Query 025186
Match_columns 256
No_of_seqs 192 out of 634
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:27:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025186.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025186hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 8.5E-70 1.8E-74 495.5 9.8 241 4-255 21-272 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 100.0 1.2E-31 2.6E-36 195.3 1.2 61 188-248 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.7 4.8E-18 1E-22 127.0 1.2 62 18-89 1-71 (71)
4 PF13639 zf-RING_2: Ring finge 99.4 6.5E-14 1.4E-18 94.6 0.9 44 140-185 1-44 (44)
5 PF12678 zf-rbx1: RING-H2 zinc 99.0 1.2E-10 2.5E-15 87.4 3.0 48 137-185 17-73 (73)
6 COG5243 HRD1 HRD ubiquitin lig 99.0 8.1E-11 1.8E-15 111.8 1.4 57 136-193 284-350 (491)
7 cd00162 RING RING-finger (Real 99.0 2.8E-10 6.1E-15 74.2 3.3 45 141-188 1-45 (45)
8 KOG4628 Predicted E3 ubiquitin 98.9 4.7E-10 1E-14 106.3 2.3 50 140-190 230-279 (348)
9 PF13923 zf-C3HC4_2: Zinc fing 98.9 8.8E-10 1.9E-14 72.7 1.6 39 142-184 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.8 2.2E-09 4.7E-14 97.3 3.9 55 135-190 170-228 (238)
11 PF13920 zf-C3HC4_3: Zinc fing 98.7 5.5E-09 1.2E-13 72.3 1.6 46 140-190 3-49 (50)
12 smart00184 RING Ring finger. E 98.7 9E-09 1.9E-13 64.7 2.4 39 142-184 1-39 (39)
13 PF00097 zf-C3HC4: Zinc finger 98.7 7.3E-09 1.6E-13 68.4 1.6 40 142-184 1-41 (41)
14 KOG0804 Cytoplasmic Zn-finger 98.6 1.8E-08 3.9E-13 97.7 3.6 82 140-249 176-259 (493)
15 PF14634 zf-RING_5: zinc-RING 98.6 2.4E-08 5.2E-13 67.7 2.8 44 141-186 1-44 (44)
16 COG5540 RING-finger-containing 98.6 3.3E-08 7.2E-13 92.2 2.8 53 135-188 319-371 (374)
17 PF15227 zf-C3HC4_4: zinc fing 98.5 6.1E-08 1.3E-12 65.5 2.6 39 142-184 1-42 (42)
18 PF13445 zf-RING_UBOX: RING-ty 98.5 6E-08 1.3E-12 66.2 1.5 40 142-182 1-43 (43)
19 PF12861 zf-Apc11: Anaphase-pr 98.4 1.4E-07 2.9E-12 73.3 3.0 48 140-189 33-82 (85)
20 KOG0802 E3 ubiquitin ligase [P 98.4 6.8E-08 1.5E-12 96.3 0.9 54 135-189 287-341 (543)
21 PLN03208 E3 ubiquitin-protein 98.4 2.1E-07 4.5E-12 82.1 3.8 56 131-190 10-80 (193)
22 PHA02926 zinc finger-like prot 98.2 4.5E-07 9.9E-12 81.6 1.9 74 122-195 153-238 (242)
23 KOG0320 Predicted E3 ubiquitin 98.1 7.8E-07 1.7E-11 77.5 1.6 46 140-189 132-178 (187)
24 smart00504 Ubox Modified RING 98.1 2.7E-06 5.9E-11 60.4 3.0 45 140-189 2-46 (63)
25 smart00744 RINGv The RING-vari 97.9 4.6E-06 1E-10 58.2 2.1 43 141-185 1-49 (49)
26 PF11793 FANCL_C: FANCL C-term 97.9 3.1E-06 6.8E-11 63.1 0.1 51 139-189 2-66 (70)
27 TIGR00599 rad18 DNA repair pro 97.8 1.4E-05 3.1E-10 77.4 4.0 47 138-189 25-71 (397)
28 KOG2177 Predicted E3 ubiquitin 97.7 1.7E-05 3.7E-10 68.1 2.6 44 138-186 12-55 (386)
29 COG5194 APC11 Component of SCF 97.7 2.5E-05 5.4E-10 60.2 2.7 30 159-189 52-81 (88)
30 KOG0317 Predicted E3 ubiquitin 97.6 2.3E-05 5E-10 72.8 1.2 45 140-189 240-284 (293)
31 TIGR00570 cdk7 CDK-activating 97.6 5.5E-05 1.2E-09 71.2 3.7 51 139-189 3-54 (309)
32 KOG0827 Predicted E3 ubiquitin 97.5 4.3E-05 9.2E-10 73.7 1.2 47 139-186 4-53 (465)
33 KOG0287 Postreplication repair 97.4 0.00012 2.5E-09 69.8 3.9 59 140-203 24-83 (442)
34 KOG0828 Predicted E3 ubiquitin 97.3 8.6E-05 1.9E-09 73.5 0.9 51 139-189 571-634 (636)
35 KOG2164 Predicted E3 ubiquitin 97.3 0.00014 3E-09 72.0 2.2 50 137-190 184-237 (513)
36 COG4357 Zinc finger domain con 97.2 7.6E-05 1.6E-09 59.3 0.2 53 16-76 13-68 (105)
37 PF04564 U-box: U-box domain; 97.2 0.00032 7E-09 52.2 3.3 48 139-190 4-51 (73)
38 KOG0823 Predicted E3 ubiquitin 97.2 0.00019 4.1E-09 64.9 2.4 50 137-190 45-96 (230)
39 PF14835 zf-RING_6: zf-RING of 97.1 0.00027 5.8E-09 52.4 1.7 56 140-202 8-65 (65)
40 KOG1734 Predicted RING-contain 97.0 0.00018 3.9E-09 66.7 0.7 52 138-189 223-281 (328)
41 KOG1493 Anaphase-promoting com 97.0 0.00024 5.2E-09 54.4 0.6 30 160-189 50-81 (84)
42 KOG4265 Predicted E3 ubiquitin 96.8 0.00066 1.4E-08 64.7 2.2 51 135-190 286-337 (349)
43 COG5574 PEX10 RING-finger-cont 96.6 0.00086 1.9E-08 61.8 1.4 46 139-189 215-262 (271)
44 KOG1941 Acetylcholine receptor 96.6 0.00062 1.3E-08 66.0 0.2 62 130-192 357-419 (518)
45 PF14570 zf-RING_4: RING/Ubox 96.5 0.0021 4.4E-08 45.1 2.3 44 142-187 1-46 (48)
46 COG5219 Uncharacterized conser 96.3 0.0023 5E-08 67.7 2.4 53 136-188 1466-1522(1525)
47 KOG0311 Predicted E3 ubiquitin 96.2 0.0013 2.8E-08 62.9 0.3 49 139-190 43-91 (381)
48 KOG1039 Predicted E3 ubiquitin 96.1 0.0012 2.5E-08 63.2 -0.5 82 137-220 159-252 (344)
49 KOG2930 SCF ubiquitin ligase, 96.1 0.0029 6.3E-08 51.1 1.7 28 160-188 80-107 (114)
50 KOG4172 Predicted E3 ubiquitin 96.1 0.0014 3E-08 47.4 -0.1 53 137-193 5-58 (62)
51 KOG1785 Tyrosine kinase negati 96.0 0.0021 4.6E-08 62.6 0.5 54 133-190 363-417 (563)
52 KOG0978 E3 ubiquitin ligase in 96.0 0.0015 3.2E-08 67.3 -0.6 47 139-189 643-689 (698)
53 KOG3002 Zn finger protein [Gen 96.0 0.0063 1.4E-07 57.2 3.5 65 138-213 47-113 (299)
54 KOG0825 PHD Zn-finger protein 95.9 0.0028 6.1E-08 65.9 1.1 75 113-189 96-171 (1134)
55 PF11789 zf-Nse: Zinc-finger o 95.8 0.0044 9.4E-08 44.6 1.5 44 137-183 9-53 (57)
56 PF10367 Vps39_2: Vacuolar sor 95.8 0.0035 7.6E-08 48.4 0.9 38 132-171 71-108 (109)
57 COG5432 RAD18 RING-finger-cont 95.5 0.008 1.7E-07 56.6 2.1 46 139-189 25-70 (391)
58 KOG1645 RING-finger-containing 95.4 0.015 3.3E-07 56.7 3.9 51 139-189 4-56 (463)
59 KOG1428 Inhibitor of type V ad 95.3 0.015 3.3E-07 64.1 3.7 74 108-189 3462-3544(3738)
60 PF12906 RINGv: RING-variant d 95.3 0.0071 1.5E-07 41.8 0.8 41 142-184 1-47 (47)
61 KOG3970 Predicted E3 ubiquitin 95.2 0.02 4.2E-07 52.3 3.7 51 137-189 48-105 (299)
62 KOG2879 Predicted E3 ubiquitin 94.6 0.026 5.6E-07 52.6 2.8 53 137-192 237-290 (298)
63 KOG4445 Uncharacterized conser 94.0 0.012 2.6E-07 55.6 -0.6 54 136-190 112-187 (368)
64 KOG0824 Predicted E3 ubiquitin 94.0 0.024 5.2E-07 53.4 1.3 49 137-189 5-53 (324)
65 PF14447 Prok-RING_4: Prokaryo 93.7 0.027 5.9E-07 40.5 0.8 33 154-189 18-50 (55)
66 PF05883 Baculo_RING: Baculovi 93.2 0.038 8.3E-07 46.4 1.1 36 139-175 26-67 (134)
67 KOG4275 Predicted E3 ubiquitin 92.8 0.019 4.2E-07 54.0 -1.4 60 128-196 286-349 (350)
68 KOG3800 Predicted E3 ubiquitin 92.6 0.078 1.7E-06 49.7 2.3 48 141-189 2-51 (300)
69 KOG3268 Predicted E3 ubiquitin 92.5 0.061 1.3E-06 47.6 1.5 52 141-192 167-232 (234)
70 KOG4739 Uncharacterized protei 92.4 0.064 1.4E-06 48.9 1.5 37 150-189 12-48 (233)
71 KOG1571 Predicted E3 ubiquitin 92.4 0.071 1.5E-06 51.2 1.8 48 135-190 301-348 (355)
72 TIGR00100 hypA hydrogenase nic 92.1 0.099 2.1E-06 42.4 2.1 37 214-252 67-103 (115)
73 PRK03824 hypA hydrogenase nick 91.4 0.15 3.3E-06 42.5 2.6 38 215-252 68-124 (135)
74 KOG0297 TNF receptor-associate 91.3 0.13 2.9E-06 49.8 2.4 54 137-194 19-72 (391)
75 PRK00564 hypA hydrogenase nick 91.0 0.14 3E-06 41.7 1.9 37 214-252 68-105 (117)
76 KOG4185 Predicted E3 ubiquitin 90.9 0.16 3.5E-06 46.6 2.5 48 140-188 4-54 (296)
77 PHA02862 5L protein; Provision 90.8 0.13 2.7E-06 44.1 1.5 57 138-200 1-63 (156)
78 PRK12380 hydrogenase nickel in 90.4 0.18 3.9E-06 40.8 2.0 36 215-252 68-103 (113)
79 PF07800 DUF1644: Protein of u 90.3 0.26 5.6E-06 42.7 3.0 33 139-175 2-47 (162)
80 KOG1814 Predicted E3 ubiquitin 90.3 0.13 2.9E-06 50.3 1.4 47 138-185 183-236 (445)
81 PF04641 Rtf2: Rtf2 RING-finge 90.2 0.2 4.3E-06 45.8 2.4 50 137-189 111-161 (260)
82 KOG2660 Locus-specific chromos 90.1 0.066 1.4E-06 50.9 -0.8 50 137-190 13-62 (331)
83 KOG2817 Predicted E3 ubiquitin 90.1 0.26 5.6E-06 48.0 3.1 48 140-188 335-384 (394)
84 PRK03681 hypA hydrogenase nick 89.9 0.21 4.7E-06 40.4 2.1 37 215-252 68-104 (114)
85 COG5175 MOT2 Transcriptional r 89.5 0.095 2.1E-06 50.5 -0.3 57 139-195 14-70 (480)
86 KOG0309 Conserved WD40 repeat- 89.2 0.19 4.1E-06 52.7 1.5 44 137-183 1026-1069(1081)
87 KOG3161 Predicted E3 ubiquitin 88.7 0.23 4.9E-06 51.3 1.7 53 140-196 12-68 (861)
88 PF01155 HypA: Hydrogenase exp 88.4 0.16 3.5E-06 41.0 0.4 36 215-252 68-103 (113)
89 PF07191 zinc-ribbons_6: zinc- 88.1 0.098 2.1E-06 39.4 -1.0 65 140-233 2-69 (70)
90 PF03854 zf-P11: P-11 zinc fin 88.0 0.26 5.7E-06 34.7 1.1 32 157-189 14-46 (50)
91 KOG4159 Predicted E3 ubiquitin 88.0 0.62 1.3E-05 45.6 4.1 49 137-190 82-130 (398)
92 KOG1002 Nucleotide excision re 87.9 0.17 3.7E-06 51.2 0.3 53 133-189 530-586 (791)
93 KOG2034 Vacuolar sorting prote 87.4 0.29 6.2E-06 51.9 1.6 43 131-175 809-851 (911)
94 KOG1813 Predicted E3 ubiquitin 87.4 0.31 6.7E-06 46.0 1.6 67 140-211 242-308 (313)
95 COG5152 Uncharacterized conser 87.1 0.34 7.4E-06 43.6 1.7 59 140-203 197-255 (259)
96 KOG2114 Vacuolar assembly/sort 86.1 0.46 9.9E-06 50.3 2.2 39 141-186 842-880 (933)
97 KOG3039 Uncharacterized conser 85.9 0.66 1.4E-05 43.0 2.9 57 134-192 216-273 (303)
98 PRK14890 putative Zn-ribbon RN 85.4 0.38 8.2E-06 35.2 0.9 32 67-104 25-56 (59)
99 PHA02825 LAP/PHD finger-like p 85.3 0.62 1.4E-05 40.4 2.3 48 137-189 6-59 (162)
100 PRK00762 hypA hydrogenase nick 84.2 0.68 1.5E-05 38.0 2.0 38 214-252 67-109 (124)
101 KOG1952 Transcription factor N 84.1 0.41 8.9E-06 50.7 0.8 52 137-189 189-247 (950)
102 TIGR02605 CxxC_CxxC_SSSS putat 84.0 1.2 2.6E-05 30.6 2.9 37 217-253 5-45 (52)
103 KOG4692 Predicted E3 ubiquitin 83.4 0.51 1.1E-05 45.8 1.1 50 136-190 419-468 (489)
104 PF14353 CpXC: CpXC protein 83.2 0.25 5.3E-06 40.1 -1.0 56 179-236 2-57 (128)
105 COG0375 HybF Zn finger protein 82.1 1.1 2.3E-05 36.9 2.3 38 213-252 66-103 (115)
106 COG5236 Uncharacterized conser 81.7 1 2.2E-05 43.8 2.3 65 120-188 42-107 (493)
107 COG2888 Predicted Zn-ribbon RN 80.5 0.77 1.7E-05 33.7 0.9 32 67-104 27-58 (61)
108 PF08746 zf-RING-like: RING-li 78.6 1.2 2.6E-05 30.1 1.3 25 160-184 18-43 (43)
109 PF14446 Prok-RING_1: Prokaryo 77.9 1.8 3.9E-05 31.1 2.1 36 137-173 3-39 (54)
110 KOG0801 Predicted E3 ubiquitin 77.3 0.96 2.1E-05 39.6 0.6 31 136-167 174-204 (205)
111 KOG2462 C2H2-type Zn-finger pr 76.0 2.6 5.6E-05 39.5 3.2 114 75-227 126-253 (279)
112 PRK00398 rpoP DNA-directed RNA 76.0 2.5 5.3E-05 28.6 2.3 36 216-251 2-37 (46)
113 COG5220 TFB3 Cdk activating ki 74.7 1.1 2.3E-05 41.7 0.2 50 139-189 10-64 (314)
114 smart00734 ZnF_Rad18 Rad18-lik 73.3 2.9 6.4E-05 25.4 1.9 21 179-200 2-22 (26)
115 KOG0269 WD40 repeat-containing 73.3 2.8 6E-05 44.2 2.8 78 95-192 752-836 (839)
116 smart00132 LIM Zinc-binding do 72.7 1.8 3.8E-05 26.9 0.8 37 142-189 2-38 (39)
117 KOG0827 Predicted E3 ubiquitin 72.3 0.39 8.3E-06 47.0 -3.3 51 138-189 195-245 (465)
118 KOG1001 Helicase-like transcri 72.0 3 6.6E-05 43.5 2.8 45 140-189 455-500 (674)
119 PF02891 zf-MIZ: MIZ/SP-RING z 70.7 2.2 4.8E-05 29.7 1.1 42 140-187 3-50 (50)
120 PF13894 zf-C2H2_4: C2H2-type 70.3 3.1 6.6E-05 23.0 1.4 20 179-198 1-20 (24)
121 COG5222 Uncharacterized conser 68.0 3.6 7.9E-05 39.3 2.2 44 140-186 275-318 (427)
122 COG5109 Uncharacterized conser 67.9 4.4 9.6E-05 39.0 2.7 45 140-185 337-383 (396)
123 KOG2068 MOT2 transcription fac 67.4 3.9 8.6E-05 39.1 2.3 52 137-189 247-298 (327)
124 smart00249 PHD PHD zinc finger 66.6 1.9 4.2E-05 27.5 0.1 41 142-184 2-47 (47)
125 PHA03096 p28-like protein; Pro 66.6 2.9 6.3E-05 39.2 1.3 47 140-186 179-231 (284)
126 smart00659 RPOLCX RNA polymera 66.6 4.3 9.2E-05 27.7 1.8 27 217-244 2-28 (44)
127 COG1996 RPC10 DNA-directed RNA 66.1 4.5 9.7E-05 28.5 1.8 30 215-244 4-33 (49)
128 PF03107 C1_2: C1 domain; Int 64.8 5.3 0.00012 24.8 1.8 20 101-120 2-22 (30)
129 PF09538 FYDLN_acid: Protein o 63.6 4.3 9.3E-05 32.9 1.6 25 68-104 10-34 (108)
130 PF06524 NOA36: NOA36 protein; 62.3 3.3 7.1E-05 38.8 0.8 52 33-88 140-191 (314)
131 PF05605 zf-Di19: Drought indu 62.3 7.7 0.00017 26.9 2.5 22 178-200 2-23 (54)
132 KOG2066 Vacuolar assembly/sort 61.3 2.9 6.3E-05 44.2 0.3 43 141-185 786-831 (846)
133 PRK12286 rpmF 50S ribosomal pr 60.4 8.3 0.00018 27.8 2.4 30 216-250 26-55 (57)
134 KOG3053 Uncharacterized conser 59.6 2.9 6.3E-05 39.0 -0.1 69 136-204 17-104 (293)
135 PF12773 DZR: Double zinc ribb 57.9 8.3 0.00018 26.0 2.0 12 67-78 12-23 (50)
136 PF13597 NRDD: Anaerobic ribon 57.8 7.6 0.00016 39.4 2.5 57 190-252 465-521 (546)
137 PRK04023 DNA polymerase II lar 57.8 8.1 0.00018 42.2 2.8 49 67-124 626-674 (1121)
138 PF05502 Dynactin_p62: Dynacti 57.6 5.3 0.00012 40.0 1.3 58 80-152 6-65 (483)
139 smart00834 CxxC_CXXC_SSSS Puta 57.1 12 0.00027 23.9 2.6 27 217-243 5-34 (41)
140 KOG1812 Predicted E3 ubiquitin 56.9 5.1 0.00011 38.9 1.1 37 139-175 146-182 (384)
141 KOG4367 Predicted Zn-finger pr 56.8 5.6 0.00012 39.9 1.3 33 139-175 4-36 (699)
142 KOG0298 DEAD box-containing he 54.6 8 0.00017 43.1 2.2 52 137-192 1151-1202(1394)
143 COG1656 Uncharacterized conser 54.1 8.9 0.00019 33.5 2.0 49 178-233 97-146 (165)
144 PRK00398 rpoP DNA-directed RNA 53.9 11 0.00023 25.4 2.0 8 96-103 21-28 (46)
145 PF09723 Zn-ribbon_8: Zinc rib 53.6 13 0.00029 24.7 2.4 32 217-248 5-39 (42)
146 cd01675 RNR_III Class III ribo 53.4 10 0.00022 38.5 2.6 56 190-251 493-548 (555)
147 PF10058 DUF2296: Predicted in 52.4 18 0.0004 25.7 3.1 47 196-245 4-54 (54)
148 PHA00626 hypothetical protein 52.3 11 0.00023 27.5 1.8 30 69-104 2-31 (59)
149 PF07282 OrfB_Zn_ribbon: Putat 51.9 9.1 0.0002 27.5 1.5 27 67-104 28-54 (69)
150 PRK14714 DNA polymerase II lar 49.7 14 0.00031 41.3 3.1 33 68-104 668-700 (1337)
151 PF00096 zf-C2H2: Zinc finger, 49.6 10 0.00022 21.2 1.2 15 179-193 1-15 (23)
152 KOG1609 Protein involved in mR 49.3 6.5 0.00014 35.6 0.4 51 139-189 78-134 (323)
153 TIGR01031 rpmF_bact ribosomal 48.5 14 0.00031 26.3 2.0 29 216-249 25-53 (55)
154 PF10122 Mu-like_Com: Mu-like 48.1 15 0.00032 26.2 1.9 35 217-251 4-40 (51)
155 PRK03564 formate dehydrogenase 48.1 19 0.00041 34.3 3.3 23 217-243 212-234 (309)
156 PRK00366 ispG 4-hydroxy-3-meth 47.2 26 0.00057 34.1 4.2 53 179-235 269-323 (360)
157 PF15353 HECA: Headcase protei 46.5 9.6 0.00021 31.0 0.9 16 160-175 39-54 (107)
158 COG1996 RPC10 DNA-directed RNA 46.4 12 0.00026 26.4 1.3 29 76-104 3-32 (49)
159 PF02701 zf-Dof: Dof domain, z 46.1 10 0.00022 28.1 0.9 14 235-248 5-18 (63)
160 PF04423 Rad50_zn_hook: Rad50 45.9 16 0.00034 25.4 1.9 13 178-190 20-32 (54)
161 PF14569 zf-UDP: Zinc-binding 45.6 19 0.00041 27.9 2.4 52 137-188 7-61 (80)
162 PF01529 zf-DHHC: DHHC palmito 45.5 12 0.00027 31.0 1.5 48 73-126 42-89 (174)
163 KOG1312 DHHC-type Zn-finger pr 45.2 7.2 0.00016 37.1 0.1 32 100-134 149-180 (341)
164 PF07649 C1_3: C1-like domain; 45.0 13 0.00028 22.8 1.2 21 102-122 3-24 (30)
165 KOG4399 C2HC-type Zn-finger pr 44.8 3.9 8.4E-05 38.3 -1.7 74 72-148 197-270 (325)
166 TIGR02159 PA_CoA_Oxy4 phenylac 44.5 11 0.00024 31.9 1.1 17 235-251 105-121 (146)
167 COG3809 Uncharacterized protei 43.2 18 0.00038 28.2 1.9 51 141-214 3-55 (88)
168 PRK00432 30S ribosomal protein 41.9 19 0.00041 25.2 1.8 9 95-103 36-44 (50)
169 PF03833 PolC_DP2: DNA polymer 41.9 8.5 0.00018 41.3 0.0 46 67-121 655-700 (900)
170 cd00350 rubredoxin_like Rubred 41.2 22 0.00048 22.4 1.8 25 79-104 1-25 (33)
171 KOG1311 DHHC-type Zn-finger pr 41.1 17 0.00036 33.5 1.8 45 74-124 108-152 (299)
172 PF04438 zf-HIT: HIT zinc fing 40.6 14 0.0003 23.2 0.8 19 68-87 3-21 (30)
173 KOG4185 Predicted E3 ubiquitin 38.8 6.5 0.00014 36.0 -1.3 50 139-188 207-266 (296)
174 PF04216 FdhE: Protein involve 38.7 11 0.00025 34.7 0.3 30 216-249 196-225 (290)
175 TIGR01562 FdhE formate dehydro 38.4 35 0.00075 32.4 3.5 23 217-243 210-232 (305)
176 KOG1100 Predicted E3 ubiquitin 38.1 13 0.00028 33.2 0.6 39 142-189 161-200 (207)
177 PLN02189 cellulose synthase 38.1 27 0.00059 38.4 3.0 56 134-189 29-87 (1040)
178 cd02337 ZZ_CBP Zinc finger, ZZ 37.8 25 0.00054 23.5 1.8 20 97-120 1-20 (41)
179 KOG2907 RNA polymerase I trans 37.4 12 0.00026 30.8 0.2 19 233-251 72-94 (116)
180 TIGR02300 FYDLN_acid conserved 35.7 23 0.00049 29.8 1.6 26 68-105 10-35 (129)
181 PF00628 PHD: PHD-finger; Int 35.4 4.2 9.1E-05 27.4 -2.4 42 142-185 2-49 (51)
182 PF14952 zf-tcix: Putative tre 34.6 19 0.00041 24.9 0.8 13 236-248 12-24 (44)
183 PF05129 Elf1: Transcription e 34.2 24 0.00052 27.0 1.4 39 177-233 21-62 (81)
184 smart00451 ZnF_U1 U1-like zinc 34.0 19 0.00042 22.1 0.7 12 77-88 1-12 (35)
185 KOG0802 E3 ubiquitin ligase [P 33.9 28 0.00061 35.1 2.2 44 137-189 477-520 (543)
186 PF00412 LIM: LIM domain; Int 33.8 14 0.0003 25.1 0.1 40 142-192 1-40 (58)
187 PRK00420 hypothetical protein; 33.5 23 0.00051 28.9 1.3 29 139-189 23-51 (112)
188 PF01529 zf-DHHC: DHHC palmito 33.1 32 0.0007 28.4 2.2 30 102-134 51-80 (174)
189 PF03604 DNA_RNApol_7kD: DNA d 32.7 30 0.00065 22.1 1.4 24 80-103 1-24 (32)
190 PRK14559 putative protein seri 32.4 30 0.00065 36.1 2.2 19 68-86 16-34 (645)
191 PLN02436 cellulose synthase A 32.2 38 0.00083 37.4 3.0 56 134-189 31-89 (1094)
192 TIGR01206 lysW lysine biosynth 32.2 41 0.00089 24.0 2.2 32 179-229 3-34 (54)
193 cd02249 ZZ Zinc finger, ZZ typ 32.2 35 0.00076 22.9 1.8 21 97-120 1-21 (46)
194 PF00643 zf-B_box: B-box zinc 32.2 26 0.00056 22.6 1.1 21 68-88 4-24 (42)
195 PF06220 zf-U1: U1 zinc finger 32.1 19 0.00041 23.8 0.4 13 77-89 1-13 (38)
196 KOG2272 Focal adhesion protein 31.6 33 0.00072 32.2 2.1 130 26-192 70-235 (332)
197 KOG4399 C2HC-type Zn-finger pr 31.5 12 0.00026 35.2 -0.8 53 68-124 250-302 (325)
198 KOG4443 Putative transcription 31.5 56 0.0012 34.3 3.9 79 133-216 139-227 (694)
199 PF01907 Ribosomal_L37e: Ribos 31.1 22 0.00048 25.7 0.7 28 212-242 10-37 (55)
200 PRK07111 anaerobic ribonucleos 29.0 59 0.0013 34.5 3.7 44 202-251 666-709 (735)
201 PF05290 Baculo_IE-1: Baculovi 29.0 29 0.00064 29.4 1.2 47 140-190 81-133 (140)
202 PRK06266 transcription initiat 28.6 71 0.0015 27.8 3.6 27 177-203 135-163 (178)
203 PRK14714 DNA polymerase II lar 28.4 48 0.001 37.3 3.0 36 69-105 681-718 (1337)
204 PF06937 EURL: EURL protein; 28.4 37 0.0008 32.0 1.8 46 136-182 27-74 (285)
205 TIGR03826 YvyF flagellar opero 27.8 7.4 0.00016 32.8 -2.6 20 67-86 81-101 (137)
206 PRK14892 putative transcriptio 27.8 48 0.001 26.5 2.2 32 111-148 19-51 (99)
207 PRK04023 DNA polymerase II lar 27.4 37 0.0008 37.4 1.9 33 68-105 639-672 (1121)
208 TIGR00373 conserved hypothetic 27.2 75 0.0016 27.0 3.4 28 177-204 127-156 (158)
209 COG1144 Pyruvate:ferredoxin ox 27.0 29 0.00063 27.5 0.8 15 111-125 63-77 (91)
210 COG5273 Uncharacterized protei 26.7 31 0.00066 32.6 1.0 45 67-134 97-141 (309)
211 PF01927 Mut7-C: Mut7-C RNAse 26.6 46 0.00099 27.7 2.0 49 178-233 91-140 (147)
212 PF01783 Ribosomal_L32p: Ribos 26.5 46 0.001 23.5 1.7 29 216-249 25-53 (56)
213 PF12874 zf-met: Zinc-finger o 26.3 34 0.00073 19.4 0.8 15 179-193 1-15 (25)
214 cd02345 ZZ_dah Zinc finger, ZZ 26.2 55 0.0012 22.5 2.0 28 218-248 1-28 (49)
215 PRK01110 rpmF 50S ribosomal pr 25.9 72 0.0016 23.1 2.6 30 217-252 27-56 (60)
216 smart00661 RPOL9 RNA polymeras 25.7 51 0.0011 22.1 1.8 10 113-122 20-29 (52)
217 COG5183 SSM4 Protein involved 25.7 34 0.00075 36.9 1.3 51 137-189 10-66 (1175)
218 smart00355 ZnF_C2H2 zinc finge 25.0 62 0.0014 17.4 1.8 15 179-193 1-15 (26)
219 PF05191 ADK_lid: Adenylate ki 24.7 33 0.00071 22.4 0.6 27 69-104 3-29 (36)
220 PF03966 Trm112p: Trm112p-like 24.6 37 0.0008 24.7 0.9 12 26-37 53-64 (68)
221 TIGR02487 NrdD anaerobic ribon 24.6 70 0.0015 32.8 3.2 54 192-251 501-554 (579)
222 PF12171 zf-C2H2_jaz: Zinc-fin 24.6 54 0.0012 19.3 1.5 15 178-192 1-15 (27)
223 PF13824 zf-Mss51: Zinc-finger 24.5 61 0.0013 23.4 2.0 21 177-197 13-33 (55)
224 PF11781 RRN7: RNA polymerase 24.3 41 0.00088 22.0 1.0 25 141-165 10-35 (36)
225 KOG3579 Predicted E3 ubiquitin 24.2 70 0.0015 30.6 2.9 59 139-206 268-340 (352)
226 PRK08271 anaerobic ribonucleos 24.2 50 0.0011 34.4 2.1 54 190-249 541-594 (623)
227 KOG1311 DHHC-type Zn-finger pr 23.2 44 0.00094 30.8 1.3 34 95-134 112-145 (299)
228 KOG3507 DNA-directed RNA polym 23.1 48 0.001 24.4 1.3 29 213-242 16-44 (62)
229 PF13248 zf-ribbon_3: zinc-rib 23.0 36 0.00077 20.3 0.5 7 69-75 4-10 (26)
230 KOG1044 Actin-binding LIM Zn-f 23.0 1E+02 0.0023 32.1 4.0 79 156-243 78-168 (670)
231 PRK00564 hypA hydrogenase nick 22.9 54 0.0012 26.5 1.7 6 98-103 90-95 (117)
232 PF04710 Pellino: Pellino; In 22.8 28 0.00061 34.4 0.0 52 138-189 327-401 (416)
233 PTZ00396 Casein kinase II subu 22.6 47 0.001 30.8 1.4 35 23-84 145-180 (251)
234 PF14354 Lar_restr_allev: Rest 22.6 25 0.00054 24.6 -0.3 10 216-225 28-37 (61)
235 COG1198 PriA Primosomal protei 21.6 77 0.0017 33.7 2.9 46 178-249 444-489 (730)
236 PF00130 C1_1: Phorbol esters/ 21.3 65 0.0014 21.7 1.6 10 112-121 27-36 (53)
237 PF10571 UPF0547: Uncharacteri 21.2 49 0.0011 20.1 0.8 15 64-78 11-25 (26)
238 PRK11788 tetratricopeptide rep 21.2 1E+02 0.0022 28.2 3.4 26 219-248 356-381 (389)
239 KOG1940 Zn-finger protein [Gen 21.1 13 0.00027 35.0 -2.7 27 16-43 178-204 (276)
240 PRK00464 nrdR transcriptional 21.1 55 0.0012 28.0 1.5 38 180-228 2-39 (154)
241 PRK09263 anaerobic ribonucleos 20.8 47 0.001 35.0 1.1 29 217-245 641-669 (711)
242 PLN02638 cellulose synthase A 20.7 82 0.0018 34.9 2.9 56 134-189 12-70 (1079)
243 KOG0826 Predicted E3 ubiquitin 20.7 89 0.0019 30.4 2.9 49 137-189 298-346 (357)
244 PF01096 TFIIS_C: Transcriptio 20.6 53 0.0012 21.5 1.0 12 70-81 3-14 (39)
245 PF12172 DUF35_N: Rubredoxin-l 20.2 79 0.0017 20.1 1.7 30 213-246 7-36 (37)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=8.5e-70 Score=495.46 Aligned_cols=241 Identities=49% Similarity=1.041 Sum_probs=231.6
Q ss_pred CccccccCCCCccCCccccCCceeEcCcCCCeecCCcchhhhhccCCCCCCCceecchhhhhh-----------hhcccc
Q 025186 4 SANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQV-----------AQVCTN 72 (256)
Q Consensus 4 ~~~~~~~~~~~~~GC~HY~R~cki~apcC~~~y~CR~CHde~~~~~~~~~~~H~l~r~~v~~v-----------~~~C~~ 72 (256)
..+++.|++.+++||+||+|+|+++||+|++||+||+||+++. +|.++|+.|.+| ++.|.+
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~--------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~ 92 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE--------DHDLDRKTVYELLCMKCRKIQPVGQICSN 92 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhh--------hcccchhhhhhhhhhhHHhhhhhhhcccc
Confidence 3566889999999999999999999999999999999999976 799999998887 779999
Q ss_pred cCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhccc
Q 025186 73 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDS 152 (256)
Q Consensus 73 Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CPICle~lf~s 152 (256)
|+..||+|||.+|+||||+++ .||||+.|||||+|++++||||++|+.|+++.+.+.|+|+|++++.+||||.|+||++
T Consensus 93 c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s 171 (276)
T KOG1940|consen 93 CHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLS 171 (276)
T ss_pred chhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccc
Confidence 999999999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeee
Q 025186 153 LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFH 232 (256)
Q Consensus 153 ~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH 232 (256)
...+.+|+|||.+|..||.+++..+ |+||+|.+ ++||+.+|+++|.+|+++|||++|++++++|+||||+..++++||
T Consensus 172 ~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~ 249 (276)
T KOG1940|consen 172 FEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYH 249 (276)
T ss_pred cccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCcccee
Confidence 9999999999999999999999865 99999999 999999999999999999999999999999999999999999999
Q ss_pred EeeecCCCCCCccccccCCCCCC
Q 025186 233 IIGQKCSHCKSYNTRSIAPPVLP 255 (256)
Q Consensus 233 ~lg~kC~~C~SyNT~~~~~~~~~ 255 (256)
||++||+.|+|||||+++.|..+
T Consensus 250 ~l~~kc~~c~~~~~r~~~~~~~~ 272 (276)
T KOG1940|consen 250 ILYHKCGKCGSYNTRMISDPSKY 272 (276)
T ss_pred hhhhhCCCcccceeeeccCCCcc
Confidence 99999999999999999876654
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.96 E-value=1.2e-31 Score=195.27 Aligned_cols=61 Identities=67% Similarity=1.267 Sum_probs=22.5
Q ss_pred ccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCccccc
Q 025186 188 VIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 248 (256)
Q Consensus 188 v~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~ 248 (256)
|+||+.+|++||++|+++|||++|++++|+|+||||+++|+|+||||||||++|+||||||
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 5799999999999999999999999999999999999999999999999999999999996
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.69 E-value=4.8e-18 Score=127.04 Aligned_cols=62 Identities=47% Similarity=1.156 Sum_probs=42.1
Q ss_pred CccccCC-ceeEcCcCCCeecCCcchhhhhccCCCCCCCceecchhhhhhhhcccccCccc--------ceeeCCccccc
Q 025186 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVAQVCTNCGVNM--------GEYFCDICKFY 88 (256)
Q Consensus 18 C~HY~R~-cki~apcC~~~y~CR~CHde~~~~~~~~~~~H~l~r~~v~~v~~~C~~Cg~~f--------~~y~C~~C~l~ 88 (256)
|+||.|+ ++|++|||++|||||+||||.+ +|+|+|..+++| .|..|+..+ |+|+|++|++|
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~--------~H~~~~~~~~~v--~Cg~C~~~~~~~~~~c~~~~~C~~C~~~ 70 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE--------DHPFDRWPVKRV--ICGKCRTEQPIDEYSCGADYFCPICGLY 70 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS--------SS---TTT--EE--EETTT--EEES-SBTT--SEEETTTTEE
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc--------cCccccccccCe--ECCCCCCccChhhhhcCCCccCcCcCCC
Confidence 8999999 9999999999999999999976 799999998865 333333222 78999999998
Q ss_pred c
Q 025186 89 D 89 (256)
Q Consensus 89 d 89 (256)
|
T Consensus 71 ~ 71 (71)
T PF05495_consen 71 F 71 (71)
T ss_dssp E
T ss_pred C
Confidence 6
No 4
>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=99.39 E-value=6.5e-14 Score=94.57 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.5
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 185 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCr 185 (256)
++||||+|++.+ .+.++.|+|||.||.+|+.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 379999999655 578889999999999999999984 68999996
No 5
>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=99.04 E-value=1.2e-10 Score=87.38 Aligned_cols=48 Identities=31% Similarity=0.684 Sum_probs=36.7
Q ss_pred CCCCCCchhhhhhccc---------CCccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 025186 137 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 185 (256)
Q Consensus 137 ~~~~~CPICle~lf~s---------~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCr 185 (256)
..+.+|+||++.|.+. .-++...+|||.||..||.+||+ .+.+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-~~~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-QNNTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-TSSB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-cCCcCCCCC
Confidence 3456799999998443 23456679999999999999998 466999997
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.01 E-value=8.1e-11 Score=111.83 Aligned_cols=57 Identities=26% Similarity=0.742 Sum_probs=49.5
Q ss_pred CCCCCCCchhhhhhcccC---------CccEEeccCCccChhhHHHHhcCCCCCCCCCCcc-ccchhH
Q 025186 136 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 193 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~---------~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrks-v~dm~~ 193 (256)
.+.+..|.||+|+||.+. ...+.|||||.+|.+|++.|++ ++.+|||||.+ +.||++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCccccccCC
Confidence 577889999999998875 2347899999999999999998 57899999999 568775
No 7
>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=99.00 E-value=2.8e-10 Score=74.17 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=38.0
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
.|+||++.+ ..++..++|||.||..|++.|++....+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999986 356677789999999999999985578899999764
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=4.7e-10 Score=106.28 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.3
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
..|.||||+ |..++.+++|||+|.||..|++.||......||+|+..+..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 589999998 77789999999999999999999998544459999998874
No 9
>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=98.86 E-value=8.8e-10 Score=72.74 Aligned_cols=39 Identities=38% Similarity=0.987 Sum_probs=33.3
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 184 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiC 184 (256)
||||++.+.+ ++++++|||+|+..|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 8999997543 7789999999999999999996 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.83 E-value=2.2e-09 Score=97.30 Aligned_cols=55 Identities=29% Similarity=0.648 Sum_probs=43.2
Q ss_pred cCCCCCCCchhhhhhcccCC----ccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 135 ENSMHHHCPICYEYLFDSLR----NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 135 e~~~~~~CPICle~lf~s~~----~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
+.+.+..||||+|.+.+... -.+.++|||.||..|+.+|++ .+.+||+||+.+..
T Consensus 170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 34557899999998765321 124458999999999999998 57899999998873
No 11
>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=98.70 E-value=5.5e-09 Score=72.31 Aligned_cols=46 Identities=37% Similarity=0.935 Sum_probs=38.5
Q ss_pred CCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~-~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
..|+||++.. ..+.++||||. |...|+.+|++ ...+||+||+.|.+
T Consensus 3 ~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 3 EECPICFENP----RDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp SB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred CCCccCCccC----CceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 5799999962 45888999999 99999999998 67899999998864
No 12
>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=98.70 E-value=9e-09 Score=64.68 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.9
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 184 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiC 184 (256)
|+||++. .+...+++|||.||..|++.|++....+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899987 35788899999999999999997556789987
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=98.68 E-value=7.3e-09 Score=68.37 Aligned_cols=40 Identities=30% Similarity=0.896 Sum_probs=34.5
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 184 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~-~~~~~CPiC 184 (256)
||||++.+. +++.+++|||.|+..|+.+|++ ....+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999743 3557899999999999999998 678899998
No 14
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.64 E-value=1.8e-08 Score=97.71 Aligned_cols=82 Identities=27% Similarity=0.625 Sum_probs=67.6
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEE
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWIL 219 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~ 219 (256)
..||||||.|-+|++.+....|.|.||..|+..| ...+||+||.... |+. ...-+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w---~~~scpvcR~~q~------------------p~~----ve~~~ 230 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW---WDSSCPVCRYCQS------------------PSV----VESSL 230 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhc---ccCcChhhhhhcC------------------cch----hhhhh
Confidence 5899999999999888888999999999999999 4579999994332 211 12467
Q ss_pred ccCCCCcceeeeeEeeecCCC--CCCcccccc
Q 025186 220 CNDCNDTTEVYFHIIGQKCSH--CKSYNTRSI 249 (256)
Q Consensus 220 CnDC~~~s~~~fH~lg~kC~~--C~SyNT~~~ 249 (256)
|.+|+...++ |+-+.|++ ||.|+....
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~eghA 259 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGHA 259 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchhH
Confidence 9999998888 99999987 999987653
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.62 E-value=2.4e-08 Score=67.66 Aligned_cols=44 Identities=34% Similarity=0.849 Sum_probs=37.9
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 025186 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 186 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrk 186 (256)
.|+||++.+ +...+..+|+|||+|...|+..+. .....||+|++
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999986 555678889999999999999998 35789999986
No 16
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=3.3e-08 Score=92.17 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.8
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 135 e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
|....-+|.|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 44445799999999 667788999999999999999999986678999999765
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.51 E-value=6.1e-08 Score=65.51 Aligned_cols=39 Identities=31% Similarity=0.985 Sum_probs=28.2
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCC---CCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCPIC 184 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~---~~~CPiC 184 (256)
||||++.| + ..+.|+|||+|-..|+..|.+.. .+.||+|
T Consensus 1 CpiC~~~~-~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF-K---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh-C---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999975 3 35669999999999999998743 2579987
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.46 E-value=6e-08 Score=66.21 Aligned_cols=40 Identities=33% Similarity=0.904 Sum_probs=24.3
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcC---CCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---DKYCCP 182 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~---~~~~CP 182 (256)
||||.| +-+...+.++|+|||+|-+.|+++|++. ..++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 5455566788999999999999999974 357787
No 19
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.44 E-value=1.4e-07 Score=73.30 Aligned_cols=48 Identities=27% Similarity=0.474 Sum_probs=34.2
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC--CCCCCCCCCcccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVI 189 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~--~~~~CPiCrksv~ 189 (256)
..||.|..+--+ -+++.-.|||.||..||.+|+.. ++.+||+||+...
T Consensus 33 g~Cp~Ck~Pgd~--Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 33 GCCPDCKFPGDD--CPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred cCCCCccCCCCC--CceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 345556554211 24455579999999999999984 3578999998753
No 20
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.41 E-value=6.8e-08 Score=96.27 Aligned_cols=54 Identities=24% Similarity=0.570 Sum_probs=44.8
Q ss_pred cCCCCCCCchhhhhhcccCC-ccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 135 ENSMHHHCPICYEYLFDSLR-NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 135 e~~~~~~CPICle~lf~s~~-~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
+......|+||+|.|+++.. ..++|||||.||..|+..|++ ...+||+||..+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-r~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-RQQTCPTCRTVLY 341 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHH-HhCcCCcchhhhh
Confidence 44567899999999987422 367899999999999999998 5889999999443
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.41 E-value=2.1e-07 Score=82.07 Aligned_cols=56 Identities=23% Similarity=0.613 Sum_probs=42.6
Q ss_pred ceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC---------------CCCCCCCCCccccc
Q 025186 131 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 190 (256)
Q Consensus 131 H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~---------------~~~~CPiCrksv~d 190 (256)
-+=++...+..||||++.+ . +.++++|||.|+..|+.+|+.. ...+||+|+..+..
T Consensus 10 ~~~~~~~~~~~CpICld~~-~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQV-R---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ceeccCCCccCCccCCCcC-C---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3334445678999999974 2 3456899999999999999842 23689999999864
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.23 E-value=4.5e-07 Score=81.55 Aligned_cols=74 Identities=22% Similarity=0.396 Sum_probs=51.1
Q ss_pred cccccccCcceeecCCCCCCCchhhhhhcccC-----CccEEeccCCccChhhHHHHhcCC-----CCCCCCCCcccc--
Q 025186 122 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVI-- 189 (256)
Q Consensus 122 C~s~~l~~~H~C~e~~~~~~CPICle~lf~s~-----~~v~~LpCGH~~H~~Cl~~~~~~~-----~~~CPiCrksv~-- 189 (256)
++..-|.+-..=.+.+.+..|+||+|.+++.+ ......+|+|.|+..|+.+|.+.. ..+||+||..+.
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 44444444344445677899999999876531 123455899999999999999732 345999998876
Q ss_pred chhHHh
Q 025186 190 DMSRTW 195 (256)
Q Consensus 190 dm~~~~ 195 (256)
-++.+|
T Consensus 233 ~pSrf~ 238 (242)
T PHA02926 233 TMSKFY 238 (242)
T ss_pred ccccce
Confidence 344444
No 23
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=7.8e-07 Score=77.49 Aligned_cols=46 Identities=30% Similarity=0.844 Sum_probs=38.4
Q ss_pred CCCchhhhhhcccCCcc-EEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 140 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v-~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
-.|||||+. ++ +.+ +...|||.|.++|+++.++ ...+||+|+|.|.
T Consensus 132 ~~CPiCl~~-~s--ek~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDS-VS--EKVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecc-hh--hccccccccchhHHHHHHHHHHH-hCCCCCCcccccc
Confidence 689999998 33 234 4479999999999999998 5689999999765
No 24
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.08 E-value=2.7e-06 Score=60.38 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=37.9
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..||||++.|-+ + ++++|||+|-+.|+.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999997532 4 56799999999999999985 789999999884
No 25
>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=97.95 E-value=4.6e-06 Score=58.20 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.6
Q ss_pred CCchhhhhhcccCCccEEeccC-----CccChhhHHHHhcCC-CCCCCCCC
Q 025186 141 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 185 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~LpCG-----H~~H~~Cl~~~~~~~-~~~CPiCr 185 (256)
.|-||++ +.+.+...++||. |++|..|+.+|+..+ +.+||+|+
T Consensus 1 ~CrIC~~--~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3889998 3344566688994 999999999999643 56899995
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.87 E-value=3.1e-06 Score=63.06 Aligned_cols=51 Identities=31% Similarity=0.656 Sum_probs=24.0
Q ss_pred CCCCchhhhhhc-ccCCccEEe---ccCCccChhhHHHHhcC---C-------CCCCCCCCcccc
Q 025186 139 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKR---D-------KYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf-~s~~~v~~L---pCGH~~H~~Cl~~~~~~---~-------~~~CPiCrksv~ 189 (256)
+..|+||.+++. +...++.+- .|+..||..||.+|+.. + .-+||.|++.|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 457999999866 333444443 69999999999999872 1 136999999885
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.83 E-value=1.4e-05 Score=77.39 Aligned_cols=47 Identities=23% Similarity=0.642 Sum_probs=39.0
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
....||||++.+ . .++ +++|||.|+..|+..|+.. ...||+|+..+.
T Consensus 25 ~~l~C~IC~d~~-~--~Pv-itpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFF-D--VPV-LTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhh-h--Ccc-CCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 356899999975 3 244 6899999999999999974 568999999876
No 28
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=1.7e-05 Score=68.10 Aligned_cols=44 Identities=30% Similarity=0.848 Sum_probs=38.0
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 186 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrk 186 (256)
.+..||||++++ .. + ++|||||+|...|+..+.. ....||.||.
T Consensus 12 ~~~~C~iC~~~~-~~--p-~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYF-RE--P-VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHh-hc--C-ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 467899999985 43 3 8999999999999999987 6799999995
No 29
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.70 E-value=2.5e-05 Score=60.21 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=26.8
Q ss_pred eccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 159 MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 159 LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
=-|.|.||..|+..||. ....||+++++.+
T Consensus 52 G~CnHaFH~HCI~rWL~-Tk~~CPld~q~w~ 81 (88)
T COG5194 52 GVCNHAFHDHCIYRWLD-TKGVCPLDRQTWV 81 (88)
T ss_pred EecchHHHHHHHHHHHh-hCCCCCCCCceeE
Confidence 36999999999999998 5789999999875
No 30
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=2.3e-05 Score=72.77 Aligned_cols=45 Identities=29% Similarity=0.712 Sum_probs=38.0
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..|.+|||.. ......||||.|.-.|+.+|... ...||+||..+-
T Consensus 240 ~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENR----SNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCC----CCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCC
Confidence 5799999975 34568999999999999999984 567999997765
No 31
>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=97.58 E-value=5.5e-05 Score=71.15 Aligned_cols=51 Identities=25% Similarity=0.554 Sum_probs=38.9
Q ss_pred CCCCchhhhhhcccCCc-cEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~-v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
+..||||+...+.+..- ..+.+|||.|..+|++.++..+...||+|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 35799999965554321 1222899999999999977656789999998876
No 32
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=4.3e-05 Score=73.65 Aligned_cols=47 Identities=28% Similarity=0.596 Sum_probs=39.1
Q ss_pred CCCCchhhhhhcccCCccEEec-cCCccChhhHHHHhcCC--CCCCCCCCc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKRD--KYCCPICSK 186 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~Lp-CGH~~H~~Cl~~~~~~~--~~~CPiCrk 186 (256)
...|.|| +++|.-...+..+. |||+||.+|+.+|++.. +.+||+|+-
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence 4579999 77888777777776 99999999999999852 468999993
No 33
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.44 E-value=0.00012 Score=69.83 Aligned_cols=59 Identities=29% Similarity=0.678 Sum_probs=44.9
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccch-hHHhHHHHHHHH
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM-SRTWKRIDEEIE 203 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm-~~~~~~lD~~i~ 203 (256)
..|-||.|++ . -.++.||||+|.+-||..+|. .+..||.|..++..- -.--+.||++|+
T Consensus 24 LRC~IC~eyf-~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv~ 83 (442)
T KOG0287|consen 24 LRCGICFEYF-N---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIVK 83 (442)
T ss_pred HHHhHHHHHh-c---CceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHHH
Confidence 4699999985 3 346678999999999999997 688999999998731 122346666554
No 34
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=8.6e-05 Score=73.46 Aligned_cols=51 Identities=24% Similarity=0.563 Sum_probs=37.3
Q ss_pred CCCCchhhhhhc--ccCC-----------ccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLF--DSLR-----------NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf--~s~~-----------~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..+|+||+.++- ..+. ...+.||.|.||++|+.+|+...+..||+||..+-
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 457888887631 1111 23445999999999999999866678999998763
No 35
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.00014 Score=72.03 Aligned_cols=50 Identities=28% Similarity=0.618 Sum_probs=38.2
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC----CCCCCCCCccccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 190 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~----~~~CPiCrksv~d 190 (256)
++...|||||++ .. ....+.|||+|.-.||.+|+..+ .-.||||+.+|.-
T Consensus 184 ~t~~~CPICL~~-~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-PS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-CC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 448899999997 22 23344699999999999987532 4679999999873
No 36
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=97.24 E-value=7.6e-05 Score=59.32 Aligned_cols=53 Identities=26% Similarity=0.694 Sum_probs=42.9
Q ss_pred cCCccccC---CceeEcCcCCCeecCCcchhhhhccCCCCCCCceecchhhhhhhhcccccCcc
Q 025186 16 YGCKHYRR---RCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVAQVCTNCGVN 76 (256)
Q Consensus 16 ~GC~HY~R---~cki~apcC~~~y~CR~CHde~~~~~~~~~~~H~l~r~~v~~v~~~C~~Cg~~ 76 (256)
..|-||-. -..|++-+|+|+|+|-+||||.+ +|++.+...++.+..++-||++
T Consensus 13 tRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~--------~Hpf~p~~~~~~~~~~iiCGvC 68 (105)
T COG4357 13 TRCLHYHTPLDIIALKCKCCQKYYACYHCHDELE--------DHPFEPWGLQEFNPKAIICGVC 68 (105)
T ss_pred ceeeEecCccceEeeeechhhhhhhHHHHHhHHh--------cCCCccCChhhcCCccEEhhhh
Confidence 36999987 56799999999999999999987 6888887777766655555553
No 37
>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=97.21 E-value=0.00032 Score=52.24 Aligned_cols=48 Identities=17% Similarity=0.364 Sum_probs=35.9
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
+..|||+++-|. +.+++|+||+|=+.++.+|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~lM~----dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMR----DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-S----SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhh----CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 346999999653 345789999999999999998668999999988763
No 38
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=0.00019 Score=64.87 Aligned_cols=50 Identities=24% Similarity=0.630 Sum_probs=39.4
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC--CCCCCCCCccccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICSKSVID 190 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~--~~~CPiCrksv~d 190 (256)
+..-+|-||||- + ++.++..|||.|.-.||.+||... ...||+|+-.|.+
T Consensus 45 ~~~FdCNICLd~---a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---A-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---c-CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 456789999985 2 456677799999999999999742 4558999988764
No 39
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.08 E-value=0.00027 Score=52.38 Aligned_cols=56 Identities=25% Similarity=0.640 Sum_probs=29.3
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc--chhHHhHHHHHHH
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEI 202 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~--dm~~~~~~lD~~i 202 (256)
..|++|.+.|. +||..-.|.|+|.+.|+.+-+. ..||+|+.+.. |+. .-+.||..|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhccC
Confidence 46999999753 4777889999999999999764 46999999985 443 347777765
No 40
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.05 E-value=0.00018 Score=66.66 Aligned_cols=52 Identities=27% Similarity=0.523 Sum_probs=42.3
Q ss_pred CCCCCchhhhhhcccC------CccEEeccCCccChhhHHHHh-cCCCCCCCCCCcccc
Q 025186 138 MHHHCPICYEYLFDSL------RNTTVMKCGHTMHCECYHEMI-KRDKYCCPICSKSVI 189 (256)
Q Consensus 138 ~~~~CPICle~lf~s~------~~v~~LpCGH~~H~~Cl~~~~-~~~~~~CPiCrksv~ 189 (256)
.++.|.||...++.+. +..-.|.|+|.||.-|++-|- .....+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 4578999999877764 245679999999999999995 445789999998775
No 41
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.00024 Score=54.44 Aligned_cols=30 Identities=23% Similarity=0.662 Sum_probs=25.1
Q ss_pred ccCCccChhhHHHHhcC--CCCCCCCCCcccc
Q 025186 160 KCGHTMHCECYHEMIKR--DKYCCPICSKSVI 189 (256)
Q Consensus 160 pCGH~~H~~Cl~~~~~~--~~~~CPiCrksv~ 189 (256)
-|-|.||..|+.+|+.. ++-.||+||+...
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 59999999999999963 4577999998653
No 42
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00066 Score=64.75 Aligned_cols=51 Identities=27% Similarity=0.655 Sum_probs=41.9
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccc
Q 025186 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 135 e~~~~~~CPICle~lf~s~~~v~~LpCGH~-~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
|......|.|||.+ +.++.+|||-|+ |.+.|.+.+.- .+.+|||||..|..
T Consensus 286 ~~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 286 ESESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 33446789999986 367899999996 89999999874 56799999998874
No 43
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.59 E-value=0.00086 Score=61.81 Aligned_cols=46 Identities=30% Similarity=0.686 Sum_probs=37.5
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHH-HhcCCCCC-CCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYC-CPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~-~~~~~~~~-CPiCrksv~ 189 (256)
+-.|+||+|.. .....++|||.|...|+.. |... ++- ||+||..+.
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~-k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKK-KYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhh-ccccCchhhhhcc
Confidence 34699999974 3456789999999999999 9874 455 999997765
No 44
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.56 E-value=0.00062 Score=65.97 Aligned_cols=62 Identities=26% Similarity=0.573 Sum_probs=51.2
Q ss_pred cceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-CCCCCCCCCccccchh
Q 025186 130 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 192 (256)
Q Consensus 130 ~H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~-~~~~CPiCrksv~dm~ 192 (256)
-|.|++ .++.+|-.|.|-+-...+....|||.|+||..|+.++|++ ...+||-|||....|+
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 466665 5788999999988777677888999999999999999864 4578999997776665
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.48 E-value=0.0021 Score=45.09 Aligned_cols=44 Identities=30% Similarity=0.828 Sum_probs=24.4
Q ss_pred CchhhhhhcccCCccEEe--ccCCccChhhHHHHhcCCCCCCCCCCcc
Q 025186 142 CPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKS 187 (256)
Q Consensus 142 CPICle~lf~s~~~v~~L--pCGH~~H~~Cl~~~~~~~~~~CPiCrks 187 (256)
||+|.|+|..+ ...++ +||.-|.+-|+..-++..+.+||-||+.
T Consensus 1 cp~C~e~~d~~--d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDET--DKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CC--CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccC--CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 79999998443 44455 5799999999999987668899999975
No 46
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.28 E-value=0.0023 Score=67.74 Aligned_cols=53 Identities=26% Similarity=0.620 Sum_probs=39.5
Q ss_pred CCCCCCCchhhhhhc--ccCCccEEe-ccCCccChhhHHHHhcC-CCCCCCCCCccc
Q 025186 136 NSMHHHCPICYEYLF--DSLRNTTVM-KCGHTMHCECYHEMIKR-DKYCCPICSKSV 188 (256)
Q Consensus 136 ~~~~~~CPICle~lf--~s~~~v~~L-pCGH~~H~~Cl~~~~~~-~~~~CPiCrksv 188 (256)
-+....|+||.--|. +..-|.+.- .|.|-||..|+.+|+++ ++.+||+||.++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 456789999998764 332333332 47899999999999974 468899999765
No 47
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.23 E-value=0.0013 Score=62.89 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.5
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
+..|||||+-|-. ......|+|-|...||..-++.++..||.|||.++.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 4579999996533 456788999999999998888789999999999983
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.14 E-value=0.0012 Score=63.18 Aligned_cols=82 Identities=23% Similarity=0.489 Sum_probs=57.5
Q ss_pred CCCCCCchhhhhhcccC---CccEE-eccCCccChhhHHHHhcCC------CCCCCCCCcccc--chhHHhHHHHHHHHh
Q 025186 137 SMHHHCPICYEYLFDSL---RNTTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWKRIDEEIEA 204 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~---~~v~~-LpCGH~~H~~Cl~~~~~~~------~~~CPiCrksv~--dm~~~~~~lD~~i~~ 204 (256)
+.+..|-||+|.+.+.. ....+ ++|-|+|...|+..|.... ...||+||...- .-+.+|..-.+ +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 66789999999876643 11223 4699999999999998432 478999998875 44556754333 66
Q ss_pred cCCChhhhcCeeEEEc
Q 025186 205 TVMPEDYRHKKVWILC 220 (256)
Q Consensus 205 ~pmP~~y~~~~v~I~C 220 (256)
++++++|...+....|
T Consensus 237 ~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDC 252 (344)
T ss_pred cccHHHHHHHhhccch
Confidence 6778887776655433
No 49
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.12 E-value=0.0029 Score=51.07 Aligned_cols=28 Identities=29% Similarity=0.734 Sum_probs=25.2
Q ss_pred ccCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 160 KCGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 160 pCGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
-|.|.||..|+..||+ ....|||+.+.-
T Consensus 80 ~CNHaFH~hCisrWlk-tr~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLK-TRNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHh-hcCcCCCcCcce
Confidence 6999999999999998 578999998764
No 50
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0014 Score=47.38 Aligned_cols=53 Identities=34% Similarity=0.778 Sum_probs=38.6
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccchhH
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSR 193 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~-~H~~Cl~~~~~~~~~~CPiCrksv~dm~~ 193 (256)
+...+|.||+|.-.+ .++.-|||+ |.-.|-.+..+..+-.|||||..|.|.-+
T Consensus 5 ~~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIk 58 (62)
T KOG4172|consen 5 QWSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIK 58 (62)
T ss_pred ccccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHH
Confidence 345789999997333 344589997 66678666655467899999999887544
No 51
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.99 E-value=0.0021 Score=62.57 Aligned_cols=54 Identities=26% Similarity=0.608 Sum_probs=45.5
Q ss_pred eecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC-CCCCCCCCccccc
Q 025186 133 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVID 190 (256)
Q Consensus 133 C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~-~~~CPiCrksv~d 190 (256)
|.-+++-..|-||-|. .++|++=||||.+...|+..|-.+. ..+||.||-.|-.
T Consensus 363 ceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 363 CEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 4456888899999995 4789999999999999999998543 6899999988763
No 52
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.0015 Score=67.34 Aligned_cols=47 Identities=23% Similarity=0.624 Sum_probs=41.4
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
-..||+|-.. ..++++..|||.|...|+...+...+.+||.|..+++
T Consensus 643 ~LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 643 LLKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred ceeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 3579999854 4678888999999999999999888999999999998
No 53
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.96 E-value=0.0063 Score=57.21 Aligned_cols=65 Identities=22% Similarity=0.586 Sum_probs=50.3
Q ss_pred CCCCCchhhhhhcccCCccEEecc--CCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhc
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRH 213 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpC--GH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~ 213 (256)
.-.+||||.++|.- -++.| ||+....|-.+. ..+||.|+.+|++... +.++..+++...|=.|.+
T Consensus 47 ~lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred hhccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceecccccc
Confidence 34689999998733 35667 899999998754 4699999999997643 577888888888776654
No 54
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.93 E-value=0.0028 Score=65.94 Aligned_cols=75 Identities=16% Similarity=0.297 Sum_probs=51.3
Q ss_pred eeecCccCccccccccCcceee-cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 113 YFHCKRCGSCYSTSLRNNHLCI-ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 113 ffHC~~C~~C~s~~l~~~H~C~-e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
--.|..|-.+.|.-.-..-.|+ .+-....||+||....+ .......+|+|.||..||..|-+ ...+||+||+.+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~D-qL~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCND-QLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFG 171 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHH-HhhccccccccccHHHHhhhhhh-hcccCchhhhhhh
Confidence 3445555555555222223333 22345689999987444 34455679999999999999987 5689999999876
No 55
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.85 E-value=0.0044 Score=44.62 Aligned_cols=44 Identities=27% Similarity=0.613 Sum_probs=30.8
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCC
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 183 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~-~~~~~CPi 183 (256)
.....|||-+..| . +||+...|||+|=+.-+.+|+. ++..+||+
T Consensus 9 ~~~~~CPiT~~~~-~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPF-E--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChh-h--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 3457899999974 4 5899999999999999999993 35688998
No 56
>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=95.80 E-value=0.0035 Score=48.43 Aligned_cols=38 Identities=24% Similarity=0.528 Sum_probs=30.9
Q ss_pred eeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHH
Q 025186 132 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 171 (256)
Q Consensus 132 ~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~ 171 (256)
..+.-.....|+||...|+. ....+.||||.+|..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 34444566789999999877 478889999999999975
No 57
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.46 E-value=0.008 Score=56.57 Aligned_cols=46 Identities=24% Similarity=0.579 Sum_probs=37.6
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
...|-||-+++ . -....+|||+|..-||..+|. .+..||+|+....
T Consensus 25 ~lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhhee-e---cceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 35799999974 2 334569999999999999997 6899999997654
No 58
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.42 E-value=0.015 Score=56.69 Aligned_cols=51 Identities=25% Similarity=0.702 Sum_probs=39.1
Q ss_pred CCCCchhhhhhcccCCc-cEEeccCCccChhhHHHHhcC-CCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~-v~~LpCGH~~H~~Cl~~~~~~-~~~~CPiCrksv~ 189 (256)
...|||||+..-.+.+. ++.|.|||.|=+.|++.||.. ...+||.|.-...
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 46899999987555444 455899999999999999952 2467999985443
No 59
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.30 E-value=0.015 Score=64.15 Aligned_cols=74 Identities=26% Similarity=0.658 Sum_probs=56.3
Q ss_pred CCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC---------C
Q 025186 108 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---------K 178 (256)
Q Consensus 108 G~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~---------~ 178 (256)
||.+|-.||--|-.|-.-.. ....+..|.||.-+-. +-.|.+.|.|||+||.+|....|++. -
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE~L-~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTEAL-SAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehhhh-CCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56788888888877743321 2345678999998743 44799999999999999998877642 3
Q ss_pred CCCCCCCcccc
Q 025186 179 YCCPICSKSVI 189 (256)
Q Consensus 179 ~~CPiCrksv~ 189 (256)
..||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998876
No 60
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.26 E-value=0.0071 Score=41.75 Aligned_cols=41 Identities=27% Similarity=0.643 Sum_probs=27.1
Q ss_pred CchhhhhhcccCCccEEeccC-----CccChhhHHHHhcC-CCCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKR-DKYCCPIC 184 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCG-----H~~H~~Cl~~~~~~-~~~~CPiC 184 (256)
|-||++.-.++ +..+.||+ -..|..|+.+|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 56898874333 34567873 68999999999973 46789987
No 61
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.23 E-value=0.02 Score=52.32 Aligned_cols=51 Identities=29% Similarity=0.684 Sum_probs=43.9
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-------CCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~-------~~~~CPiCrksv~ 189 (256)
....||..|.-.|.+ .+.+.|-|=|.||-.|+++|... ..|+||-|+..|.
T Consensus 48 DY~pNC~LC~t~La~--gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLAS--GDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred CCCCCCceeCCcccc--CcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 457899999999866 36789999999999999999762 3699999999987
No 62
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.026 Score=52.62 Aligned_cols=53 Identities=25% Similarity=0.597 Sum_probs=43.2
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCCCCccccchh
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVIDMS 192 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~-~~~~~CPiCrksv~dm~ 192 (256)
.....||+|.|+ ++.|.+..+|||.+.--|+..=+. ..+++||.|+.++..|.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 456789999997 557888899999999999987554 23689999998887664
No 63
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.03 E-value=0.012 Score=55.59 Aligned_cols=54 Identities=30% Similarity=0.594 Sum_probs=42.3
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC----------------------CCCCCCCCCccccc
Q 025186 136 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 190 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~----------------------~~~~CPiCrksv~d 190 (256)
+-....|.|||-- |.+.....+.+|-|+||..||..+|.. ..--|||||-.|++
T Consensus 112 n~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 112 NHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3456799999987 555566889999999999999988761 12349999988874
No 64
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.01 E-value=0.024 Score=53.42 Aligned_cols=49 Identities=24% Similarity=0.480 Sum_probs=40.2
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
.+..+|+||+.... -| +.|+|+|.|.-.|++--..+...+||+||..|-
T Consensus 5 ~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 45679999998642 23 789999999999998766656778999999886
No 65
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.67 E-value=0.027 Score=40.54 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=26.8
Q ss_pred CccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 154 RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 154 ~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..-.+|||||++-..|++-+. -.-||+|.+.+.
T Consensus 18 ~~~~~~pCgH~I~~~~f~~~r---YngCPfC~~~~~ 50 (55)
T PF14447_consen 18 TKGTVLPCGHLICDNCFPGER---YNGCPFCGTPFE 50 (55)
T ss_pred cccccccccceeeccccChhh---ccCCCCCCCccc
Confidence 345679999999999998763 357999998875
No 66
>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=93.22 E-value=0.038 Score=46.43 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=31.7
Q ss_pred CCCCchhhhhhcccCCccEEeccC------CccChhhHHHHhc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 175 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCG------H~~H~~Cl~~~~~ 175 (256)
...|.||++.+-+ ...|+.+++| |+||..|+..|..
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 4689999999877 5789999998 9999999999953
No 67
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.77 E-value=0.019 Score=54.01 Aligned_cols=60 Identities=25% Similarity=0.654 Sum_probs=41.5
Q ss_pred cCcceeecCCC---CCCCchhhhhhcccCCccEEeccCCccC-hhhHHHHhcCCCCCCCCCCccccchhHHhH
Q 025186 128 RNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVIDMSRTWK 196 (256)
Q Consensus 128 ~~~H~C~e~~~---~~~CPICle~lf~s~~~v~~LpCGH~~H-~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~ 196 (256)
++++.+--... +..|.||++- ..+-..|+|||+.= .+|-..+ ..|||||+-|...-.+|+
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkrm-----~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKRM-----NECPICRQYIVRVVRIFR 349 (350)
T ss_pred hcccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhcccc-----ccCchHHHHHHHHHhhhc
Confidence 44455444333 7899999974 56789999999862 3444332 389999999987666654
No 68
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=92.56 E-value=0.078 Score=49.73 Aligned_cols=48 Identities=23% Similarity=0.563 Sum_probs=39.0
Q ss_pred CCchhhhhhcccCCccEEe--ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 141 HCPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~L--pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
.||+|.-+.+... .++.| +|||.+..+|++..+..+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np-~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNP-DLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCc-cceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 5899988766553 33333 899999999999999888999999998875
No 69
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.52 E-value=0.061 Score=47.62 Aligned_cols=52 Identities=31% Similarity=0.734 Sum_probs=35.0
Q ss_pred CCchhhhhhcccCCcc---EEeccCCccChhhHHHHhcC-----C-----CCCCCCCCcccc-chh
Q 025186 141 HCPICYEYLFDSLRNT---TVMKCGHTMHCECYHEMIKR-----D-----KYCCPICSKSVI-DMS 192 (256)
Q Consensus 141 ~CPICle~lf~s~~~v---~~LpCGH~~H~~Cl~~~~~~-----~-----~~~CPiCrksv~-dm~ 192 (256)
.|-||..+-.+.+.+- -...||-.||+-|+.+||+. + --.||.|+++|. .|+
T Consensus 167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 4555554433333222 23689999999999999973 1 146999999986 564
No 70
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.43 E-value=0.064 Score=48.92 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=28.4
Q ss_pred cccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 150 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 150 f~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
|.+..+..++.|+|+|...|...-. ...||+|+|+|-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCC---ccccccccceee
Confidence 4444566678999999999997543 238999999974
No 71
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.36 E-value=0.071 Score=51.24 Aligned_cols=48 Identities=21% Similarity=0.501 Sum_probs=35.8
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 135 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 135 e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
|.+...+|.||+++ ....+.+||||+-. |..... ...+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence 45778999999997 24578999999955 554443 24569999988863
No 72
>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=92.10 E-value=0.099 Score=42.42 Aligned_cols=37 Identities=19% Similarity=0.368 Sum_probs=28.9
Q ss_pred CeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 214 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 214 ~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
..+...|++|+........ ...||.|||++++.+++.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G~ 103 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAGK 103 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecCC
Confidence 3557899999987766432 357999999999988763
No 73
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.44 E-value=0.15 Score=42.48 Aligned_cols=38 Identities=18% Similarity=0.435 Sum_probs=28.2
Q ss_pred eeEEEccCCCCcceee-------------eeE------eeecCCCCCCccccccCCC
Q 025186 215 KVWILCNDCNDTTEVY-------------FHI------IGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 215 ~v~I~CnDC~~~s~~~-------------fH~------lg~kC~~C~SyNT~~~~~~ 252 (256)
.+...|++||....+. +|+ ...+|+.|||++.+.+++.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGR 124 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCc
Confidence 4678999999776553 222 3368999999999988763
No 74
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.29 E-value=0.13 Score=49.81 Aligned_cols=54 Identities=26% Similarity=0.645 Sum_probs=42.8
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHH
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 194 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~ 194 (256)
..+..||||...|-+ ++....|||.|...|+.+|+.. +..||.|+..+..-..+
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccchhhcc
Confidence 345789999987543 4555799999999999999985 88999999888754433
No 75
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.98 E-value=0.14 Score=41.71 Aligned_cols=37 Identities=24% Similarity=0.442 Sum_probs=28.8
Q ss_pred CeeEEEccCCCCcceee-eeEeeecCCCCCCccccccCCC
Q 025186 214 KKVWILCNDCNDTTEVY-FHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 214 ~~v~I~CnDC~~~s~~~-fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
..+.+.|++|+..+... +++ .+||.|||++...+++.
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G~ 105 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQGN 105 (117)
T ss_pred cCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecCC
Confidence 35678999999877665 333 47999999999988763
No 76
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.93 E-value=0.16 Score=46.58 Aligned_cols=48 Identities=31% Similarity=0.784 Sum_probs=39.4
Q ss_pred CCCchhhhhhcccCC---ccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 140 HHCPICYEYLFDSLR---NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 140 ~~CPICle~lf~s~~---~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
..|-||-++ |++.. ..++|.|||+|-..|+...+.++..-||.||...
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 568899998 44443 3467899999999999999987778899999994
No 77
>PHA02862 5L protein; Provisional
Probab=90.81 E-value=0.13 Score=44.09 Aligned_cols=57 Identities=23% Similarity=0.500 Sum_probs=39.1
Q ss_pred CCCCCchhhhhhcccCCccEEeccC-----CccChhhHHHHhcC-CCCCCCCCCccccchhHHhHHHHH
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKR-DKYCCPICSKSVIDMSRTWKRIDE 200 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpCG-----H~~H~~Cl~~~~~~-~~~~CPiCrksv~dm~~~~~~lD~ 200 (256)
|...|=||.+.- .+.+ -||. -..|+.|+.+|+.. ++..||+|+.... +...|+.+.+
T Consensus 1 ~~diCWIC~~~~---~e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~k 63 (156)
T PHA02862 1 MSDICWICNDVC---DERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKK 63 (156)
T ss_pred CCCEEEEecCcC---CCCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHH
Confidence 356788999861 1233 4652 78999999999974 3567999998875 4444444443
No 78
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=90.41 E-value=0.18 Score=40.84 Aligned_cols=36 Identities=25% Similarity=0.514 Sum_probs=27.8
Q ss_pred eeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 215 KVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 215 ~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
.+.+.|++|+........ ...||.|||++...+++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDTGD 103 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEccCC
Confidence 456899999987766432 235999999999988764
No 79
>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=90.33 E-value=0.26 Score=42.65 Aligned_cols=33 Identities=33% Similarity=0.775 Sum_probs=24.7
Q ss_pred CCCCchhhhhhcccCCccEEeccC-C------------ccChhhHHHHhc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCG-H------------TMHCECYHEMIK 175 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCG-H------------~~H~~Cl~~~~~ 175 (256)
+..||||||. +-..+.|-|. | .-|+.||+++.+
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4579999996 3456777773 2 469999999976
No 80
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.28 E-value=0.13 Score=50.34 Aligned_cols=47 Identities=19% Similarity=0.395 Sum_probs=37.8
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-------CCCCCCCCCC
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-------RDKYCCPICS 185 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~-------~~~~~CPiCr 185 (256)
+--.|-||.+. +....-.+.|||+|+|.+.|+..|.. .+..+||-+.
T Consensus 183 slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 183 SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 34689999997 55557788899999999999999976 1357898765
No 81
>PF04641 Rtf2: Rtf2 RING-finger
Probab=90.22 E-value=0.2 Score=45.83 Aligned_cols=50 Identities=18% Similarity=0.422 Sum_probs=39.4
Q ss_pred CCCCCCchhhhhhcccCCccEEe-ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~L-pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
...-.|||-...|.. ....+.| ||||+|=...+.+.- ....||+|.+++.
T Consensus 111 ~~~~~CPvt~~~~~~-~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNG-KHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCC-ceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 456689999998744 3455554 999999999999994 3568999999965
No 82
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.12 E-value=0.066 Score=50.95 Aligned_cols=50 Identities=30% Similarity=0.688 Sum_probs=42.1
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
.....|++|.-+|-+. ..+.-|=|+|.++||-++|+. +..||.|+..|..
T Consensus 13 n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHK 62 (331)
T ss_pred ccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHH-hccCCccceeccC
Confidence 4456899999998775 446789999999999999984 7899999988874
No 83
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.10 E-value=0.26 Score=48.02 Aligned_cols=48 Identities=21% Similarity=0.543 Sum_probs=40.3
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCC--CCCCCCCccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSKSV 188 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~--~~CPiCrksv 188 (256)
-.|||=-|. -+...|.+.|.|||.+-+.=++.+.+++. ++||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 369997775 55568899999999999999999998776 9999997543
No 84
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=89.91 E-value=0.21 Score=40.44 Aligned_cols=37 Identities=16% Similarity=0.400 Sum_probs=28.1
Q ss_pred eeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 215 KVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 215 ~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
.+...|++|+......-+. ...||.|||+++..+++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVADD 104 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEccCC
Confidence 4568999999876664322 146999999999998764
No 85
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=89.52 E-value=0.095 Score=50.48 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=45.3
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHh
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTW 195 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~ 195 (256)
+.-||.|+|+|--+.+....-|||=-+.+-|+....+.-+-+||-||+...|-...|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 445999999987765555566889999999999887766889999999887644444
No 86
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=89.17 E-value=0.19 Score=52.72 Aligned_cols=44 Identities=25% Similarity=0.554 Sum_probs=32.3
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCC
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 183 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPi 183 (256)
.....|.||--.+.. ....-+.|||.+|..|+.+|++. ...||.
T Consensus 1026 ~~~~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred cceeeeeeEeeEeec--cchhhccccccccHHHHHHHHhc-CCcCCC
Confidence 334458888765443 34556789999999999999984 568885
No 87
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.70 E-value=0.23 Score=51.29 Aligned_cols=53 Identities=21% Similarity=0.555 Sum_probs=40.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc----cccchhHHhH
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK----SVIDMSRTWK 196 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrk----sv~dm~~~~~ 196 (256)
..|+||+..+|.++-..+.|-|||++...|+...- +.+|| |.. ++.+.+.+++
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~De~~~~~~~~e~p~ 68 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKRDEDSSLMQLKEEPR 68 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCccccchhcChhhcch
Confidence 47999988888888888889999999999998763 56888 543 3345555543
No 88
>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=88.42 E-value=0.16 Score=40.98 Aligned_cols=36 Identities=22% Similarity=0.330 Sum_probs=25.2
Q ss_pred eeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 215 KVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 215 ~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
.+...|++|+..+.+..+. ..||.|+|++.+.+++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISGR 103 (113)
T ss_dssp --EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEESS
T ss_pred CCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccCC
Confidence 4568999999988776543 57999999998887753
No 89
>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=88.10 E-value=0.098 Score=39.44 Aligned_cols=65 Identities=26% Similarity=0.504 Sum_probs=39.3
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEE
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWIL 219 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~ 219 (256)
..||+|..+|-... ||+....|-..+.. ...||-|.+.+.-+.+ =--|+++
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~--~a~CPdC~~~Le~LkA-------------------CGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKK--EAFCPDCGQPLEVLKA-------------------CGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEE--EEE-TTT-SB-EEEEE-------------------TTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECcccccccee--cccCCCcccHHHHHHH-------------------hccccee
Confidence 57999999874432 78888888888865 4789999998874422 1247899
Q ss_pred ccCCCC---cceeeeeE
Q 025186 220 CNDCND---TTEVYFHI 233 (256)
Q Consensus 220 CnDC~~---~s~~~fH~ 233 (256)
||.|+. |+.|.|.+
T Consensus 53 C~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 53 CNHCHGLISKKRVRFEF 69 (70)
T ss_dssp -TTTT-EE-TTTSEEEE
T ss_pred eccCCceeecceEEEEe
Confidence 999994 66677654
No 90
>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=87.99 E-value=0.26 Score=34.69 Aligned_cols=32 Identities=31% Similarity=0.745 Sum_probs=23.6
Q ss_pred EEeccC-CccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 157 TVMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 157 ~~LpCG-H~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..+.|. |.+...|+..++. .+..||||.+++-
T Consensus 14 ~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHhc-cccCCCcccCcCc
Confidence 466896 9999999999998 5789999998874
No 91
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.95 E-value=0.62 Score=45.63 Aligned_cols=49 Identities=24% Similarity=0.747 Sum_probs=39.2
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
..+-.|-||..-|+ +.+.+||||.|...|++.-+. ....||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~----~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY----PPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC----CCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 55778999988653 344559999999999999776 56789999998874
No 92
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=87.91 E-value=0.17 Score=51.23 Aligned_cols=53 Identities=21% Similarity=0.487 Sum_probs=43.8
Q ss_pred eecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc----CCCCCCCCCCcccc
Q 025186 133 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK----RDKYCCPICSKSVI 189 (256)
Q Consensus 133 C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~----~~~~~CPiCrksv~ 189 (256)
=.|+..+..|-+|-|+- ++.++..|.|.|.+.|+.+|+. +.+.+||+|.+.+.
T Consensus 530 ~~enk~~~~C~lc~d~a----ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPA----EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCChh----hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 35777888999999873 4677889999999999988876 34689999998875
No 93
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.43 E-value=0.29 Score=51.94 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=34.2
Q ss_pred ceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc
Q 025186 131 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 175 (256)
Q Consensus 131 H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~ 175 (256)
+.+.--.....|-+|.-.|+. ++-.+.||||.||+.|+.+-..
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 444434556789999998776 5889999999999999988765
No 94
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.39 E-value=0.31 Score=45.99 Aligned_cols=67 Identities=22% Similarity=0.413 Sum_probs=48.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhcCCChhh
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDY 211 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y 211 (256)
..|-||-+++ . ..++..|||+|...|...-++ ...+|+||.+.+......=..|...|...++-.+|
T Consensus 242 f~c~icr~~f-~---~pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~~kks~~E~ 308 (313)
T KOG1813|consen 242 FKCFICRKYF-Y---RPVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKLKKSDSEY 308 (313)
T ss_pred cccccccccc-c---cchhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHhhhhhccc
Confidence 4599999984 3 346789999999999988776 46899999999875433223556666655555444
No 95
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=87.09 E-value=0.34 Score=43.64 Aligned_cols=59 Identities=20% Similarity=0.474 Sum_probs=42.8
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHH
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIE 203 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~ 203 (256)
-.|-||-++ |.| .++..|||.|...|+-.=.+ ...+|-+|.+..-..-.+-..||.++.
T Consensus 197 F~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 197 FLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eeehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 379999998 443 45778999999999877665 467999999987644323345565553
No 96
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.09 E-value=0.46 Score=50.35 Aligned_cols=39 Identities=28% Similarity=0.630 Sum_probs=31.0
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 025186 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 186 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrk 186 (256)
.|..|--.| .-|++-..|||.||..|+. . +...||-|+-
T Consensus 842 kCs~C~~~L---dlP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~ 880 (933)
T KOG2114|consen 842 KCSACEGTL---DLPFVHFLCGHSYHQHCLE---D-KEDKCPKCLP 880 (933)
T ss_pred eecccCCcc---ccceeeeecccHHHHHhhc---c-CcccCCccch
Confidence 566666554 2478889999999999998 2 5689999998
No 97
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.88 E-value=0.66 Score=43.04 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=46.4
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEe-ccCCccChhhHHHHhcCCCCCCCCCCccccchh
Q 025186 134 IENSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 192 (256)
Q Consensus 134 ~e~~~~~~CPICle~lf~s~~~v~~L-pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~ 192 (256)
+-.+..-.|||+.+.|... .+..+| |+||.+-..|.+.++. ..--+||+.+.+-|..
T Consensus 216 ~a~s~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 216 IAASKRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKDRD 273 (303)
T ss_pred hhhccceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcccc
Confidence 3344567899999997665 566666 8999999999999998 5788999999998643
No 98
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.40 E-value=0.38 Score=35.18 Aligned_cols=32 Identities=31% Similarity=0.862 Sum_probs=19.9
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
...|.|||.. -=|.|.+|+-+. ..|.|++||+
T Consensus 25 ~F~CPnCG~~-~I~RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEV-IIYRCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCe-eEeechhHHhcC-----CceECCCCCC
Confidence 4567777764 123477776554 3677777774
No 99
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=85.28 E-value=0.62 Score=40.35 Aligned_cols=48 Identities=29% Similarity=0.571 Sum_probs=34.6
Q ss_pred CCCCCCchhhhhhcccCCccEEeccC--C---ccChhhHHHHhcC-CCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCG--H---TMHCECYHEMIKR-DKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCG--H---~~H~~Cl~~~~~~-~~~~CPiCrksv~ 189 (256)
.++..|=||.+.- + . ..-||. . ..|++|++.|+.. +..+||+|+....
T Consensus 6 ~~~~~CRIC~~~~-~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY-D--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC-C--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3467899998862 1 1 234663 4 6799999999974 3678999998764
No 100
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.19 E-value=0.68 Score=38.05 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=26.8
Q ss_pred CeeEEEccCCCCcceee-e---eE-eeecCCCCCCccccccCCC
Q 025186 214 KKVWILCNDCNDTTEVY-F---HI-IGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 214 ~~v~I~CnDC~~~s~~~-f---H~-lg~kC~~C~SyNT~~~~~~ 252 (256)
..+...| +|+..+... + |+ ....||.|||++...+++.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 109 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGR 109 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCC
Confidence 3457899 999875432 1 11 2357999999999988763
No 101
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=84.12 E-value=0.41 Score=50.68 Aligned_cols=52 Identities=23% Similarity=0.521 Sum_probs=38.3
Q ss_pred CCCCCCchhhhhhcccCCccEE-eccCCccChhhHHHHhcC------CCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKR------DKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~-LpCGH~~H~~Cl~~~~~~------~~~~CPiCrksv~ 189 (256)
...-.|.||+|.+-.+ .++.. -.|=|+||..||.+|.+. ...+||-|.....
T Consensus 189 ~~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 189 NRKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred cCceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 3456899999987654 44433 357799999999999863 3578999984443
No 102
>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=84.04 E-value=1.2 Score=30.60 Aligned_cols=37 Identities=19% Similarity=0.329 Sum_probs=25.8
Q ss_pred EEEccCCCCcceeeeeE---eeecCCCCCCccc-cccCCCC
Q 025186 217 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNT-RSIAPPV 253 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~---lg~kC~~C~SyNT-~~~~~~~ 253 (256)
...|++|+...++-..+ ....|+.|||-+. |++++|.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~~ 45 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAVG 45 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEecccc
Confidence 46899999877764322 1247999999886 6666553
No 103
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.42 E-value=0.51 Score=45.80 Aligned_cols=50 Identities=30% Similarity=0.628 Sum_probs=41.9
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 025186 136 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 190 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~d 190 (256)
.+.+..||||... ....++-||||--...||.+.+. ++.+|=.|+.++.+
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 4667899999874 24556779999999999999988 57899999999986
No 104
>PF14353 CpXC: CpXC protein
Probab=83.16 E-value=0.25 Score=40.14 Aligned_cols=56 Identities=13% Similarity=0.384 Sum_probs=34.9
Q ss_pred CCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeee
Q 025186 179 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQ 236 (256)
Q Consensus 179 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~ 236 (256)
.+||.|+++.. ..+|..+|......-...-..+..-.+.|..||++..+.+=+|++
T Consensus 2 itCP~C~~~~~--~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFE--FEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeE--EEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 58999999886 224554443111111122234556689999999998777666654
No 105
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=82.10 E-value=1.1 Score=36.94 Aligned_cols=38 Identities=26% Similarity=0.390 Sum_probs=29.9
Q ss_pred cCeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 213 HKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 213 ~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
...+.+.|.||+......-|.+. ||.|+|-|.+++++.
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G~ 103 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGGD 103 (115)
T ss_pred EeccEEEeccCCCeecchhheeE--CCCCCCCceEEecCC
Confidence 34567999999887666555543 999999999998864
No 106
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.67 E-value=1 Score=43.80 Aligned_cols=65 Identities=17% Similarity=0.369 Sum_probs=46.4
Q ss_pred CccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCCCCccc
Q 025186 120 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSV 188 (256)
Q Consensus 120 ~~C~s~~l~~~H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~-~~~~~CPiCrksv 188 (256)
+.|....|-++-.=.....+.+|.||.+.+ +-+.++||||-|.--|.-.... .....||+||..-
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 556665555555544456678999999864 5677899999999999765432 2356899999753
No 107
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.51 E-value=0.77 Score=33.69 Aligned_cols=32 Identities=31% Similarity=0.842 Sum_probs=19.7
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
...|.|||..+ =|.|.+|+.+. .+|-|++||+
T Consensus 27 ~F~CPnCGe~~-I~Rc~~CRk~g-----~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVE-IYRCAKCRKLG-----NPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCcee-eehhhhHHHcC-----CceECCCcCc
Confidence 45677777433 35677776654 3677777774
No 108
>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=78.56 E-value=1.2 Score=30.15 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.5
Q ss_pred ccCCccChhhHHHHhcCCCC-CCCCC
Q 025186 160 KCGHTMHCECYHEMIKRDKY-CCPIC 184 (256)
Q Consensus 160 pCGH~~H~~Cl~~~~~~~~~-~CPiC 184 (256)
.|+=.||..|+..|+++... +||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 36667999999999985433 69987
No 109
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.87 E-value=1.8 Score=31.12 Aligned_cols=36 Identities=25% Similarity=0.651 Sum_probs=27.7
Q ss_pred CCCCCCchhhhhhcccCCccEE-eccCCccChhhHHHH
Q 025186 137 SMHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEM 173 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~-LpCGH~~H~~Cl~~~ 173 (256)
-+...|++|.+.|.+. +++++ --||=.+|+.|++..
T Consensus 3 ~~~~~C~~Cg~~~~~~-dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDG-DDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCC-CCEEECCCCCCcccHHHHhhC
Confidence 3467899999996655 45555 569999999998654
No 110
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.29 E-value=0.96 Score=39.65 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=25.4
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccCh
Q 025186 136 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 167 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~ 167 (256)
.....+|.||||+|... +.+..|||-=++|+
T Consensus 174 ~ddkGECvICLEdL~~G-dtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAG-DTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccCC-CceeccceEEEeec
Confidence 35578999999998664 78899999888776
No 111
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=76.05 E-value=2.6 Score=39.48 Aligned_cols=114 Identities=24% Similarity=0.510 Sum_probs=66.0
Q ss_pred cccceeeCCcc-ccccCCC---CCCcccCCCCCccccCCccceeecCccCcccccc-ccCcceeecCCCCCCCchhhhhh
Q 025186 75 VNMGEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS-LRNNHLCIENSMHHHCPICYEYL 149 (256)
Q Consensus 75 ~~f~~y~C~~C-~l~dd~~---~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~-l~~~H~C~e~~~~~~CPICle~l 149 (256)
..-++|-|..| |-|.... .-+|+||+- .-..-|.|..||-=|..- ...-|.=.- ...-.|+||.-.
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH-~l~c~C~iCGKa- 196 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTH-TLPCECGICGKA- 196 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhcc-CCCccccccccc-
Confidence 34456666666 5554432 237888753 125578888888766431 111122111 135678899875
Q ss_pred cccCCccEEeccCCccChhhHHHHhcC---------CCCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEc
Q 025186 150 FDSLRNTTVMKCGHTMHCECYHEMIKR---------DKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILC 220 (256)
Q Consensus 150 f~s~~~v~~LpCGH~~H~~Cl~~~~~~---------~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~C 220 (256)
|+- .||.. .-|.||.|+|.+.|.+ +|-+-++.. .+.+ ...|
T Consensus 197 FSR-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRS----NLRAHmQTH------S~~K-~~qC 246 (279)
T KOG2462|consen 197 FSR-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRS----NLRAHMQTH------SDVK-KHQC 246 (279)
T ss_pred ccc-------------------hHHhhcccccccCCCCccCCcccchhcchH----HHHHHHHhh------cCCc-cccC
Confidence 652 26652 3488999999999985 444544442 2333 5678
Q ss_pred cCCCCcc
Q 025186 221 NDCNDTT 227 (256)
Q Consensus 221 nDC~~~s 227 (256)
--|+++.
T Consensus 247 ~~C~KsF 253 (279)
T KOG2462|consen 247 PRCGKSF 253 (279)
T ss_pred cchhhHH
Confidence 8888654
No 112
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.02 E-value=2.5 Score=28.59 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=24.3
Q ss_pred eEEEccCCCCcceeeeeEeeecCCCCCCccccccCC
Q 025186 216 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 216 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 251 (256)
..+.|.+||+.....-.....+|+.||+.-....++
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKERP 37 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccCC
Confidence 457899999866544433367999999866544433
No 113
>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=74.65 E-value=1.1 Score=41.65 Aligned_cols=50 Identities=24% Similarity=0.602 Sum_probs=41.4
Q ss_pred CCCCchhhhhhcccCCccEEe--c-cCCccChhhHHHHhcCCCCCCC--CCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVM--K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~L--p-CGH~~H~~Cl~~~~~~~~~~CP--iCrksv~ 189 (256)
+..||||..+.+-++ ++++| | |=|-|..+|.+..+..+.-.|| -|.|.+-
T Consensus 10 d~~CPvCksDrYLnP-dik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNP-DIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCC-CeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 458999999988774 45544 5 9999999999999988888999 7888765
No 114
>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=73.29 E-value=2.9 Score=25.38 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=15.7
Q ss_pred CCCCCCCccccchhHHhHHHHH
Q 025186 179 YCCPICSKSVIDMSRTWKRIDE 200 (256)
Q Consensus 179 ~~CPiCrksv~dm~~~~~~lD~ 200 (256)
..||+|.+.+ .+....+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 55566677774
No 115
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=73.25 E-value=2.8 Score=44.22 Aligned_cols=78 Identities=19% Similarity=0.362 Sum_probs=48.4
Q ss_pred CcccCCCCCccccCCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHh
Q 025186 95 GQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMI 174 (256)
Q Consensus 95 ~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~ 174 (256)
-+|-|+.|+-=-+++++ -- |+.|-+.+. ..|.||-..+-. ..+.---|||..|..++.+|+
T Consensus 752 i~~~~~nc~a~~~~~~~--~~---c~rc~s~a~------------~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~ 812 (839)
T KOG0269|consen 752 IHYACPNCDAPMVLTKL--WQ---CDRCESRAS------------AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWF 812 (839)
T ss_pred eeccccccCCccccccc--ee---echHHHHhh------------cCceeecceeee--eEeecccccccccHHHHHHHH
Confidence 46777777655555544 33 444444331 258888776533 233334699999999999999
Q ss_pred cCCCCCCCC-------CCccccchh
Q 025186 175 KRDKYCCPI-------CSKSVIDMS 192 (256)
Q Consensus 175 ~~~~~~CPi-------Crksv~dm~ 192 (256)
. .+..||. +++++.||.
T Consensus 813 ~-~~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 813 F-KASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred h-cCCCCccccCCccccccccchhh
Confidence 8 4566776 344555653
No 116
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=72.71 E-value=1.8 Score=26.86 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=23.0
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
|+.|.+.+..+. ..+..=|..||..|| +|..|+++|.
T Consensus 2 C~~C~~~i~~~~--~~~~~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGE--LVLRALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCc--EEEEeCCccccccCC---------CCcccCCcCc
Confidence 677877765531 222222788888765 6777887764
No 117
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.35 E-value=0.39 Score=47.02 Aligned_cols=51 Identities=22% Similarity=0.446 Sum_probs=43.9
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 138 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 138 ~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
.-..+.||.+.|...-+....+.|||..|..++.+||.. ..++|.|+..+-
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~ 245 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELP 245 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhh
Confidence 345799999998776567888999999999999999984 789999998885
No 118
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=71.96 E-value=3 Score=43.48 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=36.8
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCC-CCCCCCcccc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKY-CCPICSKSVI 189 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~-~CPiCrksv~ 189 (256)
..|+||++ .+...+.+|||.|-..|+.+.+..... .||+|+-.+.
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 78999999 257788899999999999998875443 5999996554
No 119
>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=70.72 E-value=2.2 Score=29.67 Aligned_cols=42 Identities=26% Similarity=0.795 Sum_probs=20.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHH--HHhc----CCCCCCCCCCcc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYH--EMIK----RDKYCCPICSKS 187 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~--~~~~----~~~~~CPiCrks 187 (256)
..|||-...|. .|++-..|.|. +||+ .||+ ....+||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 36888887653 48888889876 4554 3444 346789999874
No 120
>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=70.26 E-value=3.1 Score=23.00 Aligned_cols=20 Identities=35% Similarity=0.737 Sum_probs=13.5
Q ss_pred CCCCCCCccccchhHHhHHH
Q 025186 179 YCCPICSKSVIDMSRTWKRI 198 (256)
Q Consensus 179 ~~CPiCrksv~dm~~~~~~l 198 (256)
|.||+|.+.+.+...+++-+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 47999999999877665543
No 121
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=68.05 E-value=3.6 Score=39.32 Aligned_cols=44 Identities=32% Similarity=0.717 Sum_probs=36.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 186 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrk 186 (256)
..||.|.--| +.+++.--|||.|..+||..-|..+.+.||.|..
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 5799998754 2466666689999999999877667899999987
No 122
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.88 E-value=4.4 Score=38.96 Aligned_cols=45 Identities=22% Similarity=0.616 Sum_probs=37.2
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC--CCCCCCCC
Q 025186 140 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 185 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~--~~~CPiCr 185 (256)
-.|||=-|. -+...|...|.|||.+=..=++.+-+++ .++||.|-
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 368987764 6666888999999999999999987754 58899996
No 123
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=67.37 E-value=3.9 Score=39.14 Aligned_cols=52 Identities=31% Similarity=0.510 Sum_probs=39.8
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
+-...||||.+++-.......--|||+-++..|+..-.. .+.+||.||+...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 334789999998744434444457899999999988877 5889999997765
No 124
>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 PHA03096 p28-like protein; Provisional
Probab=66.56 E-value=2.9 Score=39.20 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=31.5
Q ss_pred CCCchhhhhhcccC---CccEEe-ccCCccChhhHHHHhcCC--CCCCCCCCc
Q 025186 140 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSK 186 (256)
Q Consensus 140 ~~CPICle~lf~s~---~~v~~L-pCGH~~H~~Cl~~~~~~~--~~~CPiCrk 186 (256)
-.|-||+|...... ..-..| .|-|.|...|+..|.... ..+||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46889998866531 122335 699999999999998743 234555553
No 126
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=66.56 E-value=4.3 Score=27.74 Aligned_cols=27 Identities=19% Similarity=0.484 Sum_probs=18.8
Q ss_pred EEEccCCCCcceeeeeEeeecCCCCCCc
Q 025186 217 WILCNDCNDTTEVYFHIIGQKCSHCKSY 244 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~lg~kC~~C~Sy 244 (256)
...|.+||+..+... --..+|+.||+-
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCce
Confidence 467888888665552 345788888873
No 127
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=66.07 E-value=4.5 Score=28.54 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=23.3
Q ss_pred eeEEEccCCCCcceeeeeEeeecCCCCCCc
Q 025186 215 KVWILCNDCNDTTEVYFHIIGQKCSHCKSY 244 (256)
Q Consensus 215 ~v~I~CnDC~~~s~~~fH~lg~kC~~C~Sy 244 (256)
+..+.|.+||+.-+...---+.+|+.|||-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 457889999988765555678899999973
No 128
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=64.81 E-value=5.3 Score=24.76 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=14.3
Q ss_pred CCCccccCCccc-eeecCccC
Q 025186 101 DCGICRIGGREN-YFHCKRCG 120 (256)
Q Consensus 101 ~CgiCRvG~~~~-ffHC~~C~ 120 (256)
.|++|+.-.... +|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477777655444 89998888
No 129
>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=63.63 E-value=4.3 Score=32.88 Aligned_cols=25 Identities=36% Similarity=1.088 Sum_probs=18.0
Q ss_pred hcccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 68 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
.+|.+||+.| || .+|.+-.|++||.
T Consensus 10 R~Cp~CG~kF----------YD--Lnk~PivCP~CG~ 34 (108)
T PF09538_consen 10 RTCPSCGAKF----------YD--LNKDPIVCPKCGT 34 (108)
T ss_pred ccCCCCcchh----------cc--CCCCCccCCCCCC
Confidence 4577777754 75 4688888988885
No 130
>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=62.34 E-value=3.3 Score=38.81 Aligned_cols=52 Identities=27% Similarity=0.577 Sum_probs=34.7
Q ss_pred CCeecCCcchhhhhccCCCCCCCceecchhhhhhhhcccccCcccceeeCCccccc
Q 025186 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVAQVCTNCGVNMGEYFCDICKFY 88 (256)
Q Consensus 33 ~~~y~CR~CHde~~~~~~~~~~~H~l~r~~v~~v~~~C~~Cg~~f~~y~C~~C~l~ 88 (256)
|++|.|-+|++-.-. |-.-.|+-.....+.-+..|.+|+. +|.|.|..||.-
T Consensus 140 Grif~CsfC~~flCE---DDQFEHQAsCQvLe~E~~KC~SCNr-lGq~sCLRCK~c 191 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCE---DDQFEHQASCQVLESETFKCQSCNR-LGQYSCLRCKIC 191 (314)
T ss_pred CeEEEeecCCCeeec---cchhhhhhhhhhhhccccccccccc-ccchhhhheeee
Confidence 679999999986531 1122344443333333778999976 899999999864
No 131
>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=62.28 E-value=7.7 Score=26.94 Aligned_cols=22 Identities=23% Similarity=0.585 Sum_probs=14.3
Q ss_pred CCCCCCCCccccchhHHhHHHHH
Q 025186 178 KYCCPICSKSVIDMSRTWKRIDE 200 (256)
Q Consensus 178 ~~~CPiCrksv~dm~~~~~~lD~ 200 (256)
.|+||.|++ -.+....++-++.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 588999998 5665555554433
No 132
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.32 E-value=2.9 Score=44.20 Aligned_cols=43 Identities=35% Similarity=0.642 Sum_probs=29.8
Q ss_pred CCchhhhhhcccC---CccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 025186 141 HCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 185 (256)
Q Consensus 141 ~CPICle~lf~s~---~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCr 185 (256)
.|.-|.+..-.+. ..++++.|||+||..|+.....+++ |-+|.
T Consensus 786 rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 786 RCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred hhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 5666666554333 5689999999999999987665332 55554
No 133
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=60.42 E-value=8.3 Score=27.79 Aligned_cols=30 Identities=23% Similarity=0.666 Sum_probs=23.1
Q ss_pred eEEEccCCCCcceeeeeEeeecCCCCCCccccccC
Q 025186 216 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIA 250 (256)
Q Consensus 216 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~ 250 (256)
..+.|..||+. ...| +-|+.||.|+-+++-
T Consensus 26 ~l~~C~~CG~~--~~~H---~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 26 GLVECPNCGEP--KLPH---RVCPSCGYYKGREVV 55 (57)
T ss_pred cceECCCCCCc--cCCe---EECCCCCcCCCEEee
Confidence 45789999974 4456 459999999999863
No 134
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.58 E-value=2.9 Score=39.01 Aligned_cols=69 Identities=26% Similarity=0.502 Sum_probs=45.1
Q ss_pred CCCCCCCchhhhhhcccCCccEEecc---C--CccChhhHHHHhcCC-------CCCCCCCCcccc----ch---hHHhH
Q 025186 136 NSMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-------KYCCPICSKSVI----DM---SRTWK 196 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~~~v~~LpC---G--H~~H~~Cl~~~~~~~-------~~~CPiCrksv~----dm---~~~~~ 196 (256)
...+.-|=||++.=.+.....-+=|| | |..|..|+..|+.+. .-.||.|+.... .| +...+
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~Le 96 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVLE 96 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHHH
Confidence 34567899999753333222234577 3 999999999999743 347999997654 22 23345
Q ss_pred HHHHHHHh
Q 025186 197 RIDEEIEA 204 (256)
Q Consensus 197 ~lD~~i~~ 204 (256)
++|..|..
T Consensus 97 ~~d~~i~r 104 (293)
T KOG3053|consen 97 RLDILIFR 104 (293)
T ss_pred HhhhHHhh
Confidence 66766655
No 135
>PF12773 DZR: Double zinc ribbon
Probab=57.94 E-value=8.3 Score=26.02 Aligned_cols=12 Identities=33% Similarity=0.977 Sum_probs=8.5
Q ss_pred hhcccccCcccc
Q 025186 67 AQVCTNCGVNMG 78 (256)
Q Consensus 67 ~~~C~~Cg~~f~ 78 (256)
+..|.+||..+.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 456777777776
No 136
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=57.81 E-value=7.6 Score=39.41 Aligned_cols=57 Identities=23% Similarity=0.282 Sum_probs=26.4
Q ss_pred chhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 190 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 190 dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
|.++.+..++...+.+.+|-.--+ ...-.|++||..... +.+||.|||-|+.++++.
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in-~~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~Rv 521 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTIN-PPIDICPDCGYIGGE-----GDKCPKCGSENIEVYSRV 521 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE---EEEETTT---S-------EEE-CCC----EEEEB-S
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEe-cCcccccCCCcCCCC-----CCCCCCCCCcccceEEEe
Confidence 555566666666664555533222 235679999986653 468999999998887653
No 137
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.77 E-value=8.1 Score=42.19 Aligned_cols=49 Identities=24% Similarity=0.583 Sum_probs=35.9
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCcccc
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 124 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s 124 (256)
...|.+||......+|..|.-. ...+|.|+.||.--.+ ..|.+||.=.+
T Consensus 626 ~RfCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~~-----y~CPKCG~El~ 674 (1121)
T PRK04023 626 RRKCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVEE-----DECEKCGREPT 674 (1121)
T ss_pred CccCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCCC-----CcCCCCCCCCC
Confidence 5689999999888889999644 4678899999655333 44777776443
No 138
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=57.60 E-value=5.3 Score=40.01 Aligned_cols=58 Identities=28% Similarity=0.643 Sum_probs=27.7
Q ss_pred eeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCccccccc--cCcceeecCCCCCCCchhhhhhccc
Q 025186 80 YFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDS 152 (256)
Q Consensus 80 y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l--~~~H~C~e~~~~~~CPICle~lf~s 152 (256)
|||..|.-. .|+-|-....+ .+=|..|-.=++.+. .++.+|..+- -+||+|.-.|...
T Consensus 6 ~fC~~C~~i------------rc~~c~~~Ei~-~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~ 65 (483)
T PF05502_consen 6 YFCEHCHKI------------RCPRCVSEEID-SYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVR 65 (483)
T ss_pred eeccccccc------------CChhhcccccc-eeECccccccCChhhheeccceecccc--ccCCCCCCcceeE
Confidence 777777544 12233333323 333555544444332 2445555332 3677777666443
No 139
>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=57.07 E-value=12 Score=23.91 Aligned_cols=27 Identities=33% Similarity=0.587 Sum_probs=17.9
Q ss_pred EEEccCCCCcceeeeeE---eeecCCCCCC
Q 025186 217 WILCNDCNDTTEVYFHI---IGQKCSHCKS 243 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~---lg~kC~~C~S 243 (256)
...|.+||...++..-+ ....|+.||+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 46788888766554322 2467888888
No 140
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.86 E-value=5.1 Score=38.95 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=27.6
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 175 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~ 175 (256)
...|+||..+..+......++.|||.|...|..++++
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 5689999933333323333789999999999999987
No 141
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=56.78 E-value=5.6 Score=39.90 Aligned_cols=33 Identities=18% Similarity=0.773 Sum_probs=27.5
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 175 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~ 175 (256)
+..||||... |. +.++|||||.+.+.|...-+.
T Consensus 4 elkc~vc~~f-~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGSF-YR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehhh-cc---CceEeecccHHHHHHHHhhcc
Confidence 5679999985 43 568999999999999987765
No 142
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=54.64 E-value=8 Score=43.10 Aligned_cols=52 Identities=31% Similarity=0.650 Sum_probs=41.9
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchh
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 192 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~ 192 (256)
+....|+||++-|-. .-.+..|||.+-..|+..|+. .+..||+|....+|-.
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGDFG 1202 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhhhc
Confidence 344599999998743 345678999999999999998 5789999997777644
No 143
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=54.10 E-value=8.9 Score=33.46 Aligned_cols=49 Identities=24% Similarity=0.388 Sum_probs=35.4
Q ss_pred CCCCCCCCccccchhHHhHHHHHHHHhcCCC-hhhhcCeeEEEccCCCCcceeeeeE
Q 025186 178 KYCCPICSKSVIDMSRTWKRIDEEIEATVMP-EDYRHKKVWILCNDCNDTTEVYFHI 233 (256)
Q Consensus 178 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP-~~y~~~~v~I~CnDC~~~s~~~fH~ 233 (256)
-.+||.|+-.+...+. +.....+| ..|.+......|--|++.-+..-||
T Consensus 97 ~~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 97 FSRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred cccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCcccccCchHH
Confidence 5689999999986654 23333344 4577777778899999988777776
No 144
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.95 E-value=11 Score=25.40 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.4
Q ss_pred cccCCCCC
Q 025186 96 QFHCDDCG 103 (256)
Q Consensus 96 ~yHC~~Cg 103 (256)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555555
No 145
>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=53.60 E-value=13 Score=24.71 Aligned_cols=32 Identities=28% Similarity=0.491 Sum_probs=21.8
Q ss_pred EEEccCCCCcceeeeeE---eeecCCCCCCccccc
Q 025186 217 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNTRS 248 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~---lg~kC~~C~SyNT~~ 248 (256)
...|.+||...++-..+ ....|+.||+-+.++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVRR 39 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEE
Confidence 46799999777654432 346899999955543
No 146
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=53.42 E-value=10 Score=38.51 Aligned_cols=56 Identities=21% Similarity=0.310 Sum_probs=35.7
Q ss_pred chhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCC
Q 025186 190 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 190 dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 251 (256)
|-++++..++.......++-. -+..+. .|++||.... -++.+|+.|||-|+.++++
T Consensus 493 n~~al~~lv~~a~~~~~~y~~-~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~R 548 (555)
T cd01675 493 NPEALEALVKKAAKRGVIYFG-INTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVISR 548 (555)
T ss_pred CHHHHHHHHHHHHHcCCceEE-EecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEEe
Confidence 445555555655444344433 334445 9999997553 3357999999998776654
No 147
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=52.40 E-value=18 Score=25.67 Aligned_cols=47 Identities=19% Similarity=0.427 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCChhhhcCeeEEEccCCCCcc----eeeeeEeeecCCCCCCcc
Q 025186 196 KRIDEEIEATVMPEDYRHKKVWILCNDCNDTT----EVYFHIIGQKCSHCKSYN 245 (256)
Q Consensus 196 ~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s----~~~fH~lg~kC~~C~SyN 245 (256)
+.||.++..-|+.++ .+--+.|.-|.... ...|-.+--+|+.|+..|
T Consensus 4 ki~d~L~G~d~~~~~---~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPS---NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCcccc---CceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 467777777774333 23346699998644 223445567999999987
No 148
>PHA00626 hypothetical protein
Probab=52.29 E-value=11 Score=27.55 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=15.9
Q ss_pred cccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 69 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
.|++||..- -+-|.+|+.+. +.|-|++||.
T Consensus 2 ~CP~CGS~~-Ivrcg~cr~~s-----nrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGN-IAKEKTMRGWS-----DDYVCCDCGY 31 (59)
T ss_pred CCCCCCCce-eeeeceecccC-----cceEcCCCCC
Confidence 477777631 12566665542 3466666654
No 149
>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=51.86 E-value=9.1 Score=27.51 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=18.3
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
++.|..||....+ ......|.|+.||.
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCC
Confidence 7889999887765 23445666666664
No 150
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=49.73 E-value=14 Score=41.27 Aligned_cols=33 Identities=30% Similarity=0.731 Sum_probs=23.9
Q ss_pred hcccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 68 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
..|.+||...-..||+.|.-.- +.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t----e~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT----EPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCcC----CCceeCccCCC
Confidence 6799999876667888886442 35677777776
No 151
>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=49.61 E-value=10 Score=21.24 Aligned_cols=15 Identities=53% Similarity=1.006 Sum_probs=11.7
Q ss_pred CCCCCCCccccchhH
Q 025186 179 YCCPICSKSVIDMSR 193 (256)
Q Consensus 179 ~~CPiCrksv~dm~~ 193 (256)
|+||+|++++.+.+.
T Consensus 1 y~C~~C~~~f~~~~~ 15 (23)
T PF00096_consen 1 YKCPICGKSFSSKSN 15 (23)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCccCCHHH
Confidence 579999999986544
No 152
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=49.31 E-value=6.5 Score=35.63 Aligned_cols=51 Identities=24% Similarity=0.406 Sum_probs=38.6
Q ss_pred CCCCchhhhhhcccCCccEEeccC-----CccChhhHHHHhcC-CCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKR-DKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCG-----H~~H~~Cl~~~~~~-~~~~CPiCrksv~ 189 (256)
+..|=||.+..+.+.......||. ...|+.|+..|+.. ++..|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 368999999876653334556772 88899999999863 4678999998665
No 153
>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=48.47 E-value=14 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.752 Sum_probs=22.4
Q ss_pred eEEEccCCCCcceeeeeEeeecCCCCCCcccccc
Q 025186 216 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 249 (256)
Q Consensus 216 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 249 (256)
..+.|..||+. ...| +-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~~~H---~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KLPH---RVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--ccCe---eECCccCeECCEEc
Confidence 45789999973 4455 45999999999876
No 154
>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=48.12 E-value=15 Score=26.23 Aligned_cols=35 Identities=26% Similarity=0.445 Sum_probs=21.3
Q ss_pred EEEccCCCCccee--eeeEeeecCCCCCCccccccCC
Q 025186 217 WILCNDCNDTTEV--YFHIIGQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 217 ~I~CnDC~~~s~~--~fH~lg~kC~~C~SyNT~~~~~ 251 (256)
.|.|-.|++.-.. .|-.|-.||+.|+..|.-....
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 3556666642211 2335677999999998776544
No 155
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=48.06 E-value=19 Score=34.28 Aligned_cols=23 Identities=35% Similarity=1.003 Sum_probs=17.0
Q ss_pred EEEccCCCCcceeeeeEeeecCCCCCC
Q 025186 217 WILCNDCNDTTEVYFHIIGQKCSHCKS 243 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~lg~kC~~C~S 243 (256)
...|+-|+ ..+|+.-.||++||+
T Consensus 212 yL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 212 YLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 57788777 567777778888874
No 156
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=47.23 E-value=26 Score=34.10 Aligned_cols=53 Identities=25% Similarity=0.523 Sum_probs=43.6
Q ss_pred CCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEc--cCCCCcceeeeeEee
Q 025186 179 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILC--NDCNDTTEVYFHIIG 235 (256)
Q Consensus 179 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~C--nDC~~~s~~~fH~lg 235 (256)
..||.|++...|+-..=..+|+.+...++| -+....=| |.|+......+=+.|
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 579999999999988888999999999988 34556779 999987777665554
No 157
>PF15353 HECA: Headcase protein family homologue
Probab=46.52 E-value=9.6 Score=31.02 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=13.7
Q ss_pred ccCCccChhhHHHHhc
Q 025186 160 KCGHTMHCECYHEMIK 175 (256)
Q Consensus 160 pCGH~~H~~Cl~~~~~ 175 (256)
|-|+.||+.||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 3489999999999965
No 158
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=46.43 E-value=12 Score=26.43 Aligned_cols=29 Identities=34% Similarity=0.641 Sum_probs=21.4
Q ss_pred ccceeeCCcc-ccccCCCCCCcccCCCCCc
Q 025186 76 NMGEYFCDIC-KFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 76 ~f~~y~C~~C-~l~dd~~~k~~yHC~~Cgi 104 (256)
.+..|-|..| +.++.+....-.-|+.||.
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 3567778888 5556666788889999985
No 159
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=46.11 E-value=10 Score=28.10 Aligned_cols=14 Identities=36% Similarity=0.648 Sum_probs=12.3
Q ss_pred eecCCCCCCccccc
Q 025186 235 GQKCSHCKSYNTRS 248 (256)
Q Consensus 235 g~kC~~C~SyNT~~ 248 (256)
.++|+.|.|.||+.
T Consensus 5 ~~~CPRC~S~nTKF 18 (63)
T PF02701_consen 5 PLPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCCcCCCCCEE
Confidence 36999999999986
No 160
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=45.89 E-value=16 Score=25.39 Aligned_cols=13 Identities=38% Similarity=1.237 Sum_probs=7.1
Q ss_pred CCCCCCCCccccc
Q 025186 178 KYCCPICSKSVID 190 (256)
Q Consensus 178 ~~~CPiCrksv~d 190 (256)
...||+|.+++.+
T Consensus 20 ~~~CPlC~r~l~~ 32 (54)
T PF04423_consen 20 KGCCPLCGRPLDE 32 (54)
T ss_dssp SEE-TTT--EE-H
T ss_pred CCcCCCCCCCCCH
Confidence 3499999999984
No 161
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=45.60 E-value=19 Score=27.85 Aligned_cols=52 Identities=19% Similarity=0.389 Sum_probs=24.8
Q ss_pred CCCCCCchhhhhhcccCCccEE---eccCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~---LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
.....|-||.|++-...+.-.+ .-|+-.+.+.|++--++.++..||.|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 4457899999987443332222 368999999999988888889999999443
No 162
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=45.51 E-value=12 Score=30.97 Aligned_cols=48 Identities=25% Similarity=0.546 Sum_probs=35.1
Q ss_pred cCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCcccccc
Q 025186 73 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 126 (256)
Q Consensus 73 Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~ 126 (256)
.+......+|.+|+.+-- ....||..||.|..+- -.||.-=|.|+...
T Consensus 42 ~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLRF---DHHCPWLGNCIGRR 89 (174)
T ss_pred cccCCCCEECcccCCcCC---Ccceeccccccccccc---cccchhhccccccc
Confidence 357788899999998833 2477888888887762 45777777777643
No 163
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=45.22 E-value=7.2 Score=37.10 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=27.9
Q ss_pred CCCCccccCCccceeecCccCccccccccCcceee
Q 025186 100 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 134 (256)
Q Consensus 100 ~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~ 134 (256)
.+|-.|++.+.-...||..||.|+.+- +|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 578889999988899999999999864 78886
No 164
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=44.98 E-value=13 Score=22.85 Aligned_cols=21 Identities=19% Similarity=0.585 Sum_probs=6.5
Q ss_pred CCccccCCc-cceeecCccCcc
Q 025186 102 CGICRIGGR-ENYFHCKRCGSC 122 (256)
Q Consensus 102 CgiCRvG~~-~~ffHC~~C~~C 122 (256)
|++|+..+. ..+|+|..|+.=
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDFD 24 (30)
T ss_dssp -TTTS----S--EEE-TTT---
T ss_pred CCcCCCcCCCCceEECccCCCc
Confidence 455555443 367777777643
No 165
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=44.79 E-value=3.9 Score=38.34 Aligned_cols=74 Identities=27% Similarity=0.632 Sum_probs=56.8
Q ss_pred ccCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCccccccccCcceeecCCCCCCCchhhhh
Q 025186 72 NCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 148 (256)
Q Consensus 72 ~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CPICle~ 148 (256)
.=|+.-|-.||+.|..| ..+..-||..|+.|-.-.++.|-||..|-.|+-.++-.--.|-.-+...-|-||.|+
T Consensus 197 ~~~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 197 ILPTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ecccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 34777788889999988 457788999999997776778999999999998887433333333556678888875
No 166
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=44.46 E-value=11 Score=31.88 Aligned_cols=17 Identities=24% Similarity=0.470 Sum_probs=14.8
Q ss_pred eecCCCCCCccccccCC
Q 025186 235 GQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 235 g~kC~~C~SyNT~~~~~ 251 (256)
...|+.|||-||++++.
T Consensus 105 ~~~cp~c~s~~t~~~s~ 121 (146)
T TIGR02159 105 SVQCPRCGSADTTITSI 121 (146)
T ss_pred CCcCCCCCCCCcEeecC
Confidence 36999999999999863
No 167
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.21 E-value=18 Score=28.22 Aligned_cols=51 Identities=31% Similarity=0.555 Sum_probs=32.9
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHHHHHHHhc--CCChhhhcC
Q 025186 141 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEAT--VMPEDYRHK 214 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~~~~~lD~~i~~~--pmP~~y~~~ 214 (256)
.||||.-.|-.+...-+. -..||-||-.-+|. ..||.+|+.. |-|.+|+..
T Consensus 3 lCP~C~v~l~~~~rs~vE-------------------iD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 3 LCPICGVELVMSVRSGVE-------------------IDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred ccCcCCceeeeeeecCce-------------------eeeCCccccEeecc----hhHHHHHHHhcCCCCcccCCc
Confidence 699998887665321111 24699999766665 5678888765 556666543
No 168
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.94 E-value=19 Score=25.18 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=4.5
Q ss_pred CcccCCCCC
Q 025186 95 GQFHCDDCG 103 (256)
Q Consensus 95 ~~yHC~~Cg 103 (256)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 445555554
No 169
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=41.92 E-value=8.5 Score=41.25 Aligned_cols=46 Identities=28% Similarity=0.704 Sum_probs=0.0
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCc
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 121 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~ 121 (256)
...|.+||...-...|+.|.-.. ...|.|+.||+ ++.. .+|.+||.
T Consensus 655 ~r~Cp~Cg~~t~~~~Cp~CG~~T----~~~~~Cp~C~~-~~~~----~~C~~C~~ 700 (900)
T PF03833_consen 655 RRRCPKCGKETFYNRCPECGSHT----EPVYVCPDCGI-EVEE----DECPKCGR 700 (900)
T ss_dssp -------------------------------------------------------
T ss_pred cccCcccCCcchhhcCcccCCcc----ccceecccccc-ccCc----cccccccc
Confidence 35688888887777788886553 46888888887 3321 16777765
No 170
>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=41.24 E-value=22 Score=22.44 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=17.2
Q ss_pred eeeCCccccccCCCCCCcccCCCCCc
Q 025186 79 EYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 79 ~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
.|-|.+|-+.=+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 367888866533 3457888888875
No 171
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=41.06 E-value=17 Score=33.50 Aligned_cols=45 Identities=27% Similarity=0.719 Sum_probs=28.2
Q ss_pred CcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCcccc
Q 025186 74 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 124 (256)
Q Consensus 74 g~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s 124 (256)
|......||+.|+++- .+...||.-||.|-.+- =-||.==|.|+-
T Consensus 108 ~~~~~~~~C~~C~~~r---PpRs~HCsvC~~CV~rf---DHHC~WvnnCVG 152 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYR---PPRSSHCSVCNNCVLRF---DHHCPWLNNCIG 152 (299)
T ss_pred CcccceEEcCcCcccC---CCCcccchhhccccccc---CCCCCCccceEC
Confidence 5667789999999992 34456666666665441 235555555544
No 172
>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=40.63 E-value=14 Score=23.23 Aligned_cols=19 Identities=32% Similarity=0.883 Sum_probs=12.1
Q ss_pred hcccccCcccceeeCCcccc
Q 025186 68 QVCTNCGVNMGEYFCDICKF 87 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l 87 (256)
..|.-||. .++|-|..|.+
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~ 21 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGA 21 (30)
T ss_dssp EEETSSSS-EESEE-TTT--
T ss_pred CCCccCcC-CCEEECCCcCC
Confidence 35777887 88888888754
No 173
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.79 E-value=6.5 Score=35.97 Aligned_cols=50 Identities=26% Similarity=0.523 Sum_probs=37.8
Q ss_pred CCCCchhhhhhcc--cCCccEEec--------cCCccChhhHHHHhcCCCCCCCCCCccc
Q 025186 139 HHHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKSV 188 (256)
Q Consensus 139 ~~~CPICle~lf~--s~~~v~~Lp--------CGH~~H~~Cl~~~~~~~~~~CPiCrksv 188 (256)
...|.||...+.. ......++. |||.+-..|.+..+.....+||.|++..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~ 266 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCccccee
Confidence 3569999987552 223334566 9999999999999875568999999864
No 174
>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=38.66 E-value=11 Score=34.71 Aligned_cols=30 Identities=17% Similarity=0.595 Sum_probs=16.7
Q ss_pred eEEEccCCCCcceeeeeEeeecCCCCCCcccccc
Q 025186 216 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 249 (256)
Q Consensus 216 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 249 (256)
-...|.-|+ ..+|+.-.+|++||+-+-..+
T Consensus 196 R~L~Cs~C~----t~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 196 RYLHCSLCG----TEWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEEETTT------EEE--TTS-TTT---SS-EE
T ss_pred EEEEcCCCC----CeeeecCCCCcCCCCCCCcce
Confidence 468899998 678888899999998776544
No 175
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=38.35 E-value=35 Score=32.44 Aligned_cols=23 Identities=35% Similarity=0.970 Sum_probs=16.2
Q ss_pred EEEccCCCCcceeeeeEeeecCCCCCC
Q 025186 217 WILCNDCNDTTEVYFHIIGQKCSHCKS 243 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~lg~kC~~C~S 243 (256)
...|+-|+ ..+|+.-.||++|++
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 56777777 566677777777775
No 176
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.08 E-value=13 Score=33.22 Aligned_cols=39 Identities=26% Similarity=0.532 Sum_probs=28.4
Q ss_pred CchhhhhhcccCCccEEeccCCccC-hhhHHHHhcCCCCCCCCCCcccc
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H-~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
|-+|.+. ...|..|||-|..+ ..|-.. -..||+|+..+.
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 9999885 24588899997654 466643 356999997665
No 177
>PLN02189 cellulose synthase
Probab=38.07 E-value=27 Score=38.35 Aligned_cols=56 Identities=20% Similarity=0.403 Sum_probs=40.6
Q ss_pred ecCCCCCCCchhhhhhcccCC--ccEEe-ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 134 IENSMHHHCPICYEYLFDSLR--NTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 134 ~e~~~~~~CPICle~lf~s~~--~v~~L-pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
+++.....|.||.|++-...+ +-+.- -||=-+.+.||+.=.++++..||-|+...-
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 445566799999999753323 22333 378889999997666778899999997654
No 178
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=37.81 E-value=25 Score=23.51 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=12.3
Q ss_pred ccCCCCCccccCCccceeecCccC
Q 025186 97 FHCDDCGICRIGGRENYFHCKRCG 120 (256)
Q Consensus 97 yHC~~CgiCRvG~~~~ffHC~~C~ 120 (256)
|+|+.|+. +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 56777755 332 677777764
No 179
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=37.41 E-value=12 Score=30.84 Aligned_cols=19 Identities=37% Similarity=0.835 Sum_probs=15.7
Q ss_pred EeeecCCCCC----CccccccCC
Q 025186 233 IIGQKCSHCK----SYNTRSIAP 251 (256)
Q Consensus 233 ~lg~kC~~C~----SyNT~~~~~ 251 (256)
.|-+||+.|| ||+|+|++-
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 5568999997 899999974
No 180
>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=35.68 E-value=23 Score=29.79 Aligned_cols=26 Identities=27% Similarity=0.563 Sum_probs=18.3
Q ss_pred hcccccCcccceeeCCccccccCCCCCCcccCCCCCcc
Q 025186 68 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 105 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiC 105 (256)
.+|.+||+. ||| .+|.+-.|++||.=
T Consensus 10 r~Cp~cg~k----------FYD--Lnk~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSK----------FYD--LNRRPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCcc----------ccc--cCCCCccCCCcCCc
Confidence 457777764 465 46888888888864
No 181
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=35.35 E-value=4.2 Score=27.40 Aligned_cols=42 Identities=29% Similarity=0.600 Sum_probs=27.2
Q ss_pred CchhhhhhcccCCccEE-eccCCccChhhHHHHhc-----CCCCCCCCCC
Q 025186 142 CPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIK-----RDKYCCPICS 185 (256)
Q Consensus 142 CPICle~lf~s~~~v~~-LpCGH~~H~~Cl~~~~~-----~~~~~CPiCr 185 (256)
|+||... .+ ...++. -.|+-.||..|+..-+. ...+.||.|+
T Consensus 2 C~vC~~~-~~-~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS-DD-DGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS-CT-TSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc-CC-CCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 7888883 22 223333 37899999999976543 1367888775
No 182
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=34.62 E-value=19 Score=24.92 Aligned_cols=13 Identities=38% Similarity=1.004 Sum_probs=10.8
Q ss_pred ecCCCCCCccccc
Q 025186 236 QKCSHCKSYNTRS 248 (256)
Q Consensus 236 ~kC~~C~SyNT~~ 248 (256)
-||+.||.||-.+
T Consensus 12 rkCp~CGt~NG~R 24 (44)
T PF14952_consen 12 RKCPKCGTYNGTR 24 (44)
T ss_pred ccCCcCcCccCcc
Confidence 4899999999654
No 183
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=34.17 E-value=24 Score=27.03 Aligned_cols=39 Identities=13% Similarity=0.516 Sum_probs=18.8
Q ss_pred CCCCCCCCC-cccc--chhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeE
Q 025186 177 DKYCCPICS-KSVI--DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHI 233 (256)
Q Consensus 177 ~~~~CPiCr-ksv~--dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~ 233 (256)
..++||.|. ...+ .|+. ......|.|..|+...+...+.
T Consensus 21 ~~F~CPfC~~~~sV~v~idk------------------k~~~~~~~C~~Cg~~~~~~i~~ 62 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDK------------------KEGIGILSCRVCGESFQTKINP 62 (81)
T ss_dssp S----TTT--SS-EEEEEET------------------TTTEEEEEESSS--EEEEE--S
T ss_pred ceEcCCcCCCCCeEEEEEEc------------------cCCEEEEEecCCCCeEEEccCc
Confidence 469999999 3222 3322 2457889999999877665543
No 184
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=34.02 E-value=19 Score=22.07 Aligned_cols=12 Identities=25% Similarity=1.129 Sum_probs=8.7
Q ss_pred cceeeCCccccc
Q 025186 77 MGEYFCDICKFY 88 (256)
Q Consensus 77 f~~y~C~~C~l~ 88 (256)
++.|||++|+.+
T Consensus 1 ~~~~~C~~C~~~ 12 (35)
T smart00451 1 TGGFYCKLCNVT 12 (35)
T ss_pred CcCeEccccCCc
Confidence 367888888655
No 185
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.90 E-value=28 Score=35.15 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=35.0
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
..+.+|.||++.+ ..++-+|- |..|+.+|+. .+..||+|++.+.
T Consensus 477 ~~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~-~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-----SARITPCS---HALCLRKWLY-VQEVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-----Hhcccccc---chhHHHhhhh-hccccCCCchhhh
Confidence 4578999999997 23344555 9999999997 5688999998876
No 186
>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=33.76 E-value=14 Score=25.08 Aligned_cols=40 Identities=25% Similarity=0.615 Sum_probs=27.3
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchh
Q 025186 142 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 192 (256)
Q Consensus 142 CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~ 192 (256)
|+.|.+.+.. ..+.+..=|..+|..|| +|-.|+++|.+..
T Consensus 1 C~~C~~~I~~--~~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYG--TEIVIKAMGKFWHPECF---------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESS--SSEEEEETTEEEETTTS---------BETTTTCBTTTSS
T ss_pred CCCCCCCccC--cEEEEEeCCcEEEcccc---------ccCCCCCccCCCe
Confidence 5667777653 23343456888998765 7889999987543
No 187
>PRK00420 hypothetical protein; Validated
Probab=33.51 E-value=23 Score=28.92 Aligned_cols=29 Identities=38% Similarity=0.819 Sum_probs=22.2
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
...||+|.-+||.. ..+...||.|+..+.
T Consensus 23 ~~~CP~Cg~pLf~l----------------------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFEL----------------------KDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceec----------------------CCCceECCCCCCeee
Confidence 46899999988862 136788999998765
No 188
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=33.10 E-value=32 Score=28.40 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=23.1
Q ss_pred CCccccCCccceeecCccCccccccccCcceee
Q 025186 102 CGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 134 (256)
Q Consensus 102 CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~ 134 (256)
|-.|++-....-.||..||.|+-.- +|-|.
T Consensus 51 C~~C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 51 CSTCKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CcccCCcCCCcceeccccccccccc---cccch
Confidence 4456666677899999999998764 67775
No 189
>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=32.75 E-value=30 Score=22.14 Aligned_cols=24 Identities=25% Similarity=0.671 Sum_probs=13.0
Q ss_pred eeCCccccccCCCCCCcccCCCCC
Q 025186 80 YFCDICKFYDDDIEKGQFHCDDCG 103 (256)
Q Consensus 80 y~C~~C~l~dd~~~k~~yHC~~Cg 103 (256)
|-|+.|..--+....++-.|+.||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 444555333233455666888887
No 190
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=32.39 E-value=30 Score=36.09 Aligned_cols=19 Identities=26% Similarity=0.849 Sum_probs=10.4
Q ss_pred hcccccCcccceeeCCccc
Q 025186 68 QVCTNCGVNMGEYFCDICK 86 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~ 86 (256)
..|.+||..+..-.|..|.
T Consensus 16 kFC~~CG~~l~~~~Cp~CG 34 (645)
T PRK14559 16 RFCQKCGTSLTHKPCPQCG 34 (645)
T ss_pred ccccccCCCCCCCcCCCCC
Confidence 4566666666544444443
No 191
>PLN02436 cellulose synthase A
Probab=32.25 E-value=38 Score=37.40 Aligned_cols=56 Identities=16% Similarity=0.454 Sum_probs=40.3
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEe---ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 134 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 134 ~e~~~~~~CPICle~lf~s~~~v~~L---pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
+.....+.|.||.|++-.+.+.-... -||=-+.+.||+.=.++++..||-|+...-
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34455679999999974433333333 377889999997666678899999997654
No 192
>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=32.23 E-value=41 Score=24.02 Aligned_cols=32 Identities=22% Similarity=0.685 Sum_probs=21.7
Q ss_pred CCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCccee
Q 025186 179 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEV 229 (256)
Q Consensus 179 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~ 229 (256)
++||.|..+|. +|....+. .+.|.+||+.-.|
T Consensus 3 ~~CP~CG~~ie-----------------v~~~~~Ge--iV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIE-----------------LENPELGE--LVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEe-----------------cCCCccCC--EEeCCCCCCEEEE
Confidence 68999998774 23333433 6789999976544
No 193
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=32.23 E-value=35 Score=22.89 Aligned_cols=21 Identities=33% Similarity=0.800 Sum_probs=10.8
Q ss_pred ccCCCCCccccCCccceeecCccC
Q 025186 97 FHCDDCGICRIGGRENYFHCKRCG 120 (256)
Q Consensus 97 yHC~~CgiCRvG~~~~ffHC~~C~ 120 (256)
|.|+.|+. -+- ...|||..|-
T Consensus 1 ~~C~~C~~-~i~--g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIV--GVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCc--CCEEECCCCC
Confidence 44555555 222 2466776664
No 194
>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=32.19 E-value=26 Score=22.58 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=15.6
Q ss_pred hcccccCcccceeeCCccccc
Q 025186 68 QVCTNCGVNMGEYFCDICKFY 88 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l~ 88 (256)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 467888887789999888664
No 195
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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 motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=32.11 E-value=19 Score=23.76 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.6
Q ss_pred cceeeCCcccccc
Q 025186 77 MGEYFCDICKFYD 89 (256)
Q Consensus 77 f~~y~C~~C~l~d 89 (256)
|.+|||+-|+.|-
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 5689999998885
No 196
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=31.60 E-value=33 Score=32.24 Aligned_cols=130 Identities=22% Similarity=0.587 Sum_probs=72.2
Q ss_pred eeEcCcCCC--------------------eecCCcchhhhhccCCCCCCCceecchhhhhhhhcccccCcc-----ccee
Q 025186 26 RIRAPCCNE--------------------IFDCRHCHNEAASMLRNPYDRHELVRQDVKQVAQVCTNCGVN-----MGEY 80 (256)
Q Consensus 26 ki~apcC~~--------------------~y~CR~CHde~~~~~~~~~~~H~l~r~~v~~v~~~C~~Cg~~-----f~~y 80 (256)
.|.||||++ -|.|.+|--+..+. -..|.+- ...|.-|+.. -|+|
T Consensus 70 ~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~--------gf~rnqg---r~LC~~Cn~k~Ka~~~g~Y 138 (332)
T KOG2272|consen 70 VLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQ--------GFYRNQG---RALCRECNQKEKAKGRGRY 138 (332)
T ss_pred hhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhh--------hhHhhcc---hHHhhhhhhhhccccccee
Confidence 378899887 36777777654421 1112111 2335555433 5799
Q ss_pred eCCccccc-cCCC---CCCcccCCCCCccccCCccceeecCccCccccc---cccCcceeecCCCCCCCchhhhhhcccC
Q 025186 81 FCDICKFY-DDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYEYLFDSL 153 (256)
Q Consensus 81 ~C~~C~l~-dd~~---~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~---~l~~~H~C~e~~~~~~CPICle~lf~s~ 153 (256)
-|.+|+-. |+++ .-.+|| -.-|.|.+||-=+.. ++++.--|..=-...-+|||..=
T Consensus 139 vC~KCh~~iD~~~l~fr~d~yH------------~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC----- 201 (332)
T KOG2272|consen 139 VCQKCHAHIDEQPLTFRGDPYH------------PYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGAC----- 201 (332)
T ss_pred ehhhhhhhcccccccccCCCCC------------ccceecccccccccchhhhhccceeccccccccCCcccccc-----
Confidence 99999755 5544 235565 357889999876654 34444455544444556666542
Q ss_pred CccEEeccCCccChhhH----HHHhcCCCCCCCCCCccccchh
Q 025186 154 RNTTVMKCGHTMHCECY----HEMIKRDKYCCPICSKSVIDMS 192 (256)
Q Consensus 154 ~~v~~LpCGH~~H~~Cl----~~~~~~~~~~CPiCrksv~dm~ 192 (256)
--.|-..=+ +.|-. .++.|-.|-|+++.-.
T Consensus 202 --------~rpIeervi~amgKhWHv-eHFvCa~CekPFlGHr 235 (332)
T KOG2272|consen 202 --------RRPIEERVIFAMGKHWHV-EHFVCAKCEKPFLGHR 235 (332)
T ss_pred --------cCchHHHHHHHhccccch-hheeehhcCCcccchh
Confidence 111111112 22433 3678888888877543
No 197
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=31.53 E-value=12 Score=35.22 Aligned_cols=53 Identities=17% Similarity=0.172 Sum_probs=40.6
Q ss_pred hcccccCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCcccc
Q 025186 68 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 124 (256)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s 124 (256)
-.|+-|+...+.-||.||-=||.. + -|||.|.-||--..-.+-||+.|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~--R--~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK--R--STCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc--c--ccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 347778888888899999877653 2 7899998888876666778888777765
No 198
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=31.48 E-value=56 Score=34.31 Aligned_cols=79 Identities=23% Similarity=0.373 Sum_probs=49.2
Q ss_pred eecCCCCCCCchhhhhhcccCCccEEec---cCCccChhhHHHHhc-------CCCCCCCCCCccccchhHHhHHHHHHH
Q 025186 133 CIENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIK-------RDKYCCPICSKSVIDMSRTWKRIDEEI 202 (256)
Q Consensus 133 C~e~~~~~~CPICle~lf~s~~~v~~Lp---CGH~~H~~Cl~~~~~-------~~~~~CPiCrksv~dm~~~~~~lD~~i 202 (256)
|.....-..||||+-..-++ +....+. |.=..|..|..-.-. ...|+|-+|| .-+..-..|-..+
T Consensus 139 ~~~c~s~~~cPvc~~~Y~~~-e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~v 213 (694)
T KOG4443|consen 139 CAPCASLSYCPVCLIVYQDS-ESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDAL 213 (694)
T ss_pred cccccccccCchHHHhhhhc-cchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHHH
Confidence 44444457999999865554 3333333 566788888533221 1379999999 2222335666677
Q ss_pred HhcCCChhhhcCee
Q 025186 203 EATVMPEDYRHKKV 216 (256)
Q Consensus 203 ~~~pmP~~y~~~~v 216 (256)
..+-+|..|.+...
T Consensus 214 qe~~~~k~~~~~~~ 227 (694)
T KOG4443|consen 214 QETWKAKDKPDKIL 227 (694)
T ss_pred Hhhcchhhccccce
Confidence 78888888877643
No 199
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=31.10 E-value=22 Score=25.70 Aligned_cols=28 Identities=36% Similarity=0.869 Sum_probs=20.8
Q ss_pred hcCeeEEEccCCCCcceeeeeEeeecCCCCC
Q 025186 212 RHKKVWILCNDCNDTTEVYFHIIGQKCSHCK 242 (256)
Q Consensus 212 ~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~ 242 (256)
++.+..|+|.-||. ..||+--..|..||
T Consensus 10 r~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 10 RHNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp S-S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred cCCccEeeecccCC---eeeecCCCcccccC
Confidence 34567999999997 55888888899998
No 200
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.01 E-value=59 Score=34.46 Aligned_cols=44 Identities=20% Similarity=0.293 Sum_probs=27.6
Q ss_pred HHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCC
Q 025186 202 IEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 202 i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 251 (256)
+..+.+|-.--+.. .-.|++||.... +| .+||.|||-|+.++++
T Consensus 666 ~~~~~i~Y~sin~~-~~~C~~CG~~~~--~~---~~CP~CG~~~~~~~~R 709 (735)
T PRK07111 666 MKNTNIGYGSINHP-VDRCPVCGYLGV--IE---DKCPKCGSTNIQRIRR 709 (735)
T ss_pred HHhCCCceEEeCCC-CeecCCCCCCCC--cC---ccCcCCCCccceeeeh
Confidence 34445555422333 467999996443 23 6999999977666543
No 201
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.01 E-value=29 Score=29.45 Aligned_cols=47 Identities=30% Similarity=0.646 Sum_probs=32.8
Q ss_pred CCCchhhhhhcccCCccEEe-c---cCCccChhhHHHHhcC--CCCCCCCCCccccc
Q 025186 140 HHCPICYEYLFDSLRNTTVM-K---CGHTMHCECYHEMIKR--DKYCCPICSKSVID 190 (256)
Q Consensus 140 ~~CPICle~lf~s~~~v~~L-p---CGH~~H~~Cl~~~~~~--~~~~CPiCrksv~d 190 (256)
-.|-||.|- | .+.+.| | ||=.+...|+.++-+. ....||+|+.|+-.
T Consensus 81 YeCnIC~et---S-~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 81 YECNICKET---S-AEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eeccCcccc---c-chhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 357778774 2 234555 3 8999999998874332 35679999999864
No 202
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.56 E-value=71 Score=27.77 Aligned_cols=27 Identities=22% Similarity=0.553 Sum_probs=18.1
Q ss_pred CCCCCCCCCccccchh--HHhHHHHHHHH
Q 025186 177 DKYCCPICSKSVIDMS--RTWKRIDEEIE 203 (256)
Q Consensus 177 ~~~~CPiCrksv~dm~--~~~~~lD~~i~ 203 (256)
..++||.|+..+..++ .....|+..|+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 4799999999998433 34455555444
No 203
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.40 E-value=48 Score=37.30 Aligned_cols=36 Identities=25% Similarity=0.639 Sum_probs=23.8
Q ss_pred cccccCccc-ceeeCCcccccc-CCCCCCcccCCCCCcc
Q 025186 69 VCTNCGVNM-GEYFCDICKFYD-DDIEKGQFHCDDCGIC 105 (256)
Q Consensus 69 ~C~~Cg~~f-~~y~C~~C~l~d-d~~~k~~yHC~~CgiC 105 (256)
.|.+||... ..|+|..|..-- .++.. ...|+.||.=
T Consensus 681 fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CGtp 718 (1337)
T PRK14714 681 RCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCDVE 718 (1337)
T ss_pred cCcccCCcCCCceeCccCCCccCCCccc-cccCCCCCCc
Confidence 688888775 467788887742 22223 5679988853
No 204
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=28.37 E-value=37 Score=31.98 Aligned_cols=46 Identities=20% Similarity=0.345 Sum_probs=27.5
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccC--CccChhhHHHHhcCCCCCCC
Q 025186 136 NSMHHHCPICYEYLFDSLRNTTVMKCG--HTMHCECYHEMIKRDKYCCP 182 (256)
Q Consensus 136 ~~~~~~CPICle~lf~s~~~v~~LpCG--H~~H~~Cl~~~~~~~~~~CP 182 (256)
..+-..|+||+| |.-++.+...|.=. =-=|+.||+.|-.-.+..||
T Consensus 27 ~~tLsfChiCfE-l~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFE-LSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeec-cccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 455567888888 44443333333210 01389999999443467898
No 205
>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=27.78 E-value=7.4 Score=32.83 Aligned_cols=20 Identities=30% Similarity=0.904 Sum_probs=14.7
Q ss_pred hhcccccCccc-ceeeCCccc
Q 025186 67 AQVCTNCGVNM-GEYFCDICK 86 (256)
Q Consensus 67 ~~~C~~Cg~~f-~~y~C~~C~ 86 (256)
+-.|.+||+.. .--||+.|+
T Consensus 81 ~~~CE~CG~~I~~Gr~C~~C~ 101 (137)
T TIGR03826 81 GYPCERCGTSIREGRLCDSCA 101 (137)
T ss_pred cCcccccCCcCCCCCccHHHH
Confidence 67799999752 336788885
No 206
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.76 E-value=48 Score=26.50 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=22.8
Q ss_pred cceeecCccC-ccccccccCcceeecCCCCCCCchhhhh
Q 025186 111 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 148 (256)
Q Consensus 111 ~~ffHC~~C~-~C~s~~l~~~H~C~e~~~~~~CPICle~ 148 (256)
..+|+|..|| .-+++.+. + +..+..||+|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~~--k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIK--K----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecC--C----CcceEECCCCCCc
Confidence 5789999999 33333332 2 5678899999987
No 207
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.45 E-value=37 Score=37.40 Aligned_cols=33 Identities=27% Similarity=0.667 Sum_probs=15.1
Q ss_pred hcccccCcc-cceeeCCccccccCCCCCCcccCCCCCcc
Q 025186 68 QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGIC 105 (256)
Q Consensus 68 ~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~CgiC 105 (256)
..|.+||.. -..|||..|.-- -..|.|+.||.=
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~E 672 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGRE 672 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCC
Confidence 345555542 344555555211 123556666553
No 208
>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=27.15 E-value=75 Score=27.02 Aligned_cols=28 Identities=18% Similarity=0.519 Sum_probs=20.2
Q ss_pred CCCCCCCCCccccchh--HHhHHHHHHHHh
Q 025186 177 DKYCCPICSKSVIDMS--RTWKRIDEEIEA 204 (256)
Q Consensus 177 ~~~~CPiCrksv~dm~--~~~~~lD~~i~~ 204 (256)
..++||.|+..+..++ ..-+.|+..|+.
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 4799999999998443 355667766654
No 209
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=27.04 E-value=29 Score=27.53 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.4
Q ss_pred cceeecCccCccccc
Q 025186 111 ENYFHCKRCGSCYST 125 (256)
Q Consensus 111 ~~ffHC~~C~~C~s~ 125 (256)
.||-+|+.||.|.++
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 478899999999765
No 210
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=26.68 E-value=31 Score=32.63 Aligned_cols=45 Identities=27% Similarity=0.577 Sum_probs=32.2
Q ss_pred hhcccccCcccceeeCCccccccCCCCCCcccCCCCCccccCCccceeecCccCccccccccCcceee
Q 025186 67 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 134 (256)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~ 134 (256)
...+...|.-..+-||.+|+.|-- +..-||..||.|+-+- +|.|+
T Consensus 97 ~~~~~~~~~~~~~~~C~~C~~~KP--------------------~RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 97 ISRLLDDGKFGTENFCSTCNIYKP--------------------PRSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred hhhhhhcCccccceeccccccccC--------------------CCCccchhhcchhhcc---CccCc
Confidence 455666788888899999998843 3466777888887653 57764
No 211
>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=26.62 E-value=46 Score=27.74 Aligned_cols=49 Identities=22% Similarity=0.394 Sum_probs=30.4
Q ss_pred CCCCCCCCccccchhHHhHHHHHHHHhcCCChh-hhcCeeEEEccCCCCcceeeeeE
Q 025186 178 KYCCPICSKSVIDMSRTWKRIDEEIEATVMPED-YRHKKVWILCNDCNDTTEVYFHI 233 (256)
Q Consensus 178 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~-y~~~~v~I~CnDC~~~s~~~fH~ 233 (256)
-.+||.|+..+...++ +++. ..+|+. |+....--.|..|++.-+..-||
T Consensus 91 ~sRC~~CN~~L~~v~~------~~v~-~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSK------EEVK-DRVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CCccCCCCcEeeechh------hccc-cccCccccccCCeEEECCCCCCEecccccH
Confidence 3689999998875543 1122 224444 44444467799999877666554
No 212
>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=26.52 E-value=46 Score=23.54 Aligned_cols=29 Identities=24% Similarity=0.708 Sum_probs=22.3
Q ss_pred eEEEccCCCCcceeeeeEeeecCCCCCCcccccc
Q 025186 216 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 249 (256)
Q Consensus 216 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 249 (256)
..+.|..||+. ...| .-|+.||-|+.+++
T Consensus 25 ~l~~c~~cg~~--~~~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEP--KLPH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSE--ESTT---SBCTTTBBSSSSSS
T ss_pred ceeeeccCCCE--eccc---EeeCCCCeECCEEE
Confidence 46889999963 3344 56999999999986
No 213
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.33 E-value=34 Score=19.43 Aligned_cols=15 Identities=33% Similarity=0.771 Sum_probs=11.6
Q ss_pred CCCCCCCccccchhH
Q 025186 179 YCCPICSKSVIDMSR 193 (256)
Q Consensus 179 ~~CPiCrksv~dm~~ 193 (256)
|.|.+|.+++.+...
T Consensus 1 ~~C~~C~~~f~s~~~ 15 (25)
T PF12874_consen 1 FYCDICNKSFSSENS 15 (25)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCCcCCHHH
Confidence 468999999887544
No 214
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=26.20 E-value=55 Score=22.53 Aligned_cols=28 Identities=18% Similarity=0.516 Sum_probs=18.0
Q ss_pred EEccCCCCcceeeeeEeeecCCCCCCccccc
Q 025186 218 ILCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 248 (256)
Q Consensus 218 I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~ 248 (256)
|.|+-|.+...+.++ .+|..|..|+.-+
T Consensus 1 ~~C~~C~~~~i~g~R---~~C~~C~dydLC~ 28 (49)
T cd02345 1 LSCSACRKQDISGIR---FPCQVCRDYSLCL 28 (49)
T ss_pred CcCCCCCCCCceEee---EECCCCCCcCchH
Confidence 568888875544444 3777777776543
No 215
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=25.92 E-value=72 Score=23.13 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=22.3
Q ss_pred EEEccCCCCcceeeeeEeeecCCCCCCccccccCCC
Q 025186 217 WILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 252 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 252 (256)
.+.|..||.. ...|-+ |. ||.|+.+++-.+
T Consensus 27 ~~~c~~cg~~--~~pH~v---c~-cG~Y~gr~v~~~ 56 (60)
T PRK01110 27 LSVDKTTGEY--HLPHHV---SP-KGYYKGRKVLKK 56 (60)
T ss_pred eeEcCCCCce--ecccee---cC-CcccCCeEeecc
Confidence 5789999964 445543 88 999999998543
No 216
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.70 E-value=51 Score=22.08 Aligned_cols=10 Identities=40% Similarity=1.108 Sum_probs=4.7
Q ss_pred eeecCccCcc
Q 025186 113 YFHCKRCGSC 122 (256)
Q Consensus 113 ffHC~~C~~C 122 (256)
.+-|..||.=
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 4445555543
No 217
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=25.67 E-value=34 Score=36.93 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=33.9
Q ss_pred CCCCCCchhhhhhcccCCccEEecc---C--CccChhhHHHHhcCC-CCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpC---G--H~~H~~Cl~~~~~~~-~~~CPiCrksv~ 189 (256)
..+..|-||.-+= . +++.-.=|| | -.+|++|+.+|+..+ ..+|-+|...+.
T Consensus 10 ~d~~~CRICr~e~-~-~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 10 EDKRSCRICRTED-I-RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred ccchhceeecCCC-C-CCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 3446788887541 1 122222355 3 689999999999854 567999997764
No 218
>smart00355 ZnF_C2H2 zinc finger.
Probab=25.04 E-value=62 Score=17.43 Aligned_cols=15 Identities=40% Similarity=0.773 Sum_probs=11.4
Q ss_pred CCCCCCCccccchhH
Q 025186 179 YCCPICSKSVIDMSR 193 (256)
Q Consensus 179 ~~CPiCrksv~dm~~ 193 (256)
+.|+.|.+++...+.
T Consensus 1 ~~C~~C~~~f~~~~~ 15 (26)
T smart00355 1 YRCPECGKVFKSKSA 15 (26)
T ss_pred CCCCCCcchhCCHHH
Confidence 579999998876543
No 219
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=24.70 E-value=33 Score=22.41 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=15.4
Q ss_pred cccccCcccceeeCCccccccCCCCCCcccCCCCCc
Q 025186 69 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 104 (256)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 104 (256)
.|.+||..+-.+| ++.|..--||.||-
T Consensus 3 ~C~~Cg~~Yh~~~---------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEF---------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTT---------B--SSTTBCTTTTE
T ss_pred CcCCCCCcccccc---------CCCCCCCccCCCCC
Confidence 4666666664333 34566667777775
No 220
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=24.63 E-value=37 Score=24.66 Aligned_cols=12 Identities=17% Similarity=0.553 Sum_probs=10.9
Q ss_pred eeEcCcCCCeec
Q 025186 26 RIRAPCCNEIFD 37 (256)
Q Consensus 26 ki~apcC~~~y~ 37 (256)
.++||-|++|||
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 689999999997
No 221
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=24.59 E-value=70 Score=32.80 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=30.3
Q ss_pred hHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCccccccCC
Q 025186 192 SRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 251 (256)
Q Consensus 192 ~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 251 (256)
++.+..++...... ++-.--+ ...-.|++||...... .-+|+.|||-|..++++
T Consensus 501 eal~~lv~~a~~~~-i~Y~~~n-~~~~~C~~CG~~g~~~----~~~CP~Cgs~~~~~~~R 554 (579)
T TIGR02487 501 EALKDITKKAMKNG-IGYFGIN-PPVDVCEDCGYTGEGL----NDKCPKCGSHDIEVISR 554 (579)
T ss_pred HHHHHHHHHHHhcC-CceEEec-cCCccCCCCCCCCCCC----CCcCcCCCCccceehhh
Confidence 34444444443332 4433222 2345799999643321 25899999988666543
No 222
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.58 E-value=54 Score=19.29 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=11.7
Q ss_pred CCCCCCCCccccchh
Q 025186 178 KYCCPICSKSVIDMS 192 (256)
Q Consensus 178 ~~~CPiCrksv~dm~ 192 (256)
++.|++|.+.+.+..
T Consensus 1 q~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 1 QFYCDACDKYFSSEN 15 (27)
T ss_dssp -CBBTTTTBBBSSHH
T ss_pred CCCcccCCCCcCCHH
Confidence 368999999998754
No 223
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.48 E-value=61 Score=23.39 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=16.4
Q ss_pred CCCCCCCCCccccchhHHhHH
Q 025186 177 DKYCCPICSKSVIDMSRTWKR 197 (256)
Q Consensus 177 ~~~~CPiCrksv~dm~~~~~~ 197 (256)
.+|.||.|+-++---...|+.
T Consensus 13 v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred cCCcCCCCCCcCccCHHHHHH
Confidence 579999999998755566753
No 224
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=24.27 E-value=41 Score=21.96 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=18.5
Q ss_pred CCchhhhhhcccCCccEEe-ccCCcc
Q 025186 141 HCPICYEYLFDSLRNTTVM-KCGHTM 165 (256)
Q Consensus 141 ~CPICle~lf~s~~~v~~L-pCGH~~ 165 (256)
.|++|...+|.+.+....- .|||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceEc
Confidence 3999998877776666665 788864
No 225
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.24 E-value=70 Score=30.61 Aligned_cols=59 Identities=27% Similarity=0.595 Sum_probs=43.1
Q ss_pred CCCCchhhhhhcccCCccEEecc----CCccChhhHHHHhcCC----------CCCCCCCCccccchhHHhHHHHHHHHh
Q 025186 139 HHHCPICYEYLFDSLRNTTVMKC----GHTMHCECYHEMIKRD----------KYCCPICSKSVIDMSRTWKRIDEEIEA 204 (256)
Q Consensus 139 ~~~CPICle~lf~s~~~v~~LpC----GH~~H~~Cl~~~~~~~----------~~~CPiCrksv~dm~~~~~~lD~~i~~ 204 (256)
..-|.+|.|.|- +..+..| +|.|..-|-.+.|+.. ..+||+=.. ..-|.-|..||++
T Consensus 268 pLcCTLC~ERLE----DTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS-----~vPWAFMQGEIat 338 (352)
T KOG3579|consen 268 PLCCTLCHERLE----DTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGS-----NVPWAFMQGEIAT 338 (352)
T ss_pred ceeehhhhhhhc----cCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCC-----cccHHHhhhhHHH
Confidence 467999999984 4577778 6999999999998731 345665332 2358888888887
Q ss_pred cC
Q 025186 205 TV 206 (256)
Q Consensus 205 ~p 206 (256)
+.
T Consensus 339 IL 340 (352)
T KOG3579|consen 339 IL 340 (352)
T ss_pred Hh
Confidence 54
No 226
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.17 E-value=50 Score=34.37 Aligned_cols=54 Identities=20% Similarity=0.255 Sum_probs=31.6
Q ss_pred chhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCcccccc
Q 025186 190 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 249 (256)
Q Consensus 190 dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 249 (256)
|.++.+..++... .+.+|-.--+. ..-.|++||..... .+..||.|||-|+.++
T Consensus 541 n~eal~~lv~~~~-~~~i~Yf~in~-~~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 541 SEEGYRKLLNIAA-KTGCNYFAFNV-KITICNDCHHIDKR----TGKRCPICGSENIDYY 594 (623)
T ss_pred CHHHHHHHHHHHH-HcCCceEEeCC-CCccCCCCCCcCCC----CCcCCcCCCCcchhHH
Confidence 4444445555433 35555432232 34579999975221 3579999999886554
No 227
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=23.23 E-value=44 Score=30.75 Aligned_cols=34 Identities=26% Similarity=0.609 Sum_probs=24.9
Q ss_pred CcccCCCCCccccCCccceeecCccCccccccccCcceee
Q 025186 95 GQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 134 (256)
Q Consensus 95 ~~yHC~~CgiCRvG~~~~ffHC~~C~~C~s~~l~~~H~C~ 134 (256)
+...|+.|.+= ......||..||.|+..- +|-|.
T Consensus 112 ~~~~C~~C~~~---rPpRs~HCsvC~~CV~rf---DHHC~ 145 (299)
T KOG1311|consen 112 EWKYCDTCQLY---RPPRSSHCSVCNNCVLRF---DHHCP 145 (299)
T ss_pred ceEEcCcCccc---CCCCcccchhhccccccc---CCCCC
Confidence 35667766665 445789999999999864 67774
No 228
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=23.14 E-value=48 Score=24.40 Aligned_cols=29 Identities=17% Similarity=0.556 Sum_probs=17.9
Q ss_pred cCeeEEEccCCCCcceeeeeEeeecCCCCC
Q 025186 213 HKKVWILCNDCNDTTEVYFHIIGQKCSHCK 242 (256)
Q Consensus 213 ~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~ 242 (256)
...+.++|-||++....+--=+ .+|..||
T Consensus 16 ~~~miYiCgdC~~en~lk~~D~-irCReCG 44 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGDV-IRCRECG 44 (62)
T ss_pred cccEEEEeccccccccccCCCc-Eehhhcc
Confidence 3467889999998664432111 3566665
No 229
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.99 E-value=36 Score=20.35 Aligned_cols=7 Identities=57% Similarity=1.602 Sum_probs=3.2
Q ss_pred cccccCc
Q 025186 69 VCTNCGV 75 (256)
Q Consensus 69 ~C~~Cg~ 75 (256)
.|.+||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3444444
No 230
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=22.97 E-value=1e+02 Score=32.06 Aligned_cols=79 Identities=22% Similarity=0.434 Sum_probs=46.0
Q ss_pred cEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhH-Hh--HHHHHHHHhcCCChhhhcCeeEEEccCCCCcc-----
Q 025186 156 TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR-TW--KRIDEEIEATVMPEDYRHKKVWILCNDCNDTT----- 227 (256)
Q Consensus 156 v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~dm~~-~~--~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s----- 227 (256)
.++..=|-++|..|+ .|-+|++.+..=+. .| +..--+.-+++||..-.....--.|--|+..-
T Consensus 78 evvsa~gktyh~~cf---------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~ 148 (670)
T KOG1044|consen 78 EVVSTLGKTYHPKCF---------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA 148 (670)
T ss_pred eeEecccceeccccc---------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce
Confidence 344444888888776 56667766641111 11 11122345567765533334446677787521
Q ss_pred ----eeeeeEeeecCCCCCC
Q 025186 228 ----EVYFHIIGQKCSHCKS 243 (256)
Q Consensus 228 ----~~~fH~lg~kC~~C~S 243 (256)
..++|+..-||..|+-
T Consensus 149 llald~qwhv~cfkc~~c~~ 168 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSA 168 (670)
T ss_pred eeeeccceeeeeeehhhhcc
Confidence 5689999999998764
No 231
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.86 E-value=54 Score=26.55 Aligned_cols=6 Identities=33% Similarity=1.265 Sum_probs=3.0
Q ss_pred cCCCCC
Q 025186 98 HCDDCG 103 (256)
Q Consensus 98 HC~~Cg 103 (256)
+||.||
T Consensus 90 ~CP~Cg 95 (117)
T PRK00564 90 VCEKCH 95 (117)
T ss_pred cCcCCC
Confidence 355555
No 232
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=22.77 E-value=28 Score=34.39 Aligned_cols=52 Identities=25% Similarity=0.535 Sum_probs=0.0
Q ss_pred CCCCCchhhhh------------hc--ccCCcc-EEeccCCccChhhHHHHhc----CC----CCCCCCCCcccc
Q 025186 138 MHHHCPICYEY------------LF--DSLRNT-TVMKCGHTMHCECYHEMIK----RD----KYCCPICSKSVI 189 (256)
Q Consensus 138 ~~~~CPICle~------------lf--~s~~~v-~~LpCGH~~H~~Cl~~~~~----~~----~~~CPiCrksv~ 189 (256)
....||+|+.. .| ++..+. .+-||||+.=.+-..-|-+ ++ +..||.|-..+.
T Consensus 327 ~~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~ 401 (416)
T PF04710_consen 327 RSRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLD 401 (416)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred ccccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCccc
Confidence 36789999842 11 122233 3459999999999999965 12 367999998875
No 233
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=22.64 E-value=47 Score=30.79 Aligned_cols=35 Identities=20% Similarity=0.506 Sum_probs=25.4
Q ss_pred CCceeEcCcCCCeecCCcchhhhhccCCCCCCCc-eecchhhhhhhhcccccCcccceeeCCc
Q 025186 23 RRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRH-ELVRQDVKQVAQVCTNCGVNMGEYFCDI 84 (256)
Q Consensus 23 R~cki~apcC~~~y~CR~CHde~~~~~~~~~~~H-~l~r~~v~~v~~~C~~Cg~~f~~y~C~~ 84 (256)
..+|+.||.|+.+|. .+..+| .|| |+-||..|-..
T Consensus 145 ~~VKlyCP~C~DvY~-------------p~s~~~~~iD--------------GA~FGtsFph~ 180 (251)
T PTZ00396 145 SRVKVYCPRCQEVYH-------------PKKSSLLDID--------------GAFFGTSFPHL 180 (251)
T ss_pred CceeEeCCCchhhcC-------------CCCccccccc--------------cceecCcHHHH
Confidence 478999999999994 111233 788 89899888543
No 234
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.57 E-value=25 Score=24.58 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=8.8
Q ss_pred eEEEccCCCC
Q 025186 216 VWILCNDCND 225 (256)
Q Consensus 216 v~I~CnDC~~ 225 (256)
..|.|.+|+.
T Consensus 28 ~~V~C~~Cga 37 (61)
T PF14354_consen 28 YYVECTDCGA 37 (61)
T ss_pred EEEEcCCCCC
Confidence 6799999987
No 235
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.62 E-value=77 Score=33.68 Aligned_cols=46 Identities=20% Similarity=0.444 Sum_probs=33.6
Q ss_pred CCCCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcceeeeeEeeecCCCCCCcccccc
Q 025186 178 KYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 249 (256)
Q Consensus 178 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 249 (256)
-.+||-|..++.- -...-...|+=||..+.++. .|+.|||-..+..
T Consensus 444 v~~Cp~Cd~~lt~---------------------H~~~~~L~CH~Cg~~~~~p~-----~Cp~Cgs~~L~~~ 489 (730)
T COG1198 444 IAECPNCDSPLTL---------------------HKATGQLRCHYCGYQEPIPQ-----SCPECGSEHLRAV 489 (730)
T ss_pred cccCCCCCcceEE---------------------ecCCCeeEeCCCCCCCCCCC-----CCCCCCCCeeEEe
Confidence 3589999877651 12234689999999887766 7999999855443
No 236
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=21.34 E-value=65 Score=21.65 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=3.9
Q ss_pred ceeecCccCc
Q 025186 112 NYFHCKRCGS 121 (256)
Q Consensus 112 ~ffHC~~C~~ 121 (256)
.-+.|..|+.
T Consensus 27 ~g~~C~~C~~ 36 (53)
T PF00130_consen 27 QGYRCSWCGL 36 (53)
T ss_dssp CEEEETTTT-
T ss_pred CeEEECCCCC
Confidence 3444444443
No 237
>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=21.19 E-value=49 Score=20.14 Aligned_cols=15 Identities=27% Similarity=0.820 Sum_probs=10.0
Q ss_pred hhhhhcccccCcccc
Q 025186 64 KQVAQVCTNCGVNMG 78 (256)
Q Consensus 64 ~~v~~~C~~Cg~~f~ 78 (256)
...+..|.+||-.|.
T Consensus 11 ~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 11 PESAKFCPHCGYDFE 25 (26)
T ss_pred hhhcCcCCCCCCCCc
Confidence 334667888887774
No 238
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.17 E-value=1e+02 Score=28.17 Aligned_cols=26 Identities=27% Similarity=0.710 Sum_probs=19.9
Q ss_pred EccCCCCcceeeeeEeeecCCCCCCccccc
Q 025186 219 LCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 248 (256)
Q Consensus 219 ~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~ 248 (256)
.|.-||.++.. |. ..|++|+|.+|-.
T Consensus 356 ~c~~cg~~~~~---~~-~~c~~c~~~~~~~ 381 (389)
T PRK11788 356 RCRNCGFTART---LY-WHCPSCKAWETIK 381 (389)
T ss_pred ECCCCCCCCcc---ce-eECcCCCCccCcC
Confidence 38889977655 22 5799999999965
No 239
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=21.14 E-value=13 Score=35.01 Aligned_cols=27 Identities=22% Similarity=0.648 Sum_probs=23.9
Q ss_pred cCCccccCCceeEcCcCCCeecCCcchh
Q 025186 16 YGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (256)
Q Consensus 16 ~GC~HY~R~cki~apcC~~~y~CR~CHd 43 (256)
+.|.||.-.=.++.++|.. |+|+.||+
T Consensus 178 ~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 178 LKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cCcccchHHHHHHHHhccC-CCCCcccc
Confidence 5799999755688999999 99999999
No 240
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=21.10 E-value=55 Score=28.04 Aligned_cols=38 Identities=16% Similarity=0.423 Sum_probs=21.6
Q ss_pred CCCCCCccccchhHHhHHHHHHHHhcCCChhhhcCeeEEEccCCCCcce
Q 025186 180 CCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTE 228 (256)
Q Consensus 180 ~CPiCrksv~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~ 228 (256)
+||.|....... +....|++.+.-++- ..|..||.+..
T Consensus 2 ~cp~c~~~~~~~----------~~s~~~~~~~~~~~~-~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRV----------IDSRPAEDGNAIRRR-RECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEe----------EeccccCCCCceeee-eeccccCCcce
Confidence 688887544211 223456665555443 77888887653
No 241
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.84 E-value=47 Score=35.04 Aligned_cols=29 Identities=24% Similarity=0.417 Sum_probs=21.3
Q ss_pred EEEccCCCCcceeeeeEeeecCCCCCCcc
Q 025186 217 WILCNDCNDTTEVYFHIIGQKCSHCKSYN 245 (256)
Q Consensus 217 ~I~CnDC~~~s~~~fH~lg~kC~~C~SyN 245 (256)
.-.|++||...+...--.|..||.|||-|
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~ 669 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNHD 669 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCCC
Confidence 46799999865543333457899999987
No 242
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=20.75 E-value=82 Score=34.93 Aligned_cols=56 Identities=18% Similarity=0.444 Sum_probs=39.7
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEe---ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 134 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 134 ~e~~~~~~CPICle~lf~s~~~v~~L---pCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
++....+.|-||.|++--+.+.-... -||=-..+.||+-=.++++..||.|+...-
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 34556679999999964333322233 577889999997666778899999986543
No 243
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=20.75 E-value=89 Score=30.35 Aligned_cols=49 Identities=16% Similarity=0.367 Sum_probs=36.7
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 025186 137 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 189 (256)
Q Consensus 137 ~~~~~CPICle~lf~s~~~v~~LpCGH~~H~~Cl~~~~~~~~~~CPiCrksv~ 189 (256)
.+...||||+...- .|.+.--=|=.|.-.|+-.++. +..+||+=.+++.
T Consensus 298 ~~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccC---CCceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 45678999998532 2333334599999999999998 5789999877664
No 244
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.63 E-value=53 Score=21.54 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=5.3
Q ss_pred ccccCcccceee
Q 025186 70 CTNCGVNMGEYF 81 (256)
Q Consensus 70 C~~Cg~~f~~y~ 81 (256)
|.+||..-+.||
T Consensus 3 Cp~Cg~~~a~~~ 14 (39)
T PF01096_consen 3 CPKCGHNEAVFF 14 (39)
T ss_dssp -SSS-SSEEEEE
T ss_pred CcCCCCCeEEEE
Confidence 555655554444
No 245
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=20.16 E-value=79 Score=20.08 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=14.4
Q ss_pred cCeeEEEccCCCCcceeeeeEeeecCCCCCCccc
Q 025186 213 HKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNT 246 (256)
Q Consensus 213 ~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT 246 (256)
...+.-.|.+|+.... .--..|++|+|-|.
T Consensus 7 ~~l~~~rC~~Cg~~~~----pPr~~Cp~C~s~~l 36 (37)
T PF12172_consen 7 GRLLGQRCRDCGRVQF----PPRPVCPHCGSDEL 36 (37)
T ss_dssp T-EEEEE-TTT--EEE----S--SEETTTT----
T ss_pred CEEEEEEcCCCCCEec----CCCcCCCCcCcccc
Confidence 4566788999997532 23367899998663
Done!