30 113-146 2-31 (105)
159 PF08792 A2L_zn_ribbon: A2L zi 56.1 6.6 0.00014 20.5 0.9 29 112-146 3-31 (33)
160 KOG0978 E3 ubiquitin ligase in 55.3 2.2 4.8E-05 38.5 -1.5 29 141-193 660-688 (698)
161 KOG2932 E3 ubiquitin ligase in 55.1 7.8 0.00017 31.4 1.6 33 21-56 88-120 (389)
162 PF08274 PhnA_Zn_Ribbon: PhnA 54.7 4.8 0.0001 20.6 0.3 26 114-146 4-29 (30)
163 PHA02862 5L protein; Provision 54.6 13 0.00028 26.7 2.5 47 24-83 3-54 (156)
164 PF01396 zf-C4_Topoisom: Topoi 54.6 14 0.0003 20.1 2.1 21 184-205 2-25 (39)
165 TIGR00570 cdk7 CDK-activating 53.8 12 0.00027 30.4 2.6 33 113-152 4-36 (309)
166 KOG2691 RNA polymerase II subu 53.6 12 0.00026 25.4 2.0 33 111-145 3-35 (113)
167 KOG4362 Transcriptional regula 53.2 4.4 9.6E-05 36.5 -0.0 59 19-88 17-75 (684)
168 COG1998 RPS31 Ribosomal protei 52.6 7.7 0.00017 22.3 0.9 28 112-145 19-46 (51)
169 PF01363 FYVE: FYVE zinc finge 52.4 6.7 0.00015 24.0 0.7 37 108-152 5-41 (69)
170 PF02748 PyrI_C: Aspartate car 52.2 6.1 0.00013 23.1 0.5 34 111-145 5-44 (52)
171 PRK09710 lar restriction allev 52.0 10 0.00023 23.1 1.5 15 181-195 4-18 (64)
172 COG3024 Uncharacterized protei 52.0 8.5 0.00018 23.4 1.1 16 181-196 5-20 (65)
173 smart00834 CxxC_CXXC_SSSS Puta 51.9 8.8 0.00019 20.6 1.1 16 181-196 24-39 (41)
174 PF05605 zf-Di19: Drought indu 51.7 6.8 0.00015 22.8 0.6 38 23-79 2-39 (54)
175 KOG2114 Vacuolar assembly/sort 51.3 10 0.00022 35.0 1.9 40 24-79 841-880 (933)
176 PF07800 DUF1644: Protein of u 50.9 20 0.00042 26.2 3.0 83 23-125 2-120 (162)
177 PF10497 zf-4CXXC_R1: Zinc-fin 49.4 37 0.00079 23.0 4.0 32 46-79 37-69 (105)
178 TIGR00686 phnA alkylphosphonat 49.0 8.5 0.00018 26.1 0.8 26 114-146 4-29 (109)
179 TIGR03826 YvyF flagellar opero 48.8 12 0.00025 26.8 1.5 13 184-196 82-94 (137)
180 KOG3183 Predicted Zn-finger pr 48.7 13 0.00027 29.1 1.8 104 41-161 25-138 (250)
181 PF09538 FYDLN_acid: Protein o 48.6 4.7 0.0001 27.5 -0.4 30 48-84 10-39 (108)
182 PTZ00083 40S ribosomal protein 48.5 12 0.00025 24.2 1.4 31 113-148 36-66 (85)
183 COG2051 RPS27A Ribosomal prote 48.4 6.6 0.00014 24.1 0.2 32 112-148 19-50 (67)
184 PF14149 YhfH: YhfH-like prote 47.9 1.6 3.4E-05 23.5 -2.2 31 174-204 4-34 (37)
185 PF02318 FYVE_2: FYVE-type zin 47.7 26 0.00056 24.1 3.2 36 111-153 53-88 (118)
186 PF12760 Zn_Tnp_IS1595: Transp 47.3 23 0.00051 19.8 2.4 20 173-192 5-27 (46)
187 PF14353 CpXC: CpXC protein 47.1 9.7 0.00021 26.6 0.9 13 70-84 2-14 (128)
188 COG1645 Uncharacterized Zn-fin 45.8 14 0.0003 26.1 1.5 24 181-206 26-49 (131)
189 PF01428 zf-AN1: AN1-like Zinc 45.5 8.8 0.00019 21.3 0.4 28 135-164 12-39 (43)
190 PRK03681 hypA hydrogenase nick 45.5 25 0.00053 24.2 2.7 47 91-144 40-95 (114)
191 PF03604 DNA_RNApol_7kD: DNA d 45.4 11 0.00024 19.6 0.7 23 119-146 5-27 (32)
192 PF08209 Sgf11: Sgf11 (transcr 44.9 14 0.00031 19.3 1.1 14 182-195 3-16 (33)
193 PRK13130 H/ACA RNA-protein com 44.3 44 0.00095 19.9 3.3 36 69-106 17-52 (56)
194 PRK10220 hypothetical protein; 44.0 12 0.00026 25.4 0.9 28 113-147 4-31 (111)
195 TIGR01384 TFS_arch transcripti 43.4 12 0.00026 25.0 0.9 25 114-146 2-26 (104)
196 PF03884 DUF329: Domain of unk 43.1 14 0.00031 22.0 1.1 15 183-197 2-16 (57)
197 PF09151 DUF1936: Domain of un 42.8 12 0.00026 19.1 0.6 10 185-194 3-12 (36)
198 PF14471 DUF4428: Domain of un 42.8 24 0.00052 20.5 2.0 30 25-57 1-30 (51)
199 PRK03824 hypA hydrogenase nick 42.7 26 0.00055 24.9 2.5 15 111-127 69-83 (135)
200 PRK06266 transcription initiat 42.6 12 0.00025 28.0 0.8 31 109-144 114-144 (178)
201 PLN02436 cellulose synthase A 42.2 15 0.00032 35.1 1.6 52 22-82 35-89 (1094)
202 PRK13264 3-hydroxyanthranilate 42.2 9.1 0.0002 28.5 0.2 51 142-195 118-169 (177)
203 TIGR00373 conserved hypothetic 42.0 12 0.00026 27.3 0.8 32 109-145 106-137 (158)
204 smart00531 TFIIE Transcription 41.8 11 0.00024 27.1 0.6 35 109-145 96-132 (147)
205 PLN03086 PRLI-interacting fact 41.3 9.4 0.0002 33.9 0.2 31 112-146 433-463 (567)
206 PF14369 zf-RING_3: zinc-finge 40.5 18 0.00039 19.1 1.1 30 112-146 2-31 (35)
207 PLN02189 cellulose synthase 40.1 21 0.00046 34.0 2.2 63 111-202 33-95 (1040)
208 KOG1571 Predicted E3 ubiquitin 40.1 12 0.00027 30.9 0.7 46 19-81 301-346 (355)
209 PF14445 Prok-RING_2: Prokaryo 40.0 5.8 0.00013 22.9 -0.9 38 20-58 4-41 (57)
210 PF14205 Cys_rich_KTR: Cystein 39.9 16 0.00034 21.5 0.9 33 112-146 4-38 (55)
211 KOG3214 Uncharacterized Zn rib 39.8 15 0.00032 24.5 0.9 33 1-33 1-33 (109)
212 TIGR01053 LSD1 zinc finger dom 39.5 41 0.00089 17.3 2.3 23 185-207 3-25 (31)
213 KOG1039 Predicted E3 ubiquitin 39.5 10 0.00022 31.5 0.1 38 140-195 185-222 (344)
214 PF09788 Tmemb_55A: Transmembr 39.5 17 0.00036 28.7 1.2 18 18-35 60-77 (256)
215 KOG2164 Predicted E3 ubiquitin 39.4 10 0.00022 32.9 0.1 34 141-195 203-237 (513)
216 TIGR03037 anthran_nbaC 3-hydro 39.3 11 0.00024 27.6 0.3 46 143-191 113-159 (159)
217 KOG2807 RNA polymerase II tran 39.0 13 0.00028 30.4 0.6 31 23-54 330-360 (378)
218 PRK12286 rpmF 50S ribosomal pr 39.0 23 0.0005 21.1 1.5 28 107-145 22-49 (57)
219 PLN02638 cellulose synthase A 38.8 32 0.00069 33.0 3.1 52 21-81 15-69 (1079)
220 PF14354 Lar_restr_allev: Rest 38.7 21 0.00044 21.2 1.4 14 182-195 2-15 (61)
221 PRK04023 DNA polymerase II lar 38.6 27 0.00059 33.2 2.6 20 136-155 638-662 (1121)
222 PRK12380 hydrogenase nickel in 38.6 39 0.00085 23.1 2.9 46 91-144 40-94 (113)
223 PF11023 DUF2614: Protein of u 38.5 19 0.00042 24.6 1.3 22 134-155 67-96 (114)
224 TIGR00100 hypA hydrogenase nic 38.4 39 0.00085 23.2 2.9 26 111-144 69-94 (115)
225 KOG2932 E3 ubiquitin ligase in 38.4 8.2 0.00018 31.3 -0.6 18 182-199 122-139 (389)
226 TIGR03655 anti_R_Lar restricti 38.4 15 0.00034 21.3 0.7 11 184-194 2-12 (53)
227 PF10764 Gin: Inhibitor of sig 37.8 9.5 0.00021 21.7 -0.2 35 25-64 1-35 (46)
228 COG1198 PriA Primosomal protei 37.6 31 0.00067 31.8 2.8 15 90-104 405-419 (730)
229 PF04216 FdhE: Protein involve 37.5 7.7 0.00017 31.3 -0.9 15 180-194 235-249 (290)
230 PF13913 zf-C2HC_2: zinc-finge 36.9 16 0.00035 17.6 0.5 10 137-146 3-12 (25)
231 PLN02189 cellulose synthase 36.8 24 0.00052 33.6 2.0 52 22-82 33-87 (1040)
232 PF04810 zf-Sec23_Sec24: Sec23 36.5 16 0.00035 19.9 0.6 30 113-144 3-32 (40)
233 COG1579 Zn-ribbon protein, pos 36.3 41 0.0009 26.4 3.0 59 85-145 167-230 (239)
234 PF13453 zf-TFIIB: Transcripti 35.6 19 0.00042 19.5 0.8 11 185-195 1-11 (41)
235 PRK00415 rps27e 30S ribosomal 35.4 18 0.00039 21.8 0.7 32 112-148 11-42 (59)
236 KOG3113 Uncharacterized conser 35.4 1.1E+02 0.0024 24.4 5.1 76 18-105 106-182 (293)
237 smart00734 ZnF_Rad18 Rad18-lik 35.4 6 0.00013 19.4 -1.2 20 70-91 2-21 (26)
238 KOG2923 Uncharacterized conser 35.0 28 0.00062 21.2 1.5 22 174-195 35-56 (67)
239 PF02891 zf-MIZ: MIZ/SP-RING z 34.7 25 0.00054 20.2 1.2 47 24-79 3-49 (50)
240 COG1996 RPC10 DNA-directed RNA 34.6 23 0.0005 20.4 1.0 16 179-194 20-35 (49)
241 PF07191 zinc-ribbons_6: zinc- 34.1 33 0.00071 21.4 1.7 19 185-205 3-21 (70)
242 KOG1729 FYVE finger containing 34.0 22 0.00048 28.8 1.2 49 9-57 154-203 (288)
243 PLN02915 cellulose synthase A 34.0 37 0.0008 32.5 2.7 55 19-82 11-68 (1044)
244 KOG2789 Putative Zn-finger pro 33.9 15 0.00032 30.9 0.2 36 21-58 72-107 (482)
245 COG0266 Nei Formamidopyrimidin 33.8 36 0.00078 27.3 2.3 24 184-207 246-271 (273)
246 PF06943 zf-LSD1: LSD1 zinc fi 33.7 64 0.0014 15.7 2.4 22 186-207 1-22 (25)
247 COG5109 Uncharacterized conser 33.6 29 0.00063 28.4 1.8 54 22-83 335-388 (396)
248 PRK08665 ribonucleotide-diphos 33.5 27 0.00059 32.3 1.8 20 184-205 725-744 (752)
249 PRK14892 putative transcriptio 33.4 1.5E+02 0.0033 19.9 5.8 78 1-108 1-79 (99)
250 smart00659 RPOLCX RNA polymera 33.4 22 0.00047 19.9 0.8 22 119-145 7-28 (44)
251 COG5216 Uncharacterized conser 33.3 23 0.00049 21.2 0.8 21 174-194 35-55 (67)
252 TIGR01031 rpmF_bact ribosomal 32.9 30 0.00064 20.4 1.3 28 107-145 21-48 (55)
253 PF06044 DRP: Dam-replacing fa 32.7 20 0.00042 28.2 0.7 35 112-148 31-65 (254)
254 PRK14890 putative Zn-ribbon RN 32.6 29 0.00063 20.8 1.3 32 113-150 8-39 (59)
255 PRK00564 hypA hydrogenase nick 32.6 50 0.0011 22.7 2.7 47 91-144 40-96 (117)
256 PF01667 Ribosomal_S27e: Ribos 31.5 21 0.00045 21.1 0.5 32 112-148 7-38 (55)
257 COG3357 Predicted transcriptio 31.3 19 0.00042 23.6 0.4 25 114-144 60-84 (97)
258 PF09723 Zn-ribbon_8: Zinc rib 31.1 32 0.0007 18.9 1.2 15 181-195 24-39 (42)
259 PF10426 zf-RAG1: Recombinatio 30.9 12 0.00025 19.1 -0.5 14 69-82 2-15 (30)
260 PF01927 Mut7-C: Mut7-C RNAse 30.9 64 0.0014 23.1 3.1 33 93-127 69-104 (147)
261 COG3677 Transposase and inacti 30.5 72 0.0016 22.4 3.2 39 112-152 30-69 (129)
262 smart00154 ZnF_AN1 AN1-like Zi 30.4 33 0.00071 18.6 1.2 18 136-153 12-29 (39)
263 PRK09678 DNA-binding transcrip 30.3 19 0.00042 22.6 0.3 14 112-125 27-40 (72)
264 PF04236 Transp_Tc5_C: Tc5 tra 30.2 38 0.00082 20.6 1.5 30 112-152 27-56 (63)
265 TIGR01206 lysW lysine biosynth 30.1 41 0.00089 19.8 1.6 14 184-197 3-16 (54)
266 PRK02935 hypothetical protein; 30.0 35 0.00076 23.1 1.4 22 134-155 68-97 (110)
267 PF03854 zf-P11: P-11 zinc fin 30.0 12 0.00026 21.4 -0.6 43 24-82 3-46 (50)
268 COG2260 Predicted Zn-ribbon RN 29.4 1.1E+02 0.0024 18.3 3.3 34 71-106 19-52 (59)
269 PF08271 TF_Zn_Ribbon: TFIIB z 29.4 27 0.00058 19.2 0.7 14 182-195 18-31 (43)
270 PHA02325 hypothetical protein 29.0 33 0.00071 20.9 1.1 12 182-193 2-13 (72)
271 PF14255 Cys_rich_CPXG: Cystei 28.8 37 0.0008 19.8 1.2 11 185-195 2-12 (52)
272 TIGR00595 priA primosomal prot 28.7 63 0.0014 28.4 3.2 33 115-153 225-262 (505)
273 PF04981 NMD3: NMD3 family ; 28.6 16 0.00034 28.6 -0.4 13 182-194 34-46 (236)
274 PRK14810 formamidopyrimidine-D 28.5 51 0.0011 26.4 2.5 24 183-206 244-269 (272)
275 PF01783 Ribosomal_L32p: Ribos 28.5 46 0.00099 19.6 1.7 27 107-144 21-47 (56)
276 PRK01103 formamidopyrimidine/5 28.5 52 0.0011 26.3 2.5 23 184-206 246-270 (274)
277 COG4416 Com Mu-like prophage p 28.5 30 0.00065 20.3 0.8 11 184-194 25-35 (60)
278 PF14787 zf-CCHC_5: GAG-polypr 28.2 40 0.00087 18.0 1.2 21 145-165 3-23 (36)
279 PRK10445 endonuclease VIII; Pr 28.2 54 0.0012 26.1 2.5 24 183-206 235-260 (263)
280 PF07282 OrfB_Zn_ribbon: Putat 28.1 29 0.00062 21.1 0.8 28 112-145 28-55 (69)
281 COG1656 Uncharacterized conser 28.0 66 0.0014 23.7 2.7 17 110-128 95-111 (165)
282 COG1198 PriA Primosomal protei 27.6 36 0.00077 31.4 1.5 20 134-153 460-484 (730)
283 PF13824 zf-Mss51: Zinc-finger 27.5 31 0.00066 20.4 0.7 12 183-194 14-25 (55)
284 cd00350 rubredoxin_like Rubred 27.3 40 0.00086 17.4 1.1 22 115-144 4-25 (33)
285 COG2816 NPY1 NTP pyrophosphohy 27.1 61 0.0013 26.1 2.6 31 110-146 109-139 (279)
286 PRK00418 DNA gyrase inhibitor; 26.5 35 0.00075 20.8 0.9 14 182-195 5-18 (62)
287 PLN02436 cellulose synthase A 26.5 49 0.0011 31.8 2.2 61 112-201 36-96 (1094)
288 PF00096 zf-C2H2: Zinc finger, 26.4 20 0.00044 16.3 -0.1 7 139-145 3-9 (23)
289 COG3058 FdhE Uncharacterized p 26.4 19 0.0004 28.9 -0.4 12 181-192 250-261 (308)
290 COG1913 Predicted Zn-dependent 26.3 42 0.00091 25.0 1.5 49 95-143 117-169 (181)
291 PF09889 DUF2116: Uncharacteri 26.3 1.1E+02 0.0023 18.4 2.9 30 71-104 5-34 (59)
292 PF01155 HypA: Hydrogenase exp 26.1 48 0.001 22.7 1.6 48 90-145 39-95 (113)
293 PLN02638 cellulose synthase A 25.9 47 0.001 32.0 2.0 61 112-201 17-77 (1079)
294 smart00249 PHD PHD zinc finger 25.9 34 0.00073 18.3 0.7 33 25-58 1-33 (47)
295 PRK13945 formamidopyrimidine-D 25.8 60 0.0013 26.1 2.4 24 183-206 254-279 (282)
296 TIGR00577 fpg formamidopyrimid 25.8 63 0.0014 25.9 2.5 24 183-206 245-270 (272)
297 PLN02195 cellulose synthase A 25.7 64 0.0014 30.8 2.8 51 23-82 6-59 (977)
298 PRK14811 formamidopyrimidine-D 25.2 64 0.0014 25.8 2.4 23 183-205 235-259 (269)
299 COG1885 Uncharacterized protei 24.7 37 0.00081 22.9 0.8 13 182-194 48-60 (115)
300 PF01194 RNA_pol_N: RNA polyme 24.7 99 0.0021 18.7 2.6 25 68-104 3-27 (60)
301 KOG2041 WD40 repeat protein [G 24.6 62 0.0013 29.9 2.4 32 77-108 1076-1107(1189)
302 PRK01343 zinc-binding protein; 24.5 43 0.00094 20.0 1.0 15 181-195 7-21 (57)
303 PRK00893 aspartate carbamoyltr 24.4 31 0.00067 25.1 0.5 36 111-146 104-144 (152)
304 PLN02915 cellulose synthase A 24.4 44 0.00095 32.0 1.5 60 113-201 16-75 (1044)
305 PF06467 zf-FCS: MYM-type Zinc 24.4 38 0.00082 18.3 0.7 37 21-57 4-43 (43)
306 TIGR02605 CxxC_CxxC_SSSS putat 24.4 47 0.001 18.9 1.2 15 182-196 25-40 (52)
307 TIGR02300 FYDLN_acid conserved 24.2 18 0.00039 25.4 -0.7 30 48-84 10-39 (129)
308 PF01530 zf-C2HC: Zinc finger, 23.9 43 0.00092 17.3 0.8 11 70-80 2-12 (31)
309 PF14690 zf-ISL3: zinc-finger 23.8 51 0.0011 18.1 1.2 12 184-195 3-14 (47)
310 TIGR00515 accD acetyl-CoA carb 23.7 45 0.00098 27.0 1.3 30 111-145 25-54 (285)
311 PF10122 Mu-like_Com: Mu-like 23.6 31 0.00066 20.0 0.2 31 112-146 4-34 (51)
312 PF04438 zf-HIT: HIT zinc fing 23.6 39 0.00084 17.2 0.6 8 185-192 15-22 (30)
313 PF09943 DUF2175: Uncharacteri 23.5 60 0.0013 21.8 1.6 40 23-64 2-41 (101)
314 PLN02400 cellulose synthase 23.5 49 0.0011 31.9 1.7 65 8-81 21-88 (1085)
315 PF08882 Acetone_carb_G: Aceto 23.3 46 0.001 22.8 1.1 13 135-148 23-35 (112)
316 PRK11827 hypothetical protein; 22.6 45 0.00098 20.1 0.9 27 112-144 8-34 (60)
317 PF00412 LIM: LIM domain; Int 22.6 28 0.0006 20.1 -0.1 34 21-57 24-57 (58)
318 COG1781 PyrI Aspartate carbamo 22.2 32 0.00069 24.9 0.2 12 111-122 105-116 (153)
319 CHL00174 accD acetyl-CoA carbo 21.9 38 0.00081 27.6 0.5 28 112-144 38-65 (296)
320 PF13894 zf-C2H2_4: C2H2-type 21.5 34 0.00074 15.2 0.2 6 139-144 3-8 (24)
321 PRK00241 nudC NADH pyrophospha 21.4 91 0.002 24.7 2.6 32 109-146 96-127 (256)
322 PF13465 zf-H2C2_2: Zinc-finge 21.2 41 0.00089 16.1 0.4 13 134-146 12-24 (26)
323 PF11809 DUF3330: Domain of un 21.1 50 0.0011 20.3 0.8 40 19-61 7-51 (70)
324 KOG1779 40s ribosomal protein 21.0 80 0.0017 20.1 1.7 36 112-152 34-69 (84)
325 PRK05654 acetyl-CoA carboxylas 20.9 55 0.0012 26.6 1.3 31 111-146 26-56 (292)
326 KOG4218 Nuclear hormone recept 20.7 33 0.00072 28.4 0.0 10 182-191 66-75 (475)
327 PF11682 DUF3279: Protein of u 20.7 62 0.0013 22.8 1.3 13 21-33 26-38 (128)
328 PF14392 zf-CCHC_4: Zinc knuck 20.7 38 0.00082 19.2 0.2 17 145-161 32-48 (49)
329 TIGR00240 ATCase_reg aspartate 20.5 34 0.00074 24.8 0.0 36 111-146 102-142 (150)
330 PF13696 zf-CCHC_2: Zinc knuck 20.5 39 0.00086 17.5 0.3 19 144-162 8-26 (32)
331 COG1997 RPL43A Ribosomal prote 20.4 96 0.0021 20.3 2.0 30 112-147 35-64 (89)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.4e-36 Score=238.06 Aligned_cols=186 Identities=26% Similarity=0.588 Sum_probs=155.9
Q ss_pred cccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCChhHHH
Q 035729 17 EEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPSSLFS 96 (208)
Q Consensus 17 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~ 96 (208)
+.+....+.|.|||+.......| +.++|+|+||+.|++.|+...|.+|....++||+++|+...++..++.++++++++
T Consensus 178 ~~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~a 256 (445)
T KOG1814|consen 178 EKFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFA 256 (445)
T ss_pred HHHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHH
Confidence 45677889999999999665555 69999999999999999999999988899999999999999999999999999999
Q ss_pred HHHHHHHhhhhc-CCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhc--------cc
Q 035729 97 KWCDLLCEDYVR-GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGN--------LR 167 (208)
Q Consensus 97 ~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~--------~~ 167 (208)
+|+.++.++.+. ..+.++||++.|..++..+++ ...+.|.+|+..||+.|+..||+...|.--.. |.
T Consensus 257 rYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~----~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~ 332 (445)
T KOG1814|consen 257 RYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPG----RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYL 332 (445)
T ss_pred HHHHHHHHHHHHhhcccccCChhhccCccccCch----hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHh
Confidence 999999999887 788999999999999866665 68999999999999999999999999964321 11
Q ss_pred cc------------c----hHHHHHHH----HhCCcccCCCCCceeEecCCCCceEeCCC
Q 035729 168 DR------------N----DIAFGQLA----ERMKWARCPGCGHCVQRKNGCHVMQDSVL 207 (208)
Q Consensus 168 ~~------------~----~~~~~~~~----~~~~~k~CP~C~~~i~k~~GCnhm~C~~~ 207 (208)
+. . +..+.+.. ...+.|+||+|+++|+|++|||+|+|++.
T Consensus 333 ~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c 392 (445)
T KOG1814|consen 333 EADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKC 392 (445)
T ss_pred hcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccc
Confidence 10 0 00111111 12366999999999999999999999864
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.9e-34 Score=234.48 Aligned_cols=182 Identities=27% Similarity=0.631 Sum_probs=154.6
Q ss_pred CCcccccccccccccc-ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCChhHHHHHH
Q 035729 21 GSSFTCEICIEPMAAN-KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPSSLFSKWC 99 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~-~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 99 (208)
....+|.||+.+.+.. +.| .+..|+|.||.+|+++|++.+. .+...++||..+|...++.+....+|.+.+.++|+
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f-~~~~C~H~fC~~C~k~~iev~~--~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e 220 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMF-SVLKCGHRFCKDCVKQHIEVKL--LSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWE 220 (384)
T ss_pred cccccCccCccccccHhhhH-HHhcccchhhhHHhHHHhhhhh--ccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHH
Confidence 3468999999555555 455 4889999999999999999983 35678999999999999999999999999999999
Q ss_pred HHHHhhhhcCCCcccCcccccccchhcchhhc-CCCCcccCccccchhccccCcCcCCCCCChhhhccccc--chHHHHH
Q 035729 100 DLLCEDYVRGYERSYCPNRNCMALVVNECERK-GRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDR--NDIAFGQ 176 (208)
Q Consensus 100 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~--~~~~~~~ 176 (208)
.++.+.++...+..+||+++|...+......+ .......|+.|+..||..|+.+||.+.+|++++++... .+....+
T Consensus 221 ~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~ 300 (384)
T KOG1812|consen 221 QRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLK 300 (384)
T ss_pred HHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHH
Confidence 99999988866666999999999888655321 23567789999999999999999999999999998754 4444555
Q ss_pred HHHhCCcccCCCCCceeEecCCCCceEeCC
Q 035729 177 LAERMKWARCPGCGHCVQRKNGCHVMQDSV 206 (208)
Q Consensus 177 ~~~~~~~k~CP~C~~~i~k~~GCnhm~C~~ 206 (208)
.++ .+|++||+|+..|++.+|||||+|++
T Consensus 301 ~la-~~wr~CpkC~~~ie~~~GCnhm~CrC 329 (384)
T KOG1812|consen 301 YLA-KRWRQCPKCKFMIELSEGCNHMTCRC 329 (384)
T ss_pred HHH-HhcCcCcccceeeeecCCcceEEeec
Confidence 444 89999999999999999999999984
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1.7e-26 Score=194.94 Aligned_cols=179 Identities=22% Similarity=0.478 Sum_probs=149.7
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCCh-hHHHHH
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPS-SLFSKW 98 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~ 98 (208)
.....+|.||++.... ....+.|+|.||..||..|+..+|.++....|+||..+|...+..++|..++++ +..++|
T Consensus 67 ~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky 143 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKY 143 (444)
T ss_pred CCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHH
Confidence 3456899999999965 235889999999999999999999985444499999999999999999999998 489999
Q ss_pred HHHHHhhhhc-CCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHH
Q 035729 99 CDLLCEDYVR-GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQL 177 (208)
Q Consensus 99 ~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~ 177 (208)
.....+.++. .....|||+|+|+..+.... .....+.| .|++.||+.|..+||.+.+|.....|..+.......+
T Consensus 144 ~~~i~~syve~~~~lkwCP~~~C~~av~~~~---~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~ 219 (444)
T KOG1815|consen 144 QRYILRSYVEDNVPLKWCPAPGCGLAVKFGS---LESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETI 219 (444)
T ss_pred HHHHHHHHHhcCCccccCCCCCCCceeeccC---CCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhh
Confidence 9999999998 44589999999999877531 22688999 5888999999999999999999999876633222221
Q ss_pred -HHhCCcccCCCCCceeEecCCCCceEeC
Q 035729 178 -AERMKWARCPGCGHCVQRKNGCHVMQDS 205 (208)
Q Consensus 178 -~~~~~~k~CP~C~~~i~k~~GCnhm~C~ 205 (208)
-...+.++||+|.++|+|++|||||+|.
T Consensus 220 ~wi~~ntk~CP~c~~~iek~~gc~~~~~~ 248 (444)
T KOG1815|consen 220 NWILANTKECPKCKVPIEKDGGCNHMTCK 248 (444)
T ss_pred hhhhccCccCCCcccchhccCCccccccc
Confidence 1346889999999999999999999987
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=9.1e-24 Score=163.95 Aligned_cols=180 Identities=21% Similarity=0.443 Sum_probs=136.8
Q ss_pred cccCCCccccccccccccccccccccCCCC--ChhHHHHHHHHHHHHhhcCC-------CccccCCccccCCCC-Ccccc
Q 035729 17 EEGNGSSFTCEICIEPMAANKKFKNKNLCT--HPFCQECIAKYIQVMVQDNN-------TAKIECPGLNCQKNL-DPFSC 86 (208)
Q Consensus 17 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~--H~~C~~Cl~~~~~~~i~~~~-------~~~i~CP~~~C~~~l-~~~~i 86 (208)
...+....+|..|-+--++. .+++|+ |+.|.+|++-|....+++.. .+.+.||. +|...| ..-.-
T Consensus 215 i~~N~~ni~C~~Ctdv~~~v----lvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HH 289 (446)
T KOG0006|consen 215 IATNSRNITCITCTDVRSPV----LVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHH 289 (446)
T ss_pred hhcccccceeEEecCCccce----EEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhh
Confidence 45677789999998765332 367897 99999999999999997622 23467775 566543 33344
Q ss_pred cCCCChhHHHHHHHHHHhhhhcCCCcccCcccccccchhcchhhcCCCCcccCcc-ccchhccccCcCcCCCCCChhhhc
Q 035729 87 KPMIPSSLFSKWCDLLCEDYVRGYERSYCPNRNCMALVVNECERKGRMKKAQCPN-CKHWFCFRCKLKWHGGYHCEESGN 165 (208)
Q Consensus 87 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~ 165 (208)
..+|..+.|.+|+++..+.++...+-+.||+|+|+..+.+++. ..+++|+. |++.||..|...||.+. |.+...
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 5789999999999999999988788999999999999998876 68999996 99999999999999873 442111
Q ss_pred ccc-----------cchH----HHHHHHHhCCcccCCCCCceeEecCCCCceEeCC
Q 035729 166 LRD-----------RNDI----AFGQLAERMKWARCPGCGHCVQRKNGCHVMQDSV 206 (208)
Q Consensus 166 ~~~-----------~~~~----~~~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~~ 206 (208)
... .+++ ++.+......+|+||+|.+++||+|||.||.|+=
T Consensus 365 as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~ 420 (446)
T KOG0006|consen 365 ASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQ 420 (446)
T ss_pred cccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCC
Confidence 100 0111 1222233357799999999999999999999983
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.33 E-value=1e-12 Score=81.76 Aligned_cols=63 Identities=37% Similarity=0.885 Sum_probs=53.9
Q ss_pred HHHHHHHHhhhhc-CCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCC
Q 035729 96 SKWCDLLCEDYVR-GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHC 160 (208)
Q Consensus 96 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 160 (208)
++|++++.+.+++ +++++|||+++|..++..... .....+.|+.|+..||+.|+.+||.+.+|
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 4788888988887 478999999999999987631 12579999999999999999999999887
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=99.31 E-value=2.2e-13 Score=84.79 Aligned_cols=63 Identities=29% Similarity=0.778 Sum_probs=41.2
Q ss_pred HHHHHHHHhhhhc-CCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCC
Q 035729 96 SKWCDLLCEDYVR-GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHC 160 (208)
Q Consensus 96 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 160 (208)
++|.+++++.++. ++++++||+++|+.++..+.... ...+.|+.|+..||+.|+.+||.+.+|
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 4678888888776 55678999999999999887631 224999999999999999999999876
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.81 E-value=7.4e-10 Score=62.53 Aligned_cols=41 Identities=24% Similarity=0.724 Sum_probs=29.1
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
|+||++.+..+ +.++|||+||..||.+++...- ...+.||.
T Consensus 1 CpiC~~~~~~P----v~l~CGH~FC~~Cl~~~~~~~~----~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDP----VSLPCGHSFCRSCLERLWKEPS----GSGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSE----EE-SSSSEEEHHHHHHHHCCSS----SST---SS
T ss_pred CCccchhhCCc----cccCCcCHHHHHHHHHHHHccC----CcCCCCcC
Confidence 89999999776 5899999999999999986532 22278887
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.78 E-value=9.3e-09 Score=76.38 Aligned_cols=66 Identities=26% Similarity=0.663 Sum_probs=50.3
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhc--------CCCccccCCccccCCCCCcccccCCCCh
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQD--------NNTAKIECPGLNCQKNLDPFSCKPMIPS 92 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~--------~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 92 (208)
.+.++|+||++.+..+ +++.|+|.||..||.+|+...-.. .......||. |+..++...+..+.+.
T Consensus 16 ~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiygr 89 (193)
T PLN03208 16 GGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYGR 89 (193)
T ss_pred CCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeecc
Confidence 3568999999998655 468999999999999997643211 1234579999 9999988888776554
No 9
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.71 E-value=1.8e-08 Score=73.05 Aligned_cols=59 Identities=22% Similarity=0.654 Sum_probs=44.9
Q ss_pred ccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP 88 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 88 (208)
....+.+.|+||++.+... .++...|||+||..|++..+... .+||. |...|+..++..
T Consensus 126 ~~~~~~~~CPiCl~~~sek--~~vsTkCGHvFC~~Cik~alk~~--------~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 126 LRKEGTYKCPICLDSVSEK--VPVSTKCGHVFCSQCIKDALKNT--------NKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccccCCCceecchhhc--cccccccchhHHHHHHHHHHHhC--------CCCCC--cccccchhhhee
Confidence 3345569999999999654 23478999999999999977542 48999 888777655543
No 10
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.70 E-value=6.9e-09 Score=58.58 Aligned_cols=43 Identities=28% Similarity=0.716 Sum_probs=25.0
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCC
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECP 73 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP 73 (208)
|+||.+ +...++..++++|||+||++|+.++..... ...++||
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 767666667889999999999999998543 3457887
No 11
>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=98.66 E-value=4.5e-09 Score=60.17 Aligned_cols=41 Identities=32% Similarity=0.731 Sum_probs=33.0
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 25 TCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
+|+||++++...+.+ +.++|+|.||.+|+..|+... ..||.
T Consensus 2 ~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKV-VKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCE-EEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeE-EEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 699999999765555 477799999999999999762 28887
No 12
>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=98.63 E-value=9.8e-09 Score=57.12 Aligned_cols=38 Identities=37% Similarity=0.938 Sum_probs=29.3
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
|+||++.+..+ .+.++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~~---~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRDP---VVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SSE---EEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccCc---CEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 78999998654 2479999999999999998652 57876
No 13
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.61 E-value=2.3e-08 Score=56.27 Aligned_cols=40 Identities=33% Similarity=0.940 Sum_probs=33.0
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
|+||++.+..+. ..++|+|.||..||.+++.. ...++||.
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 789999996653 37899999999999999987 23467886
No 14
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.55 E-value=7.6e-08 Score=54.98 Aligned_cols=44 Identities=32% Similarity=0.899 Sum_probs=34.7
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 25 TCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
.|+||++.+...+. +.+++|+|+||..|+.+.. ...+.||. |++
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 48999999944333 4689999999999999877 24579998 763
No 15
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=1.4e-07 Score=71.56 Aligned_cols=61 Identities=28% Similarity=0.694 Sum_probs=51.0
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIP 91 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 91 (208)
+...|+|.||+|.-.++ ++..|||.||=.||-+|+....+. -.||. |+..++.+.+-.+.+
T Consensus 44 ~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeeec
Confidence 56789999999998665 588999999999999999886644 47899 999998887766654
No 16
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.35 E-value=5e-07 Score=51.34 Aligned_cols=44 Identities=34% Similarity=0.842 Sum_probs=33.5
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCC
Q 035729 25 TCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN 80 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 80 (208)
+|+||++.+... + ...+|+|.||..|++.|+.. ....||. |+..
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 2 35669999999999999875 2357988 8764
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=98.35 E-value=5.4e-07 Score=67.94 Aligned_cols=59 Identities=25% Similarity=0.567 Sum_probs=43.4
Q ss_pred CCCcccccccccccc-----ccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 20 NGSSFTCEICIEPMA-----ANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~-----~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
.....+|+||+|... ..+.|..+.+|+|.||..|+..|..++.. ....-.||. |+..+.
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 344689999999863 23346567799999999999999987532 233458999 998543
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.29 E-value=2.8e-07 Score=54.14 Aligned_cols=46 Identities=30% Similarity=0.743 Sum_probs=35.7
Q ss_pred ccccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHP-FCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
...|.||++..... .+++|+|. ||..|+.+++. ...+||. |+..++
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 47899999 99999999987 2358999 988664
No 19
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=1.1e-06 Score=71.11 Aligned_cols=112 Identities=22% Similarity=0.489 Sum_probs=71.5
Q ss_pred ccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCChhHHHH
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPSSLFSK 97 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~ 97 (208)
....+.+.|+||++.+..+ .+++|+|.||..|+...+. ..+.||. |.. ... .+.....+..
T Consensus 8 ~~~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~----~~~~n~~l~~ 68 (386)
T KOG2177|consen 8 EVLQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSR----NLRPNVLLAN 68 (386)
T ss_pred hhccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chh----ccCccHHHHH
Confidence 3445678999999999776 4889999999999999997 3489999 984 222 2222223333
Q ss_pred HHHHHHhhhhcC-C--CcccCcccccccchhcchhhcCCCCcccCccccchhccccC-cCcCCCCCCh
Q 035729 98 WCDLLCEDYVRG-Y--ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCK-LKWHGGYHCE 161 (208)
Q Consensus 98 ~~~~~~~~~~~~-~--~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C~ 161 (208)
.........+.. . ....|+. +.....+.|..|...+|..|. ...|.++.-.
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~c~~-------------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~ 123 (386)
T KOG2177|consen 69 LVERLRQLRLSRPLGSKEELCEK-------------HGEELKLFCEEDEKLLCVLCRESGEHRGHPVL 123 (386)
T ss_pred HHHHHHhcCCcccccccchhhhh-------------cCCcceEEecccccccCCCCCCcccccCCccc
Confidence 333222221110 0 1112331 111257889999999999998 6678777543
No 20
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.15 E-value=1.6e-06 Score=67.22 Aligned_cols=52 Identities=31% Similarity=0.677 Sum_probs=39.0
Q ss_pred CCccccccccccccccc----cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 21 GSSFTCEICIEPMAANK----KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~----~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
....+|+||++.+.... .+.+..+|+|.||.+|+..|... ...||. |+..+.
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 34689999999975432 13346789999999999998753 238999 998654
No 21
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.11 E-value=3.6e-06 Score=46.00 Aligned_cols=30 Identities=37% Similarity=0.972 Sum_probs=24.8
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHH
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQ 59 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 59 (208)
|+||++..... ..++|+|.||..|++.|+.
T Consensus 1 C~iC~~~~~~~----~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEELKDP----VVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCCCCc----EEecCCChHHHHHHHHHHH
Confidence 78999885322 4789999999999999987
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=1.6e-06 Score=72.78 Aligned_cols=60 Identities=27% Similarity=0.642 Sum_probs=48.8
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIP 91 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 91 (208)
...|+||+++.+.+ +.+.|||.||-.||.+|+.... -..+..||. |...|.+.++..+.-
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 67999999998655 4677999999999999998872 234679999 999988877766543
No 23
>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=98.10 E-value=3.8e-06 Score=51.68 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=41.4
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP 88 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 88 (208)
+.|+||.+.+..+ +..+|||+||+.|+.+|+.. ...||. |+..++.+++..
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 47899999999999999975 137998 888887655544
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.98 E-value=1e-05 Score=67.20 Aligned_cols=68 Identities=21% Similarity=0.509 Sum_probs=49.1
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccccc-CCCChhHHHH
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCK-PMIPSSLFSK 97 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~ 97 (208)
.-...+.|+||++.+..+ ++++|+|.||..|+..++.. ...||. |...+....++ ..+-.++++.
T Consensus 22 ~Le~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~ 87 (397)
T TIGR00599 22 PLDTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVES 87 (397)
T ss_pred ccccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHH
Confidence 334568999999999655 47899999999999998853 137999 99987655443 2333356666
Q ss_pred HHH
Q 035729 98 WCD 100 (208)
Q Consensus 98 ~~~ 100 (208)
|..
T Consensus 88 ~~~ 90 (397)
T TIGR00599 88 FKN 90 (397)
T ss_pred HHH
Confidence 643
No 25
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.94 E-value=4.1e-06 Score=67.95 Aligned_cols=48 Identities=29% Similarity=0.741 Sum_probs=40.9
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.+|.||+|++..++.. +.++|.|.|...|+..|+... .-.||. |+..+
T Consensus 230 ~~CaIClEdY~~Gdkl-RiLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKL-RILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCee-eEecCCCchhhccchhhHhhc-------CccCCC--CCCcC
Confidence 7999999999988877 479999999999999999763 236999 88743
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=1.2e-05 Score=63.05 Aligned_cols=53 Identities=26% Similarity=0.701 Sum_probs=43.5
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccccc
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCK 87 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 87 (208)
.....|.+|+|....+ ...+|||.||-.|+..|...+- .||. |+..+.+..+-
T Consensus 237 ~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskvi 289 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKVI 289 (293)
T ss_pred CCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCccee
Confidence 3357999999999666 4789999999999999997643 4999 99988887653
No 27
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=7.5e-06 Score=64.44 Aligned_cols=55 Identities=24% Similarity=0.651 Sum_probs=45.5
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
+.....+|.||++++...+.+ ..++|.|.|.+.|+.+|+. ....+||. |+.++++
T Consensus 319 ea~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 319 EADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred hcCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 344568999999999877765 5899999999999999984 24569999 9988765
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.88 E-value=7.3e-06 Score=65.45 Aligned_cols=66 Identities=24% Similarity=0.543 Sum_probs=50.9
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC-CCChhHHHHH
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP-MIPSSLFSKW 98 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~ 98 (208)
-.....|.||+|.|..+ .+.+|+|.||.-|++.|+.. ...||. |..++...+++. .+-+++++.|
T Consensus 20 lD~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred hHHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHHHHHHHHH
Confidence 34567999999999665 47789999999999999853 468999 999888877764 3334566665
Q ss_pred H
Q 035729 99 C 99 (208)
Q Consensus 99 ~ 99 (208)
.
T Consensus 86 ~ 86 (442)
T KOG0287|consen 86 N 86 (442)
T ss_pred H
Confidence 4
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=97.87 E-value=4.3e-05 Score=61.17 Aligned_cols=55 Identities=22% Similarity=0.528 Sum_probs=39.6
Q ss_pred ccccccccccccc-c-cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC
Q 035729 24 FTCEICIEPMAAN-K-KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP 88 (208)
Q Consensus 24 ~~C~iC~~~~~~~-~-~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 88 (208)
..|++|..+.... + .+.+. .|||.||..|+...+.. .+..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~-------~~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVR-------GSGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcC-------CCCCCCC--CCCccchhhccc
Confidence 5799999964332 2 23333 89999999999998732 2358998 999887766544
No 30
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=6.5e-05 Score=66.17 Aligned_cols=58 Identities=19% Similarity=0.521 Sum_probs=46.2
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCC
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPM 89 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~ 89 (208)
.-.....|++|...+.+ . ++..|+|.||.+|++..+.+.- =+||. |+..|...+|..+
T Consensus 639 ~yK~~LkCs~Cn~R~Kd--~--vI~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 639 EYKELLKCSVCNTRWKD--A--VITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HHHhceeCCCccCchhh--H--HHHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 33557899999955532 2 4789999999999999997643 38999 9999999888764
No 31
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.48 E-value=0.00013 Score=61.80 Aligned_cols=66 Identities=24% Similarity=0.695 Sum_probs=49.9
Q ss_pred cccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCC
Q 035729 17 EEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIP 91 (208)
Q Consensus 17 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 91 (208)
...+.+..+|.+|-++-.+. ....|.|.||+-|++.|+...... ..+.||. |...|+.+.-...+.
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 34566778999999877432 378999999999999999887755 2389999 998777664444343
No 32
>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=97.30 E-value=8.6e-05 Score=47.11 Aligned_cols=46 Identities=28% Similarity=0.607 Sum_probs=31.9
Q ss_pred cccccccccccccc---------ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccC
Q 035729 23 SFTCEICIEPMAAN---------KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQ 78 (208)
Q Consensus 23 ~~~C~iC~~~~~~~---------~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 78 (208)
...|.||++++..+ +..+....|+|.|...||.+|+..+ -.||. |+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~--CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL--CR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT--SS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC--CC
Confidence 44599999999332 1222355799999999999999532 18887 64
No 33
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.13 E-value=0.00023 Score=42.76 Aligned_cols=50 Identities=28% Similarity=0.644 Sum_probs=33.0
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQ 78 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 78 (208)
....+.|+|-+..+..+ +....|+|.|-++-+.+|+ +....++||..+|.
T Consensus 8 ~~~~~~CPiT~~~~~~P---V~s~~C~H~fek~aI~~~i------~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDP---VKSKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE---EEESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC---cCcCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 34468999999999766 3467999999999999999 13556899999884
No 34
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.10 E-value=0.00039 Score=54.67 Aligned_cols=68 Identities=21% Similarity=0.423 Sum_probs=48.2
Q ss_pred cccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC-CCChhHH
Q 035729 17 EEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP-MIPSSLF 95 (208)
Q Consensus 17 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~ 95 (208)
.........|.||-+.+..+ ...+|||.||.-|++.|+.. ...||. |....-...++. .+..+..
T Consensus 19 L~~LDs~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrlr~~s~~~ei~ 84 (391)
T COG5432 19 LKGLDSMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRLRGSSGSREIN 84 (391)
T ss_pred hhcchhHHHhhhhhheeecc----eecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhcccchhHHHHH
Confidence 44556678999999999655 58899999999999999843 357898 887554444432 3334455
Q ss_pred HHH
Q 035729 96 SKW 98 (208)
Q Consensus 96 ~~~ 98 (208)
+.|
T Consensus 85 es~ 87 (391)
T COG5432 85 ESH 87 (391)
T ss_pred Hhh
Confidence 555
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.08 E-value=0.00016 Score=45.42 Aligned_cols=59 Identities=17% Similarity=0.421 Sum_probs=27.6
Q ss_pred cccccccccccccccccc-c---cCCCCChhHHHHHHHHHHHHhhcCC-Ccc--ccCCccccCCCCCc
Q 035729 23 SFTCEICIEPMAANKKFK-N---KNLCTHPFCQECIAKYIQVMVQDNN-TAK--IECPGLNCQKNLDP 83 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~-~---~~~C~H~~C~~Cl~~~~~~~i~~~~-~~~--i~CP~~~C~~~l~~ 83 (208)
..+|.||++.+...+... + ...|+..|...||.+|+...-.... ..+ =.||. |+..|+.
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 468999999875222111 1 2368899999999999987655422 222 37999 9987654
No 36
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.05 E-value=0.00046 Score=53.61 Aligned_cols=52 Identities=23% Similarity=0.542 Sum_probs=39.3
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccc
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSC 86 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 86 (208)
.+.|.||++....+ ...+|||.||-.||-..+..+ ..-.||. |+....+..+
T Consensus 215 d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCc----ccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 56799999988554 478999999999999954332 2236999 9987766655
No 37
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.02 E-value=6e-05 Score=45.71 Aligned_cols=50 Identities=28% Similarity=0.603 Sum_probs=23.2
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccccc
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCK 87 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 87 (208)
...|++|.+.+..+ +-...|.|.||..|+.+.+. -.||. |..+--.++++
T Consensus 7 lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS----B---SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS--
T ss_pred hcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHHH
Confidence 46799999998665 23578999999999976331 25999 98765555554
No 38
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.0014 Score=53.60 Aligned_cols=95 Identities=22% Similarity=0.427 Sum_probs=59.4
Q ss_pred CCCccccccccccccccc----cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc---ccc---cCC
Q 035729 20 NGSSFTCEICIEPMAANK----KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP---FSC---KPM 89 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~----~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~---~~i---~~~ 89 (208)
..+..+|.||++.+.... .|..+..|.|.||..|++.|-...-.. ....-.||. |+..... ..+ ..-
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 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFE-SKTSKSCPF--CRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccc-cccccCCCc--ccCccccccccceeeeecc
Confidence 355789999999985432 132346799999999999998654332 455678999 8864321 111 111
Q ss_pred CChhHHHHHHHHHHhhhhc--CCCcccCcc
Q 035729 90 IPSSLFSKWCDLLCEDYVR--GYERSYCPN 117 (208)
Q Consensus 90 l~~~~~~~~~~~~~~~~~~--~~~~~~Cp~ 117 (208)
-+..+++.|...+...... ......||.
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 2335667776666544222 455677886
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=96.75 E-value=0.001 Score=42.16 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=38.3
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccccc
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCK 87 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 87 (208)
..+.|+|+.+-+..+ +.+++||.|.+.++.+|+.. ....||. ++..++.+++.
T Consensus 3 ~~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l~ 55 (73)
T PF04564_consen 3 DEFLCPITGELMRDP----VILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDLI 55 (73)
T ss_dssp GGGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGSE
T ss_pred cccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccce
Confidence 468999999999776 57889999999999999965 3458888 78777765554
No 40
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.49 E-value=0.0024 Score=52.09 Aligned_cols=52 Identities=23% Similarity=0.593 Sum_probs=39.0
Q ss_pred CCCccccccccccccccc---------cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 20 NGSSFTCEICIEPMAANK---------KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~---------~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
..+...|.||+|+.-.++ .-++.++|||.+...|++.|.+.+- .||. |+.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ--------TCPI--Cr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ--------TCPI--CRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc--------CCCc--ccCcc
Confidence 344678999999942221 2235789999999999999998742 7888 98763
No 41
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.29 E-value=0.0027 Score=55.73 Aligned_cols=51 Identities=24% Similarity=0.564 Sum_probs=39.3
Q ss_pred cCCCcccccccccccccccc-ccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 19 GNGSSFTCEICIEPMAANKK-FKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~-~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
.......|+||.|++..... -...++|+|.|+..|++.|++.+ -.||. |+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--------qtCP~--CR~ 338 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--------QTCPT--CRT 338 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--------CcCCc--chh
Confidence 44557899999999966321 02478999999999999999883 27888 776
No 42
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.24 E-value=0.01 Score=48.05 Aligned_cols=124 Identities=23% Similarity=0.422 Sum_probs=67.6
Q ss_pred Ccccccccccccccc--ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCC--CCcccccCCCCh-hHHH
Q 035729 22 SSFTCEICIEPMAAN--KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN--LDPFSCKPMIPS-SLFS 96 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~--~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--l~~~~i~~~l~~-~~~~ 96 (208)
....|.||-++++.. +..+..+.|||.+|..|+...+. ...+.||. |..+ +....++.+-.. .+++
T Consensus 2 ~~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-------~~~i~cpf--cR~~~~~~~~~~~~l~kNf~ll~ 72 (296)
T KOG4185|consen 2 SFPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-------NSRILCPF--CRETTEIPDGDVKSLQKNFALLQ 72 (296)
T ss_pred CCCceeecCccccccCcccCCcccccCceehHhHHHHHhc-------CceeeccC--CCCcccCCchhHhhhhhhHHHHH
Confidence 457899999999776 33455788999999999988773 34567787 9886 333344433222 2222
Q ss_pred HHHHHHHhhhhcCCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcC-cCCCC
Q 035729 97 KWCDLLCEDYVRGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLK-WHGGY 158 (208)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~H~~~ 158 (208)
..... ...++.......+|. .|.......... ....-.|+.....+|..|... .|.++
T Consensus 73 ~~~~~-~~~~~~~~~~~~~~~-~c~~~~~nl~~~--vc~~~~~~~~~~~~c~t~~~~~~~~~~ 131 (296)
T KOG4185|consen 73 AIEHM-KKTTVEEKGEADSPP-KCKEHPYNLAEF--VCVEPDCSSKDKLMCRTCEEFGIHKGH 131 (296)
T ss_pred HHHHH-hcccccccCcccCCc-ccccCcccccce--eecCCCcchhhhhhhhhccchhhhhhh
Confidence 22222 111222223333441 244433221110 012223555667788888874 45443
No 43
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.23 E-value=0.0038 Score=50.16 Aligned_cols=53 Identities=26% Similarity=0.653 Sum_probs=42.2
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccc
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFS 85 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 85 (208)
-...++|.+|-..+.+.. .+..|-|.||+.||-+|+.. ...||. |+..+....
T Consensus 12 ~n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih~t~ 64 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIHKTH 64 (331)
T ss_pred cccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH--------hccCCc--cceeccCcc
Confidence 345789999999997664 35689999999999999987 248999 887666553
No 44
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.0059 Score=51.11 Aligned_cols=50 Identities=30% Similarity=0.742 Sum_probs=38.5
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
....++|.||+..+..+ ++++|||.||..||.+-.. ....||. |...+..
T Consensus 81 ~~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYPP----VVTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred ccchhhhhhhHhhcCCC----ccccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 36689999999999665 4779999999999777222 3358888 8876653
No 45
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.76 E-value=0.023 Score=45.99 Aligned_cols=62 Identities=26% Similarity=0.553 Sum_probs=44.4
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC-CCChh
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP-MIPSS 93 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~ 93 (208)
.-.|++|+|+++-.+.-|...+||-.+|+.||.. |.+.++. +||. |+..++.+.++- -|+++
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~lng------rcpa--crr~y~denv~~~~~s~e 76 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNLNG------RCPA--CRRKYDDENVRYVTLSPE 76 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhccC------CChH--hhhhccccceeEEecCHH
Confidence 3349999999866543234778999999999975 4444544 8999 999888877763 24443
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.76 E-value=0.012 Score=33.80 Aligned_cols=47 Identities=23% Similarity=0.620 Sum_probs=22.1
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
|++|.+++...+.-+.--+|+..+|+.|+.+-.+ + ..=.||. |+.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----~---~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----N---EGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----S---S-SB-TT--T--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----c---cCCCCCC--CCCCC
Confidence 7899999855443223557899999999987654 1 1238998 88753
No 47
>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=95.67 E-value=0.016 Score=33.59 Aligned_cols=42 Identities=21% Similarity=0.479 Sum_probs=29.7
Q ss_pred ccccccccccccccccccCCCC-----ChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 25 TCEICIEPMAANKKFKNKNLCT-----HPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~-----H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
.|-||++...+.+.+ ..+|. |.+...||.+|+...-+ ..||.
T Consensus 1 ~CrIC~~~~~~~~~l--~~PC~C~G~~~~vH~~Cl~~W~~~~~~------~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPL--VSPCRCKGSLKYVHQECLERWINESGN------KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCee--EeccccCCchhHHHHHHHHHHHHHcCC------CcCCC
Confidence 388999844333333 56774 89999999999987532 37776
No 48
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.52 E-value=0.012 Score=49.86 Aligned_cols=55 Identities=25% Similarity=0.660 Sum_probs=40.9
Q ss_pred cCCCccccccccccccccc--------------cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 19 GNGSSFTCEICIEPMAANK--------------KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~--------------~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
.......|.||+.+++.-. ++ -+.+|.|.|.+.||++|+.. ..+.||. |+.+|++
T Consensus 567 ~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nY-m~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 567 FVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNY-MLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred hhhccccceEeccccceeeccCcchhhhhhhhccc-cccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 3455779999999984321 11 14589999999999999953 4478999 9887764
No 49
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.47 E-value=0.014 Score=46.50 Aligned_cols=53 Identities=25% Similarity=0.423 Sum_probs=40.4
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccc
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSC 86 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 86 (208)
...-+|.||+.+-.-+ +.+.|+|.||.-|++..+... ...|+. |..+|+...+
T Consensus 5 ~~~~eC~IC~nt~n~P----v~l~C~HkFCyiCiKGsy~nd-------k~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP----VNLYCFHKFCYICIKGSYKND-------KKTCAV--CRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCcC----ccccccchhhhhhhcchhhcC-------CCCCce--ecCCCCcchh
Confidence 3456899999887544 689999999999999866432 235999 9998865543
No 50
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.43 E-value=0.011 Score=45.54 Aligned_cols=56 Identities=23% Similarity=0.590 Sum_probs=39.4
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCC
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIP 91 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 91 (208)
..+.|..|+.--+ .+.|+ ++.|.|+||..|.+.- .+-.||. |+..+-...+..-|+
T Consensus 2 ~~VhCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir~i~l~~slp 57 (233)
T KOG4739|consen 2 DFVHCNKCFRFPS-QDPFF-LTACRHVFCEPCLKAS----------SPDVCPL--CKKSIRIIQLNRSLP 57 (233)
T ss_pred ceEEeccccccCC-CCcee-eeechhhhhhhhcccC----------Ccccccc--ccceeeeeecccccc
Confidence 3567888886664 56664 8999999999997642 2228999 998765554444444
No 51
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.29 E-value=0.013 Score=43.83 Aligned_cols=36 Identities=28% Similarity=0.663 Sum_probs=29.1
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHH
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYI 58 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 58 (208)
...-.|.|.||..++..+ ++..|||.||..|.-.-+
T Consensus 192 ~e~IPF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 192 GEKIPFLCGICKKDYESP----VVTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCCCceeehhchhhccch----hhhhcchhHHHHHHHHHh
Confidence 334468999999999766 588999999999976544
No 52
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.16 E-value=0.025 Score=36.59 Aligned_cols=53 Identities=26% Similarity=0.537 Sum_probs=35.7
Q ss_pred cccccccccccccc---------ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 23 SFTCEICIEPMAAN---------KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 23 ~~~C~iC~~~~~~~---------~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
...|.||...|... +.-++.-.|+|.|...||.+|+.++-. .-.||. |++.+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence 44677776666411 111234579999999999999987521 248999 988654
No 53
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.11 E-value=0.018 Score=45.17 Aligned_cols=52 Identities=31% Similarity=0.601 Sum_probs=39.1
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
.+...+|++|-++=..+ .+..+|+|.||-.|+....... ..+.||. |+....
T Consensus 236 ~t~~~~C~~Cg~~PtiP---~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP---HVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCC---eeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 34568999999876555 2466799999999998866432 3479999 998654
No 54
>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=95.10 E-value=0.0071 Score=46.46 Aligned_cols=52 Identities=23% Similarity=0.508 Sum_probs=37.8
Q ss_pred ccccccccccccc-cccccccC-CCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 23 SFTCEICIEPMAA-NKKFKNKN-LCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 23 ~~~C~iC~~~~~~-~~~~~~~~-~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
...|+||..+.-. ++..+.+. .|-|.+|.+|+.+-|. ..|-.||.++|+..|
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHHH
Confidence 4579999988533 33222233 4999999999998774 457799999999743
No 55
>PF04641 Rtf2: Rtf2 RING-finger
Probab=95.01 E-value=0.039 Score=43.84 Aligned_cols=72 Identities=18% Similarity=0.397 Sum_probs=53.8
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCCh-hHHHHH
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPS-SLFSKW 98 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~ 98 (208)
....+.|+|...++.....|+.+.+|||+|....|+..- .+ -.||. |+.++...+|-.|-+. +.++.+
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 566899999999997666777788999999999999872 12 25999 9999998877766544 344444
Q ss_pred HHHH
Q 035729 99 CDLL 102 (208)
Q Consensus 99 ~~~~ 102 (208)
...+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4433
No 56
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.74 E-value=0.0093 Score=34.83 Aligned_cols=45 Identities=24% Similarity=0.544 Sum_probs=33.6
Q ss_pred cccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHP-FCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.+|.||+|.-.+. ++..|||. +|.+|-.+.+.. .+ -.||. |+.++
T Consensus 8 dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~-~~------g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKA-LH------GCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchH----HHHHcchHHhHHHHHHHHHHc-cC------CcCcc--hhhHH
Confidence 6899999875333 47799996 999998887764 22 27888 87754
No 57
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.60 E-value=0.017 Score=47.82 Aligned_cols=111 Identities=19% Similarity=0.484 Sum_probs=66.6
Q ss_pred cccccc--ccccc-cc-cccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCC-----C--
Q 035729 23 SFTCEI--CIEPM-AA-NKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMI-----P-- 91 (208)
Q Consensus 23 ~~~C~i--C~~~~-~~-~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l-----~-- 91 (208)
...||- |.-+. .+ .+.+..-..|.-+||..|...|-. + .+ |+...+ +.++..+ +
T Consensus 273 v~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG--~-------s~-----Ck~~~~-~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 273 VVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG--V-------SP-----CKVKAE-KLIELYLEYLEADEA 337 (445)
T ss_pred cccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC--C-------Cc-----ccCchH-HHHHHHHHHhhcCHH
Confidence 456665 44441 11 222323456889999999888763 1 12 555422 1111111 1
Q ss_pred --hhHHHHHHHHHHhhhh----c----CCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCc
Q 035729 92 --SSLFSKWCDLLCEDYV----R----GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKW 154 (208)
Q Consensus 92 --~~~~~~~~~~~~~~~~----~----~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 154 (208)
.++-++|..+..+..+ . ..+...|| .|...+....+ ...+.|..|++.||+.|...-
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG----CnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG----CNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC----ccceeeccccccceeehhhhc
Confidence 1344556544333222 1 24578899 79998887776 789999999999999999743
No 58
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.037 Score=44.42 Aligned_cols=91 Identities=20% Similarity=0.554 Sum_probs=55.2
Q ss_pred CCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc---cccCCCCh--hHHHHHHHHHHhhhhcCCCcccCccc
Q 035729 44 LCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF---SCKPMIPS--SLFSKWCDLLCEDYVRGYERSYCPNR 118 (208)
Q Consensus 44 ~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~---~i~~~l~~--~~~~~~~~~~~~~~~~~~~~~~Cp~~ 118 (208)
.|+-+||++|++.|-+-. |...+... ...--++. ..-.+|+.+..+. +. .....||
T Consensus 341 gCgf~FCR~C~e~yh~ge---------------C~~~~~as~t~tc~y~vde~~a~~arwd~as~~T-Ik-~tTkpCP-- 401 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGE---------------CSAVFEASGTTTCAYRVDERAAEQARWDAASKET-IK-KTTKPCP-- 401 (446)
T ss_pred CchhHhHHHHHhhhcccc---------------ceeeeccccccceeeecChhhhhhhhhhhhhhhh-hh-hccCCCC--
Confidence 488899999999886421 22111110 00111222 2345666654432 21 2356788
Q ss_pred ccccchhcchhhcCCCCcccCcc--ccchhccccCcCcCCC
Q 035729 119 NCMALVVNECERKGRMKKAQCPN--CKHWFCFRCKLKWHGG 157 (208)
Q Consensus 119 ~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~~ 157 (208)
.|......+.+ ...+.|+. |+..+|+.|+.+|.+.
T Consensus 402 kChvptErnGG----CmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 402 KCHVPTERNGG----CMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred CccCccccCCc----eEEeecCCCCCCceeEeccCChhhhh
Confidence 78776655544 67889975 9999999999999653
No 59
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=94.09 E-value=0.095 Score=31.76 Aligned_cols=32 Identities=19% Similarity=0.495 Sum_probs=25.0
Q ss_pred HHHHHHh-CCcccCC--CCCceeEecC--CCCceEeC
Q 035729 174 FGQLAER-MKWARCP--GCGHCVQRKN--GCHVMQDS 205 (208)
Q Consensus 174 ~~~~~~~-~~~k~CP--~C~~~i~k~~--GCnhm~C~ 205 (208)
+..++.. ..++.|| +|+..|+..+ |..+|+|.
T Consensus 8 ~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~ 44 (64)
T smart00647 8 LESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCP 44 (64)
T ss_pred HHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECC
Confidence 3444444 5789999 9999999975 99999993
No 60
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.05 E-value=0.032 Score=46.81 Aligned_cols=42 Identities=24% Similarity=0.661 Sum_probs=34.7
Q ss_pred CCcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCC
Q 035729 110 YERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGY 158 (208)
Q Consensus 110 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~ 158 (208)
...+.|| .|...+....+ .+.++|. |++.||+.|..+|..+.
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 4578899 79998866555 7999997 99999999999986544
No 61
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.95 E-value=0.028 Score=45.46 Aligned_cols=47 Identities=23% Similarity=0.629 Sum_probs=36.9
Q ss_pred ccCCCccccccccccccccccccccCCC--CChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLC--THPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
......++|+||++.+..+ ..+| ||..|.+|-.+ ..-+||. |...+.
T Consensus 43 ~~~~~lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSPP-----IFQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG 91 (299)
T ss_pred ccchhhccCchhhccCccc-----ceecCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence 4466788999999999766 5677 89999999652 2348999 988776
No 62
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.94 E-value=0.051 Score=45.47 Aligned_cols=34 Identities=21% Similarity=0.529 Sum_probs=28.1
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHH
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQ 59 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 59 (208)
+..-|+||..-+..+ .+++|+|..|+.|.+....
T Consensus 3 eelkc~vc~~f~~ep----iil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFYREP----IILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhccCc----eEeecccHHHHHHHHhhcc
Confidence 457899999999766 4899999999999986554
No 63
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=93.82 E-value=0.029 Score=39.49 Aligned_cols=79 Identities=18% Similarity=0.259 Sum_probs=45.2
Q ss_pred CCCccccccccccccccccccccCCCC------ChhHHHHHHHHHHHHhhcCC----CccccCCcc---ccCCCCCcccc
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCT------HPFCQECIAKYIQVMVQDNN----TAKIECPGL---NCQKNLDPFSC 86 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~------H~~C~~Cl~~~~~~~i~~~~----~~~i~CP~~---~C~~~l~~~~i 86 (208)
.....+|.||++.+...+.+ +...++ |.||.+|+++|-...-.+.- .+.+.-|.. .|...| +..
T Consensus 23 ~~~~~EC~IC~~~I~~~~Gv-V~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR~I~y~F~fPf~~~~ec~~~L--~~~ 99 (134)
T PF05883_consen 23 PRCTVECQICFDRIDNNDGV-VYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNRNIKYWFNFPFKNLEECKSFL--EKS 99 (134)
T ss_pred cccCeeehhhhhhhhcCCCE-EEEecCCeehHHHHHHHHHHHHHHhhccCCCcccceEEEEeCCCCCHHHHHHHH--Hhc
Confidence 34478999999999773333 355663 89999999999533332311 123455542 355433 234
Q ss_pred cCCCChh-HHHHHHHH
Q 035729 87 KPMIPSS-LFSKWCDL 101 (208)
Q Consensus 87 ~~~l~~~-~~~~~~~~ 101 (208)
+.+++++ ..+.|...
T Consensus 100 ~~FIGde~~d~~f~~~ 115 (134)
T PF05883_consen 100 KGFIGDEEKDEVFKDE 115 (134)
T ss_pred cCcCCChHHHHHHHHH
Confidence 4555654 33444433
No 64
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=93.60 E-value=0.084 Score=44.52 Aligned_cols=51 Identities=24% Similarity=0.709 Sum_probs=38.5
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
......|++|...+.++ + ....|+|.||..|+..+... ...||. |...+..
T Consensus 18 ~~~~l~C~~C~~vl~~p--~-~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~~~ 68 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDP--V-QTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQELTQ 68 (391)
T ss_pred CcccccCccccccccCC--C-CCCCCCCcccccccchhhcc--------CcCCcc--cccccch
Confidence 46678999999999766 1 23599999999999998754 357887 7654433
No 65
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.54 E-value=0.054 Score=41.94 Aligned_cols=58 Identities=16% Similarity=0.261 Sum_probs=45.8
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP 88 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 88 (208)
...+.|+||-+.++..-...++.+++|+||.+|++++|.. ...+|. |+..+...+|-.
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdiI~ 276 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDIIG 276 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccceEe
Confidence 3678999999999766555567799999999999998853 346787 888888776643
No 66
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.49 E-value=0.056 Score=51.72 Aligned_cols=71 Identities=17% Similarity=0.363 Sum_probs=53.8
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCC--CccccCCccccCCCCCcccccCCCCh
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNN--TAKIECPGLNCQKNLDPFSCKPMIPS 92 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~l~~~~i~~~l~~ 92 (208)
.....-.|.|||.+-...... ..+.|+|.|...|.+..++.+-.... ...|.||. |.+.|+-..++.+|++
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred hcccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 344456899999886554433 37899999999999999887665522 23589999 9999887777877775
No 67
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.45 E-value=0.043 Score=45.52 Aligned_cols=56 Identities=25% Similarity=0.570 Sum_probs=42.1
Q ss_pred cccccccccccccc-ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccc
Q 035729 23 SFTCEICIEPMAAN-KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSC 86 (208)
Q Consensus 23 ~~~C~iC~~~~~~~-~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 86 (208)
..+|+||++.+..+ +...+.+.|+|.|=.+|+++|+. + .....||. |...-...+|
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k-----~~~~~cp~--c~~katkr~i 60 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-K-----KTKMQCPL--CSGKATKRQI 60 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-h-----hhhhhCcc--cCChhHHHHH
Confidence 46899999998654 33457889999999999999994 2 34579999 8875444333
No 68
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.15 E-value=0.016 Score=45.30 Aligned_cols=56 Identities=27% Similarity=0.507 Sum_probs=41.8
Q ss_pred Cccccccccccccccc-------cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccc
Q 035729 22 SSFTCEICIEPMAANK-------KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSC 86 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~-------~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 86 (208)
+...|.||-..+.... +. ..++|+|+|...|++.|...- ..-.||. |++.++.+.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvient-y~LsCnHvFHEfCIrGWcivG------KkqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENT-YKLSCNHVFHEFCIRGWCIVG------KKQTCPY--CKEKVDLKRM 285 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhh-eeeecccchHHHhhhhheeec------CCCCCch--HHHHhhHhhh
Confidence 3568999998875442 22 368999999999999998652 2348999 9998776544
No 69
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.82 E-value=0.018 Score=46.84 Aligned_cols=50 Identities=34% Similarity=0.792 Sum_probs=36.2
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
-...+.|+||++-+... + ....|.|.||.+||-.-+.. ++ -.||. |++.+
T Consensus 40 ~~~~v~c~icl~llk~t--m-ttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~l 89 (381)
T KOG0311|consen 40 FDIQVICPICLSLLKKT--M-TTKECLHRFCFDCIWKALRS----GN---NECPT--CRKKL 89 (381)
T ss_pred hhhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhhc
Confidence 34567999999998544 2 36789999999998775543 22 37888 88643
No 70
>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=92.62 E-value=0.031 Score=32.58 Aligned_cols=43 Identities=28% Similarity=0.732 Sum_probs=21.7
Q ss_pred ccccchhcchhhcCCCCcccCccccchhccccCcCcCCCC-CCh
Q 035729 119 NCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGY-HCE 161 (208)
Q Consensus 119 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~-~C~ 161 (208)
+|...+............+.|+.|++.||..|..-.|..+ .|+
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 4555444332211224789999999999999999888764 554
No 71
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.49 E-value=0.41 Score=37.45 Aligned_cols=59 Identities=24% Similarity=0.468 Sum_probs=43.2
Q ss_pred CCccccccccccccccccccccCCC-----CChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLC-----THPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C-----~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
...-.|-|||.+-.++..---+-+| .|-....||..|+..+-..+...++.||+ |..+.
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTEY 81 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTEY 81 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcchh
Confidence 3456899999988665321114466 47899999999998766655677899999 98753
No 72
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.41 E-value=0.13 Score=42.52 Aligned_cols=50 Identities=24% Similarity=0.590 Sum_probs=35.2
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
...|.||-+-++.....-..-.|||.|...|+.+|++..-.. -.||. |.-
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~i 53 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQI 53 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eee
Confidence 468999955554444553344599999999999999764321 37887 773
No 73
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.17 E-value=0.18 Score=41.25 Aligned_cols=49 Identities=24% Similarity=0.556 Sum_probs=37.4
Q ss_pred cCCCccccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHP-FCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.+....+|.||+.+..+. ++++|.|. .|..|.+... +.. =.||. |++.+
T Consensus 286 ~~~~gkeCVIClse~rdt----~vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi 335 (349)
T KOG4265|consen 286 ESESGKECVICLSESRDT----VVLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPI 335 (349)
T ss_pred cccCCCeeEEEecCCcce----EEecchhhehhHhHHHHHH---Hhh-----cCCCc--cccch
Confidence 345578999999998654 58999996 9999988765 111 27999 99865
No 74
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=91.63 E-value=0.091 Score=30.95 Aligned_cols=47 Identities=19% Similarity=0.353 Sum_probs=32.0
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccc
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSC 86 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 86 (208)
..|..|...... ..+++|+|.+|..||-. ...-.||. |...++..++
T Consensus 8 ~~~~~~~~~~~~----~~~~pCgH~I~~~~f~~----------~rYngCPf--C~~~~~~~~~ 54 (55)
T PF14447_consen 8 QPCVFCGFVGTK----GTVLPCGHLICDNCFPG----------ERYNGCPF--CGTPFEFDDP 54 (55)
T ss_pred eeEEEccccccc----cccccccceeeccccCh----------hhccCCCC--CCCcccCCCC
Confidence 445555544322 24899999999999864 22348999 9998876554
No 75
>PHA03096 p28-like protein; Provisional
Probab=91.61 E-value=0.14 Score=41.12 Aligned_cols=53 Identities=21% Similarity=0.305 Sum_probs=36.5
Q ss_pred ccccccccccccc---c-cccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCC
Q 035729 24 FTCEICIEPMAAN---K-KFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN 80 (208)
Q Consensus 24 ~~C~iC~~~~~~~---~-~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 80 (208)
..|.||++..... + .|-.+..|.|.||..|++.|..+.... .....||. |...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~--e~~~~c~~--~~~~ 235 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYK--ETEPENRR--LNTV 235 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhc--ccCccccc--hhhH
Confidence 6899999987532 2 333345799999999999999887633 33345555 5443
No 76
>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=91.45 E-value=0.21 Score=25.18 Aligned_cols=23 Identities=26% Similarity=0.482 Sum_probs=14.9
Q ss_pred cCCCCCceeEecCCCCceEeCCC
Q 035729 185 RCPGCGHCVQRKNGCHVMQDSVL 207 (208)
Q Consensus 185 ~CP~C~~~i~k~~GCnhm~C~~~ 207 (208)
.||.|+..+.+.+|=-...|+..
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--C
T ss_pred CcCCCCCEeEcCCCCEeEECCCC
Confidence 49999999999999888888754
No 77
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=91.37 E-value=0.13 Score=43.37 Aligned_cols=52 Identities=29% Similarity=0.582 Sum_probs=39.1
Q ss_pred ccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
..-++.-+|+||+|..++.-..+....|+|.|--.|+..|. ...||. |+-..
T Consensus 170 ~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~----------~~scpv--cR~~q 221 (493)
T KOG0804|consen 170 TGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW----------DSSCPV--CRYCQ 221 (493)
T ss_pred CCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc----------cCcChh--hhhhc
Confidence 34456679999999997665455678899999999998765 357777 76533
No 78
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=91.12 E-value=0.18 Score=45.71 Aligned_cols=59 Identities=24% Similarity=0.541 Sum_probs=43.4
Q ss_pred ccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
......++|.||++.+.....+..-..|-|+|...||+.|....-.+ ....-+||. |..
T Consensus 186 ~l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~-~~~~WrCP~--Cqs 244 (950)
T KOG1952|consen 186 QLSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKT-GQDGWRCPA--CQS 244 (950)
T ss_pred HHhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhc-cCccccCCc--ccc
Confidence 34566789999999997765544455688999999999999873333 234458887 763
No 79
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.87 E-value=0.14 Score=45.97 Aligned_cols=20 Identities=15% Similarity=0.323 Sum_probs=13.1
Q ss_pred CCcccCccccch-hccccCcC
Q 035729 134 MKKAQCPNCKHW-FCFRCKLK 153 (208)
Q Consensus 134 ~~~~~C~~C~~~-~C~~C~~~ 153 (208)
...+.|..|++. +=..|.-+
T Consensus 228 dVLLLCDsCN~~~YH~YCLDP 248 (1134)
T KOG0825|consen 228 DVLLLCDSCNKVYYHVYCLDP 248 (1134)
T ss_pred HhheeecccccceeeccccCc
Confidence 467888888777 44555544
No 80
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=90.86 E-value=0.21 Score=39.92 Aligned_cols=64 Identities=23% Similarity=0.566 Sum_probs=47.7
Q ss_pred cccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhc---------------CCCccccCCccccCCCC
Q 035729 17 EEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQD---------------NNTAKIECPGLNCQKNL 81 (208)
Q Consensus 17 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~---------------~~~~~i~CP~~~C~~~l 81 (208)
...+.....|.||+--|.+.+.| ....|.|.|...||.+|+...+.+ .....-.||. |...|
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 45667788999999999877777 488999999999999998765532 0112345998 88755
Q ss_pred Cc
Q 035729 82 DP 83 (208)
Q Consensus 82 ~~ 83 (208)
..
T Consensus 186 ~~ 187 (368)
T KOG4445|consen 186 KI 187 (368)
T ss_pred cc
Confidence 43
No 81
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=90.75 E-value=0.6 Score=37.24 Aligned_cols=50 Identities=28% Similarity=0.527 Sum_probs=39.2
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
......|+||.+.+.........++|+|..-..|++.++-. . ..||. |..
T Consensus 155 ~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 155 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 34445599999998776655668899999999999988743 2 68998 877
No 82
>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=89.79 E-value=0.14 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.648 Sum_probs=15.6
Q ss_pred CCcccCCC--CCceeEecCCCCc--eEeC
Q 035729 181 MKWARCPG--CGHCVQRKNGCHV--MQDS 205 (208)
Q Consensus 181 ~~~k~CP~--C~~~i~k~~GCnh--m~C~ 205 (208)
..++.||+ |+..|++.+|.++ |+|.
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~ 44 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCP 44 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTT
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECC
Confidence 45689987 9999999999999 9998
No 83
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=89.63 E-value=0.14 Score=42.51 Aligned_cols=46 Identities=26% Similarity=0.561 Sum_probs=33.3
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
...-|-||-|.-.+. .+-+|||..|..||..|-...- --.||. |+-
T Consensus 368 TFeLCKICaendKdv----kIEPCGHLlCt~CLa~WQ~sd~------gq~CPF--CRc 413 (563)
T KOG1785|consen 368 TFELCKICAENDKDV----KIEPCGHLLCTSCLAAWQDSDE------GQTCPF--CRC 413 (563)
T ss_pred hHHHHHHhhccCCCc----ccccccchHHHHHHHhhcccCC------CCCCCc--eee
Confidence 345799999876433 4789999999999999864321 137888 554
No 84
>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=89.44 E-value=0.2 Score=24.80 Aligned_cols=23 Identities=39% Similarity=0.800 Sum_probs=16.7
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.|| .|+..+.. ....||.||+.|
T Consensus 2 ~CP--~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchh--------hcCcCCCCCCCC
Confidence 477 78887743 456799999876
No 85
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.34 E-value=0.2 Score=27.05 Aligned_cols=33 Identities=30% Similarity=0.676 Sum_probs=22.9
Q ss_pred cccCcccccccchhcchhh-cCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECER-KGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 146 (208)
++.|| .|+..+...+.. ......++|+.|+..|
T Consensus 2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 35688 798877655432 1236799999998765
No 86
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.33 E-value=0.29 Score=40.08 Aligned_cols=49 Identities=20% Similarity=0.410 Sum_probs=33.8
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
+.+...|+||+-.-... ++.+|+|.-|..|+.+|+-. .-.|-. |+..+.
T Consensus 419 ~sEd~lCpICyA~pi~A----vf~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~ 467 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPINA----VFAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVI 467 (489)
T ss_pred CcccccCcceecccchh----hccCCCCchHHHHHHHHHhc--------CCeeeE--ecceee
Confidence 34567899999543222 47899999999999998742 125555 776543
No 87
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=89.19 E-value=0.82 Score=32.14 Aligned_cols=53 Identities=25% Similarity=0.633 Sum_probs=39.9
Q ss_pred CCccccccccccccccccccc-cCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 21 GSSFTCEICIEPMAANKKFKN-KNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~-~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
....+|.||.|...+. .|.. .--||=.+|..|-...|+.. .....||. |+..+
T Consensus 78 ~~lYeCnIC~etS~ee-~FLKPneCCgY~iCn~Cya~LWK~~-----~~ypvCPv--CkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSAEE-RFLKPNECCGYSICNACYANLWKFC-----NLYPVCPV--CKTSF 131 (140)
T ss_pred CCceeccCcccccchh-hcCCcccccchHHHHHHHHHHHHHc-----ccCCCCCc--ccccc
Confidence 3679999999998554 3422 22479999999999999874 34579999 98754
No 88
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.04 E-value=0.89 Score=37.20 Aligned_cols=54 Identities=19% Similarity=0.602 Sum_probs=38.6
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
.+.+..-|.||-+.++-. ..++|+|.+|.-|-.+.-.- +..-.||. |+.....-
T Consensus 57 tDEen~~C~ICA~~~TYs----~~~PC~H~~CH~Ca~RlRAL------Y~~K~C~~--CrTE~e~V 110 (493)
T COG5236 57 TDEENMNCQICAGSTTYS----ARYPCGHQICHACAVRLRAL------YMQKGCPL--CRTETEAV 110 (493)
T ss_pred cccccceeEEecCCceEE----EeccCCchHHHHHHHHHHHH------HhccCCCc--cccccceE
Confidence 344567899999888543 58899999999997765432 23357888 88765443
No 89
>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=88.99 E-value=0.9 Score=36.24 Aligned_cols=52 Identities=21% Similarity=0.487 Sum_probs=36.3
Q ss_pred cccccccccc-ccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCccc
Q 035729 25 TCEICIEPMA-ANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFS 85 (208)
Q Consensus 25 ~C~iC~~~~~-~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 85 (208)
.|++|..+.- .++.+.-+.+|+|..|.+|+-..+. ..+-.||. |...|-...
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cpe--C~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCPE--CMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCCc--ccchhhhcc
Confidence 4888887753 3343333558999999999998774 34568996 998665443
No 90
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.66 E-value=0.71 Score=31.60 Aligned_cols=43 Identities=21% Similarity=0.501 Sum_probs=30.0
Q ss_pred ccCcccccccchhcchhh----cCCCCcccCccccchhccccCcCcCCC
Q 035729 113 SYCPNRNCMALVVNECER----KGRMKKAQCPNCKHWFCFRCKLKWHGG 157 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~~ 157 (208)
..|- +|...+...... ........|+.|++.||..|..-+|..
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 687766532110 011457889999999999999988865
No 91
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.58 E-value=0.32 Score=26.11 Aligned_cols=33 Identities=33% Similarity=0.611 Sum_probs=22.4
Q ss_pred cccCcccccccchhcchh-hcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECE-RKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~C~~C~~~~ 146 (208)
.+.|| .|+..+..++. .......++|+.|+..|
T Consensus 2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 35688 68877665443 22336789999998765
No 92
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.77 E-value=0.25 Score=39.37 Aligned_cols=48 Identities=27% Similarity=0.485 Sum_probs=36.4
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
..-.+-|.||-.++..+ ++..|+|.||..|....+.. .-+|+. |.+.+
T Consensus 238 ~~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk--------~~~c~v--C~~~t 285 (313)
T KOG1813|consen 238 ELLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQK--------GEKCYV--CSQQT 285 (313)
T ss_pred ccCCccccccccccccc----hhhcCCceeehhhhcccccc--------CCccee--ccccc
Confidence 34457899999999665 58999999999997765532 247877 87754
No 93
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.54 E-value=0.71 Score=39.71 Aligned_cols=47 Identities=32% Similarity=0.859 Sum_probs=33.0
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCcc--ccchhccccCcCc--CC---CCCChhh
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPN--CKHWFCFRCKLKW--HG---GYHCEES 163 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~---~~~C~~~ 163 (208)
+...|| .|...+..+.+ .....|.. |++.||+.|...| |. +..|..+
T Consensus 225 ntk~CP--~c~~~iek~~g----c~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~ 278 (444)
T KOG1815|consen 225 NTKECP--KCKVPIEKDGG----CNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRY 278 (444)
T ss_pred cCccCC--CcccchhccCC----ccccccccCCcCCeeceeeecccccccccceeeeeee
Confidence 355599 79888877665 45566755 9999999997765 54 2456444
No 94
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.01 E-value=2.2 Score=31.54 Aligned_cols=63 Identities=19% Similarity=0.459 Sum_probs=40.6
Q ss_pred cCCCcccccccccccccc---ccccccCCCCChhHHHHHHHHHHHHhhcCCCcc---ccCCccccCCCCCc
Q 035729 19 GNGSSFTCEICIEPMAAN---KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAK---IECPGLNCQKNLDP 83 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~---~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~---i~CP~~~C~~~l~~ 83 (208)
.+.....|.||+-.-.+. +..-...+|+..|..-||..|+..-+.....+. =.||. |..++..
T Consensus 161 kdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred cchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 345567788887654332 111125579999999999999987665422222 37998 9886643
No 95
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=85.72 E-value=1 Score=28.60 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=23.2
Q ss_pred CCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 43 NLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 43 ~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
-.|.|.|..-|+.+|+.++ =.||. +.+.+.
T Consensus 52 G~CnHaFH~HCI~rWL~Tk--------~~CPl--d~q~w~ 81 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDTK--------GVCPL--DRQTWV 81 (88)
T ss_pred EecchHHHHHHHHHHHhhC--------CCCCC--CCceeE
Confidence 3599999999999999872 26887 666543
No 96
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.46 E-value=0.7 Score=38.46 Aligned_cols=60 Identities=17% Similarity=0.367 Sum_probs=41.5
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCC
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPM 89 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~ 89 (208)
+.|.|||=-+.-+. ++-+..+.|||+++++=+.+.... +...++||. |...-..++.+++
T Consensus 333 SvF~CPVlKeqtsd-eNPPm~L~CGHVISkdAlnrLS~n-----g~~sfKCPY--CP~e~~~~~~kql 392 (394)
T KOG2817|consen 333 SVFICPVLKEQTSD-ENPPMMLICGHVISKDALNRLSKN-----GSQSFKCPY--CPVEQLASDTKQL 392 (394)
T ss_pred ceeecccchhhccC-CCCCeeeeccceecHHHHHHHhhC-----CCeeeeCCC--CCcccCHHhcccc
Confidence 35789986655533 333458899999999887765543 344799999 9887666655543
No 97
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.29 E-value=1.5 Score=35.18 Aligned_cols=44 Identities=27% Similarity=0.836 Sum_probs=33.6
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
+-|++|.-.+..+ + ....|+|.||.+||..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Llrnp--~-kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP--M-KTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhhCc--c-cCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 7899999888655 2 34578999999999865432 3579999 986
No 98
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.76 E-value=0.54 Score=43.50 Aligned_cols=54 Identities=19% Similarity=0.552 Sum_probs=38.9
Q ss_pred CCccccccccccccccc-ccc--ccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 21 GSSFTCEICIEPMAANK-KFK--NKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~-~~~--~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
.+..+|+||+.-+...+ .++ .-..|.|.|...|+-+|+...-+. +||. |+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s------~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARS------NCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCC------CCCc--cccccc
Confidence 34679999998875332 121 133588999999999999875433 8999 987664
No 99
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.74 E-value=0.44 Score=25.23 Aligned_cols=30 Identities=20% Similarity=0.623 Sum_probs=15.5
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccch
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
+|| .|+..+.......+...+..|+.|+..
T Consensus 2 fC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 688 788877544332234789999999864
No 100
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=84.69 E-value=0.59 Score=27.06 Aligned_cols=28 Identities=18% Similarity=0.661 Sum_probs=19.3
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccch
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
+|| .|+..+...... ....+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~--~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGK--EKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCC--CCCEEECCcCCCe
Confidence 688 799988765431 1247889888854
No 101
>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=83.83 E-value=0.26 Score=33.25 Aligned_cols=32 Identities=28% Similarity=0.594 Sum_probs=25.7
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHH
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIA 55 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~ 55 (208)
+...|.+|...+.. ..| ...+|+|.|...|++
T Consensus 77 ~~~~C~vC~k~l~~-~~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN-SVF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCC-ceE-EEeCCCeEEeccccc
Confidence 35579999999954 444 688999999999975
No 102
>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=83.32 E-value=0.35 Score=25.80 Aligned_cols=28 Identities=21% Similarity=0.662 Sum_probs=18.2
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
.+|| .|++.+.+..... ... .|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~--~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKE--KRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETT--TTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCc--cCc-CCCCCCCc
Confidence 4788 8999998776532 222 78888764
No 103
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.98 E-value=0.76 Score=42.09 Aligned_cols=41 Identities=22% Similarity=0.555 Sum_probs=32.4
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhh
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQ 63 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~ 63 (208)
....+|.+|...+.. +.| .+.+|||.|..+|+.+++.....
T Consensus 815 ep~d~C~~C~~~ll~-~pF-~vf~CgH~FH~~Cl~~~v~~~~~ 855 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI-KPF-YVFPCGHCFHRDCLIRHVLSLLS 855 (911)
T ss_pred cCccchHHhcchhhc-Ccc-eeeeccchHHHHHHHHHHHcccc
Confidence 345689999999854 456 47899999999999998865443
No 104
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=82.78 E-value=0.54 Score=39.05 Aligned_cols=50 Identities=22% Similarity=0.590 Sum_probs=37.8
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN 80 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 80 (208)
...|..|-+.+-..+.-...++|.|.|...|+..++.. ..+-.||. |++.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~------n~~rsCP~--Crkl 414 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN------NGTRSCPN--CRKL 414 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh------CCCCCCcc--HHHH
Confidence 57899999987443322357899999999999999943 34458998 8853
No 105
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=82.02 E-value=0.32 Score=43.86 Aligned_cols=48 Identities=35% Similarity=0.755 Sum_probs=35.2
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
+.|.||.+ . +.+ +...|+|.||.+|+...+...- .-.||. |...+...
T Consensus 455 ~~c~ic~~-~---~~~-~it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD-L---DSF-FITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKEK 502 (674)
T ss_pred cccccccc-c---ccc-eeecccchHHHHHHHhcccccc------CCCCcH--HHHHHHHH
Confidence 89999999 2 222 4789999999999999886422 127777 88765443
No 106
>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=81.93 E-value=0.8 Score=24.65 Aligned_cols=32 Identities=25% Similarity=0.496 Sum_probs=20.5
Q ss_pred ccCcccccccchhcchhhc-CCCCcccCccccchh
Q 035729 113 SYCPNRNCMALVVNECERK-GRMKKAQCPNCKHWF 146 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~ 146 (208)
+.|| .|+..+...+... .....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688 7888665543321 223479999998764
No 107
>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=81.35 E-value=0.7 Score=25.87 Aligned_cols=42 Identities=24% Similarity=0.649 Sum_probs=20.9
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCc
Q 035729 26 CEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPG 74 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 74 (208)
|.+|.+-......- ....|+-.+...|++.|+..+- ..+||.
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 66777777555322 1336888899999999997542 227886
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=81.32 E-value=0.63 Score=26.57 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=20.7
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
...||++.|+..+..... ..+..|-+|+.
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 578999999997765544 46788888875
No 109
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.12 E-value=1.5 Score=34.98 Aligned_cols=49 Identities=22% Similarity=0.571 Sum_probs=37.1
Q ss_pred CCCccccccccccccccccccccCCC----CChhHHHHHHHHHHHHhhcCCCccccCCcc
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLC----THPFCQECIAKYIQVMVQDNNTAKIECPGL 75 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C----~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~ 75 (208)
....+-|.+|.|.+.+. . +.+| .|.||..|-+..|+.+-.. -.+.||..
T Consensus 265 ~~apLcCTLC~ERLEDT--H--FVQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSG 317 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDT--H--FVQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSG 317 (352)
T ss_pred CCCceeehhhhhhhccC--c--eeecCCCcccceecccCHHHHHhhcCC---CceeCCCC
Confidence 34568999999999543 3 4566 7999999999999987654 35777753
No 110
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=79.00 E-value=2.6 Score=28.27 Aligned_cols=29 Identities=28% Similarity=0.700 Sum_probs=22.8
Q ss_pred CCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 43 NLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 43 ~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
-.|+|.|..-|+.+|++++ -.||. +.+..
T Consensus 79 G~CNHaFH~hCisrWlktr--------~vCPL--dn~eW 107 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR--------NVCPL--DNKEW 107 (114)
T ss_pred eecchHHHHHHHHHHHhhc--------CcCCC--cCcce
Confidence 3699999999999999764 27888 65543
No 111
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.88 E-value=0.83 Score=40.45 Aligned_cols=37 Identities=19% Similarity=0.562 Sum_probs=29.9
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHH
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQ 59 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 59 (208)
..-|.||+..+.......+++.|+|.+|..|++....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 4679999888866555567899999999999987654
No 112
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=78.82 E-value=2.3 Score=25.04 Aligned_cols=36 Identities=17% Similarity=0.451 Sum_probs=29.2
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHH
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAK 56 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~ 56 (208)
....-|++|-+.|.+.+..++-..|+-.+.++||..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 345679999999976666666778999999999875
No 113
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.72 E-value=1.4 Score=39.64 Aligned_cols=15 Identities=33% Similarity=0.742 Sum_probs=9.9
Q ss_pred CCcccCCCCCceeEe
Q 035729 181 MKWARCPGCGHCVQR 195 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k 195 (208)
.+.+.||+||..+.+
T Consensus 39 ~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 39 VDEAHCPNCGAETGT 53 (645)
T ss_pred cccccccccCCcccc
Confidence 366778888776543
No 114
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=77.72 E-value=1.1 Score=25.57 Aligned_cols=34 Identities=21% Similarity=0.629 Sum_probs=22.7
Q ss_pred cccccccccccccccccCCCC-----ChhHHHHHHHHHHHH
Q 035729 26 CEICIEPMAANKKFKNKNLCT-----HPFCQECIAKYIQVM 61 (208)
Q Consensus 26 C~iC~~~~~~~~~~~~~~~C~-----H~~C~~Cl~~~~~~~ 61 (208)
|-||+++....+.+ +.+|. ..+...||.+|+..+
T Consensus 1 CrIC~~~~~~~~~l--i~pC~C~Gs~~~vH~~CL~~W~~~~ 39 (47)
T PF12906_consen 1 CRICLEGEEEDEPL--ISPCRCKGSMKYVHRSCLERWIRES 39 (47)
T ss_dssp ETTTTEE-SSSS-E--E-SSS-SSCCGSEECCHHHHHHHHH
T ss_pred CeEeCCcCCCCCce--ecccccCCCcchhHHHHHHHHHHhc
Confidence 67899888655434 45653 267889999999873
No 115
>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=77.69 E-value=2 Score=26.23 Aligned_cols=17 Identities=24% Similarity=0.876 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHHHHhhc
Q 035729 48 PFCQECIAKYIQVMVQD 64 (208)
Q Consensus 48 ~~C~~Cl~~~~~~~i~~ 64 (208)
-||++||.+|+.....+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999887765
No 116
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.94 E-value=2 Score=41.19 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=8.3
Q ss_pred cccCCCCCceeE
Q 035729 183 WARCPGCGHCVQ 194 (208)
Q Consensus 183 ~k~CP~C~~~i~ 194 (208)
+..||+|+.++.
T Consensus 709 a~~CP~CGtplv 720 (1337)
T PRK14714 709 RVECPRCDVELT 720 (1337)
T ss_pred cccCCCCCCccc
Confidence 556888887654
No 117
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.70 E-value=1.3 Score=21.11 Aligned_cols=12 Identities=33% Similarity=1.027 Sum_probs=9.1
Q ss_pred cCCCCCceeEec
Q 035729 185 RCPGCGHCVQRK 196 (208)
Q Consensus 185 ~CP~C~~~i~k~ 196 (208)
.||+||..|+.+
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 488888888754
No 118
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=75.57 E-value=3.3 Score=22.91 Aligned_cols=22 Identities=32% Similarity=0.617 Sum_probs=17.3
Q ss_pred cccCCCCCceeEe-cCCCCceEeCC
Q 035729 183 WARCPGCGHCVQR-KNGCHVMQDSV 206 (208)
Q Consensus 183 ~k~CP~C~~~i~k-~~GCnhm~C~~ 206 (208)
...||.|+.|..+ .+| .+.|..
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~ 39 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVS 39 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCC
Confidence 3789999999998 566 577764
No 119
>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=75.21 E-value=1.6 Score=23.25 Aligned_cols=26 Identities=23% Similarity=0.507 Sum_probs=22.1
Q ss_pred CCcccCccccchhccccCcCcCCCCC
Q 035729 134 MKKAQCPNCKHWFCFRCKLKWHGGYH 159 (208)
Q Consensus 134 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 159 (208)
...++|..|+..+|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 46889999999999999987687764
No 120
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=75.03 E-value=1.5 Score=21.58 Aligned_cols=11 Identities=36% Similarity=0.827 Sum_probs=6.3
Q ss_pred CcccCCCCCce
Q 035729 182 KWARCPGCGHC 192 (208)
Q Consensus 182 ~~k~CP~C~~~ 192 (208)
..+.||+||..
T Consensus 15 ~~~fC~~CG~~ 25 (26)
T PF13248_consen 15 DAKFCPNCGAK 25 (26)
T ss_pred ccccChhhCCC
Confidence 45666666554
No 121
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=74.69 E-value=1.2 Score=36.08 Aligned_cols=73 Identities=22% Similarity=0.493 Sum_probs=43.2
Q ss_pred ccccCCccccCCCCCcccccCCCChhHHHHHHHHHHhhhh------cCCCcccCcccccccchhcchhhcCCCCcccCcc
Q 035729 68 AKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCEDYV------RGYERSYCPNRNCMALVVNECERKGRMKKAQCPN 141 (208)
Q Consensus 68 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~------~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~ 141 (208)
.|+.||. |+- ..+++..+.+.|..+.--+.. ...+...|- .|+.-.. ....++|..
T Consensus 289 LP~eCpi--C~l-------tLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~~~~-------~~~~y~C~~ 350 (378)
T KOG2807|consen 289 LPIECPI--CSL-------TLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQGELL-------SSGRYRCES 350 (378)
T ss_pred CCccCCc--cce-------eEecchHHHHHHHhhcCCcchhhccccccCCCccee--eeccccC-------CCCcEEchh
Confidence 3556665 554 233455566666655432211 123445576 5622111 156899999
Q ss_pred ccchhccccCcCcCCCC
Q 035729 142 CKHWFCFRCKLKWHGGY 158 (208)
Q Consensus 142 C~~~~C~~C~~~~H~~~ 158 (208)
|+..||..|..-.|..+
T Consensus 351 Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 351 CKNVFCLDCDVFIHESL 367 (378)
T ss_pred ccceeeccchHHHHhhh
Confidence 99999999998888653
No 122
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.01 E-value=0.47 Score=37.84 Aligned_cols=40 Identities=28% Similarity=0.665 Sum_probs=28.4
Q ss_pred ccccccccccccccccccccCCCCC-hhHHHHHHHHHHHHhhcCCCccccCCccccCCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTH-PFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN 80 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H-~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 80 (208)
...|.|||+.-. +.| ++.||| +.|..|-+++ . .||. |++.
T Consensus 300 ~~LC~ICmDaP~--DCv--fLeCGHmVtCt~CGkrm-----------~-eCPI--CRqy 340 (350)
T KOG4275|consen 300 RRLCAICMDAPR--DCV--FLECGHMVTCTKCGKRM-----------N-ECPI--CRQY 340 (350)
T ss_pred HHHHHHHhcCCc--ceE--EeecCcEEeehhhcccc-----------c-cCch--HHHH
Confidence 678999997653 333 899999 5799884432 2 7887 7653
No 123
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=73.24 E-value=1.7 Score=24.53 Aligned_cols=29 Identities=21% Similarity=0.336 Sum_probs=20.0
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFC 147 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 147 (208)
..|+ +|+..+..++. ...+.||.||..+=
T Consensus 4 y~C~--~CG~~~~~~~~----~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCA--RCGREVELDEY----GTGVRCPYCGYRIL 32 (46)
T ss_pred EECC--CCCCEEEECCC----CCceECCCCCCeEE
Confidence 4588 68887766544 23789998887553
No 124
>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=72.68 E-value=1.8 Score=23.07 Aligned_cols=32 Identities=19% Similarity=0.597 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 49 FCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 49 ~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
+|.+|++.|....-.--....+.|+. |+-.++
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 58899998865433222345689988 886554
No 125
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.43 E-value=8.9 Score=29.62 Aligned_cols=55 Identities=22% Similarity=0.621 Sum_probs=40.6
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.-.|.+|--++...+.. .+.|-|.|.-.||..+-.+--....-.-..||. |..+|
T Consensus 50 ~pNC~LC~t~La~gdt~--RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTT--RLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcce--eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 45799999999777754 789999999999998765543331122368998 99754
No 126
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=72.26 E-value=2.3 Score=24.65 Aligned_cols=27 Identities=19% Similarity=0.668 Sum_probs=19.3
Q ss_pred cccCccccccc-chhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMA-LVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~-~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
..+|| .|+. ++... ...+.|..|++.+
T Consensus 20 ~~fCP--~Cg~~~m~~~------~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCP--RCGSGFMAEH------LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCc--CCCcchhecc------CCcEECCCcCCEE
Confidence 56899 6888 55443 3578899998764
No 127
>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=71.66 E-value=0.83 Score=25.09 Aligned_cols=26 Identities=23% Similarity=0.554 Sum_probs=22.7
Q ss_pred CCcccCccccchhccccCcCcCCCCC
Q 035729 134 MKKAQCPNCKHWFCFRCKLKWHGGYH 159 (208)
Q Consensus 134 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 159 (208)
...++|..|+..+|..|....|.+|.
T Consensus 13 ~~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp BEEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred ceEEEecCCCCccCccCCCCCCCCCE
Confidence 37899999999999999998898863
No 128
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=70.79 E-value=7.1 Score=28.48 Aligned_cols=51 Identities=20% Similarity=0.421 Sum_probs=36.3
Q ss_pred CCccccccccccccccccccccCCCC--C---hhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCT--H---PFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~--H---~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
...-.|-||+++... . ..+|. . ....+|+++|+... ....|+. |...+...
T Consensus 6 ~~~~~CRIC~~~~~~-~----~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDV-V----TNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCC-c----cCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 345689999988642 2 24553 3 67999999999853 3568999 99876554
No 129
>PHA02926 zinc finger-like protein; Provisional
Probab=70.54 E-value=1 Score=34.71 Aligned_cols=37 Identities=30% Similarity=0.702 Sum_probs=26.7
Q ss_pred ccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 140 PNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 140 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
+.|+..||+.|...|..... .....+.||-|+.....
T Consensus 195 ~~CnHsFCl~CIr~Wr~~r~-------------------~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 195 DSCNHIFCITCINIWHRTRR-------------------ETGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCchHHHHHHHHHHHhcc-------------------ccCcCCcCCCCcceeee
Confidence 47999999999998875321 11245789999988653
No 130
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=70.54 E-value=2.3 Score=23.76 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=11.1
Q ss_pred CCcccCCCCCcee
Q 035729 181 MKWARCPGCGHCV 193 (208)
Q Consensus 181 ~~~k~CP~C~~~i 193 (208)
.++++||+||+.-
T Consensus 9 RGirkCp~CGt~N 21 (44)
T PF14952_consen 9 RGIRKCPKCGTYN 21 (44)
T ss_pred hccccCCcCcCcc
Confidence 4789999999874
No 131
>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=69.02 E-value=4.4 Score=23.97 Aligned_cols=47 Identities=23% Similarity=0.650 Sum_probs=31.3
Q ss_pred cccccccccccccccccccCCC--CChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 24 FTCEICIEPMAANKKFKNKNLC--THPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
-.|..|-.++++... ...-| ...||.+|....+. -.||. |+..|...
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 368888888865431 12234 45899999887552 27998 99877543
No 132
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=68.93 E-value=3.1 Score=24.90 Aligned_cols=35 Identities=26% Similarity=0.544 Sum_probs=23.3
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
...|. .|+..+..... ...+.||.||...=++|..
T Consensus 9 ~~~Ct--SCg~~i~p~e~----~v~F~CPnCGe~~I~Rc~~ 43 (61)
T COG2888 9 PPVCT--SCGREIAPGET----AVKFPCPNCGEVEIYRCAK 43 (61)
T ss_pred Cceec--cCCCEeccCCc----eeEeeCCCCCceeeehhhh
Confidence 44566 58877754443 5789999999666555543
No 133
>PF12773 DZR: Double zinc ribbon
Probab=68.78 E-value=3.6 Score=23.47 Aligned_cols=28 Identities=29% Similarity=0.702 Sum_probs=14.9
Q ss_pred CCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 110 YERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 110 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
.+..+|| .|+..+.... ...+.|+.|+.
T Consensus 10 ~~~~fC~--~CG~~l~~~~-----~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCP--HCGTPLPPPD-----QSKKICPNCGA 37 (50)
T ss_pred ccccCCh--hhcCChhhcc-----CCCCCCcCCcC
Confidence 3456677 5766665111 34566665543
No 134
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=68.43 E-value=3.8 Score=25.97 Aligned_cols=61 Identities=20% Similarity=0.325 Sum_probs=22.0
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGH 191 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 191 (208)
...|- -|+.-+.....+ ...+-|..|++-.|..|.. +....+.+.||.|++
T Consensus 9 ~qiCq--iCGD~VGl~~~G---e~FVAC~eC~fPvCr~CyE------------------------YErkeg~q~CpqCkt 59 (80)
T PF14569_consen 9 GQICQ--ICGDDVGLTENG---EVFVACHECAFPVCRPCYE------------------------YERKEGNQVCPQCKT 59 (80)
T ss_dssp S-B-S--SS--B--B-SSS---SB--S-SSS-----HHHHH------------------------HHHHTS-SB-TTT--
T ss_pred Ccccc--cccCccccCCCC---CEEEEEcccCCccchhHHH------------------------HHhhcCcccccccCC
Confidence 34455 455544433222 5788899999988886633 234568899999999
Q ss_pred eeEecCCCCc
Q 035729 192 CVQRKNGCHV 201 (208)
Q Consensus 192 ~i~k~~GCnh 201 (208)
+..+.-|+-.
T Consensus 60 ~ykr~kgsp~ 69 (80)
T PF14569_consen 60 RYKRHKGSPR 69 (80)
T ss_dssp B----TT---
T ss_pred CcccccCCCC
Confidence 9988777643
No 135
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.57 E-value=1.7 Score=33.56 Aligned_cols=38 Identities=29% Similarity=0.664 Sum_probs=25.7
Q ss_pred CCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 134 MKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 134 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
.+.+++ ||..|||-|.-.|-. ...+.+.||.|+..|..
T Consensus 59 dPVvTl--CGHLFCWpClyqWl~----------------------~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 59 DPVVTL--CGHLFCWPCLYQWLQ----------------------TRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCEEee--cccceehHHHHHHHh----------------------hcCCCeeCCcccccccc
Confidence 356665 999999999876631 12355667888776653
No 136
>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=66.13 E-value=8.9 Score=19.67 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=10.2
Q ss_pred cccCCCCCceeEecCCCCceEeC
Q 035729 183 WARCPGCGHCVQRKNGCHVMQDS 205 (208)
Q Consensus 183 ~k~CP~C~~~i~k~~GCnhm~C~ 205 (208)
.+-||.||.+.+...|=--|.|+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~ 25 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCP 25 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEES
T ss_pred CcccCcCCccccCCCCcCEeECC
Confidence 35566666666665554445543
No 137
>smart00336 BBOX B-Box-type zinc finger.
Probab=65.75 E-value=4.2 Score=21.95 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=21.9
Q ss_pred CCcccCccccchhccccCcCcCCCCC
Q 035729 134 MKKAQCPNCKHWFCFRCKLKWHGGYH 159 (208)
Q Consensus 134 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 159 (208)
...++|..|....|..|....|.++.
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred ceEEECCCCCcccccccChhhcCCCc
Confidence 46789999999999999987787653
No 138
>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 KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.32 E-value=7.3 Score=30.54 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=32.3
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhc
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQD 64 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 64 (208)
.+..-|.+|+.+...+ +..+=||.||++||..||.++-++
T Consensus 41 K~FdcCsLtLqPc~dP----vit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDP----VITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred CCcceeeeecccccCC----ccCCCCeeeeHHHHHHHHHHHHHH
Confidence 3456788999998766 467889999999999999877654
No 140
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=63.12 E-value=14 Score=29.16 Aligned_cols=48 Identities=23% Similarity=0.431 Sum_probs=35.8
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
...|+|=+-++..+ .....|+|+|=++=+..++.. ...+.||..+|..
T Consensus 176 s~rdPis~~~I~nP---viSkkC~HvydrDsI~~~l~~------~~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPIVNP---VISKKCGHVYDRDSIMQILCD------EITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhhhch---hhhcCcCcchhhhhHHHHhcc------CceeecccccCCc
Confidence 35788777676554 247789999998877776643 4568999999994
No 141
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.12 E-value=6.3 Score=24.57 Aligned_cols=59 Identities=20% Similarity=0.673 Sum_probs=37.3
Q ss_pred ccccccccccccccccccCCC--CChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCChhHHHHHHH
Q 035729 25 TCEICIEPMAANKKFKNKNLC--THPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCD 100 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~ 100 (208)
.|..|-.++++... ..+-| .|.||.+|.+.-+ .. .||. |+..|...-++ +...+.+|-.
T Consensus 7 nCECCDrDLpp~s~--dA~ICtfEcTFCadCae~~l----~g------~CPn--CGGelv~RP~R---Paa~L~r~PA 67 (84)
T COG3813 7 NCECCDRDLPPDST--DARICTFECTFCADCAENRL----HG------LCPN--CGGELVARPIR---PAAKLARYPA 67 (84)
T ss_pred CCcccCCCCCCCCC--ceeEEEEeeehhHhHHHHhh----cC------cCCC--CCchhhcCcCC---hHHHHhhCch
Confidence 47778778855432 13345 6899999987543 22 7998 99877654443 4455666543
No 142
>PHA00626 hypothetical protein
Probab=62.05 E-value=4.6 Score=23.88 Aligned_cols=15 Identities=13% Similarity=0.078 Sum_probs=10.9
Q ss_pred CCcccCccccchhcc
Q 035729 134 MKKAQCPNCKHWFCF 148 (208)
Q Consensus 134 ~~~~~C~~C~~~~C~ 148 (208)
.+...|+.|++.|=.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 467888888887643
No 143
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=61.86 E-value=1.8 Score=35.01 Aligned_cols=79 Identities=22% Similarity=0.410 Sum_probs=46.2
Q ss_pred ccccCCccccCCCCCcccccCCCChhHHHHHHHHHHhh-hhc-----CCCcccCcccccccchhcchh---h-cCCCCcc
Q 035729 68 AKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCED-YVR-----GYERSYCPNRNCMALVVNECE---R-KGRMKKA 137 (208)
Q Consensus 68 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~-~~~-----~~~~~~Cp~~~C~~~~~~~~~---~-~~~~~~~ 137 (208)
.|+.||. |.. ..+|+..+.+.|..+.--+ +++ ++....|- .|...++..+. + .....+.
T Consensus 321 LPi~CP~--Csl-------~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY 389 (421)
T COG5151 321 LPISCPI--CSL-------QLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VCQGPFPKPPVSPFDESTSSGRY 389 (421)
T ss_pred CCccCcc--hhH-------HHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--eccCCCCCCCCCcccccccccce
Confidence 4566665 543 3344555666676554322 222 23345566 57665543321 1 1125789
Q ss_pred cCccccchhccccCcCcCCC
Q 035729 138 QCPNCKHWFCFRCKLKWHGG 157 (208)
Q Consensus 138 ~C~~C~~~~C~~C~~~~H~~ 157 (208)
.|+.|+..||..|..-.|..
T Consensus 390 ~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 390 QCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred echhhhhhhhhhhHHHHHHH
Confidence 99999999999998877743
No 144
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=61.50 E-value=2.6 Score=26.62 Aligned_cols=51 Identities=27% Similarity=0.647 Sum_probs=34.1
Q ss_pred cccccccccccc--------ccc-cccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 25 TCEICIEPMAAN--------KKF-KNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 25 ~C~iC~~~~~~~--------~~~-~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
+|.||--+|... +.. .+.-.|.|.|-.-|+.+++.+.-++ -.||. |++.+.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~~ 81 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTWQ 81 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chheeE
Confidence 788887776431 111 1122478999999999998775543 48998 887653
No 145
>PRK00420 hypothetical protein; Validated
Probab=61.50 E-value=13 Score=25.57 Aligned_cols=42 Identities=19% Similarity=0.258 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhhhcCCCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 94 LFSKWCDLLCEDYVRGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
...+.-+++...+.. -...|| .|+..+.... ....+||.||.
T Consensus 7 ~~k~~a~~Ll~Ga~m--l~~~CP--~Cg~pLf~lk-----~g~~~Cp~Cg~ 48 (112)
T PRK00420 7 IVKKAAELLLKGAKM--LSKHCP--VCGLPLFELK-----DGEVVCPVHGK 48 (112)
T ss_pred HHHHHHHHHHhHHHH--ccCCCC--CCCCcceecC-----CCceECCCCCC
Confidence 344444444443222 237799 7998777532 24677776665
No 146
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.90 E-value=10 Score=24.84 Aligned_cols=17 Identities=18% Similarity=0.770 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHHhhc
Q 035729 48 PFCQECIAKYIQVMVQD 64 (208)
Q Consensus 48 ~~C~~Cl~~~~~~~i~~ 64 (208)
-||++||.+|+......
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887765
No 147
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=60.59 E-value=6.2 Score=32.24 Aligned_cols=63 Identities=19% Similarity=0.354 Sum_probs=39.0
Q ss_pred CCCCCCCCCCcc-cccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccC
Q 035729 5 LQRPTENRGRQE-EEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQ 78 (208)
Q Consensus 5 ~~~~~~~~~~~~-~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 78 (208)
.++|.+.....+ +........|+||+...-.+. +...=|=+||-.|+-.|+.. .=+||.-++.
T Consensus 281 ~PpPPh~~~~se~e~l~~~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~--------~~~CPVT~~p 344 (357)
T KOG0826|consen 281 IPPPPHKQYNSESELLPPDREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVN--------YGHCPVTGYP 344 (357)
T ss_pred CCcCChhhcccccccCCCccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHh--------cCCCCccCCc
Confidence 344443333333 333445689999998884442 23334889999999999972 1278874443
No 148
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=60.21 E-value=15 Score=33.76 Aligned_cols=18 Identities=11% Similarity=0.350 Sum_probs=11.0
Q ss_pred CCChhHHHHHHHHHHHHh
Q 035729 45 CTHPFCQECIAKYIQVMV 62 (208)
Q Consensus 45 C~H~~C~~Cl~~~~~~~i 62 (208)
|+|.+|-.||..+....+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhHHHHHHHHHhh
Confidence 666666666666655444
No 149
>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=60.03 E-value=5.6 Score=23.23 Aligned_cols=36 Identities=22% Similarity=0.569 Sum_probs=24.9
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHH
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQ 59 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 59 (208)
..|.+|-..|.....-..-..||++||.+|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 468888877754322223457999999999887654
No 150
>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=59.85 E-value=6.7 Score=17.39 Aligned_cols=16 Identities=31% Similarity=0.627 Sum_probs=13.1
Q ss_pred hccccCcCcCCCCCCh
Q 035729 146 FCFRCKLKWHGGYHCE 161 (208)
Q Consensus 146 ~C~~C~~~~H~~~~C~ 161 (208)
.|+.|.+.-|....|.
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 5889999999887775
No 151
>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=59.37 E-value=11 Score=29.51 Aligned_cols=56 Identities=16% Similarity=0.400 Sum_probs=39.2
Q ss_pred ccCCccccCCC-CCcccccCCCChhHHHHHHHHHHhhhhcCCCcccCcccccccchhcch
Q 035729 70 IECPGLNCQKN-LDPFSCKPMIPSSLFSKWCDLLCEDYVRGYERSYCPNRNCMALVVNEC 128 (208)
Q Consensus 70 i~CP~~~C~~~-l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 128 (208)
-+||. |... .-..+|.-+++++-|.++-+.-..+.+ ..+-..||.++|+.++....
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIF-s~GpAqCP~~gC~kILRK~k 67 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIF-SRGPAQCPYKGCGKILRKIK 67 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHh-cCCCCCCCCccHHHHHHHhc
Confidence 48999 9862 223577888899888877665554433 34557799999998876544
No 152
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=58.46 E-value=4.8 Score=27.69 Aligned_cols=31 Identities=23% Similarity=0.488 Sum_probs=22.5
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
..+|| .|++++.+..... ...+.|++|++..
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 35799 8999998765422 3588888887765
No 153
>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=58.42 E-value=4.9 Score=20.27 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=8.0
Q ss_pred ccCCCCCceeEec
Q 035729 184 ARCPGCGHCVQRK 196 (208)
Q Consensus 184 k~CP~C~~~i~k~ 196 (208)
++||+|+..|++.
T Consensus 2 ~~C~rC~~~~~~~ 14 (30)
T PF06827_consen 2 EKCPRCWNYIEDI 14 (30)
T ss_dssp SB-TTT--BBEEE
T ss_pred CcCccCCCcceEe
Confidence 5899999999763
No 154
>PLN00209 ribosomal protein S27; Provisional
Probab=58.11 E-value=8.3 Score=24.99 Aligned_cols=31 Identities=16% Similarity=0.498 Sum_probs=23.5
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
+.|| +|.+.-..-... ...+.|..|+...+.
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 7899 898876654432 578999999988875
No 155
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=57.80 E-value=8.5 Score=22.63 Aligned_cols=21 Identities=19% Similarity=0.556 Sum_probs=15.8
Q ss_pred HHHHHHHHhCCcccCCCCCce
Q 035729 172 IAFGQLAERMKWARCPGCGHC 192 (208)
Q Consensus 172 ~~~~~~~~~~~~k~CP~C~~~ 192 (208)
+.+.++........||+|+..
T Consensus 35 ~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 35 QELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHHHcCCCeEECcCCCcc
Confidence 455566666788999999975
No 156
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=57.31 E-value=5.4 Score=31.51 Aligned_cols=50 Identities=28% Similarity=0.614 Sum_probs=28.5
Q ss_pred CCcccCccc---cchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 134 MKKAQCPNC---KHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 134 ~~~~~C~~C---~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
...+.|.+| |+..|++|+.-+-..| .. ...+ . .......+||+|+..+.-
T Consensus 169 ~E~~KC~SCNrlGq~sCLRCK~cfCddH-----vr-----rKg~-k-y~k~k~~PCPKCg~et~e 221 (314)
T PF06524_consen 169 SETFKCQSCNRLGQYSCLRCKICFCDDH-----VR-----RKGF-K-YEKGKPIPCPKCGYETQE 221 (314)
T ss_pred cccccccccccccchhhhheeeeehhhh-----hh-----hccc-c-cccCCCCCCCCCCCcccc
Confidence 456677777 6778888887442221 00 0000 1 122356789999988764
No 157
>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=56.86 E-value=7.4 Score=18.81 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=8.4
Q ss_pred CCcccCccccc
Q 035729 134 MKKAQCPNCKH 144 (208)
Q Consensus 134 ~~~~~C~~C~~ 144 (208)
...+.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 56788988873
No 158
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=56.35 E-value=4.4 Score=26.89 Aligned_cols=30 Identities=23% Similarity=0.710 Sum_probs=21.1
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.+|| .|++.++.+.+.. ...+.|..|.+.+
T Consensus 2 ~FCP--~Cgn~Live~g~~--~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGES--CNRFSCRTCPYVF 31 (105)
T ss_pred cccC--CCCCEEEEecCCe--EeeEEcCCCCcee
Confidence 4688 7999999887632 4667777666554
No 159
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=56.06 E-value=6.6 Score=20.55 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=18.6
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
...|+ .|++..+.... ....+|+.|+..+
T Consensus 3 ~~~C~--~C~~~~i~~~~----~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNKE----DDYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEec----CCeEEcccCCcEe
Confidence 45677 58877766322 3577888887653
No 160
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=55.34 E-value=2.2 Score=38.50 Aligned_cols=29 Identities=28% Similarity=0.761 Sum_probs=21.1
Q ss_pred cccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCcee
Q 035729 141 NCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCV 193 (208)
Q Consensus 141 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i 193 (208)
+|++.||..|..+ .-+.+.++||+|+..+
T Consensus 660 kC~H~FC~~Cvq~------------------------r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 660 KCGHVFCEECVQT------------------------RYETRQRKCPKCNAAF 688 (698)
T ss_pred hcchHHHHHHHHH------------------------HHHHhcCCCCCCCCCC
Confidence 6799999988652 1124778999999875
No 161
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=55.11 E-value=7.8 Score=31.44 Aligned_cols=33 Identities=30% Similarity=0.659 Sum_probs=23.5
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHH
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAK 56 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~ 56 (208)
....-|.-|--.+. .+-.+.+|.|+||.+|.+.
T Consensus 88 p~VHfCd~Cd~PI~---IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 88 PRVHFCDRCDFPIA---IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred cceEeecccCCcce---eeecccccchhhhhhhhhc
Confidence 33567887866652 3345789999999999664
No 162
>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=54.70 E-value=4.8 Score=20.62 Aligned_cols=26 Identities=31% Similarity=0.600 Sum_probs=12.1
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.|| .|+.-....+ ...+.|+.|+..+
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 5665544433 4678888887653
No 163
>PHA02862 5L protein; Provisional
Probab=54.63 E-value=13 Score=26.70 Aligned_cols=47 Identities=23% Similarity=0.523 Sum_probs=34.1
Q ss_pred cccccccccccccccccccCCCC-----ChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 24 FTCEICIEPMAANKKFKNKNLCT-----HPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~-----H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
..|-||+++-... ..+|. .....+||.+|+.. ..+..|+. |+.++..
T Consensus 3 diCWIC~~~~~e~-----~~PC~C~GS~K~VHq~CL~~WIn~------S~k~~CeL--CkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDER-----NNFCGCNEEYKVVHIKCMQLWINY------SKKKECNL--CKTKYNI 54 (156)
T ss_pred CEEEEecCcCCCC-----cccccccCcchhHHHHHHHHHHhc------CCCcCccC--CCCeEEE
Confidence 4689999986332 34553 47999999999943 34579999 9986644
No 164
>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=54.61 E-value=14 Score=20.06 Aligned_cols=21 Identities=33% Similarity=0.706 Sum_probs=14.3
Q ss_pred ccCCCCCceeEe---cCCCCceEeC
Q 035729 184 ARCPGCGHCVQR---KNGCHVMQDS 205 (208)
Q Consensus 184 k~CP~C~~~i~k---~~GCnhm~C~ 205 (208)
+.||.|+..+.. ..| ..+.|+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECC
Confidence 579999977664 245 666665
No 165
>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=53.82 E-value=12 Score=30.44 Aligned_cols=33 Identities=21% Similarity=0.406 Sum_probs=19.5
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhccccCc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
..|| .|..-....+.- ...+. .||+.||..|..
T Consensus 4 ~~CP--~Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~ 36 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSL---KLMVN--VCGHTLCESCVD 36 (309)
T ss_pred CCCC--cCCCCCccCccc---ccccC--CCCCcccHHHHH
Confidence 4588 677643332220 12333 689999998865
No 166
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=53.58 E-value=12 Score=25.37 Aligned_cols=33 Identities=18% Similarity=0.535 Sum_probs=21.7
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
.+++|+ .|++.+.+....+++...+.|..|.+.
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~v 35 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYV 35 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcce
Confidence 467788 899988876654444556666655443
No 167
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=53.17 E-value=4.4 Score=36.48 Aligned_cols=59 Identities=20% Similarity=0.475 Sum_probs=44.9
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccC
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKP 88 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 88 (208)
......+|+||+..+-.+ ..+.|.|.||..|+-.-+...- ....||. |+..++...++.
T Consensus 17 ~~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 17 AMQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKK-----GPKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HHhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccC-----ccccchh--hhhhhhhhhccc
Confidence 345578999999999665 4789999999999988776532 2678888 887666655554
No 168
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=52.59 E-value=7.7 Score=22.32 Aligned_cols=28 Identities=21% Similarity=0.482 Sum_probs=19.0
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
...|| .|+..++.... ..++.|-.|++.
T Consensus 19 ~~~CP--rCG~gvfmA~H----~dR~~CGkCgyT 46 (51)
T COG1998 19 NRFCP--RCGPGVFMADH----KDRWACGKCGYT 46 (51)
T ss_pred cccCC--CCCCcchhhhc----CceeEeccccce
Confidence 46799 68865554444 458888888764
No 169
>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=52.39 E-value=6.7 Score=24.01 Aligned_cols=37 Identities=24% Similarity=0.452 Sum_probs=19.6
Q ss_pred cCCCcccCcccccccchhcchhhcCCCCcccCccccchhccccCc
Q 035729 108 RGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 108 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
++.+...|. .|+.-+... .....|..||..+|..|..
T Consensus 5 ~d~~~~~C~--~C~~~F~~~------~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 5 PDSEASNCM--ICGKKFSLF------RRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp SGGG-SB-T--TT--B-BSS------S-EEE-TTT--EEECCCS-
T ss_pred CCCCCCcCc--CcCCcCCCc------eeeEccCCCCCEECCchhC
Confidence 344466787 587766432 4788999999999999986
No 170
>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=52.22 E-value=6.1 Score=23.10 Aligned_cols=34 Identities=29% Similarity=0.478 Sum_probs=17.4
Q ss_pred CcccCcccccccchhcchh------hcCCCCcccCccccch
Q 035729 111 ERSYCPNRNCMALVVNECE------RKGRMKKAQCPNCKHW 145 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~------~~~~~~~~~C~~C~~~ 145 (208)
+.+.||||.|-.- ..++. .+.....++|..|...
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 4688999999654 11110 1122567788777654
No 171
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=52.05 E-value=10 Score=23.10 Aligned_cols=15 Identities=27% Similarity=0.419 Sum_probs=12.0
Q ss_pred CCcccCCCCCceeEe
Q 035729 181 MKWARCPGCGHCVQR 195 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k 195 (208)
...|+||.|+..+.+
T Consensus 4 d~lKPCPFCG~~~~~ 18 (64)
T PRK09710 4 DNVKPCPFCGCPSVT 18 (64)
T ss_pred ccccCCCCCCCceeE
Confidence 367999999987765
No 172
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.99 E-value=8.5 Score=23.42 Aligned_cols=16 Identities=31% Similarity=0.516 Sum_probs=13.1
Q ss_pred CCcccCCCCCceeEec
Q 035729 181 MKWARCPGCGHCVQRK 196 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k~ 196 (208)
....+||.||.+|+..
T Consensus 5 ~~~v~CP~Cgkpv~w~ 20 (65)
T COG3024 5 RITVPCPTCGKPVVWG 20 (65)
T ss_pred cccccCCCCCCccccc
Confidence 3567899999999873
No 173
>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=51.90 E-value=8.8 Score=20.64 Aligned_cols=16 Identities=44% Similarity=0.775 Sum_probs=12.4
Q ss_pred CCcccCCCCCceeEec
Q 035729 181 MKWARCPGCGHCVQRK 196 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k~ 196 (208)
.....||.|+..++|.
T Consensus 24 ~~~~~CP~Cg~~~~r~ 39 (41)
T smart00834 24 DPLATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCCCcceec
Confidence 3567899999987764
No 174
>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=51.68 E-value=6.8 Score=22.84 Aligned_cols=38 Identities=21% Similarity=0.524 Sum_probs=23.1
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
.+.|+.|.+.++. .=|..++...=.. ....+.||. |..
T Consensus 2 ~f~CP~C~~~~~~----------------~~L~~H~~~~H~~-~~~~v~CPi--C~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKGFSE----------------SSLVEHCEDEHRS-ESKNVVCPI--CSS 39 (54)
T ss_pred CcCCCCCCCccCH----------------HHHHHHHHhHCcC-CCCCccCCC--chh
Confidence 5789999985532 2244444433222 334689999 976
No 175
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.28 E-value=10 Score=35.05 Aligned_cols=40 Identities=28% Similarity=0.674 Sum_probs=32.3
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
..|..|--++..| +|...|+|.|.+.|+. + ..-.||. |..
T Consensus 841 skCs~C~~~LdlP---~VhF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLP---FVHFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeecccCCccccc---eeeeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 5899999999777 3567999999999998 2 2358998 876
No 176
>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=50.90 E-value=20 Score=26.23 Aligned_cols=83 Identities=17% Similarity=0.442 Sum_probs=44.3
Q ss_pred ccccccccccccccccccccCCC-------CCh------hHHHHHHHHHHHHhhcC-----------------------C
Q 035729 23 SFTCEICIEPMAANKKFKNKNLC-------THP------FCQECIAKYIQVMVQDN-----------------------N 66 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C-------~H~------~C~~Cl~~~~~~~i~~~-----------------------~ 66 (208)
..+|+||+|.= -+. |++-| .-. --.+||.+|-.+..... .
T Consensus 2 d~~CpICme~P-HNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHP-HNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCC-Cce---EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 46899999753 332 24443 112 23578888876544331 1
Q ss_pred CccccCCccccCCCCCcccccCCCChhHHHHHHHHHHhhhhcCCCcccCcccccccchh
Q 035729 67 TAKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCEDYVRGYERSYCPNRNCMALVV 125 (208)
Q Consensus 67 ~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~ 125 (208)
...+.||. |...+..-.+- +..++|.+ ...+-|+.-+|.....
T Consensus 78 ~~~L~CPL--CRG~V~GWtvv-----e~AR~~LN---------~K~RsC~~e~C~F~Gt 120 (162)
T PF07800_consen 78 QPELACPL--CRGEVKGWTVV-----EPARRFLN---------AKKRSCSQESCSFSGT 120 (162)
T ss_pred cccccCcc--ccCceeceEEc-----hHHHHHhc---------cCCccCcccccccccC
Confidence 23578988 88765433222 22343322 3345577666765443
No 177
>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=49.37 E-value=37 Score=23.00 Aligned_cols=32 Identities=22% Similarity=0.599 Sum_probs=22.7
Q ss_pred CChhHHHHHHHHHHHHhhc-CCCccccCCccccCC
Q 035729 46 THPFCQECIAKYIQVMVQD-NNTAKIECPGLNCQK 79 (208)
Q Consensus 46 ~H~~C~~Cl~~~~~~~i~~-~~~~~i~CP~~~C~~ 79 (208)
.-.||..||...+...+.+ .....-.||. |..
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCC--CCC
Confidence 6689999999988776654 1223468887 655
No 178
>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=49.01 E-value=8.5 Score=26.11 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=17.7
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.|| .|+.-+..+++ ..+.||.|++.|
T Consensus 4 ~CP--~C~seytY~dg-----~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG-----TQLICPSCLYEW 29 (109)
T ss_pred cCC--cCCCcceEecC-----CeeECccccccc
Confidence 477 68777766654 568888777655
No 179
>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=48.80 E-value=12 Score=26.79 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=10.5
Q ss_pred ccCCCCCceeEec
Q 035729 184 ARCPGCGHCVQRK 196 (208)
Q Consensus 184 k~CP~C~~~i~k~ 196 (208)
-+|.+||.+|...
T Consensus 82 ~~CE~CG~~I~~G 94 (137)
T TIGR03826 82 YPCERCGTSIREG 94 (137)
T ss_pred CcccccCCcCCCC
Confidence 6799999998643
No 180
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=48.73 E-value=13 Score=29.06 Aligned_cols=104 Identities=20% Similarity=0.399 Sum_probs=55.3
Q ss_pred ccCCCCChhHHHHHHHHHHHHhhc------CCCccccCCccccCCCCCcccccCCCChhHHHHHHHHHHhh----hhcCC
Q 035729 41 NKNLCTHPFCQECIAKYIQVMVQD------NNTAKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCED----YVRGY 110 (208)
Q Consensus 41 ~~~~C~H~~C~~Cl~~~~~~~i~~------~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~----~~~~~ 110 (208)
+-..|.+.||.+= ....-+. ++.....||. |...++.. ..-.....+..+...-... .-...
T Consensus 25 ~Cd~C~~~FC~eH----rsye~H~Cp~~~~~~~~v~icp~--cs~pv~~~--~de~~~~~v~~h~~~dC~~~~~~~~~k~ 96 (250)
T KOG3183|consen 25 KCDGCSGIFCLEH----RSYESHHCPKGLRIDVQVPICPL--CSKPVPTK--KDEAPDKVVEPHISNDCDRHPEQKKRKV 96 (250)
T ss_pred eeCCccchhhhcc----chHhhcCCCcccccceeecccCC--CCCCCCCC--CCcchhhhhchhhccccccCchhhhccc
Confidence 3557899998752 2222211 2344568888 88766543 1111111222221111110 00111
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCCh
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCE 161 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~ 161 (208)
....||.+.|...... ...+.|..|+..||.+-+.+. +++|.
T Consensus 97 ~t~kc~~~~c~k~~~~-------~~~~~c~~c~~~~c~khr~~~--dhsc~ 138 (250)
T KOG3183|consen 97 FTNKCPVPRCKKTLTL-------ANKITCSKCGRNFCLKHRHPL--DHSCN 138 (250)
T ss_pred ccccCCchhhHHHHHH-------HHhhhhHhhcchhhhhccCCC--Cchhh
Confidence 2456998888876654 355889999999999876632 23555
No 181
>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=48.59 E-value=4.7 Score=27.50 Aligned_cols=30 Identities=33% Similarity=0.699 Sum_probs=22.1
Q ss_pred hhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 48 PFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 48 ~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
+.|.+|-++|+- .+..||.||. |+..+.+.
T Consensus 10 R~Cp~CG~kFYD-----Lnk~PivCP~--CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-----LNKDPIVCPK--CGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-----CCCCCccCCC--CCCccCcc
Confidence 456667666663 3568999999 99988776
No 182
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=48.49 E-value=12 Score=24.24 Aligned_cols=31 Identities=19% Similarity=0.524 Sum_probs=23.7
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
+.|| +|.+.-..-... ...+.|..|+...|.
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 7899 898876654442 578999999988875
No 183
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=48.37 E-value=6.6 Score=24.09 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=23.2
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
++.|| +|++....-... ...+.|..||...+.
T Consensus 19 ~VkCp--dC~N~q~vFsha---st~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFSHA---STVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEeccC---ceEEEecccccEEEe
Confidence 47899 898866554332 578999999887764
No 184
>PF14149 YhfH: YhfH-like protein
Probab=47.86 E-value=1.6 Score=23.54 Aligned_cols=31 Identities=13% Similarity=0.364 Sum_probs=21.6
Q ss_pred HHHHHHhCCcccCCCCCceeEecCCCCceEe
Q 035729 174 FGQLAERMKWARCPGCGHCVQRKNGCHVMQD 204 (208)
Q Consensus 174 ~~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C 204 (208)
..++.++...|.|+.||..|+-.--|-.++|
T Consensus 4 ~~eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 4 IVEFFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHHHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 3456677889999999998875544444444
No 185
>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=47.68 E-value=26 Score=24.14 Aligned_cols=36 Identities=22% Similarity=0.502 Sum_probs=24.5
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccchhccccCcC
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLK 153 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 153 (208)
+...|. .|...+.... .....|..|+..+|..|...
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 456787 6876443221 24589999999999999985
No 186
>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=47.27 E-value=23 Score=19.79 Aligned_cols=20 Identities=35% Similarity=0.921 Sum_probs=13.5
Q ss_pred HHHHHHHhCCc---ccCCCCCce
Q 035729 173 AFGQLAERMKW---ARCPGCGHC 192 (208)
Q Consensus 173 ~~~~~~~~~~~---k~CP~C~~~ 192 (208)
...+++....| ..||+|+..
T Consensus 5 ~c~~~l~~~RW~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 5 ACREYLEEIRWPDGFVCPHCGST 27 (46)
T ss_pred HHHHHHHHhcCCCCCCCCCCCCe
Confidence 44455566666 469999974
No 187
>PF14353 CpXC: CpXC protein
Probab=47.07 E-value=9.7 Score=26.58 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=10.0
Q ss_pred ccCCccccCCCCCcc
Q 035729 70 IECPGLNCQKNLDPF 84 (208)
Q Consensus 70 i~CP~~~C~~~l~~~ 84 (208)
|+||. |+..+..+
T Consensus 2 itCP~--C~~~~~~~ 14 (128)
T PF14353_consen 2 ITCPH--CGHEFEFE 14 (128)
T ss_pred cCCCC--CCCeeEEE
Confidence 78999 99876544
No 188
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.76 E-value=14 Score=26.14 Aligned_cols=24 Identities=38% Similarity=0.627 Sum_probs=18.0
Q ss_pred CCcccCCCCCceeEecCCCCceEeCC
Q 035729 181 MKWARCPGCGHCVQRKNGCHVMQDSV 206 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k~~GCnhm~C~~ 206 (208)
+-...||.||.|..+..| -++|++
T Consensus 26 ML~~hCp~Cg~PLF~KdG--~v~CPv 49 (131)
T COG1645 26 MLAKHCPKCGTPLFRKDG--EVFCPV 49 (131)
T ss_pred HHHhhCcccCCcceeeCC--eEECCC
Confidence 345789999999998776 455554
No 189
>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=45.53 E-value=8.8 Score=21.26 Aligned_cols=28 Identities=21% Similarity=0.624 Sum_probs=16.1
Q ss_pred CcccCccccchhccccCcCcCCCCCChhhh
Q 035729 135 KKAQCPNCKHWFCFRCKLKWHGGYHCEESG 164 (208)
Q Consensus 135 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~ 164 (208)
..+.|+.|+..||...+.+ ..|.|....
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~--e~H~C~~~~ 39 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP--EDHNCSKLQ 39 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST--TTCT-SSTT
T ss_pred CCeECCCCCcccCccccCc--cccCCcchh
Confidence 4578999999999988764 223565443
No 190
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.52 E-value=25 Score=24.17 Aligned_cols=47 Identities=23% Similarity=0.542 Sum_probs=25.9
Q ss_pred ChhHHHHHHHHHHhhhhc---------CCCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 91 PSSLFSKWCDLLCEDYVR---------GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
.++.++.......+..+. .+...+|+ +|+..+..... ..+.||.||.
T Consensus 40 ~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 95 (114)
T PRK03681 40 ETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ-----RVRRCPQCHG 95 (114)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc-----cCCcCcCcCC
Confidence 345555544445444332 23457888 78876654322 2366887774
No 191
>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=45.36 E-value=11 Score=19.57 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=12.5
Q ss_pred ccccchhcchhhcCCCCcccCccccchh
Q 035729 119 NCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 119 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
+|+..+.... ...++|+.||+.+
T Consensus 5 ~Cg~~~~~~~-----~~~irC~~CG~RI 27 (32)
T PF03604_consen 5 ECGAEVELKP-----GDPIRCPECGHRI 27 (32)
T ss_dssp SSSSSE-BST-----SSTSSBSSSS-SE
T ss_pred cCCCeeEcCC-----CCcEECCcCCCeE
Confidence 5666555332 3567888887653
No 192
>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=44.89 E-value=14 Score=19.32 Aligned_cols=14 Identities=36% Similarity=0.992 Sum_probs=9.7
Q ss_pred CcccCCCCCceeEe
Q 035729 182 KWARCPGCGHCVQR 195 (208)
Q Consensus 182 ~~k~CP~C~~~i~k 195 (208)
.+-.||+|+.+|.-
T Consensus 3 ~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 3 PYVECPNCGRPVAA 16 (33)
T ss_dssp -EEE-TTTSSEEEG
T ss_pred CeEECCCCcCCcch
Confidence 35679999999864
No 193
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=44.32 E-value=44 Score=19.86 Aligned_cols=36 Identities=19% Similarity=0.269 Sum_probs=26.8
Q ss_pred cccCCccccCCCCCcccccCCCChhHHHHHHHHHHhhh
Q 035729 69 KIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCEDY 106 (208)
Q Consensus 69 ~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~ 106 (208)
...||. |+.......-..+-+++-+.+|...+.++.
T Consensus 17 k~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 17 KEICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred cccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 357888 998776666667777788898988777653
No 194
>PRK10220 hypothetical protein; Provisional
Probab=43.99 E-value=12 Score=25.45 Aligned_cols=28 Identities=29% Similarity=0.625 Sum_probs=18.4
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFC 147 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 147 (208)
-.|| .|+.-+..++. ..+.||.|++.|=
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 4577 68776666554 4678887766553
No 195
>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=43.39 E-value=12 Score=25.02 Aligned_cols=25 Identities=28% Similarity=0.692 Sum_probs=18.2
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
+|| .|+.++... ...+.|+.|++.+
T Consensus 2 fC~--~Cg~~l~~~------~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCP--KCGSLMTPK------NGVYVCPSCGYEK 26 (104)
T ss_pred CCc--ccCcccccC------CCeEECcCCCCcc
Confidence 588 799998653 2468888888763
No 196
>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=43.09 E-value=14 Score=22.03 Aligned_cols=15 Identities=33% Similarity=0.716 Sum_probs=8.4
Q ss_pred cccCCCCCceeEecC
Q 035729 183 WARCPGCGHCVQRKN 197 (208)
Q Consensus 183 ~k~CP~C~~~i~k~~ 197 (208)
...||.|+.+++...
T Consensus 2 ~v~CP~C~k~~~~~~ 16 (57)
T PF03884_consen 2 TVKCPICGKPVEWSP 16 (57)
T ss_dssp EEE-TTT--EEE-SS
T ss_pred cccCCCCCCeecccC
Confidence 468999999998743
No 197
>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=42.82 E-value=12 Score=19.14 Aligned_cols=10 Identities=50% Similarity=1.056 Sum_probs=6.7
Q ss_pred cCCCCCceeE
Q 035729 185 RCPGCGHCVQ 194 (208)
Q Consensus 185 ~CP~C~~~i~ 194 (208)
-||+|++-|-
T Consensus 3 lcpkcgvgvl 12 (36)
T PF09151_consen 3 LCPKCGVGVL 12 (36)
T ss_dssp B-TTTSSSBE
T ss_pred cCCccCceEE
Confidence 5999998653
No 198
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=42.81 E-value=24 Score=20.45 Aligned_cols=30 Identities=30% Similarity=0.661 Sum_probs=21.2
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHH
Q 035729 25 TCEICIEPMAANKKFKNKNLCTHPFCQECIAKY 57 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~ 57 (208)
.|.||-..+.....+ .+.=+ .+|.+|++..
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 488999888544322 34556 8999999875
No 199
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.66 E-value=26 Score=24.91 Aligned_cols=15 Identities=20% Similarity=0.173 Sum_probs=10.8
Q ss_pred CcccCcccccccchhcc
Q 035729 111 ERSYCPNRNCMALVVNE 127 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~ 127 (208)
...+|+ +|++.+...
T Consensus 69 ~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCR--NCGNEWSLK 83 (135)
T ss_pred eEEECC--CCCCEEecc
Confidence 467898 798776654
No 200
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.60 E-value=12 Score=28.04 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=18.9
Q ss_pred CCCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 109 GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 109 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
+..+..|| .|+.-+....-- ...+.||.||.
T Consensus 114 ~~~~Y~Cp--~C~~rytf~eA~---~~~F~Cp~Cg~ 144 (178)
T PRK06266 114 NNMFFFCP--NCHIRFTFDEAM---EYGFRCPQCGE 144 (178)
T ss_pred CCCEEECC--CCCcEEeHHHHh---hcCCcCCCCCC
Confidence 34578898 587655544322 35688886654
No 201
>PLN02436 cellulose synthase A
Probab=42.21 E-value=15 Score=35.08 Aligned_cols=52 Identities=31% Similarity=0.776 Sum_probs=34.4
Q ss_pred Ccccccccccccc---ccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 22 SSFTCEICIEPMA---ANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 22 ~~~~C~iC~~~~~---~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
....|.||-|++- ..+.|+.--.|+-..|+.|. .|-.. +|+ -.||. |+..+.
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~---eg~---~~Cpq--ckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERR---EGN---QACPQ--CKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---cCC---ccCcc--cCCchh
Confidence 3459999999962 23445444458889999998 44332 222 37998 887543
No 202
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=42.17 E-value=9.1 Score=28.55 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=30.6
Q ss_pred ccchhccccCcCcCCCC-CChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 142 CKHWFCFRCKLKWHGGY-HCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 142 C~~~~C~~C~~~~H~~~-~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
.-..||..|....|... .|.+... +-...+.++..+...+.|++||..-..
T Consensus 118 ~~~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 118 GFQWYCDECNHKVHEVEVQLTDIET---DLPPVFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred ceEEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhcCHhhccCCcCCcccCc
Confidence 34444556666555321 3433222 223467777888899999999987653
No 203
>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=42.04 E-value=12 Score=27.31 Aligned_cols=32 Identities=19% Similarity=0.261 Sum_probs=20.1
Q ss_pred CCCcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 109 GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 109 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
++.+..|| .|+.-+....-- ...+.||.||..
T Consensus 106 ~~~~Y~Cp--~c~~r~tf~eA~---~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICP--NMCVRFTFNEAM---ELNFTCPRCGAM 137 (158)
T ss_pred CCCeEECC--CCCcEeeHHHHH---HcCCcCCCCCCE
Confidence 45678898 577555443322 357888877754
No 204
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.82 E-value=11 Score=27.07 Aligned_cols=35 Identities=20% Similarity=0.339 Sum_probs=19.9
Q ss_pred CCCcccCcccccccchhcchhhc--CCCCcccCccccch
Q 035729 109 GYERSYCPNRNCMALVVNECERK--GRMKKAQCPNCKHW 145 (208)
Q Consensus 109 ~~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~ 145 (208)
......|| .|+.-+....... +....+.||.||..
T Consensus 96 ~~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 44578899 6887665433211 11233888877653
No 205
>PLN03086 PRLI-interacting factor K; Provisional
Probab=41.34 E-value=9.4 Score=33.87 Aligned_cols=31 Identities=23% Similarity=0.580 Sum_probs=19.6
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.+.||+.+|+..+..... ...+.|+.|+..|
T Consensus 433 ~V~Cp~~~Cg~v~~r~el----~~H~~C~~Cgk~f 463 (567)
T PLN03086 433 NVVCPHDGCGIVLRVEEA----KNHVHCEKCGQAF 463 (567)
T ss_pred ceeCCcccccceeecccc----ccCccCCCCCCcc
Confidence 456776667777754444 3456777776655
No 206
>PF14369 zf-RING_3: zinc-finger
Probab=40.50 E-value=18 Score=19.13 Aligned_cols=30 Identities=27% Similarity=0.601 Sum_probs=17.8
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
..||- .|+..+...... ...+.||.|+.-|
T Consensus 2 ~ywCh--~C~~~V~~~~~~---~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSP---DSDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCC---CCCcCCcCCCCcE
Confidence 35777 688877764331 2234688876543
No 207
>PLN02189 cellulose synthase
Probab=40.14 E-value=21 Score=33.99 Aligned_cols=63 Identities=19% Similarity=0.353 Sum_probs=43.0
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCC
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCG 190 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~ 190 (208)
+...|. -|+..+.....+ ...+-|..|++-.|.-|.+ + ..+.+.+.||.|+
T Consensus 33 ~~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr~Cye----------y--------------er~eg~q~CpqCk 83 (1040)
T PLN02189 33 DGQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCRPCYE----------Y--------------ERREGTQNCPQCK 83 (1040)
T ss_pred cCcccc--ccccccCcCCCC---CEEEeeccCCCccccchhh----------h--------------hhhcCCccCcccC
Confidence 345677 587777654332 4789999999999997753 1 2335778888888
Q ss_pred ceeEecCCCCce
Q 035729 191 HCVQRKNGCHVM 202 (208)
Q Consensus 191 ~~i~k~~GCnhm 202 (208)
....+--|+..+
T Consensus 84 t~Y~r~kgs~~v 95 (1040)
T PLN02189 84 TRYKRLKGSPRV 95 (1040)
T ss_pred CchhhccCCCCc
Confidence 887765565543
No 208
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.07 E-value=12 Score=30.89 Aligned_cols=46 Identities=20% Similarity=0.483 Sum_probs=30.2
Q ss_pred cCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.......|.||.+..... +..+|||.-| |..-+ ...+.||. |.+.+
T Consensus 301 ~~~~p~lcVVcl~e~~~~----~fvpcGh~cc--ct~cs---------~~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSA----VFVPCGHVCC--CTLCS---------KHLPQCPV--CRQRI 346 (355)
T ss_pred ccCCCCceEEecCCccce----eeecCCcEEE--chHHH---------hhCCCCch--hHHHH
Confidence 344467899999988542 5789999865 43321 11246998 87644
No 209
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=40.00 E-value=5.8 Score=22.87 Aligned_cols=38 Identities=18% Similarity=0.509 Sum_probs=28.5
Q ss_pred CCCccccccccccccccccccccCCCCChhHHHHHHHHH
Q 035729 20 NGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYI 58 (208)
Q Consensus 20 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 58 (208)
....++|.+|-+.++..+ .+.-.-||..-|..||+.-+
T Consensus 4 SFsry~CDLCn~~~p~~~-LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 4 SFSRYSCDLCNSSHPISE-LRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred HHhhHhHHhhcccCcHHH-HHHHhhhchhhhhhhhhhhH
Confidence 345789999999986543 33455689999999998643
No 210
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=39.91 E-value=16 Score=21.54 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=18.1
Q ss_pred cccCcccccccchhcchhhc--CCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERK--GRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~~ 146 (208)
.+.|| .|++.-...-..+ -...-++||+|.+.+
T Consensus 4 Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 4 WILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred EEECC--CCCCccceeeecCceeccccccCCCCCceE
Confidence 56788 6875432221111 125677888776653
No 211
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=39.83 E-value=15 Score=24.51 Aligned_cols=33 Identities=21% Similarity=0.383 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCCCcccccCCCccccccccccc
Q 035729 1 MGNSLQRPTENRGRQEEEGNGSSFTCEICIEPM 33 (208)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~ 33 (208)
||....+................|.|+.|.-..
T Consensus 1 MgkRk~K~k~~~k~r~~~~ldt~FnClfcnHek 33 (109)
T KOG3214|consen 1 MGKRKSKRKEPPKERRVEPLDTQFNCLFCNHEK 33 (109)
T ss_pred CCcccccccCCchhhhccchheeeccCcccccc
Confidence 677666665555545555566678899888665
No 212
>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=39.53 E-value=41 Score=17.28 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=17.4
Q ss_pred cCCCCCceeEecCCCCceEeCCC
Q 035729 185 RCPGCGHCVQRKNGCHVMQDSVL 207 (208)
Q Consensus 185 ~CP~C~~~i~k~~GCnhm~C~~~ 207 (208)
.|..|+..+.--.|=..+.|++.
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C 25 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALC 25 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCC
Confidence 57888888887777777777753
No 213
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.50 E-value=10 Score=31.45 Aligned_cols=38 Identities=37% Similarity=0.736 Sum_probs=26.5
Q ss_pred ccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 140 PNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 140 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
|.|.+.||..|...|+.-. + ......+.||-|++....
T Consensus 185 pnC~H~~Cl~Cir~wr~~~-----------------q-~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 185 PNCNHSFCLNCIRKWRQAT-----------------Q-FESKTSKSCPFCRVPSSF 222 (344)
T ss_pred CCcchhhhhcHhHhhhhhh-----------------c-cccccccCCCcccCcccc
Confidence 6799999999999887221 0 123456788888877653
No 214
>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=39.49 E-value=17 Score=28.73 Aligned_cols=18 Identities=22% Similarity=0.623 Sum_probs=12.8
Q ss_pred ccCCCccccccccccccc
Q 035729 18 EGNGSSFTCEICIEPMAA 35 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~ 35 (208)
.......+|.+|...++-
T Consensus 60 ~~~~p~v~CrVCq~~I~i 77 (256)
T PF09788_consen 60 SGGAPVVTCRVCQSLIDI 77 (256)
T ss_pred CCCCceEEeecCCceecc
Confidence 344567899999887743
No 215
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.39 E-value=10 Score=32.91 Aligned_cols=34 Identities=32% Similarity=0.724 Sum_probs=24.8
Q ss_pred cccchhccccCcC-cCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCceeEe
Q 035729 141 NCKHWFCFRCKLK-WHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 141 ~C~~~~C~~C~~~-~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k 195 (208)
.||..||+.|... |-. .....|+.||=|+..|-.
T Consensus 203 ~CGHiFC~~CiLqy~~~---------------------s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQYWNY---------------------SAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHHHhh---------------------hcccCCccCCchhhhccc
Confidence 4899999999763 221 234688999999988764
No 216
>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=39.32 E-value=11 Score=27.57 Aligned_cols=46 Identities=26% Similarity=0.525 Sum_probs=26.7
Q ss_pred cchhccccCcCcCCCC-CChhhhcccccchHHHHHHHHhCCcccCCCCCc
Q 035729 143 KHWFCFRCKLKWHGGY-HCEESGNLRDRNDIAFGQLAERMKWARCPGCGH 191 (208)
Q Consensus 143 ~~~~C~~C~~~~H~~~-~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 191 (208)
-..||..|....|... .|.+... +-...+.++......+.|++||.
T Consensus 113 ~~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 113 FQWFCPQCGHKLHRAEVQLENIVT---DLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred eEEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhCChhhccCCccCC
Confidence 3444445555555321 3433221 22346777788889999999984
No 217
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=38.99 E-value=13 Score=30.44 Aligned_cols=31 Identities=23% Similarity=0.611 Sum_probs=23.3
Q ss_pred ccccccccccccccccccccCCCCChhHHHHH
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECI 54 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl 54 (208)
...|-.|.+...+...+ .-..|.+.||.+|=
T Consensus 330 ~~~Cf~C~~~~~~~~~y-~C~~Ck~~FCldCD 360 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRY-RCESCKNVFCLDCD 360 (378)
T ss_pred CcceeeeccccCCCCcE-Echhccceeeccch
Confidence 34499998877665544 46789999999993
No 218
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.98 E-value=23 Score=21.09 Aligned_cols=28 Identities=25% Similarity=0.644 Sum_probs=18.6
Q ss_pred hcCCCcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 107 VRGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 107 ~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
+..+.+..|| .|+.+.. ....|+.||++
T Consensus 22 l~~~~l~~C~--~CG~~~~---------~H~vC~~CG~Y 49 (57)
T PRK12286 22 LKAPGLVECP--NCGEPKL---------PHRVCPSCGYY 49 (57)
T ss_pred ccCCcceECC--CCCCccC---------CeEECCCCCcC
Confidence 3456778888 6877654 45667777754
No 219
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=38.75 E-value=32 Score=33.01 Aligned_cols=52 Identities=29% Similarity=0.853 Sum_probs=34.7
Q ss_pred CCccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 21 GSSFTCEICIEPMAA---NKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
.....|.||-|++-. .+.|+.--.|+-..|+.|. .|-. ++|+. .||. |+..+
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr---~eG~q---~CPq--CktrY 69 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER---KDGNQ---SCPQ--CKTKY 69 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh---hcCCc---cCCc--cCCch
Confidence 345599999999733 2445445568889999998 3332 23333 7998 88643
No 220
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=38.74 E-value=21 Score=21.20 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=10.4
Q ss_pred CcccCCCCCceeEe
Q 035729 182 KWARCPGCGHCVQR 195 (208)
Q Consensus 182 ~~k~CP~C~~~i~k 195 (208)
..|+||.||.....
T Consensus 2 ~LkPCPFCG~~~~~ 15 (61)
T PF14354_consen 2 ELKPCPFCGSADVL 15 (61)
T ss_pred CCcCCCCCCCcceE
Confidence 46899999965543
No 221
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.63 E-value=27 Score=33.21 Aligned_cols=20 Identities=30% Similarity=0.840 Sum_probs=11.4
Q ss_pred cccCccccc-----hhccccCcCcC
Q 035729 136 KAQCPNCKH-----WFCFRCKLKWH 155 (208)
Q Consensus 136 ~~~C~~C~~-----~~C~~C~~~~H 155 (208)
.+.||.||. .+|..|.....
T Consensus 638 ~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 638 YRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cccCCCCCCCCCcceeCccccCcCC
Confidence 456776764 36666655433
No 222
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=38.55 E-value=39 Score=23.12 Aligned_cols=46 Identities=24% Similarity=0.509 Sum_probs=24.5
Q ss_pred ChhHHHHHHHHHHhhhhc---------CCCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 91 PSSLFSKWCDLLCEDYVR---------GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
.++.++-....+.+.++. .+...+|+ .|+..+.... ..+.||.||.
T Consensus 40 ~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~------~~~~CP~Cgs 94 (113)
T PRK12380 40 EESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQ------HDAQCPHCHG 94 (113)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC------cCccCcCCCC
Confidence 345555544555444332 23457788 6886554432 3455877763
No 223
>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=38.46 E-value=19 Score=24.60 Aligned_cols=22 Identities=32% Similarity=0.816 Sum_probs=15.7
Q ss_pred CCcccCccccchh--------ccccCcCcC
Q 035729 134 MKKAQCPNCKHWF--------CFRCKLKWH 155 (208)
Q Consensus 134 ~~~~~C~~C~~~~--------C~~C~~~~H 155 (208)
...+.||.|++.+ |..|+.+-+
T Consensus 67 av~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred ceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 5667777776665 888887655
No 224
>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=38.43 E-value=39 Score=23.19 Aligned_cols=26 Identities=27% Similarity=0.625 Sum_probs=15.9
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
...+|+ +|+..+.... ..+.||.||.
T Consensus 69 ~~~~C~--~Cg~~~~~~~------~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECE--DCSEEVSPEI------DLYRCPKCHG 94 (115)
T ss_pred cEEEcc--cCCCEEecCC------cCccCcCCcC
Confidence 457788 6886655432 2456776664
No 225
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=38.41 E-value=8.2 Score=31.34 Aligned_cols=18 Identities=33% Similarity=0.447 Sum_probs=10.4
Q ss_pred CcccCCCCCceeEecCCC
Q 035729 182 KWARCPGCGHCVQRKNGC 199 (208)
Q Consensus 182 ~~k~CP~C~~~i~k~~GC 199 (208)
..|.||.|.-.|+|.+-|
T Consensus 122 ~dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 122 SDKICPLCDDRVQRIEQI 139 (389)
T ss_pred ccccCcCcccHHHHHHHh
Confidence 355666666666665433
No 226
>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=38.37 E-value=15 Score=21.27 Aligned_cols=11 Identities=36% Similarity=0.769 Sum_probs=9.2
Q ss_pred ccCCCCCceeE
Q 035729 184 ARCPGCGHCVQ 194 (208)
Q Consensus 184 k~CP~C~~~i~ 194 (208)
|+||.||-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 78999997666
No 227
>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=37.84 E-value=9.5 Score=21.66 Aligned_cols=35 Identities=17% Similarity=0.462 Sum_probs=25.8
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhc
Q 035729 25 TCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQD 64 (208)
Q Consensus 25 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 64 (208)
.|.||-.....+ ..--+..+|.+|-+..+.....+
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 378888877543 34558899999999888776654
No 228
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.57 E-value=31 Score=31.82 Aligned_cols=15 Identities=13% Similarity=0.160 Sum_probs=9.5
Q ss_pred CChhHHHHHHHHHHh
Q 035729 90 IPSSLFSKWCDLLCE 104 (208)
Q Consensus 90 l~~~~~~~~~~~~~~ 104 (208)
++..+++...+.+.+
T Consensus 405 lS~~Ll~~i~~~l~~ 419 (730)
T COG1198 405 LSPALLEAIRKTLER 419 (730)
T ss_pred CCHHHHHHHHHHHhc
Confidence 667777776655543
No 229
>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=37.50 E-value=7.7 Score=31.32 Aligned_cols=15 Identities=20% Similarity=0.654 Sum_probs=10.3
Q ss_pred hCCcccCCCCCceeE
Q 035729 180 RMKWARCPGCGHCVQ 194 (208)
Q Consensus 180 ~~~~k~CP~C~~~i~ 194 (208)
....-.|-+|+..+-
T Consensus 235 ~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 235 AYRVEVCESCGSYLK 249 (290)
T ss_dssp SEEEEEETTTTEEEE
T ss_pred cEEEEECCcccchHH
Confidence 345567989987764
No 230
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=36.90 E-value=16 Score=17.61 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=6.3
Q ss_pred ccCccccchh
Q 035729 137 AQCPNCKHWF 146 (208)
Q Consensus 137 ~~C~~C~~~~ 146 (208)
+.|+.|+..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5566666655
No 231
>PLN02189 cellulose synthase
Probab=36.85 E-value=24 Score=33.64 Aligned_cols=52 Identities=27% Similarity=0.719 Sum_probs=34.4
Q ss_pred Cccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 22 SSFTCEICIEPMAA---NKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 22 ~~~~C~iC~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
....|.||.|++-. .+.|+.--.|+-..|+.|. .|-.. +|+ -.||. |+..+.
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~---eg~---q~Cpq--Ckt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERR---EGT---QNCPQ--CKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhh---cCC---ccCcc--cCCchh
Confidence 34599999999742 2345444458889999998 44332 222 37998 887543
No 232
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=36.54 E-value=16 Score=19.87 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=14.6
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
+.|. .|++++-.-...+.....+.|+-|+.
T Consensus 3 ~rC~--~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCR--RCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -B-T--TT--BS-TTSEEETTTTEEEETTT--
T ss_pred cccC--CCCCEECCcceEcCCCCEEECcCCCC
Confidence 4566 67777765544443457888887765
No 233
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=36.29 E-value=41 Score=26.43 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=37.1
Q ss_pred cccCCCChhHHHHHHHHHHhh-hhc--CCCcccCcccccccchhcchhh--cCCCCcccCccccch
Q 035729 85 SCKPMIPSSLFSKWCDLLCED-YVR--GYERSYCPNRNCMALVVNECER--KGRMKKAQCPNCKHW 145 (208)
Q Consensus 85 ~i~~~l~~~~~~~~~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 145 (208)
.+..-++++++..|+++.... .+. .-.-..|. +|...++..... ......++||.||..
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 445667889999998887765 222 12335677 787666543221 123578999988864
No 234
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.63 E-value=19 Score=19.55 Aligned_cols=11 Identities=36% Similarity=1.156 Sum_probs=8.6
Q ss_pred cCCCCCceeEe
Q 035729 185 RCPGCGHCVQR 195 (208)
Q Consensus 185 ~CP~C~~~i~k 195 (208)
.||+|+...+.
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 59999987664
No 235
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=35.44 E-value=18 Score=21.75 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=22.0
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
.+.|| +|++....-... ...+.|..|+...+.
T Consensus 11 ~VkCp--~C~n~q~vFsha---~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 11 KVKCP--DCGNEQVVFSHA---STVVRCLVCGKTLAE 42 (59)
T ss_pred EEECC--CCCCeEEEEecC---CcEEECcccCCCccc
Confidence 36788 788766554332 578888888877654
No 236
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.43 E-value=1.1e+02 Score=24.35 Aligned_cols=76 Identities=12% Similarity=0.187 Sum_probs=50.9
Q ss_pred ccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcccccCCCC-hhHHH
Q 035729 18 EGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPFSCKPMIP-SSLFS 96 (208)
Q Consensus 18 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~-~~~~~ 96 (208)
..+...|-|+|=--++...-.|..+-.|||+|=..=|++ |. .-.|+. |+..+..+++--+-+ .+.++
T Consensus 106 D~~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKe-----ik-----as~C~~--C~a~y~~~dvIvlNg~~E~~d 173 (293)
T KOG3113|consen 106 DTQRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKE-----IK-----ASVCHV--CGAAYQEDDVIVLNGTEEDVD 173 (293)
T ss_pred ccccceeecccccceecceEEEEEEeccceeccHHHHHH-----hh-----hccccc--cCCcccccCeEeeCCCHHHHH
Confidence 334567899998888877667877889999985443332 22 247988 999988877665433 35666
Q ss_pred HHHHHHHhh
Q 035729 97 KWCDLLCED 105 (208)
Q Consensus 97 ~~~~~~~~~ 105 (208)
.|..++.++
T Consensus 174 llk~rme~~ 182 (293)
T KOG3113|consen 174 LLKTRMEER 182 (293)
T ss_pred HHHHHHHHH
Confidence 665555443
No 237
>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=35.38 E-value=6 Score=19.42 Aligned_cols=20 Identities=15% Similarity=0.491 Sum_probs=12.8
Q ss_pred ccCCccccCCCCCcccccCCCC
Q 035729 70 IECPGLNCQKNLDPFSCKPMIP 91 (208)
Q Consensus 70 i~CP~~~C~~~l~~~~i~~~l~ 91 (208)
+.||. |...++...+...|+
T Consensus 2 v~CPi--C~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLD 21 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHH
Confidence 57888 888775555544443
No 238
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.96 E-value=28 Score=21.16 Aligned_cols=22 Identities=27% Similarity=0.607 Sum_probs=17.3
Q ss_pred HHHHHHhCCcccCCCCCceeEe
Q 035729 174 FGQLAERMKWARCPGCGHCVQR 195 (208)
Q Consensus 174 ~~~~~~~~~~k~CP~C~~~i~k 195 (208)
...+..+....+||+|...|.-
T Consensus 35 ~edL~~ge~Va~CpsCSL~I~V 56 (67)
T KOG2923|consen 35 LEDLENGEDVARCPSCSLIIRV 56 (67)
T ss_pred HHHHhCCCeeecCCCceEEEEE
Confidence 4456677888999999988864
No 239
>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=34.65 E-value=25 Score=20.21 Aligned_cols=47 Identities=19% Similarity=0.556 Sum_probs=23.4
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQK 79 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 79 (208)
..|+|-+..+..+ .....|.|.-|-+ +..|+......+ .-+||. |++
T Consensus 3 L~CPls~~~i~~P---~Rg~~C~H~~CFD-l~~fl~~~~~~~---~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP---VRGKNCKHLQCFD-LESFLESNQRTP---KWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE---EEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeC---ccCCcCcccceEC-HHHHHHHhhccC---CeECcC--CcC
Confidence 4677777777554 2367899997643 667777666542 268998 865
No 240
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.64 E-value=23 Score=20.40 Aligned_cols=16 Identities=31% Similarity=0.758 Sum_probs=12.6
Q ss_pred HhCCcccCCCCCceeE
Q 035729 179 ERMKWARCPGCGHCVQ 194 (208)
Q Consensus 179 ~~~~~k~CP~C~~~i~ 194 (208)
.....-+||.|+..|.
T Consensus 20 ~~~~~irCp~Cg~rIl 35 (49)
T COG1996 20 QETRGIRCPYCGSRIL 35 (49)
T ss_pred hccCceeCCCCCcEEE
Confidence 3457789999998875
No 241
>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=34.10 E-value=33 Score=21.40 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=11.4
Q ss_pred cCCCCCceeEecCCCCceEeC
Q 035729 185 RCPGCGHCVQRKNGCHVMQDS 205 (208)
Q Consensus 185 ~CP~C~~~i~k~~GCnhm~C~ 205 (208)
.||.|+.+++.++ .+..|.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~ 21 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE 21 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET
T ss_pred cCCCCCCccEEeC--CEEECc
Confidence 5888888888777 445554
No 242
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=34.03 E-value=22 Score=28.76 Aligned_cols=49 Identities=12% Similarity=0.255 Sum_probs=33.1
Q ss_pred CCCCCCcccccCCCccccccccc-cccccccccccCCCCChhHHHHHHHH
Q 035729 9 TENRGRQEEEGNGSSFTCEICIE-PMAANKKFKNKNLCTHPFCQECIAKY 57 (208)
Q Consensus 9 ~~~~~~~~~~~~~~~~~C~iC~~-~~~~~~~~~~~~~C~H~~C~~Cl~~~ 57 (208)
........-..+.....|.+|.- .|...+.--.--.||++||..|-..-
T Consensus 154 ~~~~~~~~W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~ 203 (288)
T KOG1729|consen 154 PSNNSAAVWLPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNR 203 (288)
T ss_pred CCCCcCCcccCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCc
Confidence 33334444556667889999998 66554332235679999999998763
No 243
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=34.00 E-value=37 Score=32.48 Aligned_cols=55 Identities=24% Similarity=0.707 Sum_probs=36.5
Q ss_pred cCCCccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 19 GNGSSFTCEICIEPMAA---NKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
.......|.||-|++-. .+.|+.--.|+-..|+.|. .|-. ++|+ -.||. |+..+.
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~---~~g~---~~cp~--c~t~y~ 68 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYER---SEGN---QCCPQ--CNTRYK 68 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhhh---hcCC---ccCCc--cCCchh
Confidence 34456789999999733 2345445568889999998 3332 2333 37988 887543
No 244
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=33.85 E-value=15 Score=30.94 Aligned_cols=36 Identities=25% Similarity=0.609 Sum_probs=28.2
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHHH
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYI 58 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 58 (208)
....+|+|||-.++...++ +.-|...+|..||..+-
T Consensus 72 rr~~ecpicflyyps~~n~--~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNL--VRCCSETICGECFAPFG 107 (482)
T ss_pred cccccCceeeeecccccch--hhhhccchhhhheeccc
Confidence 3457999999999765443 56789999999998754
No 245
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=33.77 E-value=36 Score=27.33 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=20.3
Q ss_pred ccCCCCCceeEe--cCCCCceEeCCC
Q 035729 184 ARCPGCGHCVQR--KNGCHVMQDSVL 207 (208)
Q Consensus 184 k~CP~C~~~i~k--~~GCnhm~C~~~ 207 (208)
++|+.|+.+|+| .+|=+-..|+.+
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 789999999998 488888888754
No 246
>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=33.71 E-value=64 Score=15.71 Aligned_cols=22 Identities=18% Similarity=0.431 Sum_probs=16.4
Q ss_pred CCCCCceeEecCCCCceEeCCC
Q 035729 186 CPGCGHCVQRKNGCHVMQDSVL 207 (208)
Q Consensus 186 CP~C~~~i~k~~GCnhm~C~~~ 207 (208)
|-+|++.+.--.|=.++.|++.
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C 22 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACC 22 (25)
T ss_pred CCCCCceEEcCCCCCCeECCcc
Confidence 5578888887778788877753
No 247
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.65 E-value=29 Score=28.35 Aligned_cols=54 Identities=20% Similarity=0.338 Sum_probs=34.4
Q ss_pred CccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCc
Q 035729 22 SSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDP 83 (208)
Q Consensus 22 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 83 (208)
+.|.|++=.+.-.. ++-++.+.|||++=+.=+.+.- .++...++||. |...-..
T Consensus 335 s~FiCPVlKe~~t~-ENpP~ml~CgHVIskeal~~LS-----~nG~~~FKCPY--CP~~~~~ 388 (396)
T COG5109 335 SLFICPVLKELCTD-ENPPVMLECGHVISKEALSVLS-----QNGVLSFKCPY--CPEMSKY 388 (396)
T ss_pred ceeeccccHhhhcc-cCCCeeeeccceeeHHHHHHHh-----hcCcEEeeCCC--CCcchhh
Confidence 45788886655432 3445689999998665544332 22455899999 9864333
No 248
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=33.51 E-value=27 Score=32.35 Aligned_cols=20 Identities=30% Similarity=0.873 Sum_probs=17.3
Q ss_pred ccCCCCCceeEecCCCCceEeC
Q 035729 184 ARCPGCGHCVQRKNGCHVMQDS 205 (208)
Q Consensus 184 k~CP~C~~~i~k~~GCnhm~C~ 205 (208)
..||.|+..+...+||. +|.
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~ 744 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH 744 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC
Confidence 35999999999999998 665
No 249
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.41 E-value=1.5e+02 Score=19.86 Aligned_cols=78 Identities=19% Similarity=0.306 Sum_probs=47.2
Q ss_pred CCCCCCCCCCCCCCcccccCCCccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCC
Q 035729 1 MGNSLQRPTENRGRQEEEGNGSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKN 80 (208)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 80 (208)
||....+.. ............++|+-|-+.. ..- .+ .+ +...+.||. |+..
T Consensus 1 MGkRk~~~k--~~~k~k~klpt~f~CP~Cge~~-v~v----~~--~k------------------~~~h~~C~~--CG~y 51 (99)
T PRK14892 1 MGRRRKKRK--KIIRPKPKLPKIFECPRCGKVS-ISV----KI--KK------------------NIAIITCGN--CGLY 51 (99)
T ss_pred CCCccccCC--CCcccccCCCcEeECCCCCCeE-eee----ec--CC------------------CcceEECCC--CCCc
Confidence 787766643 1222234445689999998532 210 11 01 244579999 9886
Q ss_pred CCcccccCCCCh-hHHHHHHHHHHhhhhc
Q 035729 81 LDPFSCKPMIPS-SLFSKWCDLLCEDYVR 108 (208)
Q Consensus 81 l~~~~i~~~l~~-~~~~~~~~~~~~~~~~ 108 (208)
... .|..|..+ +.|..|.....+..+.
T Consensus 52 ~~~-~V~~l~epIDVY~~wiD~~~eg~i~ 79 (99)
T PRK14892 52 TEF-EVPSVYDEVDVYNKFIDLYLEGKIE 79 (99)
T ss_pred cCE-ECCccccchhhHHHHHHHHHhcCCC
Confidence 544 46665554 8889998887776553
No 250
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.36 E-value=22 Score=19.92 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=12.1
Q ss_pred ccccchhcchhhcCCCCcccCccccch
Q 035729 119 NCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 119 ~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
.|+.-+.... ...+.|+.||..
T Consensus 7 ~Cg~~~~~~~-----~~~irC~~CG~r 28 (44)
T smart00659 7 ECGRENEIKS-----KDVVRCRECGYR 28 (44)
T ss_pred CCCCEeecCC-----CCceECCCCCce
Confidence 4655444331 356777777654
No 251
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=33.25 E-value=23 Score=21.18 Aligned_cols=21 Identities=33% Similarity=0.566 Sum_probs=15.8
Q ss_pred HHHHHHhCCcccCCCCCceeE
Q 035729 174 FGQLAERMKWARCPGCGHCVQ 194 (208)
Q Consensus 174 ~~~~~~~~~~k~CP~C~~~i~ 194 (208)
+..+..+....+||+|..+|-
T Consensus 35 LeDl~~GE~VArCPSCSLiv~ 55 (67)
T COG5216 35 LEDLRNGEVVARCPSCSLIVC 55 (67)
T ss_pred HHHhhCCceEEEcCCceEEEE
Confidence 455666778899999987764
No 252
>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=32.88 E-value=30 Score=20.42 Aligned_cols=28 Identities=25% Similarity=0.688 Sum_probs=17.8
Q ss_pred hcCCCcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 107 VRGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 107 ~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
+..+.++.|| .|+.+.. ....|+.||++
T Consensus 21 l~~p~l~~C~--~cG~~~~---------~H~vc~~cG~Y 48 (55)
T TIGR01031 21 LTAPTLVVCP--NCGEFKL---------PHRVCPSCGYY 48 (55)
T ss_pred ccCCcceECC--CCCCccc---------CeeECCccCeE
Confidence 3456677888 6777553 44667777754
No 253
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=32.65 E-value=20 Score=28.20 Aligned_cols=35 Identities=29% Similarity=0.703 Sum_probs=11.4
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
..+|| .|+..-...-..-.....+.|+.|+..|=.
T Consensus 31 n~yCP--~Cg~~~L~~f~NN~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 31 NMYCP--NCGSKPLSKFENNRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp H---T--TT--SS-EE--------EEE-TTT--EEEE
T ss_pred CCcCC--CCCChhHhhccCCCccceeECCCCchHHhh
Confidence 57899 688773322111112567888877665533
No 254
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.61 E-value=29 Score=20.81 Aligned_cols=32 Identities=28% Similarity=0.680 Sum_probs=21.3
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhcccc
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRC 150 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 150 (208)
..|. .|+..+..... ...+.||.||...=++|
T Consensus 8 ~~Ct--SCg~~i~~~~~----~~~F~CPnCG~~~I~RC 39 (59)
T PRK14890 8 PKCT--SCGIEIAPREK----AVKFLCPNCGEVIIYRC 39 (59)
T ss_pred cccc--CCCCcccCCCc----cCEeeCCCCCCeeEeec
Confidence 3466 57777654443 57899999998754444
No 255
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.60 E-value=50 Score=22.74 Aligned_cols=47 Identities=19% Similarity=0.336 Sum_probs=24.4
Q ss_pred ChhHHHHHHHHHHhhh-hc-C--------CCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 91 PSSLFSKWCDLLCEDY-VR-G--------YERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 91 ~~~~~~~~~~~~~~~~-~~-~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
.++.++-....+.+.. +. + +-..+|. .|+..+..... ....||.||.
T Consensus 40 ~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 96 (117)
T PRK00564 40 DKSLFVSAFETFREESLVCKDAILDIVDEKVELECK--DCSHVFKPNAL-----DYGVCEKCHS 96 (117)
T ss_pred CHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhh--hCCCccccCCc-----cCCcCcCCCC
Confidence 3455555444444444 32 2 3356788 78866554321 2335777764
No 256
>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=31.53 E-value=21 Score=21.14 Aligned_cols=32 Identities=16% Similarity=0.377 Sum_probs=19.4
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhcc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCF 148 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 148 (208)
.+.|| +|.+.-..-... ...+.|..|+...|.
T Consensus 7 ~VkCp--~C~~~q~vFSha---~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 7 DVKCP--GCYNIQTVFSHA---QTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEE-T--TT-SEEEEETT----SS-EE-SSSTSEEEE
T ss_pred EEECC--CCCCeeEEEecC---CeEEEcccCCCEecC
Confidence 36788 788766554332 578999999888775
No 257
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=31.25 E-value=19 Score=23.61 Aligned_cols=25 Identities=28% Similarity=0.647 Sum_probs=12.7
Q ss_pred cCcccccccchhcchhhcCCCCcccCccccc
Q 035729 114 YCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 114 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
.|- .|++-+..+.. ..-..||.|+.
T Consensus 60 ~Ck--kCGfef~~~~i----k~pSRCP~CKS 84 (97)
T COG3357 60 RCK--KCGFEFRDDKI----KKPSRCPKCKS 84 (97)
T ss_pred hhc--ccCcccccccc----CCcccCCcchh
Confidence 355 56665554333 34556665543
No 258
>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=31.07 E-value=32 Score=18.86 Aligned_cols=15 Identities=40% Similarity=0.767 Sum_probs=11.3
Q ss_pred CCcccCCCCCc-eeEe
Q 035729 181 MKWARCPGCGH-CVQR 195 (208)
Q Consensus 181 ~~~k~CP~C~~-~i~k 195 (208)
.....||.|+. .++|
T Consensus 24 ~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRR 39 (42)
T ss_pred CCCCcCCCCCCCceEE
Confidence 45678999998 6665
No 259
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=30.88 E-value=12 Score=19.15 Aligned_cols=14 Identities=21% Similarity=0.821 Sum_probs=6.2
Q ss_pred cccCCccccCCCCC
Q 035729 69 KIECPGLNCQKNLD 82 (208)
Q Consensus 69 ~i~CP~~~C~~~l~ 82 (208)
.++||..+|...+.
T Consensus 2 ~vrCPvkdC~EEv~ 15 (30)
T PF10426_consen 2 VVRCPVKDCDEEVS 15 (30)
T ss_dssp EEE--STT---EEE
T ss_pred ccccccccCcchhh
Confidence 37899999987653
No 260
>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=30.87 E-value=64 Score=23.11 Aligned_cols=33 Identities=15% Similarity=0.112 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHhhhhc---CCCcccCcccccccchhcc
Q 035729 93 SLFSKWCDLLCEDYVR---GYERSYCPNRNCMALVVNE 127 (208)
Q Consensus 93 ~~~~~~~~~~~~~~~~---~~~~~~Cp~~~C~~~~~~~ 127 (208)
+..+++.+....-.+. .+.+..|+ .|+..+...
T Consensus 69 ~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v 104 (147)
T PF01927_consen 69 DPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPV 104 (147)
T ss_pred CHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeec
Confidence 4444444444333222 34478999 799876544
No 261
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.51 E-value=72 Score=22.45 Aligned_cols=39 Identities=18% Similarity=0.423 Sum_probs=24.6
Q ss_pred cccCcccccccchhcchh-hcCCCCcccCccccchhccccCc
Q 035729 112 RSYCPNRNCMALVVNECE-RKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
-..|| .|..+.....+ .....+.+.|+.|+..|=..=..
T Consensus 30 ~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~ 69 (129)
T COG3677 30 KVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGS 69 (129)
T ss_pred cCcCC--CCCccceeeECCccccccccccCCcCcceeeeccC
Confidence 47788 68877632222 22226889999998887554443
No 262
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=30.36 E-value=33 Score=18.57 Aligned_cols=18 Identities=28% Similarity=0.728 Sum_probs=15.3
Q ss_pred cccCccccchhccccCcC
Q 035729 136 KAQCPNCKHWFCFRCKLK 153 (208)
Q Consensus 136 ~~~C~~C~~~~C~~C~~~ 153 (208)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 578999999999987764
No 263
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.34 E-value=19 Score=22.56 Aligned_cols=14 Identities=36% Similarity=0.657 Sum_probs=10.2
Q ss_pred cccCcccccccchh
Q 035729 112 RSYCPNRNCMALVV 125 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~ 125 (208)
+..|.|+.|+.-+.
T Consensus 27 Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 27 YHQCQNVNCSATFI 40 (72)
T ss_pred eeecCCCCCCCEEE
Confidence 45699999987554
No 264
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.20 E-value=38 Score=20.64 Aligned_cols=30 Identities=23% Similarity=0.584 Sum_probs=23.3
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
...|..++|+. ...+.|..|...+|+....
T Consensus 27 ~~~C~~~gC~~-----------~s~I~C~~Ckk~~Cf~Hfi 56 (63)
T PF04236_consen 27 AGDCDITGCNN-----------TSFIRCAYCKKSLCFNHFI 56 (63)
T ss_pred cCcCCCCCCCC-----------cCEEEccccCCccccccee
Confidence 45677666755 5678999999999998765
No 265
>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=30.09 E-value=41 Score=19.79 Aligned_cols=14 Identities=36% Similarity=0.933 Sum_probs=11.0
Q ss_pred ccCCCCCceeEecC
Q 035729 184 ARCPGCGHCVQRKN 197 (208)
Q Consensus 184 k~CP~C~~~i~k~~ 197 (208)
..||.|+..|+..+
T Consensus 3 ~~CP~CG~~iev~~ 16 (54)
T TIGR01206 3 FECPDCGAEIELEN 16 (54)
T ss_pred cCCCCCCCEEecCC
Confidence 47999999888754
No 266
>PRK02935 hypothetical protein; Provisional
Probab=30.03 E-value=35 Score=23.08 Aligned_cols=22 Identities=23% Similarity=0.699 Sum_probs=13.9
Q ss_pred CCcccCccccch--------hccccCcCcC
Q 035729 134 MKKAQCPNCKHW--------FCFRCKLKWH 155 (208)
Q Consensus 134 ~~~~~C~~C~~~--------~C~~C~~~~H 155 (208)
...+.||.|++. .|..|++|-+
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 456677766554 3777777654
No 267
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=29.95 E-value=12 Score=21.36 Aligned_cols=43 Identities=26% Similarity=0.633 Sum_probs=21.1
Q ss_pred cccccccccccccccccccCCC-CChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 24 FTCEICIEPMAANKKFKNKNLC-THPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 24 ~~C~iC~~~~~~~~~~~~~~~C-~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
+.|-.|.-... ....| .|..|..|+..++.. .-.||. |+.+|+
T Consensus 3 ~nCKsCWf~~k------~Li~C~dHYLCl~CLt~ml~~--------s~~C~i--C~~~LP 46 (50)
T PF03854_consen 3 YNCKSCWFANK------GLIKCSDHYLCLNCLTLMLSR--------SDRCPI--CGKPLP 46 (50)
T ss_dssp ----SS-S--S------SEEE-SS-EEEHHHHHHT-SS--------SSEETT--TTEE--
T ss_pred ccChhhhhcCC------CeeeecchhHHHHHHHHHhcc--------ccCCCc--ccCcCc
Confidence 44666664442 24456 799999999887632 236887 887664
No 268
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=29.43 E-value=1.1e+02 Score=18.34 Aligned_cols=34 Identities=18% Similarity=0.325 Sum_probs=24.0
Q ss_pred cCCccccCCCCCcccccCCCChhHHHHHHHHHHhhh
Q 035729 71 ECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCEDY 106 (208)
Q Consensus 71 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~ 106 (208)
+||. |+...-...-..+-.++-+.+|...+.+..
T Consensus 19 ~Cp~--CG~~t~~~~PprFSPeD~y~kYR~~lkk~~ 52 (59)
T COG2260 19 KCPV--CGGDTKVPHPPRFSPEDKYGKYRRELKKRL 52 (59)
T ss_pred cCCC--CCCccccCCCCCCCccchHHHHHHHHHHHh
Confidence 6888 887555554555566678888988777653
No 269
>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=29.36 E-value=27 Score=19.19 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=8.7
Q ss_pred CcccCCCCCceeEe
Q 035729 182 KWARCPGCGHCVQR 195 (208)
Q Consensus 182 ~~k~CP~C~~~i~k 195 (208)
+---|++||.+++-
T Consensus 18 g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 18 GELVCPNCGLVLEE 31 (43)
T ss_dssp TEEEETTT-BBEE-
T ss_pred CeEECCCCCCEeec
Confidence 34478888888874
No 270
>PHA02325 hypothetical protein
Probab=29.00 E-value=33 Score=20.89 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=9.6
Q ss_pred CcccCCCCCcee
Q 035729 182 KWARCPGCGHCV 193 (208)
Q Consensus 182 ~~k~CP~C~~~i 193 (208)
..|.||+|++.-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 468899999864
No 271
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.76 E-value=37 Score=19.81 Aligned_cols=11 Identities=36% Similarity=1.041 Sum_probs=9.2
Q ss_pred cCCCCCceeEe
Q 035729 185 RCPGCGHCVQR 195 (208)
Q Consensus 185 ~CP~C~~~i~k 195 (208)
.||.||..+.-
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 69999998875
No 272
>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=28.70 E-value=63 Score=28.44 Aligned_cols=33 Identities=27% Similarity=0.607 Sum_probs=21.8
Q ss_pred CcccccccchhcchhhcCCCCcccCccccch-----hccccCcC
Q 035729 115 CPNRNCMALVVNECERKGRMKKAQCPNCKHW-----FCFRCKLK 153 (208)
Q Consensus 115 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 153 (208)
|| .|+..+..... .....|..||+. .|..|+..
T Consensus 225 C~--~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 225 CP--NCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CC--CCCCceEEecC----CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 55 56665554432 467888888877 48888764
No 273
>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=28.60 E-value=16 Score=28.58 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=6.6
Q ss_pred CcccCCCCCceeE
Q 035729 182 KWARCPGCGHCVQ 194 (208)
Q Consensus 182 ~~k~CP~C~~~i~ 194 (208)
....||.|+....
T Consensus 34 ~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 34 EVTICPKCGRYRI 46 (236)
T ss_pred CceECCCCCCEEC
Confidence 4455555555443
No 274
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.55 E-value=51 Score=26.37 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=18.2
Q ss_pred cccCCCCCceeEe--cCCCCceEeCC
Q 035729 183 WARCPGCGHCVQR--KNGCHVMQDSV 206 (208)
Q Consensus 183 ~k~CP~C~~~i~k--~~GCnhm~C~~ 206 (208)
-++||+||.+|++ .+|=.--.|+.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~ 269 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPH 269 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcC
Confidence 4789999999997 46766666653
No 275
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=28.51 E-value=46 Score=19.61 Aligned_cols=27 Identities=26% Similarity=0.646 Sum_probs=16.3
Q ss_pred hcCCCcccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 107 VRGYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 107 ~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
+..+++..|| .|+.+.. ....|+.||+
T Consensus 21 l~~~~l~~c~--~cg~~~~---------~H~vc~~cG~ 47 (56)
T PF01783_consen 21 LKAPNLVKCP--NCGEPKL---------PHRVCPSCGY 47 (56)
T ss_dssp --TTSEEESS--SSSSEES---------TTSBCTTTBB
T ss_pred ccccceeeec--cCCCEec---------ccEeeCCCCe
Confidence 3345678888 5776543 4566777764
No 276
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=28.50 E-value=52 Score=26.34 Aligned_cols=23 Identities=17% Similarity=0.453 Sum_probs=17.4
Q ss_pred ccCCCCCceeEe--cCCCCceEeCC
Q 035729 184 ARCPGCGHCVQR--KNGCHVMQDSV 206 (208)
Q Consensus 184 k~CP~C~~~i~k--~~GCnhm~C~~ 206 (208)
++||.|+.+|+| .+|=.-..|+.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPR 270 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcC
Confidence 689999999997 46666666653
No 277
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=28.47 E-value=30 Score=20.27 Aligned_cols=11 Identities=27% Similarity=0.930 Sum_probs=9.3
Q ss_pred ccCCCCCceeE
Q 035729 184 ARCPGCGHCVQ 194 (208)
Q Consensus 184 k~CP~C~~~i~ 194 (208)
++||+|+..-+
T Consensus 25 ~KCPrCK~vN~ 35 (60)
T COG4416 25 KKCPRCKEVNE 35 (60)
T ss_pred ecCCccceeee
Confidence 78999998755
No 278
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=28.20 E-value=40 Score=18.00 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=12.0
Q ss_pred hhccccCcCcCCCCCChhhhc
Q 035729 145 WFCFRCKLKWHGGYHCEESGN 165 (208)
Q Consensus 145 ~~C~~C~~~~H~~~~C~~~~~ 165 (208)
..|.+|++..|+...|..-.+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 358899999999998875443
No 279
>PRK10445 endonuclease VIII; Provisional
Probab=28.19 E-value=54 Score=26.10 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=18.5
Q ss_pred cccCCCCCceeEe--cCCCCceEeCC
Q 035729 183 WARCPGCGHCVQR--KNGCHVMQDSV 206 (208)
Q Consensus 183 ~k~CP~C~~~i~k--~~GCnhm~C~~ 206 (208)
-+.||.|+.+|++ .+|=.-..|+.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~ 260 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPG 260 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCC
Confidence 4789999999997 47766666653
No 280
>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=28.13 E-value=29 Score=21.13 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=18.6
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
...|| .|+........ ...+.|+.||..
T Consensus 28 Sq~C~--~CG~~~~~~~~----~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCP--RCGHRNKKRRS----GRVFTCPNCGFE 55 (69)
T ss_pred ccCcc--Ccccccccccc----cceEEcCCCCCE
Confidence 46788 78887766222 567888877654
No 281
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=28.00 E-value=66 Score=23.70 Aligned_cols=17 Identities=29% Similarity=0.464 Sum_probs=12.6
Q ss_pred CCcccCcccccccchhcch
Q 035729 110 YERSYCPNRNCMALVVNEC 128 (208)
Q Consensus 110 ~~~~~Cp~~~C~~~~~~~~ 128 (208)
++...|| .|+..+...+
T Consensus 95 ~e~~RCp--~CN~~L~~vs 111 (165)
T COG1656 95 PEFSRCP--ECNGELEKVS 111 (165)
T ss_pred cccccCc--ccCCEeccCc
Confidence 5578899 8998776443
No 282
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.57 E-value=36 Score=31.43 Aligned_cols=20 Identities=20% Similarity=0.491 Sum_probs=10.2
Q ss_pred CCcccCccccch-----hccccCcC
Q 035729 134 MKKAQCPNCKHW-----FCFRCKLK 153 (208)
Q Consensus 134 ~~~~~C~~C~~~-----~C~~C~~~ 153 (208)
.....|..||+. .|..|+..
T Consensus 460 ~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 460 TGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 345555555554 35555543
No 283
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.46 E-value=31 Score=20.44 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=9.1
Q ss_pred cccCCCCCceeE
Q 035729 183 WARCPGCGHCVQ 194 (208)
Q Consensus 183 ~k~CP~C~~~i~ 194 (208)
.-.||.||+++-
T Consensus 14 ~~~Cp~cGipth 25 (55)
T PF13824_consen 14 NFECPDCGIPTH 25 (55)
T ss_pred CCcCCCCCCcCc
Confidence 357999999864
No 284
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=27.30 E-value=40 Score=17.37 Aligned_cols=22 Identities=32% Similarity=0.665 Sum_probs=13.2
Q ss_pred CcccccccchhcchhhcCCCCcccCccccc
Q 035729 115 CPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 115 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
|+ .|+++.... .....||.|+.
T Consensus 4 C~--~CGy~y~~~------~~~~~CP~Cg~ 25 (33)
T cd00350 4 CP--VCGYIYDGE------EAPWVCPVCGA 25 (33)
T ss_pred CC--CCCCEECCC------cCCCcCcCCCC
Confidence 55 577665432 24567887765
No 285
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.14 E-value=61 Score=26.12 Aligned_cols=31 Identities=19% Similarity=0.405 Sum_probs=23.4
Q ss_pred CCcccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 110 YERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 110 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
...++|+ .|+........ .....|+.|+..+
T Consensus 109 ~~~RFCg--~CG~~~~~~~~----g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREG----GWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCC--CCCCcCccccC----ceeeeCCCCCCcc
Confidence 4568999 79988876655 5788899887654
No 286
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=26.53 E-value=35 Score=20.76 Aligned_cols=14 Identities=36% Similarity=0.760 Sum_probs=11.4
Q ss_pred CcccCCCCCceeEe
Q 035729 182 KWARCPGCGHCVQR 195 (208)
Q Consensus 182 ~~k~CP~C~~~i~k 195 (208)
...+||.|+.+++-
T Consensus 5 ~~v~CP~C~k~~~w 18 (62)
T PRK00418 5 ITVNCPTCGKPVEW 18 (62)
T ss_pred ccccCCCCCCcccc
Confidence 45789999999864
No 287
>PLN02436 cellulose synthase A
Probab=26.50 E-value=49 Score=31.80 Aligned_cols=61 Identities=20% Similarity=0.358 Sum_probs=40.4
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGH 191 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 191 (208)
...|. -|+.-+.....+ ...+-|..|++-.|..|.. + ..+.+.+.||.|+.
T Consensus 36 ~~iCq--ICGD~Vg~t~dG---e~FVACn~C~fpvCr~Cye----------y--------------er~eg~~~Cpqckt 86 (1094)
T PLN02436 36 GQTCQ--ICGDEIELTVDG---EPFVACNECAFPVCRPCYE----------Y--------------ERREGNQACPQCKT 86 (1094)
T ss_pred Ccccc--ccccccCcCCCC---CEEEeeccCCCccccchhh----------h--------------hhhcCCccCcccCC
Confidence 44566 577666544332 4789999999999997753 1 23346777888888
Q ss_pred eeEecCCCCc
Q 035729 192 CVQRKNGCHV 201 (208)
Q Consensus 192 ~i~k~~GCnh 201 (208)
...+--|+..
T Consensus 87 ~Y~r~kgs~~ 96 (1094)
T PLN02436 87 RYKRIKGSPR 96 (1094)
T ss_pred chhhccCCCC
Confidence 7776555543
No 288
>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=26.43 E-value=20 Score=16.29 Aligned_cols=7 Identities=43% Similarity=1.141 Sum_probs=3.1
Q ss_pred Cccccch
Q 035729 139 CPNCKHW 145 (208)
Q Consensus 139 C~~C~~~ 145 (208)
|+.|+..
T Consensus 3 C~~C~~~ 9 (23)
T PF00096_consen 3 CPICGKS 9 (23)
T ss_dssp ETTTTEE
T ss_pred CCCCCCc
Confidence 4444443
No 289
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.36 E-value=19 Score=28.92 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=8.0
Q ss_pred CCcccCCCCCce
Q 035729 181 MKWARCPGCGHC 192 (208)
Q Consensus 181 ~~~k~CP~C~~~ 192 (208)
.+...|+.|+..
T Consensus 250 vkAEtC~~C~sY 261 (308)
T COG3058 250 VKAETCGDCNSY 261 (308)
T ss_pred hhhhcCCcHHHH
Confidence 455678888754
No 290
>COG1913 Predicted Zn-dependent proteases [General function prediction only]
Probab=26.33 E-value=42 Score=25.01 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhhhc----CCCcccCcccccccchhcchhhcCCCCcccCcccc
Q 035729 95 FSKWCDLLCEDYVR----GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCK 143 (208)
Q Consensus 95 ~~~~~~~~~~~~~~----~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 143 (208)
-+.|.++..+..+. .-+..+||++.|-.-+...-.+.+...-..|..|.
T Consensus 117 ~~lf~ERv~KEv~HElGH~~GL~HC~N~~CVM~FSnSl~dvDrKs~~fC~~C~ 169 (181)
T COG1913 117 RELFKERVVKEVLHELGHLLGLSHCPNPRCVMNFSNSLRDVDRKSPNFCNSCL 169 (181)
T ss_pred hHHHHHHHHHHHHHHhhhhcCcccCCCCCcEEeCCccHHhhhccchhhhHHHH
Confidence 46677777666553 23578999999977666554444445666666553
No 291
>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=26.33 E-value=1.1e+02 Score=18.43 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=19.9
Q ss_pred cCCccccCCCCCcccccCCCChhHHHHHHHHHHh
Q 035729 71 ECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCE 104 (208)
Q Consensus 71 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~ 104 (208)
.||. |+.+++++ +.+-+++--+.|.+...+
T Consensus 5 HC~~--CG~~Ip~~--~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 5 HCPV--CGKPIPPD--ESFCSPKCREEYRKRQKR 34 (59)
T ss_pred cCCc--CCCcCCcc--hhhhCHHHHHHHHHHHHH
Confidence 6888 99998876 445666555556554443
No 292
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=26.11 E-value=48 Score=22.67 Aligned_cols=48 Identities=19% Similarity=0.339 Sum_probs=23.8
Q ss_pred CChhHHHHHHHHHHhhhhc-C--------CCcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 90 IPSSLFSKWCDLLCEDYVR-G--------YERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 90 l~~~~~~~~~~~~~~~~~~-~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
+.++.++.....+.+..+. + +-..+|. .|+.-+..+.. ...||.|+..
T Consensus 39 V~pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~--~Cg~~~~~~~~------~~~CP~Cgs~ 95 (113)
T PF01155_consen 39 VEPEALRFAFEVLAEGTILEGAELEIEEVPARARCR--DCGHEFEPDEF------DFSCPRCGSP 95 (113)
T ss_dssp --HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEET--TTS-EEECHHC------CHH-SSSSSS
T ss_pred CCHHHHHHHHHHHhCCCCccCCEEEEEecCCcEECC--CCCCEEecCCC------CCCCcCCcCC
Confidence 3445565555555544332 2 3356787 68877766543 3667777643
No 293
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.90 E-value=47 Score=31.96 Aligned_cols=61 Identities=20% Similarity=0.368 Sum_probs=41.0
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGH 191 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 191 (208)
...|- -|+.-+.....+ ...+-|..|+.-.|.-|.+ | ..+.+.+.||.|++
T Consensus 17 ~qiCq--ICGD~vg~~~~G---e~FVAC~eC~FPVCrpCYE----------Y--------------Er~eG~q~CPqCkt 67 (1079)
T PLN02638 17 GQVCQ--ICGDNVGKTVDG---EPFVACDVCAFPVCRPCYE----------Y--------------ERKDGNQSCPQCKT 67 (1079)
T ss_pred Cceee--ecccccCcCCCC---CEEEEeccCCCccccchhh----------h--------------hhhcCCccCCccCC
Confidence 34566 577666554332 4789999999999987743 1 23457788888888
Q ss_pred eeEecCCCCc
Q 035729 192 CVQRKNGCHV 201 (208)
Q Consensus 192 ~i~k~~GCnh 201 (208)
...+--|+..
T Consensus 68 rYkr~kgspr 77 (1079)
T PLN02638 68 KYKRHKGSPA 77 (1079)
T ss_pred chhhhcCCCC
Confidence 8776556544
No 294
>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 PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.84 E-value=60 Score=26.14 Aligned_cols=24 Identities=21% Similarity=0.296 Sum_probs=18.7
Q ss_pred cccCCCCCceeEe--cCCCCceEeCC
Q 035729 183 WARCPGCGHCVQR--KNGCHVMQDSV 206 (208)
Q Consensus 183 ~k~CP~C~~~i~k--~~GCnhm~C~~ 206 (208)
-++||.|+.+|+| .+|=.-..|+.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~ 279 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPN 279 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCC
Confidence 4789999999997 47766666654
No 296
>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=25.76 E-value=63 Score=25.86 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=18.4
Q ss_pred cccCCCCCceeEe--cCCCCceEeCC
Q 035729 183 WARCPGCGHCVQR--KNGCHVMQDSV 206 (208)
Q Consensus 183 ~k~CP~C~~~i~k--~~GCnhm~C~~ 206 (208)
-++||.|+.+|++ .+|=.-..|+-
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCC
Confidence 3689999999997 46766666653
No 297
>PLN02195 cellulose synthase A
Probab=25.70 E-value=64 Score=30.77 Aligned_cols=51 Identities=24% Similarity=0.640 Sum_probs=35.4
Q ss_pred cccccccccccccc---ccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCCC
Q 035729 23 SFTCEICIEPMAAN---KKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLD 82 (208)
Q Consensus 23 ~~~C~iC~~~~~~~---~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 82 (208)
...|.||-+++-.. +.|+.--.|+-..|+.|. .|-. ++|+ -.||. |+..+.
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer---~eg~---q~Cpq--Ckt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEI---KEGR---KVCLR--CGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchh-hhhh---hcCC---ccCCc--cCCccc
Confidence 45799999987332 445555578999999998 3332 2333 38999 998766
No 298
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.20 E-value=64 Score=25.81 Aligned_cols=23 Identities=22% Similarity=0.439 Sum_probs=17.3
Q ss_pred cccCCCCCceeEe--cCCCCceEeC
Q 035729 183 WARCPGCGHCVQR--KNGCHVMQDS 205 (208)
Q Consensus 183 ~k~CP~C~~~i~k--~~GCnhm~C~ 205 (208)
-++||.|+.+|++ .+|=.--.|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp 259 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP 259 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC
Confidence 4789999999997 4666666665
No 299
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.66 E-value=37 Score=22.86 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=10.6
Q ss_pred CcccCCCCCceeE
Q 035729 182 KWARCPGCGHCVQ 194 (208)
Q Consensus 182 ~~k~CP~C~~~i~ 194 (208)
+...||.||.+++
T Consensus 48 G~t~CP~Cg~~~e 60 (115)
T COG1885 48 GSTSCPKCGEPFE 60 (115)
T ss_pred ccccCCCCCCccc
Confidence 4578999998875
No 300
>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=24.66 E-value=99 Score=18.66 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=15.5
Q ss_pred ccccCCccccCCCCCcccccCCCChhHHHHHHHHHHh
Q 035729 68 AKIECPGLNCQKNLDPFSCKPMIPSSLFSKWCDLLCE 104 (208)
Q Consensus 68 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~ 104 (208)
.|++|+. |+..+. +.++.|.+++.+
T Consensus 3 iPVRCFT--CGkvi~----------~~~e~y~~~~~~ 27 (60)
T PF01194_consen 3 IPVRCFT--CGKVIG----------NKWEEYLERLEN 27 (60)
T ss_dssp -SSS-ST--TTSBTC----------GHHHHHHHHHHT
T ss_pred CceecCC--CCCChh----------HhHHHHHHHHHc
Confidence 5899999 998764 345666655543
No 301
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=24.58 E-value=62 Score=29.86 Aligned_cols=32 Identities=9% Similarity=0.185 Sum_probs=20.0
Q ss_pred cCCCCCcccccCCCChhHHHHHHHHHHhhhhc
Q 035729 77 CQKNLDPFSCKPMIPSSLFSKWCDLLCEDYVR 108 (208)
Q Consensus 77 C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~ 108 (208)
|++.+-.-.-..-|++...++|+++.++-+..
T Consensus 1076 CSKAfmkLe~~e~l~~a~kq~ye~La~~iFsk 1107 (1189)
T KOG2041|consen 1076 CSKAFMKLEAFEELDDAEKQEYENLAFRIFSK 1107 (1189)
T ss_pred hHHHHHHHHhhhhCCHHHHHHHHHHHHHHhcc
Confidence 55433222223446778889999998887654
No 302
>PRK01343 zinc-binding protein; Provisional
Probab=24.49 E-value=43 Score=19.96 Aligned_cols=15 Identities=33% Similarity=0.674 Sum_probs=12.0
Q ss_pred CCcccCCCCCceeEe
Q 035729 181 MKWARCPGCGHCVQR 195 (208)
Q Consensus 181 ~~~k~CP~C~~~i~k 195 (208)
...+.||.|+.++..
T Consensus 7 ~p~~~CP~C~k~~~~ 21 (57)
T PRK01343 7 RPTRPCPECGKPSTR 21 (57)
T ss_pred CCCCcCCCCCCcCcC
Confidence 467899999998763
No 303
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=24.42 E-value=31 Score=25.07 Aligned_cols=36 Identities=25% Similarity=0.417 Sum_probs=19.6
Q ss_pred CcccCcccccccchh-cchh----hcCCCCcccCccccchh
Q 035729 111 ERSYCPNRNCMALVV-NECE----RKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~-~~~~----~~~~~~~~~C~~C~~~~ 146 (208)
+...||||.|=.-.. +... .+.....++|..|...+
T Consensus 104 gi~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~ 144 (152)
T PRK00893 104 GVLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEF 144 (152)
T ss_pred ceEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEe
Confidence 568899999954310 0000 01124577787776543
No 304
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=24.41 E-value=44 Score=32.01 Aligned_cols=60 Identities=22% Similarity=0.390 Sum_probs=38.1
Q ss_pred ccCcccccccchhcchhhcCCCCcccCccccchhccccCcCcCCCCCChhhhcccccchHHHHHHHHhCCcccCCCCCce
Q 035729 113 SYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKLKWHGGYHCEESGNLRDRNDIAFGQLAERMKWARCPGCGHC 192 (208)
Q Consensus 113 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 192 (208)
..|- -|+.-+.....+ ...+-|..|++-.|..|.. + ..+.+.+.||.|+..
T Consensus 16 ~~c~--iCGd~vg~~~~G---e~FVAC~eC~fpvCr~cye----------y--------------e~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 16 KTCR--VCGDEVGVKEDG---QPFVACHVCGFPVCKPCYE----------Y--------------ERSEGNQCCPQCNTR 66 (1044)
T ss_pred chhh--ccccccCcCCCC---CEEEEeccCCCccccchhh----------h--------------hhhcCCccCCccCCc
Confidence 3444 466655544332 4789999999999987753 1 223466778888877
Q ss_pred eEecCCCCc
Q 035729 193 VQRKNGCHV 201 (208)
Q Consensus 193 i~k~~GCnh 201 (208)
..+--|.+.
T Consensus 67 y~~~~~~~~ 75 (1044)
T PLN02915 67 YKRHKGCPR 75 (1044)
T ss_pred hhhhcCCCC
Confidence 775445543
No 305
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=24.40 E-value=38 Score=18.31 Aligned_cols=37 Identities=19% Similarity=0.405 Sum_probs=19.2
Q ss_pred CCcccccccccccccccc--ccccCCCCChhHH-HHHHHH
Q 035729 21 GSSFTCEICIEPMAANKK--FKNKNLCTHPFCQ-ECIAKY 57 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~--~~~~~~C~H~~C~-~Cl~~~ 57 (208)
.....|.-|..++..... ......-.|.||. .|+..|
T Consensus 4 ~~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp -SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHHH
T ss_pred CcCCcCcccCCcccCCCccccccccCcccChhCHHHHhhC
Confidence 346789999988865542 1123345677776 676654
No 306
>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=24.38 E-value=47 Score=18.88 Aligned_cols=15 Identities=40% Similarity=0.866 Sum_probs=10.9
Q ss_pred CcccCCCCCc-eeEec
Q 035729 182 KWARCPGCGH-CVQRK 196 (208)
Q Consensus 182 ~~k~CP~C~~-~i~k~ 196 (208)
....||.|+. .++|.
T Consensus 25 ~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 25 PLATCPECGGEKLRRL 40 (52)
T ss_pred CCCCCCCCCCCceeEE
Confidence 4567999998 56653
No 307
>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=24.17 E-value=18 Score=25.38 Aligned_cols=30 Identities=17% Similarity=0.254 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHHHHhhcCCCccccCCccccCCCCCcc
Q 035729 48 PFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNLDPF 84 (208)
Q Consensus 48 ~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 84 (208)
+.|.+|-++|+- .+..|+.||. |+..+.+.
T Consensus 10 r~Cp~cg~kFYD-----Lnk~p~vcP~--cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD-----LNRRPAVSPY--TGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc-----cCCCCccCCC--cCCccCcc
Confidence 445566666553 2568999999 99877665
No 308
>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=23.95 E-value=43 Score=17.28 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=7.1
Q ss_pred ccCCccccCCC
Q 035729 70 IECPGLNCQKN 80 (208)
Q Consensus 70 i~CP~~~C~~~ 80 (208)
.+||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 58999999863
No 309
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.81 E-value=51 Score=18.15 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=8.7
Q ss_pred ccCCCCCceeEe
Q 035729 184 ARCPGCGHCVQR 195 (208)
Q Consensus 184 k~CP~C~~~i~k 195 (208)
..||.||..-.+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 469999977544
No 310
>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=23.72 E-value=45 Score=26.98 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=22.3
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccch
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHW 145 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 145 (208)
-...|| .|+..+...... .+...||.|++.
T Consensus 25 ~~~~c~--~c~~~~~~~~l~---~~~~vc~~c~~h 54 (285)
T TIGR00515 25 VWTKCP--KCGQVLYTKELE---RNLEVCPKCDHH 54 (285)
T ss_pred CeeECC--CCcchhhHHHHH---hhCCCCCCCCCc
Confidence 367799 799988876553 356899988874
No 311
>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=23.60 E-value=31 Score=20.05 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=18.1
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.+.|+ .|+..+....... ...+.||.|+...
T Consensus 4 eiRC~--~CnklLa~~g~~~--~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCG--HCNKLLAKAGEVI--ELEIKCPRCKTIN 34 (51)
T ss_pred ceecc--chhHHHhhhcCcc--EEEEECCCCCccc
Confidence 35677 6887776532211 3567777666543
No 312
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=23.57 E-value=39 Score=17.16 Aligned_cols=8 Identities=63% Similarity=1.576 Sum_probs=2.8
Q ss_pred cCCCCCce
Q 035729 185 RCPGCGHC 192 (208)
Q Consensus 185 ~CP~C~~~ 192 (208)
+||+|+.+
T Consensus 15 ~Cp~C~~~ 22 (30)
T PF04438_consen 15 RCPRCGAR 22 (30)
T ss_dssp E-TTT--E
T ss_pred ECCCcCCc
Confidence 46666554
No 313
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=23.55 E-value=60 Score=21.85 Aligned_cols=40 Identities=20% Similarity=0.411 Sum_probs=30.1
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhc
Q 035729 23 SFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKYIQVMVQD 64 (208)
Q Consensus 23 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 64 (208)
.+.|.||-.++-..+.|. +++ +-+...+||..-....+..
T Consensus 2 kWkC~iCg~~I~~gqlFT-F~~-kG~VH~~C~~~~~~~k~~~ 41 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFT-FTK-KGPVHYECFREKASKKLYG 41 (101)
T ss_pred ceEEEecCCeeeecceEE-Eec-CCcEeHHHHHHHHhhhccc
Confidence 578999999998887774 333 2778889999877766543
No 314
>PLN02400 cellulose synthase
Probab=23.54 E-value=49 Score=31.86 Aligned_cols=65 Identities=22% Similarity=0.506 Sum_probs=0.0
Q ss_pred CCCCCCCcccccCCCccccccccccc---cccccccccCCCCChhHHHHHHHHHHHHhhcCCCccccCCccccCCCC
Q 035729 8 PTENRGRQEEEGNGSSFTCEICIEPM---AANKKFKNKNLCTHPFCQECIAKYIQVMVQDNNTAKIECPGLNCQKNL 81 (208)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~C~iC~~~~---~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 81 (208)
............+.....|.||-|++ ...+.|+.--.|+-..|+.|. .|-...-++ .||. |+..+
T Consensus 21 ~~d~~~g~kp~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq------~CPQ--CkTrY 88 (1085)
T PLN02400 21 RHDSDSGPKPLKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQ------CCPQ--CKTRY 88 (1085)
T ss_pred cccccccCCCccccCCceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCc------cCcc--cCCcc
No 315
>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=23.33 E-value=46 Score=22.75 Aligned_cols=13 Identities=46% Similarity=1.099 Sum_probs=10.6
Q ss_pred CcccCccccchhcc
Q 035729 135 KKAQCPNCKHWFCF 148 (208)
Q Consensus 135 ~~~~C~~C~~~~C~ 148 (208)
..++| .||+.||-
T Consensus 23 k~vkc-~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKC-DCGHEFCD 35 (112)
T ss_pred ceeec-cCCCeecC
Confidence 47888 79999986
No 316
>PRK11827 hypothetical protein; Provisional
Probab=22.61 E-value=45 Score=20.11 Aligned_cols=27 Identities=19% Similarity=0.247 Sum_probs=15.0
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
+.-|| .|..-+..+.. .....|..|+.
T Consensus 8 ILaCP--~ckg~L~~~~~----~~~Lic~~~~l 34 (60)
T PRK11827 8 IIACP--VCNGKLWYNQE----KQELICKLDNL 34 (60)
T ss_pred heECC--CCCCcCeEcCC----CCeEECCccCe
Confidence 56688 67766654332 34555654443
No 317
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=22.57 E-value=28 Score=20.09 Aligned_cols=34 Identities=26% Similarity=0.732 Sum_probs=24.5
Q ss_pred CCccccccccccccccccccccCCCCChhHHHHHHHH
Q 035729 21 GSSFTCEICIEPMAANKKFKNKNLCTHPFCQECIAKY 57 (208)
Q Consensus 21 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~ 57 (208)
..-+.|..|...+.... + ...=+..||..|..+.
T Consensus 24 ~~Cf~C~~C~~~l~~~~-~--~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGD-F--YEKDGKPYCKDCYQKR 57 (58)
T ss_dssp TTTSBETTTTCBTTTSS-E--EEETTEEEEHHHHHHH
T ss_pred ccccccCCCCCccCCCe-e--EeECCEEECHHHHhhh
Confidence 45679999999986654 3 2334589999998764
No 318
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=22.18 E-value=32 Score=24.90 Aligned_cols=12 Identities=42% Similarity=0.935 Sum_probs=9.7
Q ss_pred CcccCccccccc
Q 035729 111 ERSYCPNRNCMA 122 (208)
Q Consensus 111 ~~~~Cp~~~C~~ 122 (208)
+...||||.|-.
T Consensus 105 gvlkCpN~nCIT 116 (153)
T COG1781 105 GVLRCPNPNCIT 116 (153)
T ss_pred cEEEcCCCCccc
Confidence 468899999954
No 319
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.86 E-value=38 Score=27.59 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=20.8
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKH 144 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 144 (208)
...|| .|+..+...... .+...||.|++
T Consensus 38 w~kc~--~C~~~~~~~~l~---~~~~vcp~c~~ 65 (296)
T CHL00174 38 WVQCE--NCYGLNYKKFLK---SKMNICEQCGY 65 (296)
T ss_pred eeECC--CccchhhHHHHH---HcCCCCCCCCC
Confidence 56788 799888876653 35678998887
No 320
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.49 E-value=34 Score=15.20 Aligned_cols=6 Identities=50% Similarity=1.514 Sum_probs=1.7
Q ss_pred Cccccc
Q 035729 139 CPNCKH 144 (208)
Q Consensus 139 C~~C~~ 144 (208)
|+.|+.
T Consensus 3 C~~C~~ 8 (24)
T PF13894_consen 3 CPICGK 8 (24)
T ss_dssp -SSTS-
T ss_pred CcCCCC
Confidence 444443
No 321
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=21.41 E-value=91 Score=24.73 Aligned_cols=32 Identities=16% Similarity=0.413 Sum_probs=22.5
Q ss_pred CCCcccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 109 GYERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 109 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
.....+|| .|+..+..... .....|+.|+...
T Consensus 96 ~~~~~fC~--~CG~~~~~~~~----~~~~~C~~c~~~~ 127 (256)
T PRK00241 96 YRSHRFCG--YCGHPMHPSKT----EWAMLCPHCRERY 127 (256)
T ss_pred hhcCcccc--ccCCCCeecCC----ceeEECCCCCCEE
Confidence 34578999 79987765433 4667898887544
No 322
>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=21.16 E-value=41 Score=16.14 Aligned_cols=13 Identities=38% Similarity=0.828 Sum_probs=8.9
Q ss_pred CCcccCccccchh
Q 035729 134 MKKAQCPNCKHWF 146 (208)
Q Consensus 134 ~~~~~C~~C~~~~ 146 (208)
...+.|+.|++.|
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 4567788887654
No 323
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=21.13 E-value=50 Score=20.34 Aligned_cols=40 Identities=18% Similarity=0.524 Sum_probs=28.0
Q ss_pred cCCCccccccccccccccccccccCCC----CChhHH-HHHHHHHHHH
Q 035729 19 GNGSSFTCEICIEPMAANKKFKNKNLC----THPFCQ-ECIAKYIQVM 61 (208)
Q Consensus 19 ~~~~~~~C~iC~~~~~~~~~~~~~~~C----~H~~C~-~Cl~~~~~~~ 61 (208)
.+.+..+|.+|+.+++....+ .+= -+.||. +|..+|....
T Consensus 7 ~~~~~~sC~vC~KEIPl~~a~---t~E~~eYV~hFCGLeCY~~w~a~~ 51 (70)
T PF11809_consen 7 NDPKTTSCCVCCKEIPLDAAF---TPEAAEYVEHFCGLECYQRWQARA 51 (70)
T ss_pred cccccchHHHHhhhCChhhcc---CcchHHHHHHHhhHHHHHHHHHHH
Confidence 344568999999999766533 222 256786 9999998654
No 324
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=21.01 E-value=80 Score=20.12 Aligned_cols=36 Identities=17% Similarity=0.430 Sum_probs=24.4
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhccccCc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFCFRCKL 152 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 152 (208)
.+.|| +|..+-..-... ...+.|+.|+...|.-=..
T Consensus 34 ~VkC~--gc~~iT~vfSHa---qtvVvc~~c~~il~~~tgg 69 (84)
T KOG1779|consen 34 DVKCP--GCFKITTVFSHA---QTVVVCEGCSTILCQPTGG 69 (84)
T ss_pred EEEcC--CceEEEEEeecC---ceEEEcCCCceEEEEecCC
Confidence 37788 787765444332 5788999999888874433
No 325
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.85 E-value=55 Score=26.58 Aligned_cols=31 Identities=23% Similarity=0.589 Sum_probs=22.6
Q ss_pred CcccCcccccccchhcchhhcCCCCcccCccccchh
Q 035729 111 ERSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWF 146 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 146 (208)
-...|| .|+..+...... .+...||.|++.+
T Consensus 26 ~~~~c~--~c~~~~~~~~l~---~~~~vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCP--SCGQVLYRKELE---ANLNVCPKCGHHM 56 (292)
T ss_pred CeeECC--CccchhhHHHHH---hcCCCCCCCCCCe
Confidence 367798 799988876653 3457899888754
No 326
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=20.74 E-value=33 Score=28.42 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=7.8
Q ss_pred CcccCCCCCc
Q 035729 182 KWARCPGCGH 191 (208)
Q Consensus 182 ~~k~CP~C~~ 191 (208)
-.|+||.|+.
T Consensus 66 qRKRCP~CRF 75 (475)
T KOG4218|consen 66 QRKRCPSCRF 75 (475)
T ss_pred hhccCCchhH
Confidence 4589999975
No 327
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.67 E-value=62 Score=22.82 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=6.4
Q ss_pred CCccccccccccc
Q 035729 21 GSSFTCEICIEPM 33 (208)
Q Consensus 21 ~~~~~C~iC~~~~ 33 (208)
...++|..|-..+
T Consensus 26 ~~~~tC~~Cg~~L 38 (128)
T PF11682_consen 26 YDHWTCHSCGCPL 38 (128)
T ss_pred CCeEEEecCCceE
Confidence 3445555554444
No 328
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=20.66 E-value=38 Score=19.24 Aligned_cols=17 Identities=35% Similarity=0.831 Sum_probs=12.6
Q ss_pred hhccccCcCcCCCCCCh
Q 035729 145 WFCFRCKLKWHGGYHCE 161 (208)
Q Consensus 145 ~~C~~C~~~~H~~~~C~ 161 (208)
.||+.|+...|....|+
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 57888888888776664
No 329
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=20.52 E-value=34 Score=24.80 Aligned_cols=36 Identities=19% Similarity=0.423 Sum_probs=19.3
Q ss_pred CcccCcccccccchhcchhh---cCCC--CcccCccccchh
Q 035729 111 ERSYCPNRNCMALVVNECER---KGRM--KKAQCPNCKHWF 146 (208)
Q Consensus 111 ~~~~Cp~~~C~~~~~~~~~~---~~~~--~~~~C~~C~~~~ 146 (208)
+...||||.|-.-....... .+.. ..++|..|...+
T Consensus 102 gi~kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~~ 142 (150)
T TIGR00240 102 GVLKCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKEI 142 (150)
T ss_pred eeEECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCEE
Confidence 56899999995432211100 0112 367777776543
No 330
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.50 E-value=39 Score=17.54 Aligned_cols=19 Identities=32% Similarity=0.597 Sum_probs=15.8
Q ss_pred chhccccCcCcCCCCCChh
Q 035729 144 HWFCFRCKLKWHGGYHCEE 162 (208)
Q Consensus 144 ~~~C~~C~~~~H~~~~C~~ 162 (208)
.+.|..|.++-|.-..|..
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 4678899999998888876
No 331
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.36 E-value=96 Score=20.26 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=18.3
Q ss_pred cccCcccccccchhcchhhcCCCCcccCccccchhc
Q 035729 112 RSYCPNRNCMALVVNECERKGRMKKAQCPNCKHWFC 147 (208)
Q Consensus 112 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 147 (208)
...|| .|+.....-.. .-.+.|..|++.|=
T Consensus 35 ~~~Cp--~C~~~~VkR~a----~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCP--FCGRTTVKRIA----TGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCC--CCCCcceeeec----cCeEEcCCCCCeec
Confidence 45688 68776322211 46788887776653
Done!