Query 039237
Match_columns 98
No_of_seqs 109 out of 117
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:40:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039237hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12861 zf-Apc11: Anaphase-pr 99.0 3.5E-10 7.6E-15 77.4 3.3 42 2-45 42-83 (85)
2 PF13639 zf-RING_2: Ring finge 98.3 4.2E-07 9.2E-12 52.9 2.0 31 5-40 14-44 (44)
3 COG5219 Uncharacterized conser 98.2 4.8E-07 1E-11 83.5 2.5 35 8-44 1489-1523(1525)
4 PF12678 zf-rbx1: RING-H2 zinc 98.1 7.4E-07 1.6E-11 57.8 1.0 26 11-40 48-73 (73)
5 PF11793 FANCL_C: FANCL C-term 98.1 6.4E-07 1.4E-11 58.0 -0.4 39 5-43 18-65 (70)
6 cd00162 RING RING-finger (Real 97.8 1.4E-05 3.1E-10 43.7 2.2 30 11-43 16-45 (45)
7 COG5194 APC11 Component of SCF 97.7 1.8E-05 4E-10 54.8 2.2 31 11-45 52-82 (88)
8 KOG1493 Anaphase-promoting com 97.6 1.9E-05 4.1E-10 54.3 0.9 33 11-44 49-81 (84)
9 PHA02929 N1R/p28-like protein; 97.6 3.2E-05 7E-10 60.8 1.7 30 11-44 198-227 (238)
10 smart00184 RING Ring finger. E 96.9 0.00079 1.7E-08 35.4 2.1 26 11-39 14-39 (39)
11 smart00744 RINGv The RING-vari 96.8 0.0012 2.6E-08 40.2 2.4 24 15-40 26-49 (49)
12 PHA02926 zinc finger-like prot 96.6 0.0014 3.1E-08 52.3 2.7 34 11-44 195-230 (242)
13 PLN03208 E3 ubiquitin-protein 96.6 0.0018 3.9E-08 50.0 2.8 37 11-47 34-82 (193)
14 KOG2930 SCF ubiquitin ligase, 96.6 0.0023 4.9E-08 46.3 3.0 31 11-45 79-109 (114)
15 PF13920 zf-C3HC4_3: Zinc fing 96.6 0.0014 2.9E-08 39.0 1.6 30 11-44 18-48 (50)
16 PF00097 zf-C3HC4: Zinc finger 96.5 0.0014 3.1E-08 37.0 1.5 27 11-39 15-41 (41)
17 COG5243 HRD1 HRD ubiquitin lig 96.5 0.0012 2.7E-08 56.5 1.6 29 12-44 317-345 (491)
18 KOG0802 E3 ubiquitin ligase [P 96.4 0.0019 4.1E-08 54.7 2.2 30 8-41 308-338 (543)
19 KOG0827 Predicted E3 ubiquitin 96.2 0.0025 5.3E-08 54.6 1.9 29 11-40 24-52 (465)
20 PHA02862 5L protein; Provision 96.0 0.0051 1.1E-07 46.5 2.4 36 7-44 16-53 (156)
21 PF13923 zf-C3HC4_2: Zinc fing 95.7 0.0045 9.8E-08 35.1 1.0 27 9-39 13-39 (39)
22 PF14634 zf-RING_5: zinc-RING 95.6 0.0089 1.9E-07 34.9 2.0 29 9-41 15-44 (44)
23 PF12906 RINGv: RING-variant d 95.6 0.0031 6.6E-08 38.1 -0.1 29 8-39 16-47 (47)
24 PF08746 zf-RING-like: RING-li 95.4 0.0083 1.8E-07 35.8 1.3 30 8-39 12-43 (43)
25 PF10272 Tmpp129: Putative tra 95.2 0.011 2.5E-07 49.1 1.9 26 18-43 316-350 (358)
26 PHA02825 LAP/PHD finger-like p 95.0 0.018 3.8E-07 43.8 2.4 29 15-45 32-60 (162)
27 KOG3268 Predicted E3 ubiquitin 94.9 0.02 4.3E-07 45.3 2.5 36 9-44 184-228 (234)
28 smart00504 Ubox Modified RING 94.5 0.026 5.7E-07 33.8 1.8 30 11-44 17-46 (63)
29 KOG4628 Predicted E3 ubiquitin 94.4 0.02 4.2E-07 47.7 1.5 33 12-47 249-281 (348)
30 KOG0828 Predicted E3 ubiquitin 94.2 0.026 5.7E-07 49.9 1.9 30 12-44 605-634 (636)
31 KOG1734 Predicted RING-contain 94.2 0.015 3.3E-07 48.0 0.3 35 11-47 250-294 (328)
32 COG5540 RING-finger-containing 94.1 0.03 6.6E-07 47.0 2.0 30 12-44 343-372 (374)
33 PF15227 zf-C3HC4_4: zinc fing 93.9 0.026 5.6E-07 33.2 0.9 28 12-39 15-42 (42)
34 PF14446 Prok-RING_1: Prokaryo 93.8 0.047 1E-06 34.8 2.0 22 3-24 17-38 (54)
35 KOG3053 Uncharacterized conser 93.3 0.051 1.1E-06 44.6 1.8 31 14-44 48-82 (293)
36 KOG0823 Predicted E3 ubiquitin 91.5 0.15 3.3E-06 40.5 2.5 41 4-47 58-98 (230)
37 PF15353 HECA: Headcase protei 91.3 0.15 3.3E-06 36.6 2.1 15 14-28 41-55 (107)
38 smart00249 PHD PHD zinc finger 90.8 0.094 2E-06 28.7 0.5 22 3-24 10-31 (47)
39 KOG0825 PHD Zn-finger protein 90.3 0.15 3.3E-06 47.5 1.6 32 11-46 142-173 (1134)
40 TIGR00599 rad18 DNA repair pro 90.2 0.19 4.1E-06 42.4 2.0 32 11-46 42-73 (397)
41 KOG0317 Predicted E3 ubiquitin 86.7 0.42 9.2E-06 39.3 1.9 32 10-45 254-285 (293)
42 KOG1785 Tyrosine kinase negati 86.4 0.38 8.2E-06 42.1 1.5 34 12-47 386-419 (563)
43 PRK11088 rrmA 23S rRNA methylt 86.4 0.38 8.2E-06 36.6 1.4 11 48-58 29-39 (272)
44 KOG1609 Protein involved in mR 86.1 0.47 1E-05 35.9 1.7 30 15-46 107-136 (323)
45 PF13445 zf-RING_UBOX: RING-ty 84.1 0.63 1.4E-05 27.8 1.3 26 12-37 18-43 (43)
46 KOG0269 WD40 repeat-containing 83.4 0.96 2.1E-05 41.7 2.7 42 5-46 791-835 (839)
47 KOG1952 Transcription factor N 82.8 1.2 2.5E-05 41.6 3.0 45 1-45 201-248 (950)
48 KOG0804 Cytoplasmic Zn-finger 81.8 0.44 9.6E-06 41.6 -0.0 27 12-44 196-222 (493)
49 PF00628 PHD: PHD-finger; Int 80.6 0.34 7.3E-06 28.2 -0.8 39 3-41 10-50 (51)
50 PF13901 DUF4206: Domain of un 80.3 0.49 1.1E-05 35.8 -0.2 28 5-41 170-197 (202)
51 COG1996 RPC10 DNA-directed RNA 79.7 0.7 1.5E-05 29.0 0.4 31 6-44 5-35 (49)
52 KOG3899 Uncharacterized conser 79.3 1.5 3.2E-05 37.1 2.3 32 13-44 325-365 (381)
53 PF13831 PHD_2: PHD-finger; PD 79.1 0.76 1.7E-05 26.5 0.4 19 5-23 2-20 (36)
54 PF04564 U-box: U-box domain; 78.1 1.1 2.4E-05 28.5 1.0 31 12-45 21-51 (73)
55 KOG0309 Conserved WD40 repeat- 78.1 1.2 2.7E-05 41.6 1.6 22 8-29 1043-1064(1081)
56 PRK00398 rpoP DNA-directed RNA 77.9 0.69 1.5E-05 27.2 -0.1 30 7-44 3-32 (46)
57 COG5432 RAD18 RING-finger-cont 77.2 1.5 3.3E-05 37.0 1.8 35 8-46 37-72 (391)
58 PF10146 zf-C4H2: Zinc finger- 77.1 0.7 1.5E-05 36.2 -0.2 24 8-43 195-218 (230)
59 KOG4718 Non-SMC (structural ma 76.0 1.9 4.1E-05 34.6 1.9 36 8-47 195-230 (235)
60 KOG0320 Predicted E3 ubiquitin 74.7 2.4 5.1E-05 33.1 2.1 29 11-43 149-177 (187)
61 KOG4323 Polycomb-like PHD Zn-f 74.6 1.6 3.4E-05 37.9 1.3 38 4-41 182-223 (464)
62 KOG2177 Predicted E3 ubiquitin 74.4 2.1 4.6E-05 29.7 1.6 26 12-41 30-55 (386)
63 PF09538 FYDLN_acid: Protein o 74.1 1.8 4E-05 30.4 1.3 30 8-46 10-39 (108)
64 TIGR01562 FdhE formate dehydro 72.9 1.8 3.8E-05 35.4 1.1 52 7-58 184-243 (305)
65 PF07800 DUF1644: Protein of u 71.9 3.2 6.9E-05 31.7 2.2 32 13-44 32-91 (162)
66 KOG0955 PHD finger protein BR1 71.2 1.2 2.6E-05 41.9 -0.2 38 5-42 234-282 (1051)
67 KOG4172 Predicted E3 ubiquitin 70.8 2.3 4.9E-05 28.0 1.0 20 22-45 36-55 (62)
68 PF05605 zf-Di19: Drought indu 70.7 4.4 9.5E-05 24.4 2.3 34 9-42 4-40 (54)
69 TIGR00570 cdk7 CDK-activating 70.0 2.8 6.1E-05 34.6 1.7 32 12-46 25-56 (309)
70 KOG1829 Uncharacterized conser 67.4 2.1 4.5E-05 38.1 0.4 34 5-45 529-562 (580)
71 PF05883 Baculo_RING: Baculovi 65.3 5.2 0.00011 29.6 2.1 14 16-29 56-69 (134)
72 smart00109 C1 Protein kinase C 64.9 4.3 9.3E-05 22.6 1.3 18 7-24 27-44 (49)
73 PF15446 zf-PHD-like: PHD/FYVE 64.7 3.2 7E-05 32.1 1.0 19 5-23 15-33 (175)
74 KOG4451 Uncharacterized conser 64.6 1.6 3.5E-05 35.7 -0.8 25 8-44 250-274 (286)
75 PF12773 DZR: Double zinc ribb 64.4 4.1 9E-05 23.7 1.2 29 5-42 10-38 (50)
76 KOG1941 Acetylcholine receptor 64.4 4.2 9.2E-05 35.6 1.7 27 13-41 387-413 (518)
77 PF13408 Zn_ribbon_recom: Reco 63.9 2.6 5.7E-05 24.6 0.3 34 5-46 3-36 (58)
78 KOG2164 Predicted E3 ubiquitin 63.5 4.7 0.0001 35.5 1.9 40 6-45 196-237 (513)
79 COG5574 PEX10 RING-finger-cont 61.7 5.6 0.00012 32.6 1.9 33 8-43 228-261 (271)
80 cd00029 C1 Protein kinase C co 60.2 3.5 7.7E-05 23.3 0.4 19 6-24 27-45 (50)
81 KOG2114 Vacuolar assembly/sort 60.0 4.5 9.8E-05 37.9 1.2 25 12-43 858-882 (933)
82 TIGR02300 FYDLN_acid conserved 60.0 5 0.00011 29.7 1.2 30 8-46 10-39 (129)
83 KOG4443 Putative transcription 59.6 4.4 9.6E-05 36.9 1.0 35 5-40 33-69 (694)
84 KOG1538 Uncharacterized conser 58.9 5.4 0.00012 37.3 1.5 39 3-45 1040-1078(1081)
85 PF14570 zf-RING_4: RING/Ubox 57.0 8.6 0.00019 23.9 1.7 36 4-43 12-47 (48)
86 PF00130 C1_1: Phorbol esters/ 56.1 1.6 3.5E-05 25.6 -1.6 20 5-24 26-45 (53)
87 smart00647 IBR In Between Ring 54.8 10 0.00022 22.3 1.7 16 5-20 16-33 (64)
88 COG3809 Uncharacterized protei 53.3 3.9 8.4E-05 28.5 -0.3 30 33-62 21-55 (88)
89 smart00659 RPOLCX RNA polymera 52.9 4.4 9.6E-05 24.3 -0.0 26 9-43 4-29 (44)
90 PF08772 NOB1_Zn_bind: Nin one 52.5 5.4 0.00012 26.5 0.3 13 4-16 21-33 (73)
91 PF13719 zinc_ribbon_5: zinc-r 51.8 6.3 0.00014 22.5 0.5 15 30-44 22-36 (37)
92 PF02591 DUF164: Putative zinc 51.4 9.4 0.0002 23.1 1.3 31 9-41 24-54 (56)
93 PF06676 DUF1178: Protein of u 50.8 3.3 7.1E-05 30.9 -1.0 27 20-46 12-45 (148)
94 COG5141 PHD zinc finger-contai 50.6 9.2 0.0002 34.4 1.5 40 5-44 208-258 (669)
95 PF09237 GAGA: GAGA factor; I 50.0 2.9 6.2E-05 26.9 -1.3 20 25-44 16-35 (54)
96 KOG1039 Predicted E3 ubiquitin 49.5 9.6 0.00021 31.8 1.4 30 13-42 187-219 (344)
97 COG5183 SSM4 Protein involved 49.2 12 0.00026 35.7 2.0 31 15-47 39-69 (1175)
98 PF10497 zf-4CXXC_R1: Zinc-fin 49.1 11 0.00025 26.1 1.5 50 11-60 31-104 (105)
99 KOG3816 Cell differentiation r 48.8 11 0.00025 33.0 1.8 17 12-28 105-121 (526)
100 KOG0311 Predicted E3 ubiquitin 47.6 9.7 0.00021 32.6 1.2 33 11-46 60-92 (381)
101 COG4357 Zinc finger domain con 47.4 13 0.00028 26.8 1.6 33 6-46 61-93 (105)
102 COG3357 Predicted transcriptio 46.6 9 0.00019 27.2 0.7 31 9-47 60-90 (97)
103 PF14369 zf-RING_3: zinc-finge 46.5 7.5 0.00016 22.2 0.3 29 8-43 3-31 (35)
104 TIGR02605 CxxC_CxxC_SSSS putat 45.8 3.6 7.8E-05 24.2 -1.2 29 9-42 7-35 (52)
105 KOG3271 Translation initiation 45.4 9.1 0.0002 29.1 0.6 45 48-93 94-138 (156)
106 PF13717 zinc_ribbon_4: zinc-r 45.4 9.3 0.0002 21.8 0.5 34 8-44 3-36 (36)
107 KOG0287 Postreplication repair 44.2 15 0.00032 31.8 1.7 32 12-47 40-71 (442)
108 PF05810 NinF: NinF protein; 44.1 13 0.00029 24.2 1.2 19 10-28 20-45 (58)
109 KOG1002 Nucleotide excision re 43.0 17 0.00037 33.2 2.0 34 12-45 553-587 (791)
110 PF04423 Rad50_zn_hook: Rad50 42.9 17 0.00036 21.8 1.4 27 19-45 6-32 (54)
111 PRK11657 dsbG disulfide isomer 42.5 6.1 0.00013 30.6 -0.7 13 33-45 126-138 (251)
112 TIGR00100 hypA hydrogenase nic 41.6 12 0.00027 26.0 0.8 28 6-43 69-96 (115)
113 PF14447 Prok-RING_4: Prokaryo 41.1 7.5 0.00016 24.9 -0.3 29 12-46 24-52 (55)
114 KOG0978 E3 ubiquitin ligase in 41.0 22 0.00048 32.5 2.4 33 12-47 660-692 (698)
115 TIGR02098 MJ0042_CXXC MJ0042 f 39.2 12 0.00027 20.7 0.4 14 31-44 23-36 (38)
116 COG4391 Uncharacterized protei 38.1 12 0.00027 24.6 0.3 14 31-44 46-59 (62)
117 COG1579 Zn-ribbon protein, pos 37.9 19 0.00042 28.7 1.4 31 9-41 199-229 (239)
118 PF02891 zf-MIZ: MIZ/SP-RING z 37.7 3.9 8.5E-05 24.8 -2.0 25 18-42 23-50 (50)
119 PF00659 POLO_box: POLO box du 36.8 24 0.00051 21.8 1.4 9 90-98 15-23 (68)
120 PF04828 GFA: Glutathione-depe 36.1 17 0.00036 22.4 0.7 9 35-43 50-58 (92)
121 PRK00564 hypA hydrogenase nick 35.2 17 0.00036 25.5 0.6 31 5-44 69-99 (117)
122 PF11789 zf-Nse: Zinc-finger o 34.6 18 0.00039 22.5 0.7 29 8-38 25-53 (57)
123 PF03604 DNA_RNApol_7kD: DNA d 34.6 17 0.00038 20.6 0.5 11 31-41 15-25 (32)
124 PF06937 EURL: EURL protein; 34.5 22 0.00047 29.4 1.3 26 4-29 27-69 (285)
125 KOG0006 E3 ubiquitin-protein l 34.2 39 0.00084 29.2 2.7 23 3-25 331-354 (446)
126 PF13240 zinc_ribbon_2: zinc-r 34.2 16 0.00034 19.2 0.3 10 7-16 13-22 (23)
127 PF14169 YdjO: Cold-inducible 34.0 18 0.00039 23.4 0.6 21 25-45 29-51 (59)
128 PF14353 CpXC: CpXC protein 33.6 16 0.00036 25.0 0.4 14 33-46 1-14 (128)
129 KOG1940 Zn-finger protein [Gen 32.6 29 0.00062 28.3 1.6 27 11-41 178-204 (276)
130 PRK03564 formate dehydrogenase 32.4 17 0.00037 29.9 0.3 41 6-47 186-226 (309)
131 KOG0827 Predicted E3 ubiquitin 32.4 18 0.0004 31.6 0.5 33 11-47 216-248 (465)
132 TIGR01384 TFS_arch transcripti 31.1 24 0.00053 23.3 0.9 28 9-46 2-29 (104)
133 PF11781 RRN7: RNA polymerase 30.7 31 0.00067 19.8 1.1 18 33-53 8-25 (36)
134 PF14835 zf-RING_6: zf-RING of 30.5 6.1 0.00013 26.1 -2.1 33 8-46 20-54 (65)
135 PF13248 zf-ribbon_3: zinc-rib 30.5 20 0.00043 18.9 0.3 12 8-19 3-14 (26)
136 PF10276 zf-CHCC: Zinc-finger 29.9 19 0.00041 21.4 0.2 12 32-43 28-39 (40)
137 PF13451 zf-trcl: Probable zin 29.6 27 0.00058 21.8 0.8 36 7-42 4-42 (49)
138 PHA03096 p28-like protein; Pro 29.3 42 0.00092 27.2 2.1 29 12-41 203-231 (284)
139 PRK10877 protein disulfide iso 29.2 13 0.00028 28.4 -0.8 13 33-45 116-128 (232)
140 TIGR01295 PedC_BrcD bacterioci 29.1 16 0.00035 25.1 -0.3 10 33-42 32-41 (122)
141 PRK00241 nudC NADH pyrophospha 28.8 19 0.00041 28.1 0.0 31 6-44 98-128 (256)
142 PF14569 zf-UDP: Zinc-binding 28.6 56 0.0012 22.5 2.3 40 4-46 25-64 (80)
143 KOG4236 Serine/threonine prote 28.5 26 0.00056 32.5 0.8 17 7-23 173-189 (888)
144 KOG1645 RING-finger-containing 28.0 34 0.00075 30.0 1.5 30 11-42 25-54 (463)
145 KOG1086 Cytosolic sorting prot 27.9 15 0.00033 32.8 -0.7 18 6-23 68-86 (594)
146 cd03020 DsbA_DsbC_DsbG DsbA fa 27.5 15 0.00033 26.5 -0.7 13 33-45 86-98 (197)
147 KOG0824 Predicted E3 ubiquitin 27.4 31 0.00068 29.0 1.1 30 17-46 26-55 (324)
148 PF10571 UPF0547: Uncharacteri 27.1 25 0.00055 19.0 0.3 12 35-46 2-13 (26)
149 cd03023 DsbA_Com1_like DsbA fa 26.0 18 0.00039 23.7 -0.5 12 33-44 14-25 (154)
150 PRK00418 DNA gyrase inhibitor; 25.6 36 0.00079 22.2 0.9 14 33-46 6-21 (62)
151 smart00132 LIM Zinc-binding do 25.5 14 0.00031 19.2 -0.8 10 14-23 20-29 (39)
152 PF02150 RNA_POL_M_15KD: RNA p 24.9 28 0.0006 19.8 0.3 12 7-18 1-12 (35)
153 PRK12495 hypothetical protein; 24.7 31 0.00068 27.6 0.6 35 3-47 38-72 (226)
154 KOG4265 Predicted E3 ubiquitin 24.5 27 0.00058 29.6 0.2 23 19-45 315-337 (349)
155 smart00661 RPOL9 RNA polymeras 24.5 31 0.00066 19.9 0.4 32 9-46 2-33 (52)
156 PF07649 C1_3: C1-like domain; 24.4 40 0.00087 18.0 0.8 17 6-22 14-30 (30)
157 PF13098 Thioredoxin_2: Thiore 24.4 21 0.00045 22.7 -0.4 13 33-45 14-26 (112)
158 PF07282 OrfB_Zn_ribbon: Putat 24.3 27 0.00058 21.4 0.1 12 32-43 45-56 (69)
159 KOG1140 N-end rule pathway, re 24.2 44 0.00096 33.6 1.6 34 11-44 1149-1198(1738)
160 KOG4275 Predicted E3 ubiquitin 24.2 27 0.00059 29.6 0.2 19 8-42 322-340 (350)
161 PF05280 FlhC: Flagellar trans 23.4 13 0.00027 28.1 -1.8 31 6-42 133-163 (175)
162 COG5319 Uncharacterized protei 23.0 24 0.00052 26.5 -0.3 23 22-44 14-43 (142)
163 KOG1100 Predicted E3 ubiquitin 21.8 34 0.00073 26.3 0.3 11 33-43 189-199 (207)
164 PHA03050 glutaredoxin; Provisi 21.5 29 0.00063 23.7 -0.1 9 33-41 20-28 (108)
165 PF11672 DUF3268: Protein of u 21.3 41 0.00088 23.7 0.6 13 32-44 1-13 (102)
166 TIGR01385 TFSII transcription 21.1 17 0.00036 29.6 -1.6 40 2-44 253-297 (299)
167 PF03264 Cytochrom_NNT: NapC/N 20.8 58 0.0013 23.4 1.3 35 7-43 35-74 (173)
168 PF04502 DUF572: Family of unk 20.7 35 0.00077 27.5 0.2 38 7-44 40-88 (324)
169 KOG1245 Chromatin remodeling c 20.6 49 0.0011 32.4 1.1 43 2-44 1118-1160(1404)
170 PF04720 DUF506: Protein of un 20.6 89 0.0019 24.5 2.4 30 18-47 85-115 (218)
171 COG5175 MOT2 Transcriptional r 20.5 90 0.002 27.3 2.6 40 12-57 35-74 (480)
172 PLN02189 cellulose synthase 20.4 60 0.0013 31.1 1.6 38 4-44 50-87 (1040)
173 KOG2462 C2H2-type Zn-finger pr 20.2 55 0.0012 27.0 1.2 35 9-47 189-229 (279)
174 PRK03681 hypA hydrogenase nick 20.0 51 0.0011 22.9 0.8 30 5-43 68-97 (114)
No 1
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.98 E-value=3.5e-10 Score=77.44 Aligned_cols=42 Identities=26% Similarity=0.685 Sum_probs=35.1
Q ss_pred CCCCceeecccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 2 GSGERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 2 gs~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
|.+-.|||+ .|+++||..|+.+|.++.+. +.+||+||++|+-
T Consensus 42 gd~Cplv~g-~C~H~FH~hCI~kWl~~~~~-~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 42 GDDCPLVWG-KCSHNFHMHCILKWLSTQSS-KGQCPMCRQPWKF 83 (85)
T ss_pred CCCCceeec-cCccHHHHHHHHHHHccccC-CCCCCCcCCeeee
Confidence 344567777 59999999999999999754 4699999999974
No 2
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.28 E-value=4.2e-07 Score=52.86 Aligned_cols=31 Identities=32% Similarity=0.889 Sum_probs=24.6
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICR 40 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CR 40 (98)
+.++... ||+.||.+|+++|.+++ .+||+||
T Consensus 14 ~~~~~l~-C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 14 EKVVKLP-CGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp SCEEEET-TSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CeEEEcc-CCCeeCHHHHHHHHHhC----CcCCccC
Confidence 4444444 99999999999999995 4899998
No 3
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.25 E-value=4.8e-07 Score=83.50 Aligned_cols=35 Identities=34% Similarity=0.832 Sum_probs=31.2
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
-.|++|.|.||..|+.+|+++++ ..+||.||+...
T Consensus 1489 krC~TCknKFH~~CLyKWf~Ss~--~s~CPlCRseit 1523 (1525)
T COG5219 1489 KRCATCKNKFHTRCLYKWFASSA--RSNCPLCRSEIT 1523 (1525)
T ss_pred cccchhhhhhhHHHHHHHHHhcC--CCCCCccccccc
Confidence 46999999999999999999986 589999998653
No 4
>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=98.14 E-value=7.4e-07 Score=57.78 Aligned_cols=26 Identities=31% Similarity=1.005 Sum_probs=22.8
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICR 40 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CR 40 (98)
+.||..||..|+.+|..++ .+||+||
T Consensus 48 ~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp ETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred cccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 6799999999999999885 4999998
No 5
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.06 E-value=6.4e-07 Score=57.97 Aligned_cols=39 Identities=26% Similarity=0.463 Sum_probs=20.6
Q ss_pred Cceeec--ccccchhHHHHHHHHHHhcC--C-----CCcccccccccc
Q 039237 5 ERLVAC--GTCKNLIHEECWVTWKRSRG--R-----RAASCVICRGRW 43 (98)
Q Consensus 5 e~lVwC--~~CGnniHkeCf~~W~~s~~--~-----~~vtCp~CRs~W 43 (98)
...++| .+|++.+|..||.+|+++.. + -..+||+|+++-
T Consensus 18 ~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 18 IPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp ---B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred cCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 356899 69999999999999999832 1 135799999874
No 6
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.82 E-value=1.4e-05 Score=43.73 Aligned_cols=30 Identities=23% Similarity=0.645 Sum_probs=25.6
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
..||..||..|++.|.+. ...+||.||.++
T Consensus 16 ~~C~H~~c~~C~~~~~~~---~~~~Cp~C~~~~ 45 (45)
T cd00162 16 LPCGHVFCRSCIDKWLKS---GKNTCPLCRTPI 45 (45)
T ss_pred cCCCChhcHHHHHHHHHh---CcCCCCCCCCcC
Confidence 459999999999999987 257799999864
No 7
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.73 E-value=1.8e-05 Score=54.81 Aligned_cols=31 Identities=29% Similarity=0.860 Sum_probs=28.2
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+.|..+||..|+++|.+|++ -||++|.+|+-
T Consensus 52 G~CnHaFH~HCI~rWL~Tk~----~CPld~q~w~~ 82 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDTKG----VCPLDRQTWVL 82 (88)
T ss_pred EecchHHHHHHHHHHHhhCC----CCCCCCceeEE
Confidence 68999999999999999964 49999999983
No 8
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=1.9e-05 Score=54.35 Aligned_cols=33 Identities=27% Similarity=0.890 Sum_probs=29.8
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
+.|..+||..|+.+|..++.. +..||+||..|.
T Consensus 49 G~C~h~fh~hCI~~wl~~~ts-q~~CPmcRq~~~ 81 (84)
T KOG1493|consen 49 GYCLHAFHAHCILKWLNTPTS-QGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHHhcCccc-cccCCcchheeE
Confidence 479999999999999999875 478999999997
No 9
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.57 E-value=3.2e-05 Score=60.78 Aligned_cols=30 Identities=27% Similarity=0.803 Sum_probs=26.4
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
..||+.||.+|+.+|.+. ..+||+||.+..
T Consensus 198 ~~C~H~FC~~CI~~Wl~~----~~tCPlCR~~~~ 227 (238)
T PHA02929 198 SNCNHVFCIECIDIWKKE----KNTCPVCRTPFI 227 (238)
T ss_pred CCCCCcccHHHHHHHHhc----CCCCCCCCCEee
Confidence 479999999999999876 468999999876
No 10
>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=96.91 E-value=0.00079 Score=35.35 Aligned_cols=26 Identities=27% Similarity=0.721 Sum_probs=21.9
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~C 39 (98)
..||..||.+|++.|.+. +..+||.|
T Consensus 14 ~~C~H~~c~~C~~~~~~~---~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLKS---GNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHHh---CcCCCCCC
Confidence 469999999999999983 35779987
No 11
>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=96.76 E-value=0.0012 Score=40.22 Aligned_cols=24 Identities=33% Similarity=0.992 Sum_probs=21.1
Q ss_pred chhHHHHHHHHHHhcCCCCccccccc
Q 039237 15 NLIHEECWVTWKRSRGRRAASCVICR 40 (98)
Q Consensus 15 nniHkeCf~~W~~s~~~~~vtCp~CR 40 (98)
+.||..|+++|...++ ..+||+|.
T Consensus 26 ~~vH~~Cl~~W~~~~~--~~~C~iC~ 49 (49)
T smart00744 26 KYVHQECLERWINESG--NKTCEICK 49 (49)
T ss_pred hHHHHHHHHHHHHHcC--CCcCCCCC
Confidence 7899999999999986 46899995
No 12
>PHA02926 zinc finger-like protein; Provisional
Probab=96.65 E-value=0.0014 Score=52.34 Aligned_cols=34 Identities=32% Similarity=0.865 Sum_probs=28.6
Q ss_pred ccccchhHHHHHHHHHHhcC--CCCccccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRG--RRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~--~~~vtCp~CRs~W~ 44 (98)
..|++.|.-.|+.+|++++. +...+||+||.+-.
T Consensus 195 ~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 195 DSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 48999999999999999752 34678999999865
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=96.57 E-value=0.0018 Score=50.01 Aligned_cols=37 Identities=19% Similarity=0.546 Sum_probs=29.2
Q ss_pred ccccchhHHHHHHHHHHhc------------CCCCcccccccccccCCC
Q 039237 11 GTCKNLIHEECWVTWKRSR------------GRRAASCVICRGRWRDNR 47 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~------------~~~~vtCp~CRs~W~~~~ 47 (98)
..||+.|...|+.+|.... ..+..+||.||++-....
T Consensus 34 T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 34 TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 3799999999999998642 123579999999987544
No 14
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0023 Score=46.28 Aligned_cols=31 Identities=26% Similarity=0.723 Sum_probs=28.5
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+.|...||-.|+.+|.+++ ..||+|..+|.-
T Consensus 79 G~CNHaFH~hCisrWlktr----~vCPLdn~eW~~ 109 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR----NVCPLDNKEWVF 109 (114)
T ss_pred eecchHHHHHHHHHHHhhc----CcCCCcCcceeE
Confidence 7999999999999999997 559999999973
No 15
>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=96.56 E-value=0.0014 Score=38.96 Aligned_cols=30 Identities=30% Similarity=0.552 Sum_probs=25.3
Q ss_pred ccccch-hHHHHHHHHHHhcCCCCccccccccccc
Q 039237 11 GTCKNL-IHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnn-iHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
.-||+. |-.+|+.+|.++ ..+||+||++-.
T Consensus 18 ~pCgH~~~C~~C~~~~~~~----~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 18 LPCGHLCFCEECAERLLKR----KKKCPICRQPIE 48 (50)
T ss_dssp ETTCEEEEEHHHHHHHHHT----TSBBTTTTBB-S
T ss_pred eCCCChHHHHHHhHHhccc----CCCCCcCChhhc
Confidence 479999 999999999994 578999999753
No 16
>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=96.54 E-value=0.0014 Score=36.96 Aligned_cols=27 Identities=19% Similarity=0.672 Sum_probs=23.8
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~C 39 (98)
..||+.|+..|+.+|.+.+ ..++||.|
T Consensus 15 ~~C~H~fC~~C~~~~~~~~--~~~~CP~C 41 (41)
T PF00097_consen 15 LPCGHSFCRDCLRKWLENS--GSVKCPLC 41 (41)
T ss_dssp TTTSEEEEHHHHHHHHHHT--SSSBTTTT
T ss_pred ecCCCcchHHHHHHHHHhc--CCccCCcC
Confidence 5799999999999999973 46889998
No 17
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.0012 Score=56.46 Aligned_cols=29 Identities=28% Similarity=0.788 Sum_probs=26.0
Q ss_pred cccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
.||+=+|=+|++.|...+ -|||+||.|-.
T Consensus 317 pCGHilHl~CLknW~ERq----QTCPICr~p~i 345 (491)
T COG5243 317 PCGHILHLHCLKNWLERQ----QTCPICRRPVI 345 (491)
T ss_pred cccceeeHHHHHHHHHhc----cCCCcccCccc
Confidence 699999999999999984 78999999944
No 18
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.42 E-value=0.0019 Score=54.73 Aligned_cols=30 Identities=23% Similarity=0.713 Sum_probs=26.5
Q ss_pred eec-ccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 8 VAC-GTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 8 VwC-~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
+-. --||.-||-.|+++|.+. ..|||.||.
T Consensus 308 ~~~rL~C~Hifh~~CL~~W~er----~qtCP~CR~ 338 (543)
T KOG0802|consen 308 TPKRLPCGHIFHDSCLRSWFER----QQTCPTCRT 338 (543)
T ss_pred ccceeecccchHHHHHHHHHHH----hCcCCcchh
Confidence 345 579999999999999999 478999999
No 19
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.23 E-value=0.0025 Score=54.63 Aligned_cols=29 Identities=31% Similarity=0.883 Sum_probs=25.2
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICR 40 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CR 40 (98)
.+||.-||..|+.||+.+... ..+||.||
T Consensus 24 ~~cGhifh~~cl~qwfe~~Ps-~R~cpic~ 52 (465)
T KOG0827|consen 24 GTCGHIFHTTCLTQWFEGDPS-NRGCPICQ 52 (465)
T ss_pred cchhhHHHHHHHHHHHccCCc-cCCCCcee
Confidence 579999999999999999642 26899999
No 20
>PHA02862 5L protein; Provisional
Probab=95.98 E-value=0.0051 Score=46.52 Aligned_cols=36 Identities=17% Similarity=0.573 Sum_probs=28.8
Q ss_pred eeec--ccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 7 LVAC--GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 7 lVwC--~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
+-.| .+--+-+|++|+++|.+++ ++.+|+.|+.+..
T Consensus 16 ~~PC~C~GS~K~VHq~CL~~WIn~S--~k~~CeLCkteY~ 53 (156)
T PHA02862 16 NNFCGCNEEYKVVHIKCMQLWINYS--KKKECNLCKTKYN 53 (156)
T ss_pred cccccccCcchhHHHHHHHHHHhcC--CCcCccCCCCeEE
Confidence 4555 4556789999999999876 4799999998754
No 21
>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=95.74 E-value=0.0045 Score=35.14 Aligned_cols=27 Identities=19% Similarity=0.599 Sum_probs=22.4
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~C 39 (98)
.-..||+.|.++|+++|.+.+ .+||.|
T Consensus 13 ~~~~CGH~fC~~C~~~~~~~~----~~CP~C 39 (39)
T PF13923_consen 13 VVTPCGHSFCKECIEKYLEKN----PKCPVC 39 (39)
T ss_dssp EECTTSEEEEHHHHHHHHHCT----SB-TTT
T ss_pred EECCCCCchhHHHHHHHHHCc----CCCcCC
Confidence 346899999999999999883 689987
No 22
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=95.63 E-value=0.0089 Score=34.89 Aligned_cols=29 Identities=28% Similarity=0.700 Sum_probs=25.1
Q ss_pred ec-ccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 9 AC-GTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 9 wC-~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
.- .+||.-|...|+++.. ...+.||+||.
T Consensus 15 ~~l~~CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 15 PRLTSCGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred eEEcccCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 45 7899999999999999 34789999985
No 23
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.58 E-value=0.0031 Score=38.14 Aligned_cols=29 Identities=38% Similarity=1.054 Sum_probs=20.3
Q ss_pred eecccccc---hhHHHHHHHHHHhcCCCCcccccc
Q 039237 8 VACGTCKN---LIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 8 VwC~~CGn---niHkeCf~~W~~s~~~~~vtCp~C 39 (98)
-.| .|.- .+|.+|+++|..+++ ..+|+.|
T Consensus 16 ~pC-~C~Gs~~~vH~~CL~~W~~~~~--~~~C~~C 47 (47)
T PF12906_consen 16 SPC-RCKGSMKYVHRSCLERWIRESG--NRKCEIC 47 (47)
T ss_dssp -SS-S-SSCCGSEECCHHHHHHHHHT---SB-TTT
T ss_pred ccc-ccCCCcchhHHHHHHHHHHhcC--CCcCCCC
Confidence 345 4555 999999999999975 5779887
No 24
>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=95.38 E-value=0.0083 Score=35.82 Aligned_cols=30 Identities=27% Similarity=0.832 Sum_probs=18.6
Q ss_pred eecc--cccchhHHHHHHHHHHhcCCCCcccccc
Q 039237 8 VACG--TCKNLIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 8 VwC~--~CGnniHkeCf~~W~~s~~~~~vtCp~C 39 (98)
+-|. .|+-.+|..||++++++++. .+||-|
T Consensus 12 ~~C~~~~C~~r~H~~C~~~y~r~~~~--~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVRLHDDCFKKYFRHRSN--PKCPNC 43 (43)
T ss_dssp EE-SS--S--EE-HHHHHHHTTT-SS---B-TTT
T ss_pred ccCCCCccCchHHHHHHHHHHhcCCC--CCCcCC
Confidence 5673 79999999999999999763 389987
No 25
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=95.16 E-value=0.011 Score=49.08 Aligned_cols=26 Identities=31% Similarity=0.698 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcC---------CCCcccccccccc
Q 039237 18 HEECWVTWKRSRG---------RRAASCVICRGRW 43 (98)
Q Consensus 18 HkeCf~~W~~s~~---------~~~vtCp~CRs~W 43 (98)
=-+|+-||++++. .+..+||.||++.
T Consensus 316 C~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred HHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 3689999999964 3589999999985
No 26
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.04 E-value=0.018 Score=43.80 Aligned_cols=29 Identities=31% Similarity=0.831 Sum_probs=25.2
Q ss_pred chhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 15 NLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 15 nniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+-+|++|+++|...++ ..+|+.|+++..-
T Consensus 32 k~VH~sCL~rWi~~s~--~~~CeiC~~~Y~i 60 (162)
T PHA02825 32 KIVHKECLEEWINTSK--NKSCKICNGPYNI 60 (162)
T ss_pred hHHHHHHHHHHHhcCC--CCcccccCCeEEE
Confidence 4789999999999874 7899999998764
No 27
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.91 E-value=0.02 Score=45.29 Aligned_cols=36 Identities=25% Similarity=0.650 Sum_probs=27.9
Q ss_pred ec--ccccchhHHHHHHHHHHhc--CCC-----Cccccccccccc
Q 039237 9 AC--GTCKNLIHEECWVTWKRSR--GRR-----AASCVICRGRWR 44 (98)
Q Consensus 9 wC--~~CGnniHkeCf~~W~~s~--~~~-----~vtCp~CRs~W~ 44 (98)
.| -+||+.||.-|+..|.+.- +++ -..||||-.|-.
T Consensus 184 tCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 184 TCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 57 7999999999999999972 111 346999987643
No 28
>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=94.48 E-value=0.026 Score=33.79 Aligned_cols=30 Identities=7% Similarity=-0.013 Sum_probs=26.0
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
..||+.|-++|+.+|.+. ..+||+||.+..
T Consensus 17 ~~~G~v~~~~~i~~~~~~----~~~cP~~~~~~~ 46 (63)
T smart00504 17 LPSGQTYERRAIEKWLLS----HGTDPVTGQPLT 46 (63)
T ss_pred CCCCCEEeHHHHHHHHHH----CCCCCCCcCCCC
Confidence 478999999999999987 368999998874
No 29
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.43 E-value=0.02 Score=47.71 Aligned_cols=33 Identities=21% Similarity=0.637 Sum_probs=27.9
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
-|+++||..|.+.|.-+.+ -.||.|+.+=..+.
T Consensus 249 PC~H~FH~~CIDpWL~~~r---~~CPvCK~di~~~~ 281 (348)
T KOG4628|consen 249 PCSHKFHVNCIDPWLTQTR---TFCPVCKRDIRTDS 281 (348)
T ss_pred cCCCchhhccchhhHhhcC---ccCCCCCCcCCCCC
Confidence 6999999999999999963 56999999776543
No 30
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.20 E-value=0.026 Score=49.86 Aligned_cols=30 Identities=23% Similarity=0.791 Sum_probs=26.3
Q ss_pred cccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
-|.+-+|..|+++|..+. +..||.||.|-+
T Consensus 605 PC~HifH~~CL~~WMd~y---kl~CPvCR~pLP 634 (636)
T KOG0828|consen 605 PCHHIFHRQCLLQWMDTY---KLICPVCRCPLP 634 (636)
T ss_pred chHHHHHHHHHHHHHhhh---cccCCccCCCCC
Confidence 488999999999999975 488999999865
No 31
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.15 E-value=0.015 Score=48.04 Aligned_cols=35 Identities=23% Similarity=0.703 Sum_probs=28.5
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccc----------ccccCCC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICR----------GRWRDNR 47 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CR----------s~W~~~~ 47 (98)
-+|++.||+.|++-|--- |+..|||||. .||+.+-
T Consensus 250 LsCnHvFHEfCIrGWciv--GKkqtCPYCKekVdl~rmfsnpWekph 294 (328)
T KOG1734|consen 250 LSCNHVFHEFCIRGWCIV--GKKQTCPYCKEKVDLKRMFSNPWEKPH 294 (328)
T ss_pred eecccchHHHhhhhheee--cCCCCCchHHHHhhHhhhccCccccch
Confidence 479999999999999876 3579999995 5677654
No 32
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.12 E-value=0.03 Score=46.97 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=25.3
Q ss_pred cccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
-|.+-||..|+++|..-- ...||.||++-+
T Consensus 343 PC~H~FH~~Cv~kW~~~y---~~~CPvCrt~iP 372 (374)
T COG5540 343 PCDHRFHVGCVDKWLLGY---SNKCPVCRTAIP 372 (374)
T ss_pred ccCceechhHHHHHHhhh---cccCCccCCCCC
Confidence 489999999999999942 366999999865
No 33
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=93.92 E-value=0.026 Score=33.18 Aligned_cols=28 Identities=18% Similarity=0.412 Sum_probs=21.9
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVIC 39 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~C 39 (98)
.||.+|=+.|+.+|.+...+....||.|
T Consensus 15 ~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 15 PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 6999999999999998876655899987
No 34
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=93.78 E-value=0.047 Score=34.83 Aligned_cols=22 Identities=32% Similarity=0.995 Sum_probs=19.2
Q ss_pred CCCceeecccccchhHHHHHHH
Q 039237 3 SGERLVACGTCKNLIHEECWVT 24 (98)
Q Consensus 3 s~e~lVwC~~CGnniHkeCf~~ 24 (98)
++..+|.|..||...|++|..+
T Consensus 17 ~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 17 DGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CCCCEEECCCCCCcccHHHHhh
Confidence 4678999999999999999753
No 35
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.26 E-value=0.051 Score=44.56 Aligned_cols=31 Identities=19% Similarity=0.629 Sum_probs=26.3
Q ss_pred cchhHHHHHHHHHHhcC----CCCccccccccccc
Q 039237 14 KNLIHEECWVTWKRSRG----RRAASCVICRGRWR 44 (98)
Q Consensus 14 GnniHkeCf~~W~~s~~----~~~vtCp~CRs~W~ 44 (98)
-+=+|..|+.+|...|. .+.|+||-|+++..
T Consensus 48 ~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 48 TKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred cHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 45699999999998853 47999999999865
No 36
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.53 E-value=0.15 Score=40.55 Aligned_cols=41 Identities=20% Similarity=0.553 Sum_probs=33.5
Q ss_pred CCceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 4 GERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 4 ~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
.+.+|.| ||+-|=--||+||..++.. ..-||.|++.=..+.
T Consensus 58 kdPVvTl--CGHLFCWpClyqWl~~~~~-~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 58 KDPVVTL--CGHLFCWPCLYQWLQTRPN-SKECPVCKAEVSIDT 98 (230)
T ss_pred CCCEEee--cccceehHHHHHHHhhcCC-CeeCCccccccccce
Confidence 4566766 9999999999999999865 566899999877654
No 37
>PF15353 HECA: Headcase protein family homologue
Probab=91.33 E-value=0.15 Score=36.58 Aligned_cols=15 Identities=33% Similarity=0.948 Sum_probs=14.2
Q ss_pred cchhHHHHHHHHHHh
Q 039237 14 KNLIHEECWVTWKRS 28 (98)
Q Consensus 14 GnniHkeCf~~W~~s 28 (98)
|+.+|++||++|..+
T Consensus 41 ~~~MH~~CF~~wE~~ 55 (107)
T PF15353_consen 41 GQYMHRECFEKWEDS 55 (107)
T ss_pred CCchHHHHHHHHHHH
Confidence 899999999999887
No 38
>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 KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.26 E-value=0.15 Score=47.49 Aligned_cols=32 Identities=28% Similarity=0.626 Sum_probs=28.3
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
+.|+..||++||..|-+- .-|||.||..+-.-
T Consensus 142 k~c~H~FC~~Ci~sWsR~----aqTCPiDR~EF~~v 173 (1134)
T KOG0825|consen 142 KHTAHYFCEECVGSWSRC----AQTCPVDRGEFGEV 173 (1134)
T ss_pred cccccccHHHHhhhhhhh----cccCchhhhhhhee
Confidence 579999999999999987 57999999998753
No 40
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.18 E-value=0.19 Score=42.36 Aligned_cols=32 Identities=16% Similarity=0.475 Sum_probs=26.8
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
..||+.|...|++.|...+ ..||.||.+-...
T Consensus 42 tpCgH~FCs~CI~~~l~~~----~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 42 TSCSHTFCSLCIRRCLSNQ----PKCPLCRAEDQES 73 (397)
T ss_pred CCCCCchhHHHHHHHHhCC----CCCCCCCCccccc
Confidence 4799999999999998763 4799999986643
No 41
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=86.71 E-value=0.42 Score=39.32 Aligned_cols=32 Identities=19% Similarity=0.737 Sum_probs=27.5
Q ss_pred cccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 10 CGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 10 C~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
|.-||+=|=-.|+..|...+. .||.||.+-..
T Consensus 254 aTpCGHiFCWsCI~~w~~ek~----eCPlCR~~~~p 285 (293)
T KOG0317|consen 254 ATPCGHIFCWSCILEWCSEKA----ECPLCREKFQP 285 (293)
T ss_pred cCcCcchHHHHHHHHHHcccc----CCCcccccCCC
Confidence 456999999999999999974 49999998764
No 42
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=86.45 E-value=0.38 Score=42.08 Aligned_cols=34 Identities=24% Similarity=0.714 Sum_probs=29.2
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
-||+-+-..|+..|..+..+ -+||+||..-++..
T Consensus 386 PCGHLlCt~CLa~WQ~sd~g--q~CPFCRcEIKGte 419 (563)
T KOG1785|consen 386 PCGHLLCTSCLAAWQDSDEG--QTCPFCRCEIKGTE 419 (563)
T ss_pred cccchHHHHHHHhhcccCCC--CCCCceeeEecccc
Confidence 58999999999999988763 78999999988654
No 43
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=86.42 E-value=0.38 Score=36.63 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=9.2
Q ss_pred CCCCCeeehhh
Q 039237 48 TDQDKYLNLAA 58 (98)
Q Consensus 48 ~~~eGYlNla~ 58 (98)
...+||+||..
T Consensus 29 ~a~~Gy~~ll~ 39 (272)
T PRK11088 29 CAKEGYVNLLP 39 (272)
T ss_pred cccCceEEecc
Confidence 56789999974
No 44
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=86.14 E-value=0.47 Score=35.86 Aligned_cols=30 Identities=23% Similarity=0.702 Sum_probs=25.3
Q ss_pred chhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 15 NLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 15 nniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
.-+|+.|+++|...++ ..+|-+|.+.-...
T Consensus 107 ~~vH~~cl~~W~~~~~--~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 107 AYVHRSCLEKWFSIKG--NITCEICKSFFINV 136 (323)
T ss_pred HHHHHHHHHhhhcccc--Ceeeecccccceec
Confidence 4569999999999886 68999999877755
No 45
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=84.08 E-value=0.63 Score=27.80 Aligned_cols=26 Identities=15% Similarity=0.520 Sum_probs=17.8
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCV 37 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp 37 (98)
.||..|=++|++++.+.+.+...+||
T Consensus 18 ~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 18 PCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 59999999999999998755578887
No 46
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=83.44 E-value=0.96 Score=41.70 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=33.0
Q ss_pred CceeecccccchhHHHHHHHHHHhcCC--C-CcccccccccccCC
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGR--R-AASCVICRGRWRDN 46 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~--~-~vtCp~CRs~W~~~ 46 (98)
...+||..||.--|.+|+++|...... + ...|+.|++.|.+.
T Consensus 791 G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~~~~~D~ 835 (839)
T KOG0269|consen 791 GVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHYSSFIDT 835 (839)
T ss_pred eeEeecccccccccHHHHHHHHhcCCCCccccCCccccccccchh
Confidence 357999999999999999999988542 1 24566788888764
No 47
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=82.83 E-value=1.2 Score=41.64 Aligned_cols=45 Identities=22% Similarity=0.606 Sum_probs=36.0
Q ss_pred CCCCCceeecccccchhHHHHHHHHHHhc---CCCCcccccccccccC
Q 039237 1 MGSGERLVACGTCKNLIHEECWVTWKRSR---GRRAASCVICRGRWRD 45 (98)
Q Consensus 1 ~gs~e~lVwC~~CGnniHkeCf~~W~~s~---~~~~vtCp~CRs~W~~ 45 (98)
|+....+.-|.+|=.-||--|+++|+++. +...-+||.|++.-..
T Consensus 201 I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~ 248 (950)
T KOG1952|consen 201 IKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKT 248 (950)
T ss_pred ccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhcc
Confidence 44556777789999999999999999993 2346689999977764
No 48
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=81.81 E-value=0.44 Score=41.57 Aligned_cols=27 Identities=33% Similarity=0.759 Sum_probs=21.6
Q ss_pred cccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
-|.+.||-.|+.+|..+ +||.||=--.
T Consensus 196 ~c~Hsfh~~cl~~w~~~------scpvcR~~q~ 222 (493)
T KOG0804|consen 196 LCNHSFHCSCLMKWWDS------SCPVCRYCQS 222 (493)
T ss_pred ecccccchHHHhhcccC------cChhhhhhcC
Confidence 58899999999999765 4888875554
No 49
>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=80.63 E-value=0.34 Score=28.23 Aligned_cols=39 Identities=21% Similarity=0.519 Sum_probs=28.2
Q ss_pred CCCceeecccccchhHHHHHHHHHHhcC--CCCcccccccc
Q 039237 3 SGERLVACGTCKNLIHEECWVTWKRSRG--RRAASCVICRG 41 (98)
Q Consensus 3 s~e~lVwC~~CGnniHkeCf~~W~~s~~--~~~vtCp~CRs 41 (98)
.+..++.|..|++-+|..|+.-=..... ...=.||.|+.
T Consensus 10 ~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 10 DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 4678999999999999999865433221 12567888864
No 50
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=80.27 E-value=0.49 Score=35.75 Aligned_cols=28 Identities=32% Similarity=0.860 Sum_probs=22.7
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
+.++-|..|+.-+|++||.+ ..||-|-.
T Consensus 170 ~~~~~C~~C~~v~H~~C~~~---------~~CpkC~R 197 (202)
T PF13901_consen 170 DTTVRCPKCKSVFHKSCFRK---------KSCPKCAR 197 (202)
T ss_pred CCeeeCCcCccccchhhcCC---------CCCCCcHh
Confidence 46789999999999999983 23998853
No 51
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.73 E-value=0.7 Score=28.97 Aligned_cols=31 Identities=19% Similarity=0.448 Sum_probs=21.7
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
.+--|+.||.-| ..-+....+.||+|.+.--
T Consensus 5 ~~Y~C~~Cg~~~--------~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 5 MEYKCARCGREV--------ELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred EEEEhhhcCCee--------ehhhccCceeCCCCCcEEE
Confidence 345689999998 2223445799999987643
No 52
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.25 E-value=1.5 Score=37.07 Aligned_cols=32 Identities=28% Similarity=0.580 Sum_probs=24.7
Q ss_pred ccchhHHHHHHHHHHhcC---------CCCccccccccccc
Q 039237 13 CKNLIHEECWVTWKRSRG---------RRAASCVICRGRWR 44 (98)
Q Consensus 13 CGnniHkeCf~~W~~s~~---------~~~vtCp~CRs~W~ 44 (98)
|.--.-.+|+.||+..+. .++.+||+||+..-
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 444456799999998743 46899999999875
No 53
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=79.13 E-value=0.76 Score=26.49 Aligned_cols=19 Identities=26% Similarity=0.838 Sum_probs=13.9
Q ss_pred CceeecccccchhHHHHHH
Q 039237 5 ERLVACGTCKNLIHEECWV 23 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~ 23 (98)
..|++|..|+-.+|+.|-.
T Consensus 2 n~ll~C~~C~v~VH~~CYG 20 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYG 20 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT
T ss_pred CceEEeCCCCCcCChhhCC
Confidence 4689999999999999964
No 54
>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=78.10 E-value=1.1 Score=28.48 Aligned_cols=31 Identities=6% Similarity=0.126 Sum_probs=23.6
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
.+|+-+=+.|+++|.+.. ..+||+||.+-..
T Consensus 21 ~~G~tyer~~I~~~l~~~---~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 21 PSGHTYERSAIERWLEQN---GGTDPFTRQPLSE 51 (73)
T ss_dssp TTSEEEEHHHHHHHHCTT---SSB-TTT-SB-SG
T ss_pred CcCCEEcHHHHHHHHHcC---CCCCCCCCCcCCc
Confidence 577889999999999993 5899999987553
No 55
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=78.05 E-value=1.2 Score=41.56 Aligned_cols=22 Identities=36% Similarity=0.896 Sum_probs=20.4
Q ss_pred eecccccchhHHHHHHHHHHhc
Q 039237 8 VACGTCKNLIHEECWVTWKRSR 29 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~ 29 (98)
-+|+.||+-.|..|+..|.++.
T Consensus 1043 ~~Cg~C~Hv~H~sc~~eWf~~g 1064 (1081)
T KOG0309|consen 1043 NFCGTCGHVGHTSCMMEWFRTG 1064 (1081)
T ss_pred hhhccccccccHHHHHHHHhcC
Confidence 4799999999999999999995
No 56
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.86 E-value=0.69 Score=27.22 Aligned_cols=30 Identities=17% Similarity=0.341 Sum_probs=20.2
Q ss_pred eeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 7 LVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 7 lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
..-|..||..|.-+ ......+||+|.++-.
T Consensus 3 ~y~C~~CG~~~~~~--------~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELD--------EYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEEC--------CCCCceECCCCCCeEE
Confidence 34688888877641 1222789999998765
No 57
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=77.18 E-value=1.5 Score=37.04 Aligned_cols=35 Identities=20% Similarity=0.497 Sum_probs=29.8
Q ss_pred eec-ccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 8 VAC-GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 8 VwC-~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
+-| -+||+-|-.-|+++...++ ..||.||.+-...
T Consensus 37 ip~~TtCgHtFCslCIR~hL~~q----p~CP~Cr~~~~es 72 (391)
T COG5432 37 IPCETTCGHTFCSLCIRRHLGTQ----PFCPVCREDPCES 72 (391)
T ss_pred cceecccccchhHHHHHHHhcCC----CCCccccccHHhh
Confidence 457 7999999999999998884 7799999987754
No 58
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=77.13 E-value=0.7 Score=36.23 Aligned_cols=24 Identities=29% Similarity=0.837 Sum_probs=19.3
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
-.|-+|++.||+ ...+||+|.+.=
T Consensus 195 K~C~sC~qqIHR------------NAPiCPlCK~Ks 218 (230)
T PF10146_consen 195 KTCQSCHQQIHR------------NAPICPLCKAKS 218 (230)
T ss_pred chhHhHHHHHhc------------CCCCCccccccc
Confidence 468899999994 379999998753
No 59
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=76.03 E-value=1.9 Score=34.64 Aligned_cols=36 Identities=25% Similarity=0.678 Sum_probs=31.6
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
+-|++||=.+|..|++.+..+ ...||.|---|+.+-
T Consensus 195 ~rCg~c~i~~h~~c~qty~q~----~~~cphc~d~w~h~I 230 (235)
T KOG4718|consen 195 IRCGSCNIQYHRGCIQTYLQR----RDICPHCGDLWTHPI 230 (235)
T ss_pred eccCcccchhhhHHHHHHhcc----cCcCCchhcccCccc
Confidence 569999999999999999988 377999999998763
No 60
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.67 E-value=2.4 Score=33.11 Aligned_cols=29 Identities=17% Similarity=0.523 Sum_probs=24.6
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
..||+-|=++|++.=.+. ..+||.||..-
T Consensus 149 TkCGHvFC~~Cik~alk~----~~~CP~C~kkI 177 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKDALKN----TNKCPTCRKKI 177 (187)
T ss_pred cccchhHHHHHHHHHHHh----CCCCCCccccc
Confidence 579999999999987776 58899999743
No 61
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=74.65 E-value=1.6 Score=37.91 Aligned_cols=38 Identities=21% Similarity=0.582 Sum_probs=27.0
Q ss_pred CCceeecccccchhHHHHHHHHHHhcC----CCCcccccccc
Q 039237 4 GERLVACGTCKNLIHEECWVTWKRSRG----RRAASCVICRG 41 (98)
Q Consensus 4 ~e~lVwC~~CGnniHkeCf~~W~~s~~----~~~vtCp~CRs 41 (98)
...+|+|..|++-||++|.+=-..-.- ...--|--|+.
T Consensus 182 ~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 182 GNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred cceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 348999999999999999876555421 22445666654
No 62
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.35 E-value=2.1 Score=29.66 Aligned_cols=26 Identities=23% Similarity=0.523 Sum_probs=23.0
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
-||.+|=+.|+..+.. ....||.||.
T Consensus 30 ~C~H~~c~~C~~~~~~----~~~~Cp~cr~ 55 (386)
T KOG2177|consen 30 PCGHNFCRACLTRSWE----GPLSCPVCRP 55 (386)
T ss_pred cccchHhHHHHHHhcC----CCcCCcccCC
Confidence 5999999999999998 3689999993
No 63
>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=74.10 E-value=1.8 Score=30.43 Aligned_cols=30 Identities=13% Similarity=0.433 Sum_probs=22.5
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
-.|.+||..|-- .+..+++||+|-+.|.-.
T Consensus 10 R~Cp~CG~kFYD---------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---------CCCCCccCCCCCCccCcc
Confidence 358899987631 233589999999999966
No 64
>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=72.92 E-value=1.8 Score=35.39 Aligned_cols=52 Identities=23% Similarity=0.414 Sum_probs=35.8
Q ss_pred eeecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC--------CCCCCeeehhh
Q 039237 7 LVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR--------TDQDKYLNLAA 58 (98)
Q Consensus 7 lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~--------~~~eGYlNla~ 58 (98)
.-+|..||..=+..=+..+....+.+-..|.+|.+.|...+ ...-+|+.+..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~ 243 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEH 243 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecC
Confidence 45899999876544444444344557899999999999776 33445777643
No 65
>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=71.86 E-value=3.2 Score=31.73 Aligned_cols=32 Identities=28% Similarity=0.812 Sum_probs=23.3
Q ss_pred ccc-hhHHHHHHHHHHhcCC---------------------------CCccccccccccc
Q 039237 13 CKN-LIHEECWVTWKRSRGR---------------------------RAASCVICRGRWR 44 (98)
Q Consensus 13 CGn-niHkeCf~~W~~s~~~---------------------------~~vtCp~CRs~W~ 44 (98)
|+. .-|.-||+|.++.... ..+.||+||..=.
T Consensus 32 c~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~V~ 91 (162)
T PF07800_consen 32 CDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGEVK 91 (162)
T ss_pred cCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCcee
Confidence 444 3589999999988321 2678999998744
No 66
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=71.17 E-value=1.2 Score=41.92 Aligned_cols=38 Identities=26% Similarity=0.809 Sum_probs=29.9
Q ss_pred CceeecccccchhHHHHHH-------HHHHh----cCCCCccccccccc
Q 039237 5 ERLVACGTCKNLIHEECWV-------TWKRS----RGRRAASCVICRGR 42 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~-------~W~~s----~~~~~vtCp~CRs~ 42 (98)
..+|||..|+-.+|.+|.. +|.=. +..+.++|.+|-+.
T Consensus 234 n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~v~c~~cp~~ 282 (1051)
T KOG0955|consen 234 NVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSPQRPVRCLLCPSK 282 (1051)
T ss_pred ceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCcCcccceEeccCC
Confidence 5789999999999999998 66533 12357899999764
No 67
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.83 E-value=2.3 Score=27.98 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=14.3
Q ss_pred HHHHHHhcCCCCcccccccccccC
Q 039237 22 WVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 22 f~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+++|+.. ..+||+||+|-++
T Consensus 36 ~rl~~~~----~g~CPiCRapi~d 55 (62)
T KOG4172|consen 36 LRLKKAL----HGCCPICRAPIKD 55 (62)
T ss_pred HHHHHcc----CCcCcchhhHHHH
Confidence 3556654 4789999998664
No 68
>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=70.69 E-value=4.4 Score=24.35 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=24.2
Q ss_pred ecccccchhHHHHHHHHHHhc---CCCCccccccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSR---GRRAASCVICRGR 42 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~---~~~~vtCp~CRs~ 42 (98)
.|.-||..+-..=|..=.... ..+.+.||+|.+.
T Consensus 4 ~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 477788877776666655552 2457999999974
No 69
>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=69.97 E-value=2.8 Score=34.59 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=25.0
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
.||++|=+.|+++.... +...||.|+.+-...
T Consensus 25 ~CGH~~C~sCv~~l~~~---~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVR---GSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcccHHHHHHHhcC---CCCCCCCCCCccchh
Confidence 69999999999996533 246899999876643
No 70
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=67.44 E-value=2.1 Score=38.09 Aligned_cols=34 Identities=24% Similarity=0.656 Sum_probs=26.5
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+...-|.+||.-||+.||.+ +...||-|-..|+.
T Consensus 529 ~~~~rC~~C~avfH~~C~~r-------~s~~CPrC~R~q~r 562 (580)
T KOG1829|consen 529 RNTRRCSTCLAVFHKKCLRR-------KSPCCPRCERRQKR 562 (580)
T ss_pred ccceeHHHHHHHHHHHHHhc-------cCCCCCchHHHHHH
Confidence 45567999999999999853 23449999888874
No 71
>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=65.26 E-value=5.2 Score=29.58 Aligned_cols=14 Identities=29% Similarity=0.859 Sum_probs=11.7
Q ss_pred hhHHHHHHHHHHhc
Q 039237 16 LIHEECWVTWKRSR 29 (98)
Q Consensus 16 niHkeCf~~W~~s~ 29 (98)
-||++|+++|.+.+
T Consensus 56 mfc~~C~~rw~~~~ 69 (134)
T PF05883_consen 56 MFCADCDKRWRRER 69 (134)
T ss_pred HHHHHHHHHHHhhc
Confidence 48999999997654
No 72
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=64.93 E-value=4.3 Score=22.57 Aligned_cols=18 Identities=28% Similarity=0.538 Sum_probs=15.4
Q ss_pred eeecccccchhHHHHHHH
Q 039237 7 LVACGTCKNLIHEECWVT 24 (98)
Q Consensus 7 lVwC~~CGnniHkeCf~~ 24 (98)
-..|..|+-.+|+.|.++
T Consensus 27 ~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 27 GLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CcCCCCCCchHHHHHHhh
Confidence 356899999999999875
No 73
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=64.75 E-value=3.2 Score=32.06 Aligned_cols=19 Identities=32% Similarity=0.655 Sum_probs=17.4
Q ss_pred CceeecccccchhHHHHHH
Q 039237 5 ERLVACGTCKNLIHEECWV 23 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~ 23 (98)
-.||+|.+|-..+|+.|+-
T Consensus 15 G~Lv~CQGCs~sYHk~CLG 33 (175)
T PF15446_consen 15 GPLVYCQGCSSSYHKACLG 33 (175)
T ss_pred CCeEEcCccChHHHhhhcC
Confidence 4799999999999999985
No 74
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=64.58 E-value=1.6 Score=35.71 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=19.7
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
-.|-+|+.+||+ ...+||.|.+.=.
T Consensus 250 K~ClsChqqIHR------------NAPiCPlCKaKsR 274 (286)
T KOG4451|consen 250 KVCLSCHQQIHR------------NAPICPLCKAKSR 274 (286)
T ss_pred hHHHHHHHHHhc------------CCCCCcchhhccc
Confidence 458899999995 2699999987544
No 75
>PF12773 DZR: Double zinc ribbon
Probab=64.44 E-value=4.1 Score=23.70 Aligned_cols=29 Identities=14% Similarity=0.389 Sum_probs=21.5
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCccccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGR 42 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~ 42 (98)
....||..||..+- ......+.||.|.++
T Consensus 10 ~~~~fC~~CG~~l~---------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP---------PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChh---------hccCCCCCCcCCcCC
Confidence 34678999999987 222346889999886
No 76
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=64.37 E-value=4.2 Score=35.59 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=21.6
Q ss_pred ccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 13 CKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 13 CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
|-+-||..|++.....++ ..+||-||+
T Consensus 387 CsHIfH~rCl~e~L~~n~--~rsCP~Crk 413 (518)
T KOG1941|consen 387 CSHIFHLRCLQEILENNG--TRSCPNCRK 413 (518)
T ss_pred hhHHHHHHHHHHHHHhCC--CCCCccHHH
Confidence 335689999999996654 788999993
No 77
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=63.88 E-value=2.6 Score=24.61 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=21.3
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
..+++|+.||+.++. ..|. + ...=-.|++.....
T Consensus 3 ~g~l~C~~CG~~m~~---~~~~---~--~~~yy~C~~~~~~~ 36 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR---RKRK---G--KYRYYRCSNRRRKG 36 (58)
T ss_pred CCcEEcccCCcEeEE---EECC---C--CceEEEcCCCcCCC
Confidence 368999999999987 2222 1 12335566666544
No 78
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.46 E-value=4.7 Score=35.54 Aligned_cols=40 Identities=20% Similarity=0.397 Sum_probs=31.8
Q ss_pred ceeec-ccccchhHHHHHHHHHHhc-CCCCcccccccccccC
Q 039237 6 RLVAC-GTCKNLIHEECWVTWKRSR-GRRAASCVICRGRWRD 45 (98)
Q Consensus 6 ~lVwC-~~CGnniHkeCf~~W~~s~-~~~~vtCp~CRs~W~~ 45 (98)
..+-+ ..||+-|=-.|+-|+..+. -.+...||+||+.-..
T Consensus 196 ~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 196 PSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 44566 6799999999998888775 3567889999987665
No 79
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.68 E-value=5.6 Score=32.58 Aligned_cols=33 Identities=24% Similarity=0.794 Sum_probs=27.0
Q ss_pred eecccccchhHHHHHHH-HHHhcCCCCcccccccccc
Q 039237 8 VACGTCKNLIHEECWVT-WKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~-W~~s~~~~~vtCp~CRs~W 43 (98)
--|..||.-|=-.|+-. |-..+ .--||.||+.=
T Consensus 228 ps~t~CgHlFC~~Cl~~~~t~~k---~~~CplCRak~ 261 (271)
T COG5574 228 PSCTPCGHLFCLSCLLISWTKKK---YEFCPLCRAKV 261 (271)
T ss_pred cccccccchhhHHHHHHHHHhhc---cccCchhhhhc
Confidence 34678999999999999 98875 35599999863
No 80
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=60.19 E-value=3.5 Score=23.26 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=15.4
Q ss_pred ceeecccccchhHHHHHHH
Q 039237 6 RLVACGTCKNLIHEECWVT 24 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~ 24 (98)
.-..|..|+-.+|+.|.++
T Consensus 27 ~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 27 QGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred ceeEcCCCCCchhhhhhcc
Confidence 3456899999999999864
No 81
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.04 E-value=4.5 Score=37.91 Aligned_cols=25 Identities=20% Similarity=0.557 Sum_probs=20.8
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
.||+.+|..||. .+.--||-|+..-
T Consensus 858 ~CgHsyHqhC~e-------~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 858 LCGHSYHQHCLE-------DKEDKCPKCLPEL 882 (933)
T ss_pred ecccHHHHHhhc-------cCcccCCccchhh
Confidence 699999999999 3467799999743
No 82
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.96 E-value=5 Score=29.67 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=22.3
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
-.|.+||..|-- .++.+++||+|-+.|...
T Consensus 10 r~Cp~cg~kFYD---------Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD---------LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc---------cCCCCccCCCcCCccCcc
Confidence 358889987631 233589999999999755
No 83
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=59.58 E-value=4.4 Score=36.89 Aligned_cols=35 Identities=31% Similarity=0.764 Sum_probs=27.8
Q ss_pred CceeecccccchhHHHHHHHHHHhc--CCCCccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSR--GRRAASCVICR 40 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~--~~~~vtCp~CR 40 (98)
-.++-|..||.-.|..|...|+.+. .+ .-+||-||
T Consensus 33 g~m~ac~~c~~~yH~~cvt~~~~~~~l~~-gWrC~~cr 69 (694)
T KOG4443|consen 33 GRLLACSDCGQKYHPYCVTSWAQHAVLSG-GWRCPSCR 69 (694)
T ss_pred CcchhhhhhcccCCcchhhHHHhHHHhcC-CcccCCce
Confidence 3578999999999999999999885 32 25566665
No 84
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=58.86 E-value=5.4 Score=37.30 Aligned_cols=39 Identities=23% Similarity=0.560 Sum_probs=32.9
Q ss_pred CCCceeecccccchhHHHHHHHHHHhcCCCCcccccccccccC
Q 039237 3 SGERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 3 s~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
+...+..|++|-.-||.+=|+.=.-+++. ||+||+.-.+
T Consensus 1040 Pd~~it~Cp~C~~~F~~eDFEl~vLqKGH----CPFCrTS~dd 1078 (1081)
T KOG1538|consen 1040 PDASITMCPSCFQMFHSEDFELLVLQKGH----CPFCRTSKDD 1078 (1081)
T ss_pred CcchhhhCchHHhhhccchhhHHHHhcCC----CCcccccccC
Confidence 45678899999999999999998888765 9999987553
No 85
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=56.98 E-value=8.6 Score=23.86 Aligned_cols=36 Identities=19% Similarity=0.505 Sum_probs=17.6
Q ss_pred CCceeecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 4 GERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 4 ~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
+..+.-| .||-.|=..|+.+=++. ....||-||.+.
T Consensus 12 d~~~~PC-~Cgf~IC~~C~~~i~~~---~~g~CPgCr~~Y 47 (48)
T PF14570_consen 12 DKDFYPC-ECGFQICRFCYHDILEN---EGGRCPGCREPY 47 (48)
T ss_dssp CTT--SS-TTS----HHHHHHHTTS---S-SB-TTT--B-
T ss_pred CCccccC-cCCCcHHHHHHHHHHhc---cCCCCCCCCCCC
Confidence 3455566 89988888887766553 357899999874
No 86
>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=56.09 E-value=1.6 Score=25.55 Aligned_cols=20 Identities=20% Similarity=0.524 Sum_probs=14.5
Q ss_pred CceeecccccchhHHHHHHH
Q 039237 5 ERLVACGTCKNLIHEECWVT 24 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~ 24 (98)
..-.-|..|+..+|+.|+++
T Consensus 26 ~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 26 KQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp SCEEEETTTT-EEETTGGCT
T ss_pred CCeEEECCCCChHhhhhhhh
Confidence 34567889999999999753
No 87
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=54.83 E-value=10 Score=22.30 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=11.7
Q ss_pred Cceeecc--cccchhHHH
Q 039237 5 ERLVACG--TCKNLIHEE 20 (98)
Q Consensus 5 e~lVwC~--~CGnniHke 20 (98)
..+.||. .|+..+-..
T Consensus 16 ~~~~~CP~~~C~~~~~~~ 33 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVT 33 (64)
T ss_pred CCccCCCCCCCcceEEec
Confidence 4678895 998887653
No 88
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.35 E-value=3.9 Score=28.51 Aligned_cols=30 Identities=27% Similarity=0.648 Sum_probs=23.4
Q ss_pred CcccccccccccCCC-----CCCCCeeehhhhcCC
Q 039237 33 AASCVICRGRWRDNR-----TDQDKYLNLAAFVSQ 62 (98)
Q Consensus 33 ~vtCp~CRs~W~~~~-----~~~eGYlNla~~~g~ 62 (98)
.--||-||..|-+.+ ....+|=|-+.|.-+
T Consensus 21 iD~CPrCrGVWLDrGELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 21 IDYCPRCRGVWLDRGELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred eeeCCccccEeecchhHHHHHHHhcCCCCcccCCc
Confidence 346999999999877 456668888887665
No 89
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.91 E-value=4.4 Score=24.31 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=17.7
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
-|+.||..+=-. ....+.||+|..+-
T Consensus 4 ~C~~Cg~~~~~~---------~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK---------SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC---------CCCceECCCCCceE
Confidence 477888765422 34579999997653
No 90
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=52.48 E-value=5.4 Score=26.53 Aligned_cols=13 Identities=23% Similarity=0.386 Sum_probs=5.4
Q ss_pred CCceeecccccch
Q 039237 4 GERLVACGTCKNL 16 (98)
Q Consensus 4 ~e~lVwC~~CGnn 16 (98)
+...+||+.|||+
T Consensus 21 ~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 21 DMTKQFCPKCGNA 33 (73)
T ss_dssp -SS--S-SSS--S
T ss_pred CCCceeCcccCCC
Confidence 4567889889885
No 91
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=51.81 E-value=6.3 Score=22.47 Aligned_cols=15 Identities=33% Similarity=0.729 Sum_probs=12.7
Q ss_pred CCCCccccccccccc
Q 039237 30 GRRAASCVICRGRWR 44 (98)
Q Consensus 30 ~~~~vtCp~CRs~W~ 44 (98)
.++.++|+-|+..|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 456899999999985
No 92
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=51.42 E-value=9.4 Score=23.11 Aligned_cols=31 Identities=13% Similarity=0.350 Sum_probs=24.7
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
.|.+|+-.|-..=+.+.++.. .-++||.|-.
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~--~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGD--EIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCC--CeEECcCCCc
Confidence 688899999888888886663 4799999953
No 93
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=50.82 E-value=3.3 Score=30.86 Aligned_cols=27 Identities=26% Similarity=0.487 Sum_probs=20.7
Q ss_pred HHHHHHHHhc-------CCCCcccccccccccCC
Q 039237 20 ECWVTWKRSR-------GRRAASCVICRGRWRDN 46 (98)
Q Consensus 20 eCf~~W~~s~-------~~~~vtCp~CRs~W~~~ 46 (98)
.=|+-|+++. ..+-++||+|-+.=...
T Consensus 12 H~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K 45 (148)
T PF06676_consen 12 HEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSK 45 (148)
T ss_pred CccceecCCHHHHHHHHHcCCccCCCCCCCeEee
Confidence 3489999984 25689999998876654
No 94
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=50.56 E-value=9.2 Score=34.45 Aligned_cols=40 Identities=20% Similarity=0.586 Sum_probs=31.6
Q ss_pred CceeecccccchhHHHHHH-------HHHHhc----CCCCccccccccccc
Q 039237 5 ERLVACGTCKNLIHEECWV-------TWKRSR----GRRAASCVICRGRWR 44 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~-------~W~~s~----~~~~vtCp~CRs~W~ 44 (98)
..||||.+|.-.+|.+|.- +|.-.+ ...-.+|-+|-+.-.
T Consensus 208 naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~~~~i~~C~fCps~dG 258 (669)
T COG5141 208 NAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDG 258 (669)
T ss_pred ceEEEecCcchhhhhhcccceecCcchhhhhhhcccccceeEEEeccCCCC
Confidence 5799999999999999974 787764 234567999977544
No 95
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=50.03 E-value=2.9 Score=26.94 Aligned_cols=20 Identities=30% Similarity=0.586 Sum_probs=10.0
Q ss_pred HHHhcCCCCccccccccccc
Q 039237 25 WKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 25 W~~s~~~~~vtCp~CRs~W~ 44 (98)
|.+.++.++.|||.|.+.-.
T Consensus 16 k~~~~S~~PatCP~C~a~~~ 35 (54)
T PF09237_consen 16 KSKSQSEQPATCPICGAVIR 35 (54)
T ss_dssp CCCCTTS--EE-TTT--EES
T ss_pred HHhhccCCCCCCCcchhhcc
Confidence 33445567899999998755
No 96
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.50 E-value=9.6 Score=31.78 Aligned_cols=30 Identities=23% Similarity=0.705 Sum_probs=21.9
Q ss_pred ccchhHHHHHHHHHHhcC---CCCccccccccc
Q 039237 13 CKNLIHEECWVTWKRSRG---RRAASCVICRGR 42 (98)
Q Consensus 13 CGnniHkeCf~~W~~s~~---~~~vtCp~CRs~ 42 (98)
|-..+=..|..+|+..+. .-.-.||.||.+
T Consensus 187 C~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~ 219 (344)
T KOG1039|consen 187 CNHSFCLNCIRKWRQATQFESKTSKSCPFCRVP 219 (344)
T ss_pred cchhhhhcHhHhhhhhhccccccccCCCcccCc
Confidence 666666789999996542 124679999986
No 97
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=49.19 E-value=12 Score=35.67 Aligned_cols=31 Identities=29% Similarity=0.763 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 15 NLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 15 nniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
+-+|++|+-.|...++ ...|-+|..+.+-..
T Consensus 39 kYiH~eCL~eW~~~s~--~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 39 KYIHRECLMEWMECSG--TKKCDICHYEYKFKD 69 (1175)
T ss_pred HHHHHHHHHHHHhcCC--Ccceeeecceeeeee
Confidence 6799999999999764 688999999988554
No 98
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=49.13 E-value=11 Score=26.07 Aligned_cols=50 Identities=16% Similarity=0.416 Sum_probs=31.2
Q ss_pred ccc---cchhHHHHHHHHHHhc-----CCCCccccccccc-----------ccCCC-----CCCCCeeehhhhc
Q 039237 11 GTC---KNLIHEECWVTWKRSR-----GRRAASCVICRGR-----------WRDNR-----TDQDKYLNLAAFV 60 (98)
Q Consensus 11 ~~C---GnniHkeCf~~W~~s~-----~~~~vtCp~CRs~-----------W~~~~-----~~~eGYlNla~~~ 60 (98)
..| ...|=..|+..+.... ....-.||.||.. |...+ +...||-||+.||
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk~g~~PTg~l~~~a~~~G~~sv~~~L 104 (105)
T PF10497_consen 31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRKRGWAPTGILYHKAKALGFKSVAHYL 104 (105)
T ss_pred CCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhccCCCCCcHHHHHHHHHhChhHHHHHh
Confidence 566 7778888887776542 2345678887751 22222 4566777777765
No 99
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=48.76 E-value=11 Score=33.04 Aligned_cols=17 Identities=29% Similarity=0.984 Sum_probs=16.0
Q ss_pred cccchhHHHHHHHHHHh
Q 039237 12 TCKNLIHEECWVTWKRS 28 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s 28 (98)
.|+.-+|.+||+-|.++
T Consensus 105 ~~~~~MH~qCF~~WEsS 121 (526)
T KOG3816|consen 105 PCSTWMHLQCFYEWESS 121 (526)
T ss_pred ChhhHHHHHHHHHHHHH
Confidence 78999999999999988
No 100
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.65 E-value=9.7 Score=32.57 Aligned_cols=33 Identities=21% Similarity=0.387 Sum_probs=22.9
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
+.|++.|-.+||-+=.+.. ..+||.||..-...
T Consensus 60 keClhrfc~~ci~~a~r~g---n~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 60 KECLHRFCFDCIWKALRSG---NNECPTCRKKLVSK 92 (381)
T ss_pred HHHHHHHHHHHHHHHHHhc---CCCCchHHhhcccc
Confidence 3577777777775544442 68899999876643
No 101
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=47.40 E-value=13 Score=26.76 Aligned_cols=33 Identities=21% Similarity=0.717 Sum_probs=21.2
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
..+-|+.|.+-+- +.++..+ +.||+|+||+...
T Consensus 61 ~~iiCGvC~~~LT---~~EY~~~-----~~Cp~C~spFNp~ 93 (105)
T COG4357 61 KAIICGVCRKLLT---RAEYGMC-----GSCPYCQSPFNPG 93 (105)
T ss_pred ccEEhhhhhhhhh---HHHHhhc-----CCCCCcCCCCCcc
Confidence 4466777765443 3444443 6699999998754
No 102
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=46.63 E-value=9 Score=27.21 Aligned_cols=31 Identities=16% Similarity=0.657 Sum_probs=20.9
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
-|..||--|-. -+-..+.+||-|.|.|-.++
T Consensus 60 ~CkkCGfef~~--------~~ik~pSRCP~CKSE~Ie~p 90 (97)
T COG3357 60 RCKKCGFEFRD--------DKIKKPSRCPKCKSEWIEEP 90 (97)
T ss_pred hhcccCccccc--------cccCCcccCCcchhhcccCC
Confidence 36677765422 12234789999999998765
No 103
>PF14369 zf-RING_3: zinc-finger
Probab=46.48 E-value=7.5 Score=22.25 Aligned_cols=29 Identities=17% Similarity=0.559 Sum_probs=18.0
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
-||-.|...|+-. ......++||.|.+..
T Consensus 3 ywCh~C~~~V~~~-------~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCHQCNRFVRIA-------PSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCccCCCEeEeC-------cCCCCCcCCcCCCCcE
Confidence 4788888777531 1122345799998754
No 104
>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=45.84 E-value=3.6 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.566 Sum_probs=18.8
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCccccccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRGR 42 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~ 42 (98)
.|..||+-|- .|+.......+.||.|.+.
T Consensus 7 ~C~~Cg~~fe-----~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFE-----VLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeE-----EEEecCCCCCCCCCCCCCC
Confidence 4777887653 4543332346789999983
No 105
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=45.38 E-value=9.1 Score=29.15 Aligned_cols=45 Identities=20% Similarity=0.173 Sum_probs=34.4
Q ss_pred CCCCCeeehhhhcCCCcccccccccCCCceeeeeeeeccceeeEEE
Q 039237 48 TDQDKYLNLAAFVSQEDHHHQAAEDSGSRICGLEAVEEDNEIQVQV 93 (98)
Q Consensus 48 ~~~eGYlNla~~~g~~~~~~~~~~~~~ggl~~~~~~~~~~~~~~~~ 93 (98)
.-++|||+|-...|.+-++.-+..++ -|-=+-+++++++.+.|+|
T Consensus 94 dIsd~~~sl~t~sG~~kdDlklp~~e-l~~~i~~~~e~g~dl~v~V 138 (156)
T KOG3271|consen 94 DISDGYLSLMTDSGETKDDLKLPEGE-LGNQIRQGFEEGKDLLVTV 138 (156)
T ss_pred EecCCeEEEEcCCCCcchhccCcchh-HHHHHHHhhcCCCcEEEEE
Confidence 34678999999998776776666655 3445778889999999887
No 106
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=45.37 E-value=9.3 Score=21.79 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=20.1
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
+-|..|+..+. +.-.+-...+..++|+.|+..|.
T Consensus 3 i~Cp~C~~~y~---i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYE---IDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEe---CCHHHCCCCCcEEECCCCCCEeC
Confidence 44555555443 12222223466899999999884
No 107
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=44.22 E-value=15 Score=31.84 Aligned_cols=32 Identities=13% Similarity=0.361 Sum_probs=28.4
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
.|+++|-.-|+....+.+ ..||.|+.+...+.
T Consensus 40 pCsHtfCSlCIR~~L~~~----p~CP~C~~~~~Es~ 71 (442)
T KOG0287|consen 40 PCSHTFCSLCIRKFLSYK----PQCPTCCVTVTESD 71 (442)
T ss_pred cccchHHHHHHHHHhccC----CCCCceecccchhh
Confidence 499999999999999885 77999999998765
No 108
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=44.05 E-value=13 Score=24.17 Aligned_cols=19 Identities=37% Similarity=0.985 Sum_probs=16.2
Q ss_pred cccccchhH-------HHHHHHHHHh
Q 039237 10 CGTCKNLIH-------EECWVTWKRS 28 (98)
Q Consensus 10 C~~CGnniH-------keCf~~W~~s 28 (98)
|+.||+.+| .+|...|...
T Consensus 20 Ca~C~~~L~~~E~h~Ce~C~~E~l~y 45 (58)
T PF05810_consen 20 CANCGQKLHPDETHVCEECCAEWLVY 45 (58)
T ss_pred HhccCcccccchhhHHHHHHHHHHhh
Confidence 999999998 5788888874
No 109
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=42.98 E-value=17 Score=33.20 Aligned_cols=34 Identities=15% Similarity=0.323 Sum_probs=28.1
Q ss_pred cccchhHHHHHHHHHHhcC-CCCcccccccccccC
Q 039237 12 TCKNLIHEECWVTWKRSRG-RRAASCVICRGRWRD 45 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~-~~~vtCp~CRs~W~~ 45 (98)
+|.+.|-+.|++.+..+-. +..+|||.|--+-.-
T Consensus 553 ~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi 587 (791)
T KOG1002|consen 553 SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI 587 (791)
T ss_pred hhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence 7899999999999998843 446999999877653
No 110
>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=42.87 E-value=17 Score=21.82 Aligned_cols=27 Identities=11% Similarity=0.220 Sum_probs=14.1
Q ss_pred HHHHHHHHHhcCCCCcccccccccccC
Q 039237 19 EECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 19 keCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
..=|+++...-......||.|.++...
T Consensus 6 ~~~~~k~i~~l~~~~~~CPlC~r~l~~ 32 (54)
T PF04423_consen 6 IEELKKYIEELKEAKGCCPLCGRPLDE 32 (54)
T ss_dssp HHHHHHHHHHHTT-SEE-TTT--EE-H
T ss_pred HHHHHHHHHHHhcCCCcCCCCCCCCCH
Confidence 344666666644334499999998753
No 111
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=42.48 E-value=6.1 Score=30.55 Aligned_cols=13 Identities=23% Similarity=0.935 Sum_probs=11.1
Q ss_pred CcccccccccccC
Q 039237 33 AASCVICRGRWRD 45 (98)
Q Consensus 33 ~vtCp~CRs~W~~ 45 (98)
..+|||||.-|..
T Consensus 126 Dp~CpyC~kl~~~ 138 (251)
T PRK11657 126 DPNCPYCKQFWQQ 138 (251)
T ss_pred CCCChhHHHHHHH
Confidence 4689999999885
No 112
>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=41.57 E-value=12 Score=25.97 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=18.5
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
...+|..||+.+... . ...+||.|.++=
T Consensus 69 ~~~~C~~Cg~~~~~~--------~--~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSEEVSPE--------I--DLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCCEEecC--------C--cCccCcCCcCCC
Confidence 457899999655322 1 146799998863
No 113
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=41.09 E-value=7.5 Score=24.92 Aligned_cols=29 Identities=21% Similarity=0.610 Sum_probs=23.7
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
.||.-|=..||.-++-+ -||+|-+|...+
T Consensus 24 pCgH~I~~~~f~~~rYn------gCPfC~~~~~~~ 52 (55)
T PF14447_consen 24 PCGHLICDNCFPGERYN------GCPFCGTPFEFD 52 (55)
T ss_pred cccceeeccccChhhcc------CCCCCCCcccCC
Confidence 69999999999887655 399999988754
No 114
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=40.96 E-value=22 Score=32.47 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=27.5
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
.||+-|=.+|++.=-.++ ..+||-|-+++...+
T Consensus 660 kC~H~FC~~Cvq~r~etR---qRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 660 KCGHVFCEECVQTRYETR---QRKCPKCNAAFGAND 692 (698)
T ss_pred hcchHHHHHHHHHHHHHh---cCCCCCCCCCCCccc
Confidence 578888899999888885 678999999998654
No 115
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=39.23 E-value=12 Score=20.69 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=11.4
Q ss_pred CCCccccccccccc
Q 039237 31 RRAASCVICRGRWR 44 (98)
Q Consensus 31 ~~~vtCp~CRs~W~ 44 (98)
+..++||.|.++|.
T Consensus 23 ~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 23 GGKVRCGKCGHVWY 36 (38)
T ss_pred CCEEECCCCCCEEE
Confidence 34799999999885
No 116
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.15 E-value=12 Score=24.56 Aligned_cols=14 Identities=29% Similarity=0.743 Sum_probs=11.3
Q ss_pred CCCccccccccccc
Q 039237 31 RRAASCVICRGRWR 44 (98)
Q Consensus 31 ~~~vtCp~CRs~W~ 44 (98)
.+.+.||||-+...
T Consensus 46 ~gev~CPYC~t~y~ 59 (62)
T COG4391 46 EGEVVCPYCSTRYR 59 (62)
T ss_pred CCcEecCccccEEE
Confidence 35899999988765
No 117
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=37.91 E-value=19 Score=28.67 Aligned_cols=31 Identities=16% Similarity=0.466 Sum_probs=17.4
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
-|++|+--+=..=...=++ ....|+||+|-+
T Consensus 199 ~C~GC~m~l~~~~~~~V~~--~d~iv~CP~CgR 229 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRK--KDEIVFCPYCGR 229 (239)
T ss_pred cccCCeeeecHHHHHHHhc--CCCCccCCccch
Confidence 4777775543322222222 345899999954
No 118
>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=37.68 E-value=3.9 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.503 Sum_probs=9.6
Q ss_pred HHHHHHH--HHHhcC-CCCccccccccc
Q 039237 18 HEECWVT--WKRSRG-RRAASCVICRGR 42 (98)
Q Consensus 18 HkeCf~~--W~~s~~-~~~vtCp~CRs~ 42 (98)
|-+||+- |..+.. .+.-.||+|..+
T Consensus 23 H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 23 HLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred ccceECHHHHHHHhhccCCeECcCCcCc
Confidence 6677753 555522 235789999864
No 119
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=36.79 E-value=24 Score=21.77 Aligned_cols=9 Identities=67% Similarity=0.962 Sum_probs=7.0
Q ss_pred eEEEeecCC
Q 039237 90 QVQVNFHDS 98 (98)
Q Consensus 90 ~~~~~~~~~ 98 (98)
.|||||.|+
T Consensus 15 ~vqv~FnD~ 23 (68)
T PF00659_consen 15 TVQVNFNDH 23 (68)
T ss_dssp EEEEEETTS
T ss_pred CEEEEEeCC
Confidence 478889884
No 120
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=36.14 E-value=17 Score=22.40 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=3.1
Q ss_pred ccccccccc
Q 039237 35 SCVICRGRW 43 (98)
Q Consensus 35 tCp~CRs~W 43 (98)
.|+.|.++=
T Consensus 50 FC~~CGs~l 58 (92)
T PF04828_consen 50 FCPTCGSPL 58 (92)
T ss_dssp EETTT--EE
T ss_pred ccCCCCCee
Confidence 344444443
No 121
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.25 E-value=17 Score=25.45 Aligned_cols=31 Identities=13% Similarity=0.406 Sum_probs=19.2
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
....+|..||+.+-.. .....+||.|-++-.
T Consensus 69 p~~~~C~~Cg~~~~~~---------~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 69 KVELECKDCSHVFKPN---------ALDYGVCEKCHSKNV 99 (117)
T ss_pred CCEEEhhhCCCccccC---------CccCCcCcCCCCCce
Confidence 3567899999554221 112346999988754
No 122
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=34.61 E-value=18 Score=22.50 Aligned_cols=29 Identities=14% Similarity=0.403 Sum_probs=19.8
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVI 38 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~ 38 (98)
|-...||+-|=++.+.+|... .+...||.
T Consensus 25 V~s~~C~H~fek~aI~~~i~~--~~~~~CPv 53 (57)
T PF11789_consen 25 VKSKKCGHTFEKEAILQYIQR--NGSKRCPV 53 (57)
T ss_dssp EEESSS--EEEHHHHHHHCTT--TS-EE-SC
T ss_pred cCcCCCCCeecHHHHHHHHHh--cCCCCCCC
Confidence 444689999999999999933 35799997
No 123
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=34.56 E-value=17 Score=20.58 Aligned_cols=11 Identities=18% Similarity=0.428 Sum_probs=7.6
Q ss_pred CCCcccccccc
Q 039237 31 RRAASCVICRG 41 (98)
Q Consensus 31 ~~~vtCp~CRs 41 (98)
...++||+|-.
T Consensus 15 ~~~irC~~CG~ 25 (32)
T PF03604_consen 15 GDPIRCPECGH 25 (32)
T ss_dssp SSTSSBSSSS-
T ss_pred CCcEECCcCCC
Confidence 45788999854
No 124
>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=34.48 E-value=22 Score=29.44 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=18.8
Q ss_pred CCceeecccccc-----------------hhHHHHHHHHHHhc
Q 039237 4 GERLVACGTCKN-----------------LIHEECWVTWKRSR 29 (98)
Q Consensus 4 ~e~lVwC~~CGn-----------------niHkeCf~~W~~s~ 29 (98)
.+.|.||.-|=- .=|++||++|----
T Consensus 27 ~~tLsfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIa 69 (285)
T PF06937_consen 27 TETLSFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIA 69 (285)
T ss_pred ccceeecceeeccccccCccccccccccccchHHHHHHHHHHH
Confidence 467888877732 23999999997663
No 125
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=34.24 E-value=39 Score=29.21 Aligned_cols=23 Identities=30% Similarity=0.673 Sum_probs=19.6
Q ss_pred CCCceeec-ccccchhHHHHHHHH
Q 039237 3 SGERLVAC-GTCKNLIHEECWVTW 25 (98)
Q Consensus 3 s~e~lVwC-~~CGnniHkeCf~~W 25 (98)
++...|.| .+||-.|-++|++.+
T Consensus 331 PD~rkvtC~~gCgf~FCR~C~e~y 354 (446)
T KOG0006|consen 331 PDQRKVTCEGGCGFAFCRECKEAY 354 (446)
T ss_pred CCCCcccCCCCchhHhHHHHHhhh
Confidence 46778999 889999999999944
No 126
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.15 E-value=16 Score=19.15 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=5.1
Q ss_pred eeecccccch
Q 039237 7 LVACGTCKNL 16 (98)
Q Consensus 7 lVwC~~CGnn 16 (98)
..||..||..
T Consensus 13 ~~fC~~CG~~ 22 (23)
T PF13240_consen 13 AKFCPNCGTP 22 (23)
T ss_pred CcchhhhCCc
Confidence 3455555544
No 127
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=34.00 E-value=18 Score=23.42 Aligned_cols=21 Identities=19% Similarity=0.586 Sum_probs=14.4
Q ss_pred HHHhc--CCCCcccccccccccC
Q 039237 25 WKRSR--GRRAASCVICRGRWRD 45 (98)
Q Consensus 25 W~~s~--~~~~vtCp~CRs~W~~ 45 (98)
|.|.. .....+||+|.++=..
T Consensus 29 WmR~nFs~~~~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 29 WMRDNFSFEEEPVCPLCKSPMVS 51 (59)
T ss_pred ccccccccCCCccCCCcCCcccc
Confidence 65553 2456899999997553
No 128
>PF14353 CpXC: CpXC protein
Probab=33.57 E-value=16 Score=24.98 Aligned_cols=14 Identities=14% Similarity=0.432 Sum_probs=10.7
Q ss_pred CcccccccccccCC
Q 039237 33 AASCVICRGRWRDN 46 (98)
Q Consensus 33 ~vtCp~CRs~W~~~ 46 (98)
.+|||.|..++..+
T Consensus 1 ~itCP~C~~~~~~~ 14 (128)
T PF14353_consen 1 EITCPHCGHEFEFE 14 (128)
T ss_pred CcCCCCCCCeeEEE
Confidence 36899999888744
No 129
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=32.59 E-value=29 Score=28.34 Aligned_cols=27 Identities=22% Similarity=0.576 Sum_probs=23.2
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
..||.-.|..||+....+. -+||+|-.
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 4799999999998877762 89999988
No 130
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.45 E-value=17 Score=29.91 Aligned_cols=41 Identities=20% Similarity=0.464 Sum_probs=26.0
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
..-+|..||..=...=..- ....+.+-..|.+|.+.|...+
T Consensus 186 ~~~~CPvCGs~P~~s~v~~-~~~~G~RyL~CslC~teW~~~R 226 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQI-GTTQGLRYLHCNLCESEWHVVR 226 (309)
T ss_pred CCCCCCCCCCcchhheeec-cCCCCceEEEcCCCCCcccccC
Confidence 3467999998643221110 1123457889999999999776
No 131
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.41 E-value=18 Score=31.58 Aligned_cols=33 Identities=18% Similarity=0.383 Sum_probs=28.3
Q ss_pred ccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
..||...|.+|+.+|..++ ..||-||+.-+...
T Consensus 216 ~~~g~~~~~~kL~k~L~~~----~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 216 IVCGHIYHHGKLSKWLATK----RKLPSCRRELPKNG 248 (465)
T ss_pred HhhcccchhhHHHHHHHHH----HHhHHHHhhhhhhh
Confidence 5899999999999999995 45999999877543
No 132
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.10 E-value=24 Score=23.34 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=21.7
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
||..||+.+... .....|+.|...+...
T Consensus 2 fC~~Cg~~l~~~----------~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 2 FCPKCGSLMTPK----------NGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCcccCcccccC----------CCeEECcCCCCccccc
Confidence 799999999531 1368999999988753
No 133
>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=30.70 E-value=31 Score=19.84 Aligned_cols=18 Identities=28% Similarity=0.883 Sum_probs=12.5
Q ss_pred CcccccccccccCCCCCCCCe
Q 039237 33 AASCVICRGRWRDNRTDQDKY 53 (98)
Q Consensus 33 ~vtCp~CRs~W~~~~~~~eGY 53 (98)
...|+.|++.|. ...+|+
T Consensus 8 ~~~C~~C~~~~~---~~~dG~ 25 (36)
T PF11781_consen 8 NEPCPVCGSRWF---YSDDGF 25 (36)
T ss_pred CCcCCCCCCeEe---EccCCE
Confidence 345999999987 344453
No 134
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=30.52 E-value=6.1 Score=26.15 Aligned_cols=33 Identities=21% Similarity=0.756 Sum_probs=15.2
Q ss_pred eec-ccccchhHHHHHHHHHHhcCCCCccccccccc-ccCC
Q 039237 8 VAC-GTCKNLIHEECWVTWKRSRGRRAASCVICRGR-WRDN 46 (98)
Q Consensus 8 VwC-~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~-W~~~ 46 (98)
..| +.|.++|=..|+..=+. ..||.|++| |..|
T Consensus 20 pv~l~~CeH~fCs~Ci~~~~~------~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 20 PVCLGGCEHIFCSSCIRDCIG------SECPVCHTPAWIQD 54 (65)
T ss_dssp -B---SSS--B-TTTGGGGTT------TB-SSS--B-S-SS
T ss_pred CceeccCccHHHHHHhHHhcC------CCCCCcCChHHHHH
Confidence 457 78888888888855222 239999987 5543
No 135
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.50 E-value=20 Score=18.91 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=6.3
Q ss_pred eecccccchhHH
Q 039237 8 VACGTCKNLIHE 19 (98)
Q Consensus 8 VwC~~CGnniHk 19 (98)
+.|..||..+..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 345555555554
No 136
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=29.94 E-value=19 Score=21.43 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=9.2
Q ss_pred CCcccccccccc
Q 039237 32 RAASCVICRGRW 43 (98)
Q Consensus 32 ~~vtCp~CRs~W 43 (98)
+.+.||||....
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 458999998653
No 137
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.58 E-value=27 Score=21.77 Aligned_cols=36 Identities=17% Similarity=0.402 Sum_probs=23.7
Q ss_pred eeecccccchhH-HHHHHHHHHhcC--CCCccccccccc
Q 039237 7 LVACGTCKNLIH-EECWVTWKRSRG--RRAASCVICRGR 42 (98)
Q Consensus 7 lVwC~~CGnniH-keCf~~W~~s~~--~~~vtCp~CRs~ 42 (98)
...|..||.-|= .+==++|...++ ..+.+||-||..
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQA 42 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHHH
Confidence 456788887652 222256666666 358999999974
No 138
>PHA03096 p28-like protein; Provisional
Probab=29.25 E-value=42 Score=27.18 Aligned_cols=29 Identities=14% Similarity=0.063 Sum_probs=21.4
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccc
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRG 41 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs 41 (98)
.|...|=-.|...|+.++.. .-+||-||.
T Consensus 203 ~c~h~fc~~ci~~wr~~~~~-~e~~~~c~~ 231 (284)
T PHA03096 203 EIKHEFNIFCIKIWMTESLY-KETEPENRR 231 (284)
T ss_pred cCCcHHHHHHHHHHHHhhhh-cccCccccc
Confidence 57788888999999998653 345666654
No 139
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=29.22 E-value=13 Score=28.42 Aligned_cols=13 Identities=15% Similarity=0.442 Sum_probs=10.6
Q ss_pred CcccccccccccC
Q 039237 33 AASCVICRGRWRD 45 (98)
Q Consensus 33 ~vtCp~CRs~W~~ 45 (98)
...|||||.-+..
T Consensus 116 Dp~CpyCkkl~~~ 128 (232)
T PRK10877 116 DITCGYCHKLHEQ 128 (232)
T ss_pred CCCChHHHHHHHH
Confidence 5689999997763
No 140
>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.
Probab=29.09 E-value=16 Score=25.07 Aligned_cols=10 Identities=30% Similarity=0.713 Sum_probs=8.2
Q ss_pred Cccccccccc
Q 039237 33 AASCVICRGR 42 (98)
Q Consensus 33 ~vtCp~CRs~ 42 (98)
..+||+||.-
T Consensus 32 ~~~Cp~C~~~ 41 (122)
T TIGR01295 32 RKTCPYCRKF 41 (122)
T ss_pred CCCChhHHHH
Confidence 5789999973
No 141
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=28.77 E-value=19 Score=28.14 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=22.0
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
..-||+.||..+... ..+....|+-|....-
T Consensus 98 ~~~fC~~CG~~~~~~--------~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 98 SHRFCGYCGHPMHPS--------KTEWAMLCPHCRERYY 128 (256)
T ss_pred cCccccccCCCCeec--------CCceeEECCCCCCEEC
Confidence 346899999988752 3345678999976554
No 142
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=28.63 E-value=56 Score=22.49 Aligned_cols=40 Identities=28% Similarity=0.708 Sum_probs=18.2
Q ss_pred CCceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 4 GERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 4 ~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
++.-|.|.-|+-.+=+.|++-=++. + .-.||-|+++....
T Consensus 25 Ge~FVAC~eC~fPvCr~CyEYErke-g--~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 25 GEVFVACHECAFPVCRPCYEYERKE-G--NQVCPQCKTRYKRH 64 (80)
T ss_dssp SSB--S-SSS-----HHHHHHHHHT-S---SB-TTT--B----
T ss_pred CCEEEEEcccCCccchhHHHHHhhc-C--cccccccCCCcccc
Confidence 4567889999999999999865444 2 46699999998843
No 143
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=28.47 E-value=26 Score=32.49 Aligned_cols=17 Identities=24% Similarity=0.509 Sum_probs=14.2
Q ss_pred eeecccccchhHHHHHH
Q 039237 7 LVACGTCKNLIHEECWV 23 (98)
Q Consensus 7 lVwC~~CGnniHkeCf~ 23 (98)
-+-|..||-|+||.|--
T Consensus 173 GlKC~gCglNyHKRCa~ 189 (888)
T KOG4236|consen 173 GLKCEGCGLNYHKRCAF 189 (888)
T ss_pred cccccCCCCcHhhhhhh
Confidence 35799999999999953
No 144
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.98 E-value=34 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.726 Sum_probs=24.6
Q ss_pred ccccchhHHHHHHHHHHhcCCCCccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRGRRAASCVICRGR 42 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~ 42 (98)
.+||.-|-..|+++|.- +. -...||.|-.+
T Consensus 25 l~cghlFgs~cie~wl~-k~-~~~~cp~c~~k 54 (463)
T KOG1645|consen 25 LQCGHLFGSQCIEKWLG-KK-TKMQCPLCSGK 54 (463)
T ss_pred ecccccccHHHHHHHHh-hh-hhhhCcccCCh
Confidence 58999999999999995 32 26789999754
No 145
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.94 E-value=15 Score=32.75 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=14.6
Q ss_pred ceeec-ccccchhHHHHHH
Q 039237 6 RLVAC-GTCKNLIHEECWV 23 (98)
Q Consensus 6 ~lVwC-~~CGnniHkeCf~ 23 (98)
.|.+| ..||..||.+|=+
T Consensus 68 vLe~cmkncGekfH~evgk 86 (594)
T KOG1086|consen 68 VLEYCMKNCGEKFHEEVGK 86 (594)
T ss_pred HHHHHHHhhhHHHHHHHHH
Confidence 46689 9999999999844
No 146
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=27.50 E-value=15 Score=26.50 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=10.9
Q ss_pred CcccccccccccC
Q 039237 33 AASCVICRGRWRD 45 (98)
Q Consensus 33 ~vtCp~CRs~W~~ 45 (98)
...|||||.-+..
T Consensus 86 D~~Cp~C~~~~~~ 98 (197)
T cd03020 86 DPDCPYCRKLEKE 98 (197)
T ss_pred CCCCccHHHHHHH
Confidence 5789999998864
No 147
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.37 E-value=31 Score=29.00 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 17 IHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 17 iHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
+|+-|+--=+-+--.+..+|+.||-|...+
T Consensus 26 ~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 26 FHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred cchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 477777665555444578899999998754
No 148
>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=27.15 E-value=25 Score=19.00 Aligned_cols=12 Identities=17% Similarity=0.556 Sum_probs=9.7
Q ss_pred ccccccccccCC
Q 039237 35 SCVICRGRWRDN 46 (98)
Q Consensus 35 tCp~CRs~W~~~ 46 (98)
+||-|++.+...
T Consensus 2 ~CP~C~~~V~~~ 13 (26)
T PF10571_consen 2 TCPECGAEVPES 13 (26)
T ss_pred cCCCCcCCchhh
Confidence 699999988754
No 149
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=26.00 E-value=18 Score=23.68 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=9.9
Q ss_pred Cccccccccccc
Q 039237 33 AASCVICRGRWR 44 (98)
Q Consensus 33 ~vtCp~CRs~W~ 44 (98)
...||+||.-++
T Consensus 14 D~~Cp~C~~~~~ 25 (154)
T cd03023 14 DYNCGYCKKLAP 25 (154)
T ss_pred CCCChhHHHhhH
Confidence 578999998775
No 150
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=25.56 E-value=36 Score=22.15 Aligned_cols=14 Identities=21% Similarity=0.769 Sum_probs=10.9
Q ss_pred Cccccccccc--ccCC
Q 039237 33 AASCVICRGR--WRDN 46 (98)
Q Consensus 33 ~vtCp~CRs~--W~~~ 46 (98)
.++||.|+.+ |...
T Consensus 6 ~v~CP~C~k~~~w~~~ 21 (62)
T PRK00418 6 TVNCPTCGKPVEWGEI 21 (62)
T ss_pred cccCCCCCCcccccCC
Confidence 5899999987 7543
No 151
>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=25.53 E-value=14 Score=19.22 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=6.7
Q ss_pred cchhHHHHHH
Q 039237 14 KNLIHEECWV 23 (98)
Q Consensus 14 GnniHkeCf~ 23 (98)
+..+|.+||.
T Consensus 20 ~~~~H~~Cf~ 29 (39)
T smart00132 20 GKVWHPECFK 29 (39)
T ss_pred CccccccCCC
Confidence 4567777763
No 152
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=24.94 E-value=28 Score=19.77 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=7.5
Q ss_pred eeecccccchhH
Q 039237 7 LVACGTCKNLIH 18 (98)
Q Consensus 7 lVwC~~CGnniH 18 (98)
+.||..|||-+.
T Consensus 1 m~FCp~C~nlL~ 12 (35)
T PF02150_consen 1 MRFCPECGNLLY 12 (35)
T ss_dssp --BETTTTSBEE
T ss_pred CeeCCCCCccce
Confidence 357888888664
No 153
>PRK12495 hypothetical protein; Provisional
Probab=24.70 E-value=31 Score=27.64 Aligned_cols=35 Identities=17% Similarity=0.395 Sum_probs=25.3
Q ss_pred CCCceeecccccchhHHHHHHHHHHhcCCCCcccccccccccCCC
Q 039237 3 SGERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 3 s~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~ 47 (98)
..-...+|..||..|= +.. +.+.||.|...-..++
T Consensus 38 atmsa~hC~~CG~PIp--------a~p--G~~~Cp~CQ~~~~~~~ 72 (226)
T PRK12495 38 ATMTNAHCDECGDPIF--------RHD--GQEFCPTCQQPVTEDG 72 (226)
T ss_pred cccchhhcccccCccc--------CCC--CeeECCCCCCcccccc
Confidence 3345678999999997 222 4788999998766543
No 154
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.55 E-value=27 Score=29.58 Aligned_cols=23 Identities=22% Similarity=0.551 Sum_probs=15.5
Q ss_pred HHHHHHHHHhcCCCCcccccccccccC
Q 039237 19 EECWVTWKRSRGRRAASCVICRGRWRD 45 (98)
Q Consensus 19 keCf~~W~~s~~~~~vtCp~CRs~W~~ 45 (98)
..|-+.-+-+ ...||+||.+-..
T Consensus 315 s~Ca~~Lr~q----~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 315 SGCAKSLRYQ----TNNCPICRQPIEE 337 (349)
T ss_pred HhHHHHHHHh----hcCCCccccchHh
Confidence 4565555422 4679999999773
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.47 E-value=31 Score=19.89 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=20.5
Q ss_pred ecccccchhHHHHHHHHHHhcCCCCcccccccccccCC
Q 039237 9 ACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDN 46 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~ 46 (98)
||..||+-+...= +. .+....||-|--.+..+
T Consensus 2 FCp~Cg~~l~~~~---~~---~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKE---GK---EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCcccccc---CC---CCCEEECCcCCCeEECC
Confidence 7999999775441 11 11257799998776643
No 156
>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=24.44 E-value=40 Score=17.96 Aligned_cols=17 Identities=35% Similarity=0.771 Sum_probs=7.6
Q ss_pred ceeecccccchhHHHHH
Q 039237 6 RLVACGTCKNLIHEECW 22 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf 22 (98)
..-.|..|.=.||.+|-
T Consensus 14 ~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 14 WFYRCSECDFDLHEECA 30 (30)
T ss_dssp -EEE-TTT-----HHHH
T ss_pred ceEECccCCCccChhcC
Confidence 34567999999999983
No 157
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=24.37 E-value=21 Score=22.69 Aligned_cols=13 Identities=15% Similarity=0.455 Sum_probs=8.6
Q ss_pred CcccccccccccC
Q 039237 33 AASCVICRGRWRD 45 (98)
Q Consensus 33 ~vtCp~CRs~W~~ 45 (98)
...||+||.-++.
T Consensus 14 ~~~C~~C~~~~~~ 26 (112)
T PF13098_consen 14 DPWCPYCKKLEKE 26 (112)
T ss_dssp -TT-HHHHHHHHH
T ss_pred CCCCHHHHHHHHH
Confidence 4789999977663
No 158
>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=24.29 E-value=27 Score=21.40 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=6.1
Q ss_pred CCcccccccccc
Q 039237 32 RAASCVICRGRW 43 (98)
Q Consensus 32 ~~vtCp~CRs~W 43 (98)
+..+||-|...+
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 345555555443
No 159
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=24.23 E-value=44 Score=33.64 Aligned_cols=34 Identities=15% Similarity=0.512 Sum_probs=25.0
Q ss_pred ccccchhHHHHHHHHHHhcC----------------CCCccccccccccc
Q 039237 11 GTCKNLIHEECWVTWKRSRG----------------RRAASCVICRGRWR 44 (98)
Q Consensus 11 ~~CGnniHkeCf~~W~~s~~----------------~~~vtCp~CRs~W~ 44 (98)
.+||+.+|..||+..+...+ .+..-||.|++.=.
T Consensus 1149 s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn 1198 (1738)
T KOG1140|consen 1149 SSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSN 1198 (1738)
T ss_pred eccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhh
Confidence 48999999999999988742 13455777776543
No 160
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.17 E-value=27 Score=29.55 Aligned_cols=19 Identities=37% Similarity=0.955 Sum_probs=13.2
Q ss_pred eecccccchhHHHHHHHHHHhcCCCCccccccccc
Q 039237 8 VACGTCKNLIHEECWVTWKRSRGRRAASCVICRGR 42 (98)
Q Consensus 8 VwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~ 42 (98)
|.|-.||+.+- .||+||..
T Consensus 322 VtCt~CGkrm~----------------eCPICRqy 340 (350)
T KOG4275|consen 322 VTCTKCGKRMN----------------ECPICRQY 340 (350)
T ss_pred Eeehhhccccc----------------cCchHHHH
Confidence 56666776553 69999964
No 161
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=23.43 E-value=13 Score=28.13 Aligned_cols=31 Identities=19% Similarity=0.495 Sum_probs=10.2
Q ss_pred ceeecccccchhHHHHHHHHHHhcCCCCccccccccc
Q 039237 6 RLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGR 42 (98)
Q Consensus 6 ~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~ 42 (98)
.+..|..||.+|=.. +.......+||+|.-|
T Consensus 133 ~l~~C~~C~~~fv~~------~~~~~~~~~Cp~C~~p 163 (175)
T PF05280_consen 133 QLAPCRRCGGHFVTH------AHDPRHSFVCPFCQPP 163 (175)
T ss_dssp EEEE-TTT--EEEEE------SS--SS----TT----
T ss_pred cccCCCCCCCCeECc------CCCCCcCcCCCCCCCc
Confidence 567888888775211 0111346899999854
No 162
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.00 E-value=24 Score=26.55 Aligned_cols=23 Identities=22% Similarity=0.498 Sum_probs=17.3
Q ss_pred HHHHHHhcC-------CCCccccccccccc
Q 039237 22 WVTWKRSRG-------RRAASCVICRGRWR 44 (98)
Q Consensus 22 f~~W~~s~~-------~~~vtCp~CRs~W~ 44 (98)
|+-|+.++. ++-+|||.|-+.=.
T Consensus 14 FEGWF~ssaDfd~Q~~rgLv~CPvCgs~~V 43 (142)
T COG5319 14 FEGWFGSSADFDRQRERGLVTCPVCGSTEV 43 (142)
T ss_pred ccccccCchhHHHHHHcCceeCCCCCcHHH
Confidence 778888742 56899999987543
No 163
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.82 E-value=34 Score=26.33 Aligned_cols=11 Identities=36% Similarity=0.676 Sum_probs=8.3
Q ss_pred Ccccccccccc
Q 039237 33 AASCVICRGRW 43 (98)
Q Consensus 33 ~vtCp~CRs~W 43 (98)
..+||+||++=
T Consensus 189 ~~~CPiC~~~~ 199 (207)
T KOG1100|consen 189 LRICPICRSPK 199 (207)
T ss_pred CccCCCCcChh
Confidence 35699999863
No 164
>PHA03050 glutaredoxin; Provisional
Probab=21.54 E-value=29 Score=23.67 Aligned_cols=9 Identities=33% Similarity=0.966 Sum_probs=7.3
Q ss_pred Ccccccccc
Q 039237 33 AASCVICRG 41 (98)
Q Consensus 33 ~vtCp~CRs 41 (98)
..+||||+.
T Consensus 20 ~~~CPyC~~ 28 (108)
T PHA03050 20 KFTCPFCRN 28 (108)
T ss_pred CCCChHHHH
Confidence 577999984
No 165
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.31 E-value=41 Score=23.66 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=9.6
Q ss_pred CCccccccccccc
Q 039237 32 RAASCVICRGRWR 44 (98)
Q Consensus 32 ~~vtCp~CRs~W~ 44 (98)
++++||||-.+=.
T Consensus 1 ~p~~CpYCg~~~~ 13 (102)
T PF11672_consen 1 KPIICPYCGGPAE 13 (102)
T ss_pred CCcccCCCCCeeE
Confidence 4689999976543
No 166
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.09 E-value=17 Score=29.57 Aligned_cols=40 Identities=28% Similarity=0.698 Sum_probs=23.9
Q ss_pred CCCCceeecccccchhHHHHHHHHHHhcCC-----CCccccccccccc
Q 039237 2 GSGERLVACGTCKNLIHEECWVTWKRSRGR-----RAASCVICRGRWR 44 (98)
Q Consensus 2 gs~e~lVwC~~CGnniHkeCf~~W~~s~~~-----~~vtCp~CRs~W~ 44 (98)
++.....-|+.|| |.+|..-=..+++. .-++|.-|.-.|.
T Consensus 253 ~~~t~~~~C~~C~---~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 253 KAVTDLFTCGKCK---QKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cCCcccccCCCCC---CccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 3455677888887 56664411222221 2457888888885
No 167
>PF03264 Cytochrom_NNT: NapC/NirT cytochrome c family, N-terminal region; InterPro: IPR005126 Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC P33932 from SWISSPROT and NirT P24038 from SWISSPROT, bind four haem groups, while others, such as TorC P33226 from SWISSPROT, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.; PDB: 2VR0_F 2J7A_C.
Probab=20.81 E-value=58 Score=23.44 Aligned_cols=35 Identities=20% Similarity=0.531 Sum_probs=23.8
Q ss_pred eeecccccchhHHHHHHHHHHhcC-----CCCcccccccccc
Q 039237 7 LVACGTCKNLIHEECWVTWKRSRG-----RRAASCVICRGRW 43 (98)
Q Consensus 7 lVwC~~CGnniHkeCf~~W~~s~~-----~~~vtCp~CRs~W 43 (98)
-.||.+|.. +... ++.|+.+.- +..++|.-|=.|=
T Consensus 35 ~~fC~sCH~-m~~~-~~~~~~s~H~~~~~~~~~~C~dCH~p~ 74 (173)
T PF03264_consen 35 PEFCASCHE-MEPY-YESWQHSSHSRNASGVNVTCVDCHLPH 74 (173)
T ss_dssp HHHHTTSGG-GHHH-HHHHHHSTTT------TS-THHHHS-S
T ss_pred cHHHHhhcC-CcHH-HHHHhhCCCccccCCCCCcCccccCCc
Confidence 358999985 4444 999998853 2589999998763
No 168
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.72 E-value=35 Score=27.54 Aligned_cols=38 Identities=21% Similarity=0.309 Sum_probs=22.7
Q ss_pred eeecccccchhHH--------HHHHH--HHHhcC-CCCccccccccccc
Q 039237 7 LVACGTCKNLIHE--------ECWVT--WKRSRG-RRAASCVICRGRWR 44 (98)
Q Consensus 7 lVwC~~CGnniHk--------eCf~~--W~~s~~-~~~vtCp~CRs~W~ 44 (98)
-+||.+||+.|-+ +.... +..+.- .=-..|+.|-+...
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 3799999998643 22222 322210 01367999999876
No 169
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=20.64 E-value=49 Score=32.43 Aligned_cols=43 Identities=23% Similarity=0.376 Sum_probs=36.7
Q ss_pred CCCCceeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 2 GSGERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 2 gs~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
+..+..+-|..|-+.+|--|++-=..+..-+.=.||.||..=.
T Consensus 1118 ~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1118 KQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred ccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 4456788999999999999999888887666899999998874
No 170
>PF04720 DUF506: Protein of unknown function (DUF506) ; InterPro: IPR006502 This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=20.63 E-value=89 Score=24.54 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhcC-CCCcccccccccccCCC
Q 039237 18 HEECWVTWKRSRG-RRAASCVICRGRWRDNR 47 (98)
Q Consensus 18 HkeCf~~W~~s~~-~~~vtCp~CRs~W~~~~ 47 (98)
.+.|+++|....- ...-..-+|++.|...+
T Consensus 85 ~~~~~rr~v~~~Lr~~GydAaiCkS~W~~s~ 115 (218)
T PF04720_consen 85 CRSCLRRSVMSRLRALGYDAAICKSRWESSG 115 (218)
T ss_pred chHHHHHHHHHHHHhCCCCEEEEEecCCCCC
Confidence 4689999988842 22355678999999755
No 171
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=20.50 E-value=90 Score=27.26 Aligned_cols=40 Identities=23% Similarity=0.645 Sum_probs=29.8
Q ss_pred cccchhHHHHHHHHHHhcCCCCcccccccccccCCCCCCCCeeehh
Q 039237 12 TCKNLIHEECWVTWKRSRGRRAASCVICRGRWRDNRTDQDKYLNLA 57 (98)
Q Consensus 12 ~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~~~~~~~eGYlNla 57 (98)
.||-.|-+-|+..-+... +.+||-||....+..+ .|+-|+
T Consensus 35 ~cgy~ic~fc~~~irq~l---ngrcpacrr~y~denv---~~~~~s 74 (480)
T COG5175 35 PCGYQICQFCYNNIRQNL---NGRCPACRRKYDDENV---RYVTLS 74 (480)
T ss_pred CcccHHHHHHHHHHHhhc---cCCChHhhhhccccce---eEEecC
Confidence 789888888877666553 5689999999886653 466655
No 172
>PLN02189 cellulose synthase
Probab=20.41 E-value=60 Score=31.13 Aligned_cols=38 Identities=29% Similarity=0.871 Sum_probs=31.1
Q ss_pred CCceeecccccchhHHHHHHHHHHhcCCCCccccccccccc
Q 039237 4 GERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRWR 44 (98)
Q Consensus 4 ~e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W~ 44 (98)
++.-|.|..||=++=+.|+ .+.+..+ +-.||-|+++.+
T Consensus 50 g~~fvaC~~C~fpvCr~Cy-eyer~eg--~q~CpqCkt~Y~ 87 (1040)
T PLN02189 50 GDLFVACNECGFPVCRPCY-EYERREG--TQNCPQCKTRYK 87 (1040)
T ss_pred CCEEEeeccCCCccccchh-hhhhhcC--CccCcccCCchh
Confidence 4567899999999999999 5555544 577999999988
No 173
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.22 E-value=55 Score=27.01 Aligned_cols=35 Identities=26% Similarity=0.687 Sum_probs=27.6
Q ss_pred ecccccchhHHHHHHHHHHh------cCCCCcccccccccccCCC
Q 039237 9 ACGTCKNLIHEECWVTWKRS------RGRRAASCVICRGRWRDNR 47 (98)
Q Consensus 9 wC~~CGnniHkeCf~~W~~s------~~~~~vtCp~CRs~W~~~~ 47 (98)
-|..||+.|++- |.-+ .+-++-.||.|+..+.+..
T Consensus 189 ~C~iCGKaFSRP----WLLQGHiRTHTGEKPF~C~hC~kAFADRS 229 (279)
T KOG2462|consen 189 ECGICGKAFSRP----WLLQGHIRTHTGEKPFSCPHCGKAFADRS 229 (279)
T ss_pred ccccccccccch----HHhhcccccccCCCCccCCcccchhcchH
Confidence 368999999975 7665 2457899999999998754
No 174
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.03 E-value=51 Score=22.89 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=17.8
Q ss_pred CceeecccccchhHHHHHHHHHHhcCCCCcccccccccc
Q 039237 5 ERLVACGTCKNLIHEECWVTWKRSRGRRAASCVICRGRW 43 (98)
Q Consensus 5 e~lVwC~~CGnniHkeCf~~W~~s~~~~~vtCp~CRs~W 43 (98)
....+|..||+.+- .. ......||.|-++=
T Consensus 68 p~~~~C~~Cg~~~~--------~~-~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 68 EAECWCETCQQYVT--------LL-TQRVRRCPQCHGDM 97 (114)
T ss_pred CcEEEcccCCCeee--------cC-CccCCcCcCcCCCC
Confidence 34678999996321 11 11125699998763
Done!