Query 021794
Match_columns 307
No_of_seqs 247 out of 1369
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:44:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021794.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021794hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 6.8E-65 1.5E-69 476.0 7.6 236 59-306 21-267 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 3.1E-27 6.7E-32 177.2 0.3 61 244-304 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.7 7.9E-18 1.7E-22 129.4 1.4 62 73-145 1-71 (71)
4 PF13639 zf-RING_2: Ring finge 99.3 8.6E-13 1.9E-17 91.6 1.9 44 196-241 1-44 (44)
5 PF12861 zf-Apc11: Anaphase-pr 99.2 2.1E-11 4.5E-16 97.3 3.9 51 193-245 30-82 (85)
6 PF12678 zf-rbx1: RING-H2 zinc 99.0 4.6E-10 1E-14 86.6 3.7 46 195-241 19-73 (73)
7 KOG4628 Predicted E3 ubiquitin 98.9 4E-10 8.7E-15 109.8 3.2 50 196-246 230-279 (348)
8 cd00162 RING RING-finger (Real 98.9 1.2E-09 2.7E-14 72.9 3.8 45 197-244 1-45 (45)
9 PF13923 zf-C3HC4_2: Zinc fing 98.8 2.2E-09 4.8E-14 72.9 2.9 39 198-240 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.8 7E-09 1.5E-13 96.7 4.5 54 192-246 171-228 (238)
11 PF15227 zf-C3HC4_4: zinc fing 98.7 6.9E-09 1.5E-13 72.3 3.2 39 198-240 1-42 (42)
12 COG5243 HRD1 HRD ubiquitin lig 98.7 5.1E-09 1.1E-13 102.6 2.3 56 192-248 284-349 (491)
13 PF13920 zf-C3HC4_3: Zinc fing 98.7 1E-08 2.3E-13 72.9 3.0 47 195-246 2-49 (50)
14 PF00097 zf-C3HC4: Zinc finger 98.7 1.4E-08 3E-13 69.0 3.1 40 198-240 1-41 (41)
15 smart00184 RING Ring finger. E 98.6 2.4E-08 5.3E-13 64.3 3.1 39 198-240 1-39 (39)
16 KOG1493 Anaphase-promoting com 98.6 6E-09 1.3E-13 81.8 -0.2 51 193-245 29-81 (84)
17 PF13445 zf-RING_UBOX: RING-ty 98.6 2.6E-08 5.7E-13 70.0 2.5 40 198-238 1-43 (43)
18 COG5540 RING-finger-containing 98.6 3.1E-08 6.8E-13 95.0 3.3 54 191-245 319-372 (374)
19 PF14634 zf-RING_5: zinc-RING 98.6 5.2E-08 1.1E-12 67.9 3.4 44 197-242 1-44 (44)
20 PLN03208 E3 ubiquitin-protein 98.5 1E-07 2.2E-12 86.5 4.6 56 187-246 10-80 (193)
21 COG5194 APC11 Component of SCF 98.5 7.8E-08 1.7E-12 76.2 3.1 50 195-245 31-81 (88)
22 KOG0804 Cytoplasmic Zn-finger 98.3 2.8E-07 6.1E-12 92.1 2.7 81 196-304 176-258 (493)
23 PHA02926 zinc finger-like prot 98.3 4.6E-07 9.9E-12 83.9 3.5 69 178-246 153-231 (242)
24 smart00504 Ubox Modified RING 98.2 1.2E-06 2.5E-11 64.0 4.0 45 196-245 2-46 (63)
25 KOG0802 E3 ubiquitin ligase [P 98.1 1.2E-06 2.5E-11 90.0 1.5 54 191-245 287-341 (543)
26 KOG0320 Predicted E3 ubiquitin 98.1 2.5E-06 5.4E-11 76.6 3.0 48 195-245 131-178 (187)
27 KOG2177 Predicted E3 ubiquitin 98.0 8.1E-06 1.8E-10 71.8 5.8 44 194-242 12-55 (386)
28 KOG0317 Predicted E3 ubiquitin 97.9 6.2E-06 1.4E-10 78.7 2.2 47 195-246 239-285 (293)
29 smart00744 RINGv The RING-vari 97.8 1.3E-05 2.9E-10 57.6 3.0 43 197-241 1-49 (49)
30 TIGR00599 rad18 DNA repair pro 97.8 1.3E-05 2.8E-10 79.9 3.5 46 195-245 26-71 (397)
31 TIGR00570 cdk7 CDK-activating 97.8 2.1E-05 4.5E-10 76.1 4.2 52 195-246 3-55 (309)
32 KOG0823 Predicted E3 ubiquitin 97.7 1.9E-05 4.1E-10 73.4 3.2 50 193-246 45-96 (230)
33 KOG2930 SCF ubiquitin ligase, 97.7 8.5E-06 1.8E-10 67.5 0.3 33 212-245 76-108 (114)
34 PF11793 FANCL_C: FANCL C-term 97.7 9.9E-06 2.2E-10 62.2 -0.1 51 195-245 2-66 (70)
35 COG4357 Zinc finger domain con 97.6 1.4E-05 3E-10 65.5 -0.3 51 72-131 14-67 (105)
36 PF04564 U-box: U-box domain; 97.5 0.00016 3.4E-09 55.5 5.2 48 195-246 4-51 (73)
37 KOG2164 Predicted E3 ubiquitin 97.4 8.2E-05 1.8E-09 75.8 2.8 49 194-246 185-237 (513)
38 KOG0828 Predicted E3 ubiquitin 97.4 6.1E-05 1.3E-09 76.6 1.5 51 195-245 571-634 (636)
39 KOG0287 Postreplication repair 97.3 0.00013 2.9E-09 71.5 3.2 46 196-246 24-69 (442)
40 KOG0827 Predicted E3 ubiquitin 97.2 0.00016 3.5E-09 71.8 2.0 47 195-242 4-53 (465)
41 COG5574 PEX10 RING-finger-cont 97.1 0.00027 5.9E-09 67.0 2.2 47 195-245 215-262 (271)
42 PF14835 zf-RING_6: zf-RING of 96.8 0.00053 1.2E-08 52.5 1.2 55 196-257 8-64 (65)
43 KOG4265 Predicted E3 ubiquitin 96.8 0.00094 2E-08 65.6 3.0 49 193-246 288-337 (349)
44 KOG4172 Predicted E3 ubiquitin 96.7 0.00042 9.2E-09 51.7 0.0 50 194-247 6-56 (62)
45 KOG0978 E3 ubiquitin ligase in 96.6 0.00067 1.4E-08 71.8 0.6 47 196-246 644-690 (698)
46 KOG1039 Predicted E3 ubiquitin 96.6 0.0007 1.5E-08 66.6 0.6 82 193-276 159-252 (344)
47 KOG0311 Predicted E3 ubiquitin 96.6 0.00056 1.2E-08 67.3 -0.2 48 195-245 43-90 (381)
48 KOG1734 Predicted RING-contain 96.5 0.00072 1.6E-08 64.6 0.5 52 194-245 223-281 (328)
49 PF14570 zf-RING_4: RING/Ubox 96.5 0.0021 4.5E-08 46.5 2.4 47 198-244 1-47 (48)
50 COG5432 RAD18 RING-finger-cont 96.4 0.0018 4E-08 62.6 2.4 46 195-245 25-70 (391)
51 KOG1941 Acetylcholine receptor 96.3 0.00079 1.7E-08 67.2 -1.0 58 186-244 357-415 (518)
52 PF11789 zf-Nse: Zinc-finger o 96.2 0.0037 8E-08 46.4 2.6 44 193-239 9-53 (57)
53 KOG1428 Inhibitor of type V ad 96.0 0.0047 1E-07 69.7 3.2 74 164-245 3462-3544(3738)
54 COG5219 Uncharacterized conser 95.9 0.0038 8.2E-08 68.0 2.0 53 193-245 1467-1523(1525)
55 KOG2879 Predicted E3 ubiquitin 95.7 0.0081 1.7E-07 57.6 3.2 53 193-248 237-290 (298)
56 KOG1785 Tyrosine kinase negati 95.7 0.0035 7.6E-08 62.9 0.5 54 188-245 362-416 (563)
57 KOG0825 PHD Zn-finger protein 95.5 0.0046 9.9E-08 66.3 0.8 49 195-245 123-171 (1134)
58 PF12906 RINGv: RING-variant d 95.5 0.0088 1.9E-07 42.6 1.8 41 198-240 1-47 (47)
59 KOG0824 Predicted E3 ubiquitin 95.4 0.0082 1.8E-07 58.2 2.1 49 193-245 5-53 (324)
60 KOG3800 Predicted E3 ubiquitin 94.6 0.026 5.6E-07 54.5 3.0 49 197-245 2-51 (300)
61 KOG4185 Predicted E3 ubiquitin 94.5 0.034 7.3E-07 52.5 3.6 49 196-245 4-55 (296)
62 PF10367 Vps39_2: Vacuolar sor 94.5 0.018 3.9E-07 45.7 1.4 33 193-227 76-108 (109)
63 KOG1645 RING-finger-containing 94.4 0.048 1E-06 55.0 4.4 50 196-245 5-56 (463)
64 PF14447 Prok-RING_4: Prokaryo 94.0 0.023 4.9E-07 42.3 0.9 33 211-246 19-51 (55)
65 KOG3268 Predicted E3 ubiquitin 93.9 0.035 7.7E-07 50.6 2.1 31 215-245 188-228 (234)
66 COG5175 MOT2 Transcriptional r 93.8 0.023 5.1E-07 56.1 0.8 57 195-251 14-70 (480)
67 KOG0297 TNF receptor-associate 93.6 0.042 9.1E-07 54.8 2.3 49 194-246 20-68 (391)
68 KOG4159 Predicted E3 ubiquitin 93.6 0.07 1.5E-06 53.7 3.8 49 193-246 82-130 (398)
69 KOG4445 Uncharacterized conser 93.3 0.027 5.9E-07 54.8 0.4 51 195-246 115-187 (368)
70 PF05883 Baculo_RING: Baculovi 93.3 0.041 8.8E-07 47.7 1.4 35 195-230 26-66 (134)
71 KOG1571 Predicted E3 ubiquitin 92.8 0.064 1.4E-06 53.1 2.2 47 191-245 301-347 (355)
72 KOG1814 Predicted E3 ubiquitin 92.7 0.13 2.9E-06 51.8 4.2 46 195-241 184-236 (445)
73 PF04641 Rtf2: Rtf2 RING-finge 91.8 0.16 3.6E-06 47.7 3.5 51 192-245 110-161 (260)
74 KOG4275 Predicted E3 ubiquitin 91.7 0.028 6.2E-07 54.5 -1.7 55 184-247 286-344 (350)
75 KOG3002 Zn finger protein [Gen 91.5 0.22 4.8E-06 48.3 4.2 62 195-267 48-111 (299)
76 KOG2817 Predicted E3 ubiquitin 91.4 0.15 3.3E-06 51.1 2.9 48 196-244 335-384 (394)
77 KOG3970 Predicted E3 ubiquitin 91.0 0.31 6.7E-06 46.1 4.4 52 193-246 48-106 (299)
78 KOG1813 Predicted E3 ubiquitin 90.7 0.17 3.7E-06 49.1 2.4 49 193-246 239-287 (313)
79 TIGR00100 hypA hydrogenase nic 90.4 0.19 4.1E-06 42.0 2.3 35 271-307 68-102 (115)
80 PRK03824 hypA hydrogenase nick 89.8 0.24 5.3E-06 42.5 2.5 37 271-307 68-123 (135)
81 COG5236 Uncharacterized conser 89.6 0.34 7.4E-06 48.3 3.6 66 176-245 42-108 (493)
82 COG5152 Uncharacterized conser 89.4 0.22 4.7E-06 46.3 1.9 59 195-258 196-254 (259)
83 PRK00564 hypA hydrogenase nick 89.3 0.27 5.8E-06 41.3 2.3 36 270-307 68-104 (117)
84 PHA02862 5L protein; Provision 89.2 0.28 6E-06 43.4 2.4 46 195-245 2-53 (156)
85 PF07800 DUF1644: Protein of u 88.4 0.48 1E-05 42.3 3.4 33 195-231 2-47 (162)
86 KOG1002 Nucleotide excision re 88.3 0.2 4.4E-06 52.2 1.1 54 188-245 529-586 (791)
87 PHA02825 LAP/PHD finger-like p 88.3 0.46 9.9E-06 42.5 3.2 47 194-245 7-59 (162)
88 KOG2114 Vacuolar assembly/sort 88.2 0.35 7.5E-06 52.7 2.8 43 196-245 841-883 (933)
89 PRK14890 putative Zn-ribbon RN 88.1 0.24 5.1E-06 37.4 1.1 32 122-160 24-56 (59)
90 PRK12380 hydrogenase nickel in 88.1 0.35 7.5E-06 40.4 2.2 35 271-307 68-102 (113)
91 PRK03681 hypA hydrogenase nick 87.7 0.39 8.3E-06 40.2 2.2 36 271-307 68-103 (114)
92 KOG3039 Uncharacterized conser 87.7 0.57 1.2E-05 44.8 3.6 54 192-247 218-272 (303)
93 PF08746 zf-RING-like: RING-li 87.3 0.4 8.6E-06 33.6 1.8 42 198-240 1-43 (43)
94 PF03854 zf-P11: P-11 zinc fin 87.2 0.26 5.6E-06 35.9 0.8 32 214-246 15-47 (50)
95 PF07191 zinc-ribbons_6: zinc- 87.0 0.12 2.5E-06 40.3 -1.2 65 196-289 2-69 (70)
96 KOG2660 Locus-specific chromos 86.7 0.18 4E-06 49.4 -0.3 49 193-245 13-61 (331)
97 PF01155 HypA: Hydrogenase exp 86.0 0.27 5.8E-06 40.9 0.4 35 271-307 68-102 (113)
98 KOG3161 Predicted E3 ubiquitin 85.7 0.33 7.2E-06 51.6 0.9 43 196-242 12-54 (861)
99 KOG4739 Uncharacterized protei 84.7 0.35 7.7E-06 45.5 0.6 37 206-245 12-48 (233)
100 KOG0309 Conserved WD40 repeat- 83.4 0.76 1.7E-05 49.8 2.4 42 195-239 1028-1069(1081)
101 COG5220 TFB3 Cdk activating ki 83.0 0.42 9E-06 45.6 0.3 51 195-245 10-64 (314)
102 COG5222 Uncharacterized conser 82.7 0.83 1.8E-05 44.9 2.2 44 196-242 275-318 (427)
103 PRK00762 hypA hydrogenase nick 82.6 0.93 2E-05 38.4 2.2 36 271-307 68-108 (124)
104 KOG4692 Predicted E3 ubiquitin 81.8 0.98 2.1E-05 45.3 2.4 51 191-246 418-468 (489)
105 PHA03096 p28-like protein; Pro 80.5 0.95 2.1E-05 43.7 1.8 47 196-242 179-231 (284)
106 COG2888 Predicted Zn-ribbon RN 80.3 0.8 1.7E-05 34.8 0.9 33 122-160 26-58 (61)
107 COG0375 HybF Zn finger protein 78.6 1.6 3.6E-05 37.0 2.4 36 270-307 67-102 (115)
108 KOG2034 Vacuolar sorting prote 76.9 1.2 2.5E-05 49.0 1.3 35 195-231 817-851 (911)
109 KOG1952 Transcription factor N 75.2 1.6 3.5E-05 47.8 1.8 48 195-245 191-247 (950)
110 KOG1001 Helicase-like transcri 74.9 1.5 3.3E-05 47.0 1.5 44 196-244 455-499 (674)
111 COG5109 Uncharacterized conser 74.0 2.3 5E-05 42.1 2.4 45 196-241 337-383 (396)
112 PF14446 Prok-RING_1: Prokaryo 74.0 3.5 7.5E-05 30.7 2.8 36 194-229 4-39 (54)
113 PF05290 Baculo_IE-1: Baculovi 73.9 2.2 4.8E-05 37.3 2.0 48 196-247 81-134 (140)
114 PF02891 zf-MIZ: MIZ/SP-RING z 73.5 4.3 9.3E-05 29.2 3.1 42 196-243 3-50 (50)
115 KOG4367 Predicted Zn-finger pr 71.9 2.1 4.6E-05 44.0 1.6 33 195-231 4-36 (699)
116 KOG1812 Predicted E3 ubiquitin 68.9 2.4 5.2E-05 42.4 1.3 50 195-245 146-203 (384)
117 KOG3053 Uncharacterized conser 66.4 3.9 8.4E-05 39.4 2.1 55 191-245 16-82 (293)
118 KOG2068 MOT2 transcription fac 62.7 5.8 0.00013 39.2 2.5 53 193-246 247-299 (327)
119 PF09538 FYDLN_acid: Protein o 62.2 4.6 0.0001 33.7 1.5 25 124-160 10-34 (108)
120 KOG2462 C2H2-type Zn-finger pr 62.0 5.4 0.00012 38.6 2.2 88 130-249 125-230 (279)
121 PF03107 C1_2: C1 domain; Int 61.3 6.5 0.00014 25.2 1.8 20 157-176 2-22 (30)
122 KOG0827 Predicted E3 ubiquitin 60.4 0.87 1.9E-05 46.0 -3.6 52 194-246 195-246 (465)
123 KOG2066 Vacuolar assembly/sort 57.6 3.9 8.4E-05 44.6 0.4 45 195-241 784-831 (846)
124 PF01529 zf-DHHC: DHHC palmito 56.5 8.3 0.00018 33.0 2.2 48 129-182 42-89 (174)
125 PF06524 NOA36: NOA36 protein; 55.9 5.4 0.00012 38.6 1.0 52 88-144 140-191 (314)
126 smart00249 PHD PHD zinc finger 55.6 4.6 0.0001 26.5 0.4 41 198-240 2-47 (47)
127 PF14353 CpXC: CpXC protein 54.8 2.5 5.5E-05 35.2 -1.2 56 235-292 2-57 (128)
128 TIGR02605 CxxC_CxxC_SSSS putat 54.6 9.5 0.00021 26.9 1.9 30 273-302 5-37 (52)
129 PRK04023 DNA polymerase II lar 53.8 11 0.00023 42.6 2.9 49 122-179 625-673 (1121)
130 PRK00398 rpoP DNA-directed RNA 53.2 11 0.00023 26.3 2.0 30 273-302 3-32 (46)
131 KOG1609 Protein involved in mR 52.7 8.4 0.00018 35.9 1.8 51 195-245 78-134 (323)
132 COG3809 Uncharacterized protei 52.2 11 0.00024 30.3 2.1 30 235-268 22-53 (88)
133 KOG1701 Focal adhesion adaptor 52.0 1.8 3.9E-05 44.2 -3.0 83 122-226 273-361 (468)
134 PRK12286 rpmF 50S ribosomal pr 51.5 15 0.00033 27.3 2.6 29 272-305 26-54 (57)
135 PF07282 OrfB_Zn_ribbon: Putat 51.0 9.7 0.00021 28.3 1.5 28 122-160 27-54 (69)
136 PF13894 zf-C2H2_4: C2H2-type 50.8 7.7 0.00017 22.0 0.8 17 235-251 1-17 (24)
137 PRK00398 rpoP DNA-directed RNA 49.7 14 0.0003 25.7 2.1 8 152-159 21-28 (46)
138 PF05605 zf-Di19: Drought indu 49.6 17 0.00037 26.0 2.6 8 235-242 3-10 (54)
139 KOG1100 Predicted E3 ubiquitin 49.4 7.8 0.00017 35.8 1.0 39 198-245 161-200 (207)
140 KOG0269 WD40 repeat-containing 49.3 16 0.00035 39.9 3.4 78 151-248 752-836 (839)
141 PF14569 zf-UDP: Zinc-binding 49.2 18 0.0004 28.9 2.9 52 194-245 8-62 (80)
142 KOG2907 RNA polymerase I trans 49.2 6.4 0.00014 33.5 0.3 19 289-307 72-94 (116)
143 PF04438 zf-HIT: HIT zinc fing 48.5 9.5 0.00021 24.9 1.0 19 124-143 3-21 (30)
144 PF12773 DZR: Double zinc ribb 48.2 14 0.00031 25.7 2.0 12 123-134 12-23 (50)
145 PRK14714 DNA polymerase II lar 48.1 16 0.00034 42.1 3.2 33 124-160 668-700 (1337)
146 COG1656 Uncharacterized conser 48.1 12 0.00027 33.7 2.0 50 234-290 97-147 (165)
147 TIGR02300 FYDLN_acid conserved 47.9 11 0.00024 32.7 1.6 26 124-161 10-35 (129)
148 KOG0298 DEAD box-containing he 45.5 8.8 0.00019 44.1 0.8 51 193-247 1151-1201(1394)
149 COG5183 SSM4 Protein involved 45.0 16 0.00034 40.5 2.5 52 192-245 9-66 (1175)
150 PHA00626 hypothetical protein 44.6 17 0.00036 27.5 1.9 30 125-160 2-31 (59)
151 COG1996 RPC10 DNA-directed RNA 44.3 14 0.0003 27.0 1.4 29 132-160 3-32 (49)
152 cd00350 rubredoxin_like Rubred 43.7 19 0.00041 23.5 1.9 25 135-160 1-25 (33)
153 PF13717 zinc_ribbon_4: zinc-r 43.4 18 0.00038 24.4 1.7 12 122-133 24-35 (36)
154 smart00734 ZnF_Rad18 Rad18-lik 42.1 22 0.00047 22.4 1.9 20 235-255 2-21 (26)
155 PF02701 zf-Dof: Dof domain, z 41.4 14 0.00029 28.4 1.0 14 291-304 5-18 (63)
156 COG1996 RPC10 DNA-directed RNA 41.1 17 0.00037 26.5 1.5 29 271-299 4-32 (49)
157 KOG0801 Predicted E3 ubiquitin 40.6 10 0.00022 34.5 0.3 29 194-223 176-204 (205)
158 TIGR01031 rpmF_bact ribosomal 40.2 24 0.00052 26.0 2.2 29 272-305 25-53 (55)
159 smart00659 RPOLCX RNA polymera 40.0 21 0.00045 25.2 1.7 26 273-299 2-27 (44)
160 PF07649 C1_3: C1-like domain; 38.7 18 0.00039 22.9 1.2 20 158-177 3-23 (30)
161 PF10272 Tmpp129: Putative tra 38.5 34 0.00073 34.3 3.6 25 221-245 315-351 (358)
162 PLN02189 cellulose synthase 38.0 26 0.00057 39.6 3.0 56 190-245 29-87 (1040)
163 KOG4185 Predicted E3 ubiquitin 38.0 5.9 0.00013 37.3 -1.7 49 196-244 208-266 (296)
164 PF00096 zf-C2H2: Zinc finger, 37.8 18 0.0004 20.9 1.0 15 235-249 1-15 (23)
165 smart00451 ZnF_U1 U1-like zinc 37.8 16 0.00034 23.3 0.8 13 133-145 1-13 (35)
166 KOG4399 C2HC-type Zn-finger pr 37.7 8.4 0.00018 37.3 -0.7 53 124-180 250-302 (325)
167 TIGR02159 PA_CoA_Oxy4 phenylac 37.5 17 0.00036 31.9 1.1 16 291-306 105-120 (146)
168 PRK04023 DNA polymerase II lar 37.3 22 0.00048 40.2 2.2 17 82-98 627-646 (1121)
169 PF03833 PolC_DP2: DNA polymer 37.2 11 0.00024 41.6 0.0 46 124-178 656-701 (900)
170 KOG0826 Predicted E3 ubiquitin 36.8 28 0.0006 34.8 2.6 49 193-245 298-346 (357)
171 PRK14559 putative protein seri 36.6 26 0.00057 37.6 2.6 21 123-143 15-35 (645)
172 PRK00432 30S ribosomal protein 36.6 25 0.00055 25.4 1.8 9 151-159 36-44 (50)
173 PF06220 zf-U1: U1 zinc finger 35.8 16 0.00034 25.0 0.5 13 133-145 1-13 (38)
174 PF00628 PHD: PHD-finger; Int 35.4 4 8.6E-05 28.4 -2.6 43 198-241 2-49 (51)
175 KOG1044 Actin-binding LIM Zn-f 35.0 44 0.00095 35.8 3.8 135 148-299 12-168 (670)
176 PF04710 Pellino: Pellino; In 34.9 13 0.00029 37.8 0.1 49 192-243 274-337 (416)
177 PLN02436 cellulose synthase A 34.6 32 0.00069 39.1 3.0 56 190-245 31-89 (1094)
178 KOG2932 E3 ubiquitin ligase in 33.7 17 0.00036 36.2 0.6 30 213-245 105-134 (389)
179 PF00643 zf-B_box: B-box zinc 33.7 26 0.00056 23.4 1.3 21 124-144 4-24 (42)
180 KOG4399 C2HC-type Zn-finger pr 33.6 8.3 0.00018 37.4 -1.5 75 127-204 196-270 (325)
181 PF06906 DUF1272: Protein of u 33.4 62 0.0013 24.4 3.4 50 194-246 4-53 (57)
182 PRK14714 DNA polymerase II lar 33.0 40 0.00086 39.1 3.4 36 125-161 681-718 (1337)
183 PF05502 Dynactin_p62: Dynacti 32.5 37 0.00079 35.2 2.8 20 185-206 44-63 (483)
184 PRK00366 ispG 4-hydroxy-3-meth 32.3 62 0.0014 32.6 4.3 53 235-291 269-323 (360)
185 KOG4362 Transcriptional regula 32.0 21 0.00045 38.7 1.0 47 195-245 21-69 (684)
186 PF03604 DNA_RNApol_7kD: DNA d 31.9 34 0.00073 22.7 1.6 24 136-159 1-24 (32)
187 KOG1311 DHHC-type Zn-finger pr 31.0 39 0.00085 32.0 2.6 46 130-181 108-153 (299)
188 cd02337 ZZ_CBP Zinc finger, ZZ 30.3 37 0.0008 23.5 1.7 20 153-176 1-20 (41)
189 cd01675 RNR_III Class III ribo 30.0 44 0.00096 35.0 3.0 29 274-306 519-547 (555)
190 cd02249 ZZ Zinc finger, ZZ typ 29.7 39 0.00084 23.5 1.7 21 153-176 1-21 (46)
191 PF14952 zf-tcix: Putative tre 29.5 26 0.00056 25.1 0.8 13 292-304 12-24 (44)
192 KOG1815 Predicted E3 ubiquitin 29.1 34 0.00074 34.7 1.9 38 192-232 67-104 (444)
193 PF05191 ADK_lid: Adenylate ki 28.9 24 0.00051 23.9 0.5 27 125-160 3-29 (36)
194 PF04423 Rad50_zn_hook: Rad50 28.2 40 0.00086 24.1 1.6 12 235-246 21-32 (54)
195 smart00661 RPOL9 RNA polymeras 28.1 43 0.00093 23.2 1.8 9 151-159 19-27 (52)
196 PF09723 Zn-ribbon_8: Zinc rib 28.0 46 0.00099 22.9 1.8 31 273-303 5-38 (42)
197 TIGR01562 FdhE formate dehydro 27.8 66 0.0014 31.5 3.6 10 234-243 184-193 (305)
198 PF01529 zf-DHHC: DHHC palmito 27.2 37 0.00081 28.9 1.6 36 149-190 45-80 (174)
199 PF01783 Ribosomal_L32p: Ribos 27.0 43 0.00093 24.6 1.6 29 272-305 25-53 (56)
200 PF06937 EURL: EURL protein; 26.4 52 0.0011 32.0 2.5 43 193-238 28-74 (285)
201 smart00132 LIM Zinc-binding do 26.4 36 0.00078 21.4 1.0 37 198-245 2-38 (39)
202 PF08271 TF_Zn_Ribbon: TFIIB z 26.0 47 0.001 22.7 1.6 9 171-179 21-29 (43)
203 PF15353 HECA: Headcase protei 25.7 41 0.00089 28.4 1.5 16 216-231 39-54 (107)
204 PF13719 zinc_ribbon_5: zinc-r 25.0 51 0.0011 22.1 1.6 12 122-133 24-35 (37)
205 KOG3842 Adaptor protein Pellin 24.8 70 0.0015 32.1 3.1 51 195-245 341-414 (429)
206 KOG3842 Adaptor protein Pellin 24.7 34 0.00073 34.2 1.0 46 192-242 287-349 (429)
207 PLN02638 cellulose synthase A 24.5 60 0.0013 37.0 2.9 55 191-245 13-70 (1079)
208 KOG1312 DHHC-type Zn-finger pr 24.2 22 0.00048 35.0 -0.4 32 156-190 149-180 (341)
209 PF03966 Trm112p: Trm112p-like 23.8 37 0.0008 25.5 0.8 12 81-92 53-64 (68)
210 cd02345 ZZ_dah Zinc finger, ZZ 23.7 57 0.0012 23.2 1.7 26 274-302 1-26 (49)
211 PRK00564 hypA hydrogenase nick 23.1 54 0.0012 27.4 1.8 6 154-159 90-95 (117)
212 PRK14890 putative Zn-ribbon RN 23.1 97 0.0021 23.5 2.9 10 233-242 47-56 (59)
213 KOG1940 Zn-finger protein [Gen 22.9 13 0.00028 36.0 -2.3 29 69-98 176-204 (276)
214 COG5273 Uncharacterized protei 22.5 49 0.0011 32.3 1.6 29 130-161 104-132 (309)
215 PF00130 C1_1: Phorbol esters/ 22.3 61 0.0013 22.5 1.7 13 148-160 24-36 (53)
216 PF10058 DUF2296: Predicted in 22.0 1.2E+02 0.0026 22.3 3.2 47 252-301 4-54 (54)
217 PF13453 zf-TFIIB: Transcripti 21.9 54 0.0012 22.2 1.3 8 151-158 18-25 (41)
218 KOG0006 E3 ubiquitin-protein l 21.8 73 0.0016 32.0 2.6 98 124-230 135-254 (446)
219 TIGR02494 PFLE_PFLC glycyl-rad 21.8 51 0.0011 30.8 1.5 33 91-134 26-58 (295)
220 PF01907 Ribosomal_L37e: Ribos 21.7 35 0.00075 25.6 0.3 27 269-298 11-37 (55)
221 smart00834 CxxC_CXXC_SSSS Puta 21.4 79 0.0017 20.7 2.0 27 273-299 5-34 (41)
222 PRK01110 rpmF 50S ribosomal pr 21.2 77 0.0017 23.8 2.1 27 273-305 27-53 (60)
223 KOG4317 Predicted Zn-finger pr 21.2 43 0.00093 33.4 0.9 20 125-144 9-28 (383)
224 PRK00420 hypothetical protein; 21.2 54 0.0012 27.8 1.3 30 194-245 22-51 (112)
225 PF13695 zf-3CxxC: Zinc-bindin 21.1 85 0.0018 25.3 2.5 46 234-303 5-50 (98)
226 KOG2462 C2H2-type Zn-finger pr 21.0 85 0.0018 30.6 2.8 115 122-250 129-259 (279)
227 KOG3113 Uncharacterized conser 20.8 1.5E+02 0.0032 28.9 4.3 50 193-245 109-158 (293)
228 PRK14892 putative transcriptio 20.7 78 0.0017 26.2 2.2 33 167-204 19-51 (99)
229 PF11405 Inhibitor_I67: Bromel 20.6 34 0.00073 23.6 0.0 16 124-139 16-31 (41)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.8e-65 Score=476.02 Aligned_cols=236 Identities=53% Similarity=1.070 Sum_probs=227.7
Q ss_pred CCchhcccCCCcCCCcccccCceeEcCccCCeecCCccccccccCcCcCCcCCcccCcccccc-----------cccccc
Q 021794 59 GSTELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQ-----------VQQVCV 127 (307)
Q Consensus 59 ~~~~~~~~~~~~~GC~HY~R~Cki~aPCC~~~y~CR~CHde~~~~~~~~~~~~H~l~R~~v~e-----------v~~~C~ 127 (307)
.+.++.|++.+.+||+||+|+|++++|||++||+||+||+++ ++|.++|+.|.+ +++.|.
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s---------~~h~~~r~~v~~~~C~~C~~~q~~~~~c~ 91 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNES---------EDHDLDRKTVYELLCMKCRKIQPVGQICS 91 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChh---------hhcccchhhhhhhhhhhHHhhhhhhhccc
Confidence 345788999999999999999999999999999999999987 489999998876 789999
Q ss_pred cCCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcceeccccCCccccCCCCCCCCccccccccc
Q 021794 128 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFE 207 (307)
Q Consensus 128 nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~ 207 (307)
+|+..||+|||.+|+||||+++ .||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.+||||.|++|+
T Consensus 92 ~c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~ 170 (276)
T KOG1940|consen 92 NCHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFL 170 (276)
T ss_pred cchhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhcc
Confidence 9999999999999999999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEEcCCCCCCccccc
Q 021794 208 TRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQF 287 (307)
Q Consensus 208 s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s~~~f 287 (307)
+...+..|+|||++|..|++++...+ |+||+|.+ +.||+.+|+++|.+|+++|||++|.+++++|+||||+..++++|
T Consensus 171 s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~ 248 (276)
T KOG1940|consen 171 SFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKY 248 (276)
T ss_pred ccccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccce
Confidence 99999999999999999999999876 99999999 99999999999999999999999999999999999999999999
Q ss_pred eeeeccCCCCCCccccccC
Q 021794 288 HVLAQKCPNCKSYNTRLTR 306 (307)
Q Consensus 288 H~lg~kC~~C~SYNT~~~~ 306 (307)
|||++||+.|+|||||+++
T Consensus 249 ~~l~~kc~~c~~~~~r~~~ 267 (276)
T KOG1940|consen 249 HILYHKCGKCGSYNTRMIS 267 (276)
T ss_pred ehhhhhCCCcccceeeecc
Confidence 9999999999999999985
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.93 E-value=3.1e-27 Score=177.20 Aligned_cols=61 Identities=66% Similarity=1.160 Sum_probs=22.6
Q ss_pred cCchhHHHHHhHHHHhcCCCChhhhcCceeEEcCCCCCCccccceeeeccCCCCCCccccc
Q 021794 244 VCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRL 304 (307)
Q Consensus 244 ~~dm~~~~~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~ 304 (307)
+.||+.+|+.||++|+++|||++|++++++|+||||+++|+++||||||||.+|+||||||
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 4689999999999999999999999999999999999999999999999999999999997
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.68 E-value=7.9e-18 Score=129.44 Aligned_cols=62 Identities=40% Similarity=1.047 Sum_probs=42.6
Q ss_pred CcccccC-ceeEcCccCCeecCCccccccccCcCcCCcCCcccCcccccccccccccCCccc--------ceeecCcccc
Q 021794 73 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVQQVCVNCGVCM--------GEYFCESCKL 143 (307)
Q Consensus 73 C~HY~R~-Cki~aPCC~~~y~CR~CHde~~~~~~~~~~~~H~l~R~~v~ev~~~C~nCg~~f--------~~YfC~~Ckl 143 (307)
|+||+|+ |+|++|||++|||||+||||.. +|+|+|..++ ...|..|+..+ |+|||++|++
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~---------~H~~~~~~~~--~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE---------DHPFDRWPVK--RVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS---------SS---TTT----EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc---------cCcccccccc--CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 8999999 9999999999999999999973 7999999988 44455554433 6799999999
Q ss_pred cc
Q 021794 144 FD 145 (307)
Q Consensus 144 ~d 145 (307)
||
T Consensus 70 ~~ 71 (71)
T PF05495_consen 70 YF 71 (71)
T ss_dssp EE
T ss_pred CC
Confidence 86
No 4
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.30 E-value=8.6e-13 Score=91.55 Aligned_cols=44 Identities=39% Similarity=1.061 Sum_probs=37.0
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 241 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 241 (307)
++||||++.+. ..+.++.|+|||.||.+||.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~-~~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFE-DGEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHH-TTSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhc-CCCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 37999999754 4667889999999999999999986 58999997
No 5
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.16 E-value=2.1e-11 Score=97.27 Aligned_cols=51 Identities=20% Similarity=0.466 Sum_probs=41.1
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCrks~~ 245 (307)
+++..||.|.. ....-++++..|+|.||.+||.+||+.. +.+||+||+.+.
T Consensus 30 ~fdg~Cp~Ck~--Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 30 PFDGCCPDCKF--PGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred ccccCCCCccC--CCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 55778999984 4445567778999999999999999863 568999998764
No 6
>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=98.96 E-value=4.6e-10 Score=86.56 Aligned_cols=46 Identities=28% Similarity=0.808 Sum_probs=35.5
Q ss_pred CCCCcccccccccC---------cceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 021794 195 HHDCPVCCEYLFET---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 241 (307)
Q Consensus 195 ~~~CPIClE~lf~s---------~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 241 (307)
+++|+||++.|.+. ..++++++|||.||..||.+||+. +.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 56699999887332 244566799999999999999985 56999997
No 7
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=4e-10 Score=109.77 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=45.2
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
..|+||||+ |..++.++.|||+|.||..|+++||...+..||+|+.++..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 589999997 88899999999999999999999998755669999998874
No 8
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.91 E-value=1.2e-09 Score=72.91 Aligned_cols=45 Identities=33% Similarity=1.041 Sum_probs=37.1
Q ss_pred CCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCccc
Q 021794 197 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 244 (307)
Q Consensus 197 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~ 244 (307)
.|+||++.+ ..++.+++|||.||..|+..|++..+.+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999975 335666779999999999999986568899999764
No 9
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.83 E-value=2.2e-09 Score=72.85 Aligned_cols=39 Identities=41% Similarity=1.110 Sum_probs=32.7
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiC 240 (307)
||||++.+.+ ++++++|||+|+.+|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 7999986443 5688999999999999999997 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.75 E-value=7e-09 Score=96.73 Aligned_cols=54 Identities=19% Similarity=0.609 Sum_probs=42.0
Q ss_pred CCCCCCCcccccccccCcc----eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 192 GAMHHDCPVCCEYLFETRQ----DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~~----~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.+.+..||||+|.+.+... -.++++|||.||.+||.+|++. +.+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEeeE
Confidence 3456899999997654321 1245689999999999999984 6899999998763
No 11
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.75 E-value=6.9e-09 Score=72.26 Aligned_cols=39 Identities=38% Similarity=1.199 Sum_probs=28.9
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcC---CCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~---~~~CPiC 240 (307)
||||++. |. +++.|+|||+|+..||..|++.. .+.||+|
T Consensus 1 CpiC~~~-~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL-FK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh-hC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999995 54 47899999999999999988753 2579998
No 12
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.71 E-value=5.1e-09 Score=102.63 Aligned_cols=56 Identities=38% Similarity=0.820 Sum_probs=47.1
Q ss_pred CCCCCCCcccccccccCc---------ceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCccc-Cchh
Q 021794 192 GAMHHDCPVCCEYLFETR---------QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV-CDMS 248 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~---------~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~-~dm~ 248 (307)
...+..|.||+|.|+.++ ..+..|||||.+|.+|++.|+++ +.+|||||.++ .|+.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~~ 349 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQS 349 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCccccccC
Confidence 466889999999988776 34578999999999999999985 68999999994 4543
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.70 E-value=1e-08 Score=72.92 Aligned_cols=47 Identities=34% Similarity=0.982 Sum_probs=38.0
Q ss_pred CCCCcccccccccCcceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
+..|+||++. ...++++||||. |+..|+..|++ ...+||+||+++.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 3579999985 235788999999 99999999998 56899999998753
No 14
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.68 E-value=1.4e-08 Score=68.98 Aligned_cols=40 Identities=43% Similarity=1.116 Sum_probs=33.4
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHh-cCCCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~-~~~~~CPiC 240 (307)
||||++.+.. +..+++|||.|+..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 7999996332 446899999999999999998 567889998
No 15
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.64 E-value=2.4e-08 Score=64.32 Aligned_cols=39 Identities=44% Similarity=1.130 Sum_probs=33.2
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiC 240 (307)
|+||++. ...++.++|||.||..|+..|++....+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899985 34678899999999999999998556789987
No 16
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.62 E-value=6e-09 Score=81.81 Aligned_cols=51 Identities=24% Similarity=0.490 Sum_probs=40.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc--CCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~--~~~~CPiCrks~~ 245 (307)
++++.||-|. +....-++++..|.|.||..||.+|+.. ++-.||+||+.+.
T Consensus 29 ~Fdg~Cp~Ck--~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 29 PFDGCCPDCK--LPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccCCcCCCCc--CCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 5678899998 4555556666689999999999999965 3456999998764
No 17
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.59 E-value=2.6e-08 Score=70.04 Aligned_cols=40 Identities=38% Similarity=1.053 Sum_probs=24.5
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcC---CCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACP 238 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~---~~~CP 238 (307)
||||+| +.+...++++|+|||+|.++|+++|++.+ .++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 55556678899999999999999998853 56687
No 18
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.58 E-value=3.1e-08 Score=95.01 Aligned_cols=54 Identities=26% Similarity=0.663 Sum_probs=45.6
Q ss_pred CCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 191 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
|....-+|+|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+.
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 33445789999998 5667789999999999999999999865688999998764
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.57 E-value=5.2e-08 Score=67.90 Aligned_cols=44 Identities=32% Similarity=0.839 Sum_probs=37.0
Q ss_pred CCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 021794 197 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 242 (307)
Q Consensus 197 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 242 (307)
.|+||++.+ .....+.+++|||+|+..|+..+. .....||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999964 555678899999999999999998 34678999986
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.51 E-value=1e-07 Score=86.47 Aligned_cols=56 Identities=25% Similarity=0.623 Sum_probs=42.8
Q ss_pred ccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc---------------CCCCCCCCCcccCc
Q 021794 187 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------------HQYACPICSKSVCD 246 (307)
Q Consensus 187 H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~---------------~~~~CPiCrks~~d 246 (307)
.+-++...+..||||++. +. ++++++|||.||..||.+|+.. ...+||+||..+..
T Consensus 10 ~~~~~~~~~~~CpICld~-~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQ-VR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ceeccCCCccCCccCCCc-CC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 344444567899999995 33 4567899999999999999852 23579999998864
No 21
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.50 E-value=7.8e-08 Score=76.18 Aligned_cols=50 Identities=20% Similarity=0.436 Sum_probs=37.7
Q ss_pred CCCCcccccccccC-cceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFET-RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s-~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.+.||-|+-.+... .-+++...|.|.||.+||..||.. +..||++|+++.
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 45677776533222 234566789999999999999986 789999999875
No 22
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.31 E-value=2.8e-07 Score=92.13 Aligned_cols=81 Identities=27% Similarity=0.646 Sum_probs=66.0
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEE
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 275 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~Il 275 (307)
-.||||||.|..+...++...|.|+||-.|+..|.. .+||+||....+ + +. ..-+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~p-~---------------~v------e~~~ 230 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQSP-S---------------VV------ESSL 230 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcCc-c---------------hh------hhhh
Confidence 479999999999998899999999999999999963 689999964331 1 11 1346
Q ss_pred cCCCCCCccccceeeeccCC--CCCCccccc
Q 021794 276 CNDCGKTSNVQFHVLAQKCP--NCKSYNTRL 304 (307)
Q Consensus 276 CnDC~~~s~~~fH~lg~kC~--~C~SYNT~~ 304 (307)
|..|+...+. |+-+.|+ .||-|+-..
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchh
Confidence 9999998888 9999998 599998654
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.29 E-value=4.6e-07 Score=83.94 Aligned_cols=69 Identities=17% Similarity=0.425 Sum_probs=46.6
Q ss_pred ceeccccCCccccCCCCCCCCcccccccccC-----cceeEEcCCCCcccHHHHHHHHhcC-----CCCCCCCCcccCc
Q 021794 178 CYSMLLKNSHPCVEGAMHHDCPVCCEYLFET-----RQDVIVLPCGHTIHKNCLKEMREHH-----QYACPICSKSVCD 246 (307)
Q Consensus 178 C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s-----~~~v~~LpCGH~fH~~Cl~~wl~~~-----~~~CPiCrks~~d 246 (307)
++..-|.+-..-...+.+..|+||||.++.. +.-.++.+|+|.||..||..|.+.. ..+||+||..+..
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 3443333322333456688999999976542 1223556999999999999998742 2459999987753
No 24
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.24 E-value=1.2e-06 Score=64.03 Aligned_cols=45 Identities=20% Similarity=0.473 Sum_probs=38.1
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
..||||++. ++ .+++++|||+|.++||.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~-~~---~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEV-MK---DPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCc-CC---CCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999995 43 2577899999999999999986 678999998874
No 25
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=1.2e-06 Score=89.96 Aligned_cols=54 Identities=31% Similarity=0.660 Sum_probs=43.8
Q ss_pred CCCCCCCCcccccccccCcc-eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 191 EGAMHHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~-~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
....+..|+||+|.|..+.. .+..|||||.||..|+..|++. ..+||+||..+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLY 341 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhh
Confidence 34558899999998876422 2568999999999999999996 689999998443
No 26
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=2.5e-06 Score=76.62 Aligned_cols=48 Identities=25% Similarity=0.742 Sum_probs=38.6
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
-..|||||+. +. .+.++..+|||.|+.+||+..++. ...||+|+|.+.
T Consensus 131 ~~~CPiCl~~-~s-ek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VS-EKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hh-hccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 3789999996 33 223355899999999999999985 589999998664
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=8.1e-06 Score=71.76 Aligned_cols=44 Identities=39% Similarity=1.050 Sum_probs=37.4
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 242 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 242 (307)
.+..||||+++ |..+ ++|||||+|+..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHH-hhcC---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 46789999996 4432 8999999999999999887 5688999994
No 28
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=6.2e-06 Score=78.71 Aligned_cols=47 Identities=28% Similarity=0.718 Sum_probs=39.1
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
...|.+|||. +..+...||||.|+-.||.+|.+. ..-||+||..+..
T Consensus 239 ~~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLEN----RSNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecC----CCCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 3579999995 345678999999999999999984 5679999987754
No 29
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=97.84 E-value=1.3e-05 Score=57.57 Aligned_cols=43 Identities=28% Similarity=0.724 Sum_probs=33.6
Q ss_pred CCcccccccccCcceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCC
Q 021794 197 DCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICS 241 (307)
Q Consensus 197 ~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCr 241 (307)
.|-||++ +.+...+.++||. |.+|..|+.+|+... +.+||+|+
T Consensus 1 ~CrIC~~--~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3889997 3445566788995 999999999999653 45799995
No 30
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.82 E-value=1.3e-05 Score=79.93 Aligned_cols=46 Identities=24% Similarity=0.699 Sum_probs=38.7
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
...|+||++. +. .+++++|||.||..||..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~-~~---~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDF-FD---VPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchh-hh---CccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 5689999995 44 3457899999999999999975 568999998876
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.78 E-value=2.1e-05 Score=76.08 Aligned_cols=52 Identities=23% Similarity=0.568 Sum_probs=39.8
Q ss_pred CCCCcccccccccCccee-EEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 195 HHDCPVCCEYLFETRQDV-IVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v-~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
+..||||+...+.+..-. .+-+|||.|+..|++.++..+...||+|++++..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 457999998655554422 2337999999999999776667789999987763
No 32
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.9e-05 Score=73.40 Aligned_cols=50 Identities=28% Similarity=0.654 Sum_probs=38.7
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCrks~~d 246 (307)
....+|-||||. .+++++..|||.|+--||-+||... +..||+|+..+..
T Consensus 45 ~~~FdCNICLd~----akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL----AKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc----cCCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 446799999983 2345566699999999999999763 3458999987763
No 33
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=8.5e-06 Score=67.54 Aligned_cols=33 Identities=24% Similarity=0.509 Sum_probs=29.0
Q ss_pred eEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 212 VIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 212 v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+...-|.|.||..||..||++ +..||++.+.+.
T Consensus 76 VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW~ 108 (114)
T KOG2930|consen 76 VAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEWV 108 (114)
T ss_pred EEeeecchHHHHHHHHHHHhh-cCcCCCcCccee
Confidence 456689999999999999995 689999999775
No 34
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.65 E-value=9.9e-06 Score=62.17 Aligned_cols=51 Identities=27% Similarity=0.656 Sum_probs=23.4
Q ss_pred CCCCcccccccccCc-ceeEEc---CCCCcccHHHHHHHHhc---CC-------CCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETR-QDVIVL---PCGHTIHKNCLKEMREH---HQ-------YACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~-~~v~~L---pCGH~fH~~Cl~~wl~~---~~-------~~CPiCrks~~ 245 (307)
+.+|+||++++.+.. .+.++- .|+..||..||.+||.. .+ -+||.|++++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 468999998766333 233332 69999999999999863 11 24999998774
No 35
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=97.58 E-value=1.4e-05 Score=65.46 Aligned_cols=51 Identities=27% Similarity=0.763 Sum_probs=40.9
Q ss_pred CCccccc---CceeEcCccCCeecCCccccccccCcCcCCcCCcccCcccccccccccccCCc
Q 021794 72 GCQHYRR---RCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVQQVCVNCGV 131 (307)
Q Consensus 72 GC~HY~R---~Cki~aPCC~~~y~CR~CHde~~~~~~~~~~~~H~l~R~~v~ev~~~C~nCg~ 131 (307)
-|-||.. ...|+|-+|+++|+|-+||||. ++|++.+....+....++-||+
T Consensus 14 RC~Hyht~~Diialkc~~C~kyYaCy~CHdel---------~~Hpf~p~~~~~~~~~~iiCGv 67 (105)
T COG4357 14 RCLHYHTPLDIIALKCKCCQKYYACYHCHDEL---------EDHPFEPWGLQEFNPKAIICGV 67 (105)
T ss_pred eeeEecCccceEeeeechhhhhhhHHHHHhHH---------hcCCCccCChhhcCCccEEhhh
Confidence 5999998 7889999999999999999997 4699998776665444444443
No 36
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.54 E-value=0.00016 Score=55.52 Aligned_cols=48 Identities=23% Similarity=0.524 Sum_probs=36.6
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
+..|||+.+- +. +++++|+||+|-+.+|..|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~l-M~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGEL-MR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB--S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcH-hh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 4579999984 44 477899999999999999998767899999988764
No 37
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.42 E-value=8.2e-05 Score=75.78 Aligned_cols=49 Identities=24% Similarity=0.626 Sum_probs=36.8
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcC----CCCCCCCCcccCc
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH----QYACPICSKSVCD 246 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~----~~~CPiCrks~~d 246 (307)
++..|||||++ +. -+ ..+.|||.|+..||.+||... .-.||+|+..+..
T Consensus 185 t~~~CPICL~~-~~--~p-~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 185 TDMQCPICLEP-PS--VP-VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred cCCcCCcccCC-CC--cc-cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 37899999986 22 23 344599999999999977643 2459999987763
No 38
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=6.1e-05 Score=76.60 Aligned_cols=51 Identities=25% Similarity=0.706 Sum_probs=38.5
Q ss_pred CCCCcccccccccC-------------cceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFET-------------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s-------------~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
..+|+|||.++..- ++..++.||.|.||..|+.+|+...+..||+||.++.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 46899999765211 1124556999999999999999855567999998764
No 39
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.35 E-value=0.00013 Score=71.45 Aligned_cols=46 Identities=30% Similarity=0.823 Sum_probs=39.6
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
..|-||.|| |. .+++.||||+|+.-||..+|. .+..||.|+.++..
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTE 69 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhc-cCCCCCceecccch
Confidence 479999996 54 467889999999999999998 47899999988863
No 40
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.20 E-value=0.00016 Score=71.82 Aligned_cols=47 Identities=28% Similarity=0.644 Sum_probs=37.8
Q ss_pred CCCCcccccccccCcceeEEcC-CCCcccHHHHHHHHhcCC--CCCCCCCc
Q 021794 195 HHDCPVCCEYLFETRQDVIVLP-CGHTIHKNCLKEMREHHQ--YACPICSK 242 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~Lp-CGH~fH~~Cl~~wl~~~~--~~CPiCrk 242 (307)
...|.|| ++++.....+..+. |||+||..|+.+|+...- ..||+|+-
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence 4579999 55787777776664 999999999999998632 47999993
No 41
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00027 Score=66.99 Aligned_cols=47 Identities=28% Similarity=0.572 Sum_probs=37.3
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHH-HHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE-MREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~-wl~~~~~~CPiCrks~~ 245 (307)
+..|+||+|.. ..+...+|||.|+..||.. |.+.....||+||.-..
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 56799999853 3467889999999999999 87754334999997654
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.79 E-value=0.00053 Score=52.46 Aligned_cols=55 Identities=24% Similarity=0.619 Sum_probs=26.6
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC--chhHHHHHhHHH
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC--DMSKVWEKYDRE 257 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~--dm~~~~~~lD~e 257 (307)
..|++|.+.|.. ++.+..|.|.|+..|+.+-+. +.||+|+.+.. |+. ..+.||..
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~ 64 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSM 64 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhcc
Confidence 479999986443 566779999999999998764 45999998874 322 23445554
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.76 E-value=0.00094 Score=65.58 Aligned_cols=49 Identities=31% Similarity=0.811 Sum_probs=39.7
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
....+|.|||.. .++.++|||-|. ++..|.+...- .+.+|||||..+..
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 445689999974 446899999998 99999999753 35789999998763
No 44
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.69 E-value=0.00042 Score=51.70 Aligned_cols=50 Identities=26% Similarity=0.695 Sum_probs=38.4
Q ss_pred CCCCCcccccccccCcceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcccCch
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDM 247 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~dm 247 (307)
...+|.||+|.- .+.++.-|||. ++-+|-...++..+-.||+||.++.+.
T Consensus 6 ~~dECTICye~p----vdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dv 56 (62)
T KOG4172|consen 6 WSDECTICYEHP----VDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDV 56 (62)
T ss_pred cccceeeeccCc----chHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHH
Confidence 347899999852 23455689997 889998886665678899999988764
No 45
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.00067 Score=71.84 Aligned_cols=47 Identities=28% Similarity=0.710 Sum_probs=40.6
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
..||+|-.. ..+.++..|||.||..|++..+...+.+||.|+.+|+.
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 579999964 44577889999999999999988778899999999984
No 46
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0007 Score=66.59 Aligned_cols=82 Identities=22% Similarity=0.483 Sum_probs=53.3
Q ss_pred CCCCCCcccccccccCc---ceeEE-cCCCCcccHHHHHHHHhcCC------CCCCCCCcccCc--hhHHHHHhHHHHhc
Q 021794 193 AMHHDCPVCCEYLFETR---QDVIV-LPCGHTIHKNCLKEMREHHQ------YACPICSKSVCD--MSKVWEKYDREIAA 260 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~---~~v~~-LpCGH~fH~~Cl~~wl~~~~------~~CPiCrks~~d--m~~~~~~lD~eia~ 260 (307)
+.+..|-||||.+.... ....+ ++|.|.|+..|+..|.+..+ ..||+||..... .+..|-.-.+ +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 55789999999766533 11223 46999999999999985433 579999977653 2333532222 56
Q ss_pred CCCChhhhcCceeEEc
Q 021794 261 TPMPEAYLNKKVWILC 276 (307)
Q Consensus 261 ~pmPeey~~~~~~IlC 276 (307)
++++++|........|
T Consensus 237 ~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDC 252 (344)
T ss_pred cccHHHHHHHhhccch
Confidence 6677777666444333
No 47
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.55 E-value=0.00056 Score=67.28 Aligned_cols=48 Identities=23% Similarity=0.568 Sum_probs=40.4
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+..|||||+-|.. ...+.-|+|.|+.+||..-+..++..||.||+.+.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 4679999995444 34567899999999999988878889999999887
No 48
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.54 E-value=0.00072 Score=64.64 Aligned_cols=52 Identities=23% Similarity=0.553 Sum_probs=40.9
Q ss_pred CCCCCcccccccccCc------ceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 194 MHHDCPVCCEYLFETR------QDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~------~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
.++.|+||...+..+. +..-.|.|+|.||.-||.-|--. ...+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3678999988766654 24567899999999999999543 4578999997665
No 49
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.47 E-value=0.0021 Score=46.52 Aligned_cols=47 Identities=34% Similarity=0.699 Sum_probs=25.4
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCccc
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 244 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~ 244 (307)
||+|.|.|..++.....=+||+.+++.|+...+.....+||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999988554444334468999999999999875678999999864
No 50
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.42 E-value=0.0018 Score=62.57 Aligned_cols=46 Identities=26% Similarity=0.597 Sum_probs=38.0
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
-..|-||-+++. .+...+|||+|+.-||..+|. .+..||+||.+..
T Consensus 25 ~lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRIS----IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheee----cceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 357999998632 356779999999999999997 4799999997664
No 51
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.27 E-value=0.00079 Score=67.17 Aligned_cols=58 Identities=34% Similarity=0.713 Sum_probs=47.9
Q ss_pred CccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCccc
Q 021794 186 SHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSV 244 (307)
Q Consensus 186 ~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~ 244 (307)
.|.|++ +++..|-.|.|.+-...+....|||.|.||..|+.++|.. ...+||-||+-.
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr 415 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR 415 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence 477886 6789999999987777777788999999999999998864 346799999433
No 52
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.22 E-value=0.0037 Score=46.42 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=29.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-CCCCCCC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPI 239 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPi 239 (307)
.....|||-+.. +. ++++...|||+|-++.|.+|++. ....||+
T Consensus 9 ~~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345789999986 43 37788899999999999999943 4567998
No 53
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.00 E-value=0.0047 Score=69.69 Aligned_cols=74 Identities=27% Similarity=0.577 Sum_probs=54.9
Q ss_pred cCCcceeeccCCCcceeccccCCccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc---------CC
Q 021794 164 GGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQ 234 (307)
Q Consensus 164 G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~---------~~ 234 (307)
||.+|--||.-|-.|-.-.. ....++-|.||+-. -.+..+...|.|||.||.+|....|.. +-
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56688889998888754322 12347789999864 455667889999999999999876653 12
Q ss_pred CCCCCCCcccC
Q 021794 235 YACPICSKSVC 245 (307)
Q Consensus 235 ~~CPiCrks~~ 245 (307)
..||+|...+.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 46999998775
No 54
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.92 E-value=0.0038 Score=68.03 Aligned_cols=53 Identities=21% Similarity=0.570 Sum_probs=37.6
Q ss_pred CCCCCCcccccccc--cCccee-EEcCCCCcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLF--ETRQDV-IVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf--~s~~~v-~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
+...+||||..-|. +..-|. +-.-|.|-||..|+-+|+.+ ++.+||+||.++.
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 45789999986443 211122 22348899999999999976 4678999997664
No 55
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.0081 Score=57.60 Aligned_cols=53 Identities=26% Similarity=0.676 Sum_probs=41.5
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHh-cCCCCCCCCCcccCchh
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPICSKSVCDMS 248 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~-~~~~~CPiCrks~~dm~ 248 (307)
+....||+|.++ +.-|.+..+|||.|+--|+..-+. ..+++||.|+.+...+.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 446789999986 445667789999999999999443 23589999998887553
No 56
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.65 E-value=0.0035 Score=62.86 Aligned_cols=54 Identities=30% Similarity=0.765 Sum_probs=43.5
Q ss_pred cccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 188 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 188 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
-|.-+++=.-|-||-| +.+++.+=||||.++..|+..|-.. +...||.||-.+.
T Consensus 362 YceMgsTFeLCKICae----ndKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAE----NDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHccchHHHHHHhhc----cCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 3556677788999998 3567888899999999999999744 3678999996654
No 57
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.54 E-value=0.0046 Score=66.26 Aligned_cols=49 Identities=14% Similarity=0.365 Sum_probs=39.7
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+..||+|+.. +.........+|+|.||.+||..|-.. -.+||+||+.|.
T Consensus 123 ~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 123 ENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhh
Confidence 5689999975 444444456799999999999999874 589999998887
No 58
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.45 E-value=0.0088 Score=42.61 Aligned_cols=41 Identities=29% Similarity=0.752 Sum_probs=26.7
Q ss_pred CcccccccccCcceeEEcCCC-----CcccHHHHHHHHhc-CCCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~-~~~~CPiC 240 (307)
|-||++...++ +..+.||+ -..|.+||.+|+.. .+.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 56888753332 35677885 57899999999974 45679987
No 59
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.0082 Score=58.18 Aligned_cols=49 Identities=18% Similarity=0.419 Sum_probs=39.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.+..+|+||+...- -++.|+|+|.|+..||+--.+....+||+||.++.
T Consensus 5 ~~~~eC~IC~nt~n----~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGN----CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCC----cCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 45678999997522 24789999999999999855545677999999886
No 60
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=94.63 E-value=0.026 Score=54.49 Aligned_cols=49 Identities=20% Similarity=0.522 Sum_probs=40.1
Q ss_pred CCcccccccccCcceeEE-cCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 197 DCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 197 ~CPIClE~lf~s~~~v~~-LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.||+|.-+.+.+..-... =+|||.++..|+...+..+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 599998777766543322 2999999999999999888999999998775
No 61
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.034 Score=52.46 Aligned_cols=49 Identities=31% Similarity=0.756 Sum_probs=38.7
Q ss_pred CCCcccccccccCc---ceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 196 HDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 196 ~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
..|-||-++ |.+. ..+++|.|||+++..|+.+.+......||.||.+..
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~ 55 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTE 55 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCccc
Confidence 457788776 4443 335788999999999999999877777999999854
No 62
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=94.49 E-value=0.018 Score=45.68 Aligned_cols=33 Identities=36% Similarity=0.850 Sum_probs=27.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHH
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK 227 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~ 227 (307)
.....|+||...|.. ....+.||||.+|..|++
T Consensus 76 ~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 446789999998776 467888999999999975
No 63
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.42 E-value=0.048 Score=54.97 Aligned_cols=50 Identities=24% Similarity=0.744 Sum_probs=38.2
Q ss_pred CCCcccccccccCcce-eEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 196 HDCPVCCEYLFETRQD-VIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~-v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
..||||++.+-.+++- ++.|.|||.|=.+|++.||-. ....||.|.....
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 5799999877665544 466899999999999999942 2245999985443
No 64
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.98 E-value=0.023 Score=42.31 Aligned_cols=33 Identities=39% Similarity=0.785 Sum_probs=26.6
Q ss_pred eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 211 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 211 ~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.-.+|||||.+...|+.-+-- .-||+|.+.+..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY---NGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhhc---cCCCCCCCcccC
Confidence 456899999999999987632 359999998864
No 65
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.88 E-value=0.035 Score=50.60 Aligned_cols=31 Identities=29% Similarity=0.808 Sum_probs=25.2
Q ss_pred cCCCCcccHHHHHHHHhc-----CC-----CCCCCCCcccC
Q 021794 215 LPCGHTIHKNCLKEMREH-----HQ-----YACPICSKSVC 245 (307)
Q Consensus 215 LpCGH~fH~~Cl~~wl~~-----~~-----~~CPiCrks~~ 245 (307)
..||-.||+-|+.+||.. .+ -.||.|++++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999963 11 24999999885
No 66
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.78 E-value=0.023 Score=56.14 Aligned_cols=57 Identities=26% Similarity=0.604 Sum_probs=44.7
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHHH
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVW 251 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~ 251 (307)
++-||.|+|+|.-+.+....-|||-.+++-|+....+.-+-+||-||+...+-...|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 455999999987766666667899999999998876655678999999887644433
No 67
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=93.60 E-value=0.042 Score=54.80 Aligned_cols=49 Identities=29% Similarity=0.690 Sum_probs=39.6
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.+..||+|..-+- +++....|||.|+..|+..|+.. +..||.|+..+..
T Consensus 20 ~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 20 ENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQ 68 (391)
T ss_pred ccccCcccccccc---CCCCCCCCCCcccccccchhhcc-CcCCcccccccch
Confidence 3578999997533 24444789999999999999986 7899999987764
No 68
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.60 E-value=0.07 Score=53.68 Aligned_cols=49 Identities=29% Similarity=0.823 Sum_probs=39.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
..+..|.||+.-++ +++++||||+|+..||..-+. ...-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~----~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY----PPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC----CCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 45789999998544 356779999999999999776 35779999988874
No 69
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.31 E-value=0.027 Score=54.81 Aligned_cols=51 Identities=24% Similarity=0.580 Sum_probs=40.3
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc----------------------CCCCCCCCCcccCc
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----------------------HQYACPICSKSVCD 246 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~----------------------~~~~CPiCrks~~d 246 (307)
.+.|.|||= =|.+.....+.+|-|+||..||..+|.. ..-.||+||-.+.+
T Consensus 115 ~gqCvICLy-gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 115 NGQCVICLY-GFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCceEEEEE-eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 679999994 4777777888999999999999887741 12349999977763
No 70
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=93.29 E-value=0.041 Score=47.75 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=30.1
Q ss_pred CCCCcccccccccCcceeEEcCCC------CcccHHHHHHHH
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCG------HTIHKNCLKEMR 230 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCG------H~fH~~Cl~~wl 230 (307)
..+|.||++.+-. .+.++.++|| |.||.+|++.|-
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 4689999998777 5678889997 889999999993
No 71
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.84 E-value=0.064 Score=53.08 Aligned_cols=47 Identities=26% Similarity=0.639 Sum_probs=35.1
Q ss_pred CCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 191 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+.+...+|.||++. ....+.+||||.-+ |..-... ..+||+||..+.
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 45678899999984 33478999999966 6655533 356999998764
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.65 E-value=0.13 Score=51.83 Aligned_cols=46 Identities=30% Similarity=0.551 Sum_probs=36.3
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-------CCCCCCCCC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICS 241 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-------~~~~CPiCr 241 (307)
-..|-||++. +....-...|||+|+|++.|+..|... ...+||-+.
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 5789999985 555567788999999999999998742 346698665
No 73
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.77 E-value=0.16 Score=47.72 Aligned_cols=51 Identities=25% Similarity=0.640 Sum_probs=39.5
Q ss_pred CCCCCCCcccccccccCcceeEE-cCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 192 GAMHHDCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~~~v~~-LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
......|||....| +.....+. .||||+|-..+|.+.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 34567899999865 44445555 4999999999999983 2467999999986
No 74
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.73 E-value=0.028 Score=54.48 Aligned_cols=55 Identities=27% Similarity=0.690 Sum_probs=37.7
Q ss_pred cCCccccCCCC---CCCCcccccccccCcceeEEcCCCCcc-cHHHHHHHHhcCCCCCCCCCcccCch
Q 021794 184 KNSHPCVEGAM---HHDCPVCCEYLFETRQDVIVLPCGHTI-HKNCLKEMREHHQYACPICSKSVCDM 247 (307)
Q Consensus 184 ~~~H~CiE~~~---~~~CPIClE~lf~s~~~v~~LpCGH~f-H~~Cl~~wl~~~~~~CPiCrks~~dm 247 (307)
+++|.+-.... +..|.||++ .+.+-++|+|||.. +.+|-+.+ ..|||||+-+...
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmD----aP~DCvfLeCGHmVtCt~CGkrm-----~eCPICRqyi~rv 344 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMD----APRDCVFLECGHMVTCTKCGKRM-----NECPICRQYIVRV 344 (350)
T ss_pred hcccccccccchhHHHHHHHHhc----CCcceEEeecCcEEeehhhcccc-----ccCchHHHHHHHH
Confidence 34454443333 789999998 45678999999974 55555444 2699999866543
No 75
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=91.54 E-value=0.22 Score=48.32 Aligned_cols=62 Identities=24% Similarity=0.566 Sum_probs=45.3
Q ss_pred CCCCcccccccccCcceeEEcCC--CCcccHHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHhcCCCChhh
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPC--GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAY 267 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpC--GH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey 267 (307)
=.+||||.++|.. -++.| ||..+..|-.+. ...||.||.++++... +.++..+++...|=.|
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~ 111 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKN 111 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceecccc
Confidence 3589999997543 24556 899999998864 3679999999996532 4466777777666444
No 76
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.37 E-value=0.15 Score=51.08 Aligned_cols=48 Identities=29% Similarity=0.647 Sum_probs=40.0
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCC--CCCCCCCccc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ--YACPICSKSV 244 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~--~~CPiCrks~ 244 (307)
..|||=.|- -+...|++.|.|||++-++-++.+.+.+. ++||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 479998873 55567889999999999999999988766 8899997543
No 77
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.04 E-value=0.31 Score=46.08 Aligned_cols=52 Identities=31% Similarity=0.662 Sum_probs=40.7
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-------CCCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-------~~~~CPiCrks~~d 246 (307)
....+|..|.-.|- ++ +.+-|.|=|.||-.|+++|-.. ..|+||-|+..+..
T Consensus 48 DY~pNC~LC~t~La-~g-dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLA-SG-DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccc-cC-cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 34679999987643 34 4567889999999999999753 35899999998873
No 78
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.67 E-value=0.17 Score=49.15 Aligned_cols=49 Identities=22% Similarity=0.610 Sum_probs=39.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.....|-||.+++. .+++..|||+|+..|...-++. ...|++|.+.+-.
T Consensus 239 ~~Pf~c~icr~~f~----~pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 239 LLPFKCFICRKYFY----RPVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHG 287 (313)
T ss_pred cCCccccccccccc----cchhhcCCceeehhhhcccccc-CCcceeccccccc
Confidence 34567999999743 3678899999999999887763 4789999998864
No 79
>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=90.43 E-value=0.19 Score=42.01 Aligned_cols=35 Identities=23% Similarity=0.601 Sum_probs=28.1
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~~ 307 (307)
.+...|++|+.......+ ...||.|||+++++++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAG 102 (115)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecC
Confidence 567899999987766432 35799999999998876
No 80
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.77 E-value=0.24 Score=42.52 Aligned_cols=37 Identities=27% Similarity=0.734 Sum_probs=27.5
Q ss_pred ceeEEcCCCCCCcccc-------------cee------eeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQ-------------FHV------LAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~-------------fH~------lg~kC~~C~SYNT~~~~~ 307 (307)
.....|.+|+...... +|+ ...+|+.|||++.++++|
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecC
Confidence 3678999999766443 222 236899999999998775
No 81
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.62 E-value=0.34 Score=48.32 Aligned_cols=66 Identities=23% Similarity=0.450 Sum_probs=46.2
Q ss_pred CcceeccccCCccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 176 RCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 176 ~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
+.|...+|.++.+=..+..+..|.||.+. ..-+.++||||.++-.|......- .+-.||+||..+.
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred ccccCCccccccccccccccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 55666565554443445567899999984 335678999999999998775321 2456999997765
No 82
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=89.36 E-value=0.22 Score=46.29 Aligned_cols=59 Identities=20% Similarity=0.459 Sum_probs=41.8
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHH
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREI 258 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~~~lD~ei 258 (307)
...|-||.++ +.| +++..|||.|+..|+-.-.+. ...|-+|.+..--.-..-..++..+
T Consensus 196 PF~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t~G~f~V~~d~~kmL 254 (259)
T COG5152 196 PFLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQK-GDECGVCGKATYGRFWVVSDLQKML 254 (259)
T ss_pred ceeehhchhh-ccc---hhhhhcchhHHHHHHHHHhcc-CCcceecchhhccceeHHhhHHHHH
Confidence 4589999987 553 567789999999998875553 4789999987764322333444443
No 83
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.26 E-value=0.27 Score=41.29 Aligned_cols=36 Identities=31% Similarity=0.624 Sum_probs=28.3
Q ss_pred CceeEEcCCCCCCcccc-ceeeeccCCCCCCccccccCC
Q 021794 270 KKVWILCNDCGKTSNVQ-FHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 270 ~~~~IlCnDC~~~s~~~-fH~lg~kC~~C~SYNT~~~~~ 307 (307)
..+...|++|+..+... +++ .+||.|||++...++|
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQG 104 (117)
T ss_pred cCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecC
Confidence 35678999999877664 333 4799999999998875
No 84
>PHA02862 5L protein; Provisional
Probab=89.22 E-value=0.28 Score=43.38 Aligned_cols=46 Identities=17% Similarity=0.471 Sum_probs=33.6
Q ss_pred CCCCcccccccccCcceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCrks~~ 245 (307)
...|=||.+. - .+. .-||. -..|++|+.+|++.. +..||+|+.++.
T Consensus 2 ~diCWIC~~~-~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV-C--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc-C--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4678899874 1 122 35774 569999999999763 456999998775
No 85
>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=88.39 E-value=0.48 Score=42.33 Aligned_cols=33 Identities=33% Similarity=0.893 Sum_probs=23.6
Q ss_pred CCCCcccccccccCcceeEEcCCC-C------------cccHHHHHHHHh
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCG-H------------TIHKNCLKEMRE 231 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCG-H------------~fH~~Cl~~wl~ 231 (307)
+..||||||. +-..++|-|. | .-|..||+++-+
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4679999995 2345667673 2 368999999864
No 86
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=88.34 E-value=0.2 Score=52.24 Aligned_cols=54 Identities=26% Similarity=0.571 Sum_probs=43.3
Q ss_pred cccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc----CCCCCCCCCcccC
Q 021794 188 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----HQYACPICSKSVC 245 (307)
Q Consensus 188 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~----~~~~CPiCrks~~ 245 (307)
.=.|+..+..|-+|-+. .+++..-.|.|.|++-|+.+|+.. .+.+||+|...+.
T Consensus 529 ~~~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CCccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 34577888999999985 235677889999999999998753 4578999998775
No 87
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=88.31 E-value=0.46 Score=42.49 Aligned_cols=47 Identities=28% Similarity=0.617 Sum_probs=33.8
Q ss_pred CCCCCcccccccccCcceeEEcCCC--C---cccHHHHHHHHhcC-CCCCCCCCcccC
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCG--H---TIHKNCLKEMREHH-QYACPICSKSVC 245 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCG--H---~fH~~Cl~~wl~~~-~~~CPiCrks~~ 245 (307)
++..|-||.+.- + ...-||. . ..|++|++.|+... ..+||+|+..+.
T Consensus 7 ~~~~CRIC~~~~---~--~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY---D--VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCCC---C--CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 466899998751 1 1234765 3 56999999999763 467999997764
No 88
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.22 E-value=0.35 Score=52.71 Aligned_cols=43 Identities=28% Similarity=0.710 Sum_probs=32.2
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
..|..|--.|- -|.+...|||.||++|+. .....||-|+-...
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 36888875433 366777899999999999 24578999998443
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.09 E-value=0.24 Score=37.44 Aligned_cols=32 Identities=38% Similarity=0.949 Sum_probs=22.4
Q ss_pred cccccccCCcc-cceeecCccccccCCCCCCccccCCCCc
Q 021794 122 VQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 122 v~~~C~nCg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
+...|.|||.. .. -|.+|+-+. ..|.|++||+
T Consensus 24 ~~F~CPnCG~~~I~--RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIY--RCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEe--echhHHhcC-----CceECCCCCC
Confidence 56778888875 43 388887664 4688888885
No 90
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=88.06 E-value=0.35 Score=40.39 Aligned_cols=35 Identities=26% Similarity=0.685 Sum_probs=27.2
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~~ 307 (307)
.....|++|+........ ...||.|||++...++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDTG 102 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEccC
Confidence 467899999987766422 23599999999998876
No 91
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.70 E-value=0.39 Score=40.17 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=27.5
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~~ 307 (307)
.....|++|+......-+. ...||.|||++++.++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVAD 103 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEccC
Confidence 4678999999876654322 14699999999998876
No 92
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.69 E-value=0.57 Score=44.83 Aligned_cols=54 Identities=26% Similarity=0.507 Sum_probs=43.6
Q ss_pred CCCCCCCcccccccccCcceeEEc-CCCCcccHHHHHHHHhcCCCCCCCCCcccCch
Q 021794 192 GAMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVCDM 247 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~~~v~~L-pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm 247 (307)
.+....||||.+.|.. ..+..+| ||||++..+|..+++.. .-.||+|.+++.+.
T Consensus 218 ~s~ryiCpvtrd~LtN-t~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTN-TTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDR 272 (303)
T ss_pred hccceecccchhhhcC-ccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCccc
Confidence 3456789999997554 5556666 99999999999999974 57899999998863
No 93
>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=87.31 E-value=0.4 Score=33.59 Aligned_cols=42 Identities=29% Similarity=0.698 Sum_probs=20.1
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcCC-CCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ-YACPIC 240 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~-~~CPiC 240 (307)
|.+|.+ +.+-+..-....|+=.+|..|+..|+++.+ .+||.|
T Consensus 1 C~~C~~-iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKE-IVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-S-B-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccch-hHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 556666 333222111224778899999999987643 369987
No 94
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=87.17 E-value=0.26 Score=35.90 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=22.9
Q ss_pred EcCCC-CcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 214 VLPCG-HTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 214 ~LpCG-H~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.+.|. |+++..|+..+++. +..||||.+++..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt 47 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT 47 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence 56786 99999999999985 6899999988753
No 95
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=87.00 E-value=0.12 Score=40.33 Aligned_cols=65 Identities=26% Similarity=0.542 Sum_probs=37.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEE
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 275 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~Il 275 (307)
..||.|...|-... ||+.+..|-..+... ..||-|..++..+. +-..+..+
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~~--a~CPdC~~~Le~Lk-------------------ACGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKKE--AFCPDCGQPLEVLK-------------------ACGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEEE--EE-TTT-SB-EEEE-------------------ETTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECccccccceec--ccCCCcccHHHHHH-------------------Hhccccee
Confidence 47999998643321 888999998887653 67999998876432 12247899
Q ss_pred cCCCCC---Ccccccee
Q 021794 276 CNDCGK---TSNVQFHV 289 (307)
Q Consensus 276 CnDC~~---~s~~~fH~ 289 (307)
||.|.+ ++.|.|.+
T Consensus 53 C~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 53 CNHCHGLISKKRVRFEF 69 (70)
T ss_dssp -TTTT-EE-TTTSEEEE
T ss_pred eccCCceeecceEEEEe
Confidence 999985 55665543
No 96
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=86.68 E-value=0.18 Score=49.44 Aligned_cols=49 Identities=29% Similarity=0.667 Sum_probs=39.6
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
..+..|++|..+|-+ +..+.-|=|+|++.||.++|.. ...||.|.-.+.
T Consensus 13 n~~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeec---chhHHHHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence 345689999998765 3345679999999999999986 688999997665
No 97
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=86.01 E-value=0.27 Score=40.92 Aligned_cols=35 Identities=26% Similarity=0.552 Sum_probs=24.8
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~~ 307 (307)
.....|++|+..+....+. ..||.|+|++.++++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G 102 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISG 102 (113)
T ss_dssp --EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEES
T ss_pred CCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccC
Confidence 4678999999998776553 6799999999888765
No 98
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.65 E-value=0.33 Score=51.62 Aligned_cols=43 Identities=28% Similarity=0.718 Sum_probs=35.9
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 242 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 242 (307)
..|+||+..++.++..++.|-|||++++.|++.... .+|| |..
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn---~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN---ASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh---ccCC-CCc
Confidence 479999887888888889999999999999998743 5788 553
No 99
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=84.68 E-value=0.35 Score=45.52 Aligned_cols=37 Identities=30% Similarity=0.737 Sum_probs=28.0
Q ss_pred ccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 206 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 206 f~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+.+..+..++.|+|.|+..|...-.. ..||+|++++.
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~~---~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASSP---DVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCCc---cccccccceee
Confidence 44444556779999999999886432 38999999965
No 100
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=83.41 E-value=0.76 Score=49.82 Aligned_cols=42 Identities=24% Similarity=0.521 Sum_probs=30.5
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI 239 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPi 239 (307)
...|.||--.+. +....-+.|||.+|..|+.+|++.+ ..||.
T Consensus 1028 ~~~C~~C~l~V~--gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVR--GSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred eeeeeeEeeEee--ccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 445888874333 3344567899999999999999864 67873
No 101
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=82.96 E-value=0.42 Score=45.60 Aligned_cols=51 Identities=25% Similarity=0.621 Sum_probs=41.1
Q ss_pred CCCCcccccccccCcceeEEc-C-CCCcccHHHHHHHHhcCCCCCC--CCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVL-P-CGHTIHKNCLKEMREHHQYACP--ICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~L-p-CGH~fH~~Cl~~wl~~~~~~CP--iCrks~~ 245 (307)
+..||||..+.+.+++-..++ | |=|.++..|.+..++.+.-.|| -|.+-+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 558999998888877543333 6 9999999999999988888899 8886554
No 102
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.69 E-value=0.83 Score=44.87 Aligned_cols=44 Identities=30% Similarity=0.763 Sum_probs=34.6
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 242 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 242 (307)
..||.|.- |.. .++.+--|||.|+.+||..-|....+.||.|.+
T Consensus 275 LkCplc~~-Llr--np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHC-LLR--NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhh-hhh--CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 68999986 333 345555689999999999866656799999986
No 103
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.59 E-value=0.93 Score=38.42 Aligned_cols=36 Identities=31% Similarity=0.608 Sum_probs=26.0
Q ss_pred ceeEEcCCCCCCcccc-c---ee-eeccCCCCCCccccccCC
Q 021794 271 KVWILCNDCGKTSNVQ-F---HV-LAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~-f---H~-lg~kC~~C~SYNT~~~~~ 307 (307)
.....| +|+..+... + |+ ....||.|||++.+.++|
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 567899 999875432 1 11 235799999999998875
No 104
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.82 E-value=0.98 Score=45.27 Aligned_cols=51 Identities=22% Similarity=0.544 Sum_probs=41.1
Q ss_pred CCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 191 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
..+.+..||||.-. +...+.-||||.-+..||.+.+.. ...|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhc-CCeeeEecceeee
Confidence 44668899999853 234567899999999999998874 5789999998876
No 105
>PHA03096 p28-like protein; Provisional
Probab=80.47 E-value=0.95 Score=43.71 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=31.9
Q ss_pred CCCcccccccccCc---ceeEEc-CCCCcccHHHHHHHHhcC--CCCCCCCCc
Q 021794 196 HDCPVCCEYLFETR---QDVIVL-PCGHTIHKNCLKEMREHH--QYACPICSK 242 (307)
Q Consensus 196 ~~CPIClE~lf~s~---~~v~~L-pCGH~fH~~Cl~~wl~~~--~~~CPiCrk 242 (307)
-.|.||+|...... .....| .|.|.|+..|+..|.... ..+||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46999998765431 122345 699999999999998653 234666653
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.29 E-value=0.8 Score=34.76 Aligned_cols=33 Identities=36% Similarity=0.960 Sum_probs=22.3
Q ss_pred cccccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 122 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 122 v~~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
+...|.|||..+ =|-|.+|+.+.+ +|-|++||+
T Consensus 26 v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 567777787443 356777776643 688888875
No 107
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=78.65 E-value=1.6 Score=36.98 Aligned_cols=36 Identities=31% Similarity=0.632 Sum_probs=29.1
Q ss_pred CceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021794 270 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 307 (307)
Q Consensus 270 ~~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~~ 307 (307)
..+.+.|-+|+......-|.+. ||.|+|-|.++++|
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G 102 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGG 102 (115)
T ss_pred eccEEEeccCCCeecchhheeE--CCCCCCCceEEecC
Confidence 3578899999887766666554 99999999999875
No 108
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.88 E-value=1.2 Score=48.96 Aligned_cols=35 Identities=31% Similarity=0.737 Sum_probs=28.4
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHh
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 231 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~ 231 (307)
...|-+|.-.|+. ++-.+.||||.||+.|+.+-..
T Consensus 817 ~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 817 QDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 5689999976543 4778889999999999998654
No 109
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=75.17 E-value=1.6 Score=47.80 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=34.8
Q ss_pred CCCCcccccccccCcceeEEcC---CCCcccHHHHHHHHhc------CCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREH------HQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Cl~~wl~~------~~~~CPiCrks~~ 245 (307)
..+|.||.|.+..+. -++. |=|.||..||.+|... ...+||-|+....
T Consensus 191 ~yeCmIC~e~I~~t~---~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 191 KYECMICTERIKRTA---PVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred ceEEEEeeeeccccC---CceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 568999999765532 2444 5599999999999753 2357999994443
No 110
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=74.94 E-value=1.5 Score=46.97 Aligned_cols=44 Identities=30% Similarity=0.896 Sum_probs=35.2
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCC-CCCCCCccc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQY-ACPICSKSV 244 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~-~CPiCrks~ 244 (307)
..|+||++ .+.....+|||.|+.+|+.+.+..... .||+||..+
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 78999998 235677899999999999998765433 599999644
No 111
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.04 E-value=2.3 Score=42.06 Aligned_cols=45 Identities=33% Similarity=0.754 Sum_probs=37.4
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCC
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICS 241 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCr 241 (307)
..|||=.| +-+...+++.|.|||.+=.+-+...-+.+ +++||.|-
T Consensus 337 FiCPVlKe-~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKE-LCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHh-hhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 36999887 56667789999999999999999987653 47899996
No 112
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.96 E-value=3.5 Score=30.68 Aligned_cols=36 Identities=25% Similarity=0.628 Sum_probs=26.2
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHH
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 229 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~w 229 (307)
+...|++|.+.|....+.++---||=.+|+.|....
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 456899999975544443344569999999997653
No 113
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=73.92 E-value=2.2 Score=37.26 Aligned_cols=48 Identities=27% Similarity=0.674 Sum_probs=35.0
Q ss_pred CCCcccccccccCcceeEEc-C---CCCcccHHHHHHHHhcC--CCCCCCCCcccCch
Q 021794 196 HDCPVCCEYLFETRQDVIVL-P---CGHTIHKNCLKEMREHH--QYACPICSKSVCDM 247 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~L-p---CGH~fH~~Cl~~wl~~~--~~~CPiCrks~~dm 247 (307)
-.|-||.|. |. +.+.| | ||-.++..|....++.. ...||+|+.|+-..
T Consensus 81 YeCnIC~et---S~-ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKET---SA-EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccc---cc-hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 468888874 22 23455 2 89999999999976653 35799999998653
No 114
>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=73.49 E-value=4.3 Score=29.20 Aligned_cols=42 Identities=29% Similarity=0.672 Sum_probs=19.7
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHHH--HHHh----cCCCCCCCCCcc
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK--EMRE----HHQYACPICSKS 243 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~--~wl~----~~~~~CPiCrks 243 (307)
..|||-...|.. +++...|.|. +|++ .||. .....||+|+++
T Consensus 3 L~CPls~~~i~~---P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRI---PVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SS---EEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEe---CccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 368888876544 7788899987 3433 2443 245789999874
No 115
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=71.88 E-value=2.1 Score=44.04 Aligned_cols=33 Identities=30% Similarity=0.926 Sum_probs=27.9
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHh
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 231 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~ 231 (307)
+..||||.. +|. ++++|||||.+++.|....+.
T Consensus 4 elkc~vc~~-f~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGS-FYR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehh-hcc---CceEeecccHHHHHHHHhhcc
Confidence 678999997 465 578999999999999998664
No 116
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.87 E-value=2.4 Score=42.43 Aligned_cols=50 Identities=32% Similarity=0.677 Sum_probs=33.7
Q ss_pred CCCCcccc-cccccCcceeEEcCCCCcccHHHHHHHHhc-----CCCCCC--CCCcccC
Q 021794 195 HHDCPVCC-EYLFETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACP--ICSKSVC 245 (307)
Q Consensus 195 ~~~CPICl-E~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-----~~~~CP--iCrks~~ 245 (307)
...|.||+ ++ ........++.|+|.|+.+|+.+++.. ...+|| .|...+.
T Consensus 146 ~~~C~iC~~e~-~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~ 203 (384)
T KOG1812|consen 146 KEECGICFVED-PEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLT 203 (384)
T ss_pred cccCccCcccc-ccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCC
Confidence 56899999 54 333233337789999999999998873 235575 3444443
No 117
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.39 E-value=3.9 Score=39.41 Aligned_cols=55 Identities=24% Similarity=0.573 Sum_probs=37.6
Q ss_pred CCCCCCCCcccccccccCcceeEEcCC---C--CcccHHHHHHHHhcC-------CCCCCCCCcccC
Q 021794 191 EGAMHHDCPVCCEYLFETRQDVIVLPC---G--HTIHKNCLKEMREHH-------QYACPICSKSVC 245 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~~v~~LpC---G--H~fH~~Cl~~wl~~~-------~~~CPiCrks~~ 245 (307)
+...+-.|=||+..-.+.+...-+=|| | |-.|+.|+..|+... .-.||.|+....
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 345677899999742222222234487 3 889999999999642 246999997664
No 118
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=62.66 E-value=5.8 Score=39.21 Aligned_cols=53 Identities=28% Similarity=0.600 Sum_probs=40.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
+-...||||-+++..........|||+.++..|+..-.. ...+||.||++...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 335789999997644444444557899999999999876 46899999987763
No 119
>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=62.21 E-value=4.6 Score=33.75 Aligned_cols=25 Identities=36% Similarity=0.971 Sum_probs=18.3
Q ss_pred cccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 124 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
.+|.+||+ ||| |.+|.+-.|++||.
T Consensus 10 R~Cp~CG~----------kFY--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 10 RTCPSCGA----------KFY--DLNKDPIVCPKCGT 34 (108)
T ss_pred ccCCCCcc----------hhc--cCCCCCccCCCCCC
Confidence 45777776 557 45788888998885
No 120
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=61.98 E-value=5.4 Score=38.58 Aligned_cols=88 Identities=26% Similarity=0.574 Sum_probs=60.0
Q ss_pred CcccceeecCcc-ccccCCC---CCCccccCCCCcccccCCcceeeccCCCcceec--ccc---CCccccCCCCCCCCcc
Q 021794 130 GVCMGEYFCESC-KLFDDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM--LLK---NSHPCVEGAMHHDCPV 200 (307)
Q Consensus 130 g~~f~~YfC~~C-kl~ddd~---~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~--~l~---~~H~CiE~~~~~~CPI 200 (307)
...-++|-|..| |-|.... .-+|+||+- .-..-|+|..||-=|.. .|+ .+|. ....|+|
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH~-----l~c~C~i 192 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGI 192 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhccC-----CCccccc
Confidence 566788999999 7775543 238999842 12578999999988843 222 3343 4678999
Q ss_pred cccccccCcceeEEcCCCCcccHHHHHHHHhc---------CCCCCCCCCcccCchhH
Q 021794 201 CCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQYACPICSKSVCDMSK 249 (307)
Q Consensus 201 ClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~---------~~~~CPiCrks~~dm~~ 249 (307)
|.-. |.. +||.+ .-|.||.|+|.|.|.+.
T Consensus 193 CGKa-FSR-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 193 CGKA-FSR-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred cccc-ccc-------------------hHHhhcccccccCCCCccCCcccchhcchHH
Confidence 9873 542 25532 24789999999999754
No 121
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=61.26 E-value=6.5 Score=25.23 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=14.1
Q ss_pred CCCcccccCCcc-eeeccCCC
Q 021794 157 GCGICRIGGCDN-FFHCNKCR 176 (307)
Q Consensus 157 ~CgiCR~G~~~~-ffHC~~C~ 176 (307)
.|++||.-.... +|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 477776655444 88888887
No 122
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.39 E-value=0.87 Score=45.99 Aligned_cols=52 Identities=19% Similarity=0.418 Sum_probs=43.7
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
.-..+.||.+.+...-+....+-|||.+|.++|.+||.. ...+|.|++.+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 345799999988776566778899999999999999985 6789999988863
No 123
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.63 E-value=3.9 Score=44.63 Aligned_cols=45 Identities=36% Similarity=0.680 Sum_probs=31.4
Q ss_pred CCCCcccccccccCc---ceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 021794 195 HHDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICS 241 (307)
Q Consensus 195 ~~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 241 (307)
++.|.-|.+....++ ..++++.|||.||..|+......+ .|-+|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~--~~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN--ACNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc--ccChhh
Confidence 346677776655444 467899999999999999865533 265554
No 124
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=56.49 E-value=8.3 Score=32.96 Aligned_cols=48 Identities=21% Similarity=0.444 Sum_probs=37.6
Q ss_pred CCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcceecc
Q 021794 129 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 182 (307)
Q Consensus 129 Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~ 182 (307)
.+......+|.+|+.+-- ...+||..||.|..+ --.||.-=|.|+...
T Consensus 42 ~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLR---FDHHCPWLGNCIGRR 89 (174)
T ss_pred cccCCCCEECcccCCcCC---Ccceecccccccccc---ccccchhhccccccc
Confidence 557888899999999832 358899999999884 446888888887643
No 125
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=55.90 E-value=5.4 Score=38.61 Aligned_cols=52 Identities=25% Similarity=0.664 Sum_probs=34.2
Q ss_pred CCeecCCccccccccCcCcCCcCCcccCcccccccccccccCCcccceeecCccccc
Q 021794 88 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVQQVCVNCGVCMGEYFCESCKLF 144 (307)
Q Consensus 88 ~~~y~CR~CHde~~~~~~~~~~~~H~l~R~~v~ev~~~C~nCg~~f~~YfC~~Ckl~ 144 (307)
|++|.|.+|++-.-++ -.-.|.-.-.-.+.-...|.+|++ +|.|.|..||.-
T Consensus 140 Grif~CsfC~~flCED----DQFEHQAsCQvLe~E~~KC~SCNr-lGq~sCLRCK~c 191 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCED----DQFEHQASCQVLESETFKCQSCNR-LGQYSCLRCKIC 191 (314)
T ss_pred CeEEEeecCCCeeecc----chhhhhhhhhhhhccccccccccc-ccchhhhheeee
Confidence 5699999999876432 112344333222335677999986 899999999863
No 126
>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 PF14353 CpXC: CpXC protein
Probab=54.76 E-value=2.5 Score=35.24 Aligned_cols=56 Identities=16% Similarity=0.390 Sum_probs=29.8
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEEcCCCCCCccccceeeec
Q 021794 235 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQ 292 (307)
Q Consensus 235 ~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s~~~fH~lg~ 292 (307)
.+||.|+..+... .|..++....+.-...-..+..-.+-|..|+.+..+.+=+|++
T Consensus 2 itCP~C~~~~~~~--v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFE--VWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEE--EEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 5799999887621 2222221000000001112334578899999988777666554
No 128
>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=54.60 E-value=9.5 Score=26.88 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=19.7
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCccc
Q 021794 273 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNT 302 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH~---lg~kC~~C~SYNT 302 (307)
...|.+|+...++-..+ ....|+.|||-+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKL 37 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCce
Confidence 45788888866653221 1237999999776
No 129
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.80 E-value=11 Score=42.57 Aligned_cols=49 Identities=27% Similarity=0.489 Sum_probs=36.7
Q ss_pred cccccccCCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcce
Q 021794 122 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCY 179 (307)
Q Consensus 122 v~~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~ 179 (307)
....|.+||.....-+|..|.=. .+.+|.|+.||.-..+ ..|.+||.=.
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~~-----y~CPKCG~El 673 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVEE-----DECEKCGREP 673 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCCC-----CcCCCCCCCC
Confidence 34579999999888889999644 5688999999665442 4588887644
No 130
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.18 E-value=11 Score=26.27 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=19.4
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCCccc
Q 021794 273 WILCNDCGKTSNVQFHVLAQKCPNCKSYNT 302 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT 302 (307)
...|.+|++.....-.....+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467888887654433333678888887543
No 131
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=52.72 E-value=8.4 Score=35.93 Aligned_cols=51 Identities=24% Similarity=0.523 Sum_probs=37.0
Q ss_pred CCCCcccccccccCcceeEEcCCC-----CcccHHHHHHHHhc-CCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~-~~~~CPiCrks~~ 245 (307)
+..|-||.+....+.......||. ...|+.|+..|+.. ++..|.+|...+.
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 367999998654432224566873 77899999999874 4577999997655
No 132
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.18 E-value=11 Score=30.31 Aligned_cols=30 Identities=30% Similarity=0.565 Sum_probs=19.3
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHhcC--CCChhhh
Q 021794 235 YACPICSKSVCDMSKVWEKYDREIAAT--PMPEAYL 268 (307)
Q Consensus 235 ~~CPiCrks~~dm~~~~~~lD~eia~~--pmPeey~ 268 (307)
..||-||..++|... ||.+|+.. |-|.+|.
T Consensus 22 D~CPrCrGVWLDrGE----LdKli~r~r~pqpa~ys 53 (88)
T COG3809 22 DYCPRCRGVWLDRGE----LDKLIERSRYPQPAEYS 53 (88)
T ss_pred eeCCccccEeecchh----HHHHHHHhcCCCCcccC
Confidence 469999999999754 44444433 3444443
No 133
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=52.00 E-value=1.8 Score=44.19 Aligned_cols=83 Identities=23% Similarity=0.571 Sum_probs=45.4
Q ss_pred cccccccCCcccceeecCccccccCCCCCCccc--cCCCCcccccC-CcceeeccC---CCcceeccccCCccccCCCCC
Q 021794 122 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYH--CDGCGICRIGG-CDNFFHCNK---CRCCYSMLLKNSHPCVEGAMH 195 (307)
Q Consensus 122 v~~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yH--C~~CgiCR~G~-~~~ffHC~~---C~~C~s~~l~~~H~CiE~~~~ 195 (307)
....|+.||+....-- .-| ...+++|| |=.|++||.-. +..||.=+. |--||-.+|
T Consensus 273 ~~~iC~~C~K~V~g~~-~ac-----~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl------------ 334 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQG-LAV-----EAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL------------ 334 (468)
T ss_pred hhhhhhhcCCcccCcc-hHH-----HHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH------------
Confidence 5558888887642210 000 13568898 77888888775 455655433 333443333
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHHH
Q 021794 196 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCL 226 (307)
Q Consensus 196 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl 226 (307)
..|..|-+.+.+ -++=.+|-.||-.|+
T Consensus 335 ekC~~Cg~~I~d----~iLrA~GkayHp~CF 361 (468)
T KOG1701|consen 335 EKCNKCGEPIMD----RILRALGKAYHPGCF 361 (468)
T ss_pred HHHhhhhhHHHH----HHHHhcccccCCCce
Confidence 346666664333 112256777776653
No 134
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=51.55 E-value=15 Score=27.32 Aligned_cols=29 Identities=31% Similarity=0.748 Sum_probs=22.5
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021794 272 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 305 (307)
Q Consensus 272 ~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~ 305 (307)
..+.|..|++. ...| +-|+.||.|+-+++
T Consensus 26 ~l~~C~~CG~~--~~~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEP--KLPH---RVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCc--cCCe---EECCCCCcCCCEEe
Confidence 45789999976 3345 45999999999886
No 135
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=51.01 E-value=9.7 Score=28.25 Aligned_cols=28 Identities=29% Similarity=0.733 Sum_probs=19.7
Q ss_pred cccccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 122 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 122 v~~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
-++.|..||....+ ......|.|+.||.
T Consensus 27 TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc-----------ccccceEEcCCCCC
Confidence 57889999887766 34456677777764
No 136
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=50.76 E-value=7.7 Score=22.01 Aligned_cols=17 Identities=41% Similarity=0.899 Sum_probs=11.0
Q ss_pred CCCCCCCcccCchhHHH
Q 021794 235 YACPICSKSVCDMSKVW 251 (307)
Q Consensus 235 ~~CPiCrks~~dm~~~~ 251 (307)
+.||+|++.+......+
T Consensus 1 ~~C~~C~~~~~~~~~l~ 17 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELR 17 (24)
T ss_dssp EE-SSTS-EESSHHHHH
T ss_pred CCCcCCCCcCCcHHHHH
Confidence 46999999998765544
No 137
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=49.71 E-value=14 Score=25.69 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.6
Q ss_pred ccccCCCC
Q 021794 152 QYHCDGCG 159 (307)
Q Consensus 152 ~yHC~~Cg 159 (307)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 55566555
No 138
>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=49.56 E-value=17 Score=25.99 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=4.5
Q ss_pred CCCCCCCc
Q 021794 235 YACPICSK 242 (307)
Q Consensus 235 ~~CPiCrk 242 (307)
|+||.|++
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 55555555
No 139
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.41 E-value=7.8 Score=35.76 Aligned_cols=39 Identities=33% Similarity=0.766 Sum_probs=28.6
Q ss_pred CcccccccccCcceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
|-.|.+. ...+++|||-|. ++..|-.. + ..||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-~----~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-L----RICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-C----ccCCCCcChhh
Confidence 9999874 334888999876 67778665 2 35999997554
No 140
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=49.30 E-value=16 Score=39.92 Aligned_cols=78 Identities=27% Similarity=0.459 Sum_probs=46.7
Q ss_pred CccccCCCCcccccCCcceeeccCCCcceeccccCCccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHH
Q 021794 151 KQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMR 230 (307)
Q Consensus 151 ~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl 230 (307)
-+|-|+.|+-=-+++++ --|++| -+.+ ...|.+|-..+-. ..+.---|||-.|.+++.+|+
T Consensus 752 i~~~~~nc~a~~~~~~~--~~c~rc---~s~a------------~~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~ 812 (839)
T KOG0269|consen 752 IHYACPNCDAPMVLTKL--WQCDRC---ESRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWF 812 (839)
T ss_pred eeccccccCCccccccc--eeechH---HHHh------------hcCceeecceeee--eEeecccccccccHHHHHHHH
Confidence 46788888755554444 334443 3322 2369999753322 122223699999999999999
Q ss_pred hcCCCCCCC--C-----CcccCchh
Q 021794 231 EHHQYACPI--C-----SKSVCDMS 248 (307)
Q Consensus 231 ~~~~~~CPi--C-----rks~~dm~ 248 (307)
.. +.-||. | +.++.|+.
T Consensus 813 ~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 813 FK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred hc-CCCCccccCCccccccccchhh
Confidence 74 455654 4 45555543
No 141
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=49.25 E-value=18 Score=28.93 Aligned_cols=52 Identities=17% Similarity=0.450 Sum_probs=24.4
Q ss_pred CCCCCcccccccccCcceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 194 MHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
....|.||.|++-.....-.+. -|+--.++.|+.--.+.++..||.|+....
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 3568999998875444333333 578889999999988888889999996554
No 142
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=49.17 E-value=6.4 Score=33.48 Aligned_cols=19 Identities=47% Similarity=0.950 Sum_probs=15.9
Q ss_pred eeeccCCCCC----CccccccCC
Q 021794 289 VLAQKCPNCK----SYNTRLTRG 307 (307)
Q Consensus 289 ~lg~kC~~C~----SYNT~~~~~ 307 (307)
.|-+||+.|| +|+|+|+|.
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 4678999997 899999973
No 143
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=48.46 E-value=9.5 Score=24.86 Aligned_cols=19 Identities=32% Similarity=0.901 Sum_probs=12.6
Q ss_pred cccccCCcccceeecCcccc
Q 021794 124 QVCVNCGVCMGEYFCESCKL 143 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl 143 (307)
..|.-||. .++|-|..|.+
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~ 21 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGA 21 (30)
T ss_dssp EEETSSSS-EESEE-TTT--
T ss_pred CCCccCcC-CCEEECCCcCC
Confidence 46777888 88888888864
No 144
>PF12773 DZR: Double zinc ribbon
Probab=48.18 E-value=14 Score=25.66 Aligned_cols=12 Identities=25% Similarity=0.791 Sum_probs=9.3
Q ss_pred ccccccCCcccc
Q 021794 123 QQVCVNCGVCMG 134 (307)
Q Consensus 123 ~~~C~nCg~~f~ 134 (307)
+..|.+||..+.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 567888888877
No 145
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=48.13 E-value=16 Score=42.12 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=25.1
Q ss_pred cccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 124 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
..|.+||...-..||+.|.-. .+.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~----te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTH----TEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCc----CCCceeCccCCC
Confidence 679999987666799999644 245788888887
No 146
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=48.06 E-value=12 Score=33.65 Aligned_cols=50 Identities=30% Similarity=0.486 Sum_probs=34.9
Q ss_pred CCCCCCCCcccCchhHHHHHhHHHHhcCCCCh-hhhcCceeEEcCCCCCCccccceee
Q 021794 234 QYACPICSKSVCDMSKVWEKYDREIAATPMPE-AYLNKKVWILCNDCGKTSNVQFHVL 290 (307)
Q Consensus 234 ~~~CPiCrks~~dm~~~~~~lD~eia~~pmPe-ey~~~~~~IlCnDC~~~s~~~fH~l 290 (307)
-.+||.|+..+...+ .+.+...+|+ .|.+......|..|++..+..-||=
T Consensus 97 ~~RCp~CN~~L~~vs-------~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 97 FSRCPECNGELEKVS-------REEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred cccCcccCCEeccCc-------HHHHhhccchhhhhcccceeECCCCcccccCchHHH
Confidence 467999999887543 2333334444 4666666777999999988888873
No 147
>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=47.88 E-value=11 Score=32.69 Aligned_cols=26 Identities=23% Similarity=0.452 Sum_probs=18.6
Q ss_pred cccccCCcccceeecCccccccCCCCCCccccCCCCcc
Q 021794 124 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 161 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiC 161 (307)
..|.+||+ ||| |.+|.+-.|++||.=
T Consensus 10 r~Cp~cg~----------kFY--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGS----------KFY--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCc----------ccc--ccCCCCccCCCcCCc
Confidence 45666666 557 457899999988864
No 148
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=45.50 E-value=8.8 Score=44.08 Aligned_cols=51 Identities=25% Similarity=0.471 Sum_probs=39.6
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCch
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDM 247 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm 247 (307)
..+..|+||++.+-. .-.+..|||.++..|+..|+.. +..||+|....++.
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~df 1201 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDF 1201 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhh
Confidence 345689999986543 1235569999999999999985 68999999666653
No 149
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=44.98 E-value=16 Score=40.49 Aligned_cols=52 Identities=29% Similarity=0.616 Sum_probs=37.2
Q ss_pred CCCCCCCcccccccccCcceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCCcccC
Q 021794 192 GAMHHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 245 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCrks~~ 245 (307)
|+....|-||--. +.++.+..-||. -.+|++|+.+|+..+ ...|-+|..++.
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 4456789999742 233445566875 469999999999863 456999997765
No 150
>PHA00626 hypothetical protein
Probab=44.56 E-value=17 Score=27.54 Aligned_cols=30 Identities=23% Similarity=0.534 Sum_probs=13.5
Q ss_pred ccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 125 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 125 ~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
.|.+||..- -+-|.+|+.+ .+.|-|++||.
T Consensus 2 ~CP~CGS~~-Ivrcg~cr~~-----snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGN-IAKEKTMRGW-----SDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCce-eeeeceeccc-----CcceEcCCCCC
Confidence 356666521 1145555443 23455555543
No 151
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=44.27 E-value=14 Score=27.00 Aligned_cols=29 Identities=31% Similarity=0.697 Sum_probs=22.5
Q ss_pred ccceeecCcc-ccccCCCCCCccccCCCCc
Q 021794 132 CMGEYFCESC-KLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 132 ~f~~YfC~~C-kl~ddd~~k~~yHC~~Cgi 160 (307)
.+..|-|..| +.|+.+....-.-|+.||.
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4567888888 5666677788899999985
No 152
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=43.68 E-value=19 Score=23.54 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=17.8
Q ss_pred eeecCccccccCCCCCCccccCCCCc
Q 021794 135 EYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 135 ~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
+|-|.+|-+.=+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 377888866533 3568888988875
No 153
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=43.42 E-value=18 Score=24.36 Aligned_cols=12 Identities=25% Similarity=0.695 Sum_probs=9.0
Q ss_pred cccccccCCccc
Q 021794 122 VQQVCVNCGVCM 133 (307)
Q Consensus 122 v~~~C~nCg~~f 133 (307)
....|.+||..|
T Consensus 24 ~~v~C~~C~~~f 35 (36)
T PF13717_consen 24 RKVRCSKCGHVF 35 (36)
T ss_pred cEEECCCCCCEe
Confidence 456799998765
No 154
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=42.13 E-value=22 Score=22.36 Aligned_cols=20 Identities=25% Similarity=0.617 Sum_probs=12.6
Q ss_pred CCCCCCCcccCchhHHHHHhH
Q 021794 235 YACPICSKSVCDMSKVWEKYD 255 (307)
Q Consensus 235 ~~CPiCrks~~dm~~~~~~lD 255 (307)
..||+|.+.+ .+....+-||
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999988 3333444455
No 155
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=41.43 E-value=14 Score=28.43 Aligned_cols=14 Identities=43% Similarity=0.971 Sum_probs=12.2
Q ss_pred eccCCCCCCccccc
Q 021794 291 AQKCPNCKSYNTRL 304 (307)
Q Consensus 291 g~kC~~C~SYNT~~ 304 (307)
.++|+.|.|.||+.
T Consensus 5 ~~~CPRC~S~nTKF 18 (63)
T PF02701_consen 5 PLPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCCcCCCCCEE
Confidence 47999999999975
No 156
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.15 E-value=17 Score=26.54 Aligned_cols=29 Identities=24% Similarity=0.627 Sum_probs=20.8
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCC
Q 021794 271 KVWILCNDCGKTSNVQFHVLAQKCPNCKS 299 (307)
Q Consensus 271 ~~~IlCnDC~~~s~~~fH~lg~kC~~C~S 299 (307)
+....|-.|++......---|.+|+.|||
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 34677888888776444556788888886
No 157
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.57 E-value=10 Score=34.49 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=23.7
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccH
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHK 223 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~ 223 (307)
...+|.||||+|. .++.+..|||=-.||+
T Consensus 176 dkGECvICLEdL~-~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLE-AGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhcc-CCCceeccceEEEeec
Confidence 3679999999865 4677889999888886
No 158
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=40.23 E-value=24 Score=26.01 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=22.3
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021794 272 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 305 (307)
Q Consensus 272 ~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~ 305 (307)
..+.|..|++. ...| +-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~~~H---~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KLPH---RVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--ccCe---eECCccCeECCEEc
Confidence 45779999974 3445 46999999999886
No 159
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.03 E-value=21 Score=25.22 Aligned_cols=26 Identities=19% Similarity=0.703 Sum_probs=16.0
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCC
Q 021794 273 WILCNDCGKTSNVQFHVLAQKCPNCKS 299 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH~lg~kC~~C~S 299 (307)
...|-+|+....... --+.+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 356777777554442 24567777776
No 160
>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=38.68 E-value=18 Score=22.95 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=6.3
Q ss_pred CCcccccCCc-ceeeccCCCc
Q 021794 158 CGICRIGGCD-NFFHCNKCRC 177 (307)
Q Consensus 158 CgiCR~G~~~-~ffHC~~C~~ 177 (307)
|.+|+..+.. .+|+|..|+.
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp -TTTS----S--EEE-TTT--
T ss_pred CCcCCCcCCCCceEECccCCC
Confidence 4455544433 5666666654
No 161
>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=38.54 E-value=34 Score=34.33 Aligned_cols=25 Identities=20% Similarity=0.623 Sum_probs=17.8
Q ss_pred ccHHHHHHHHhc------------CCCCCCCCCcccC
Q 021794 221 IHKNCLKEMREH------------HQYACPICSKSVC 245 (307)
Q Consensus 221 fH~~Cl~~wl~~------------~~~~CPiCrks~~ 245 (307)
-+.+|+.+|+.+ ++-.||+||+.+-
T Consensus 315 WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 315 WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 467777777642 3467999999874
No 162
>PLN02189 cellulose synthase
Probab=38.03 E-value=26 Score=39.60 Aligned_cols=56 Identities=18% Similarity=0.418 Sum_probs=39.6
Q ss_pred cCCCCCCCCcccccccccC--cceeEEc-CCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 190 VEGAMHHDCPVCCEYLFET--RQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 190 iE~~~~~~CPIClE~lf~s--~~~v~~L-pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.++.....|.||.|++-.. ++.-+.- -||--.++.|++-=.+.++..||.|+....
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3444567999999986533 3333332 377889999996666667889999997665
No 163
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.02 E-value=5.9 Score=37.33 Aligned_cols=49 Identities=27% Similarity=0.588 Sum_probs=36.0
Q ss_pred CCCcccccccc--cCcceeEEcC--------CCCcccHHHHHHHHhcCCCCCCCCCccc
Q 021794 196 HDCPVCCEYLF--ETRQDVIVLP--------CGHTIHKNCLKEMREHHQYACPICSKSV 244 (307)
Q Consensus 196 ~~CPIClE~lf--~s~~~v~~Lp--------CGH~fH~~Cl~~wl~~~~~~CPiCrks~ 244 (307)
..|.||..... +....+.++. |||+.+.+|++..+......||.|+...
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~ 266 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCccccee
Confidence 45888876433 2233456677 9999999999998776557899999753
No 164
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=37.85 E-value=18 Score=20.90 Aligned_cols=15 Identities=53% Similarity=1.112 Sum_probs=11.6
Q ss_pred CCCCCCCcccCchhH
Q 021794 235 YACPICSKSVCDMSK 249 (307)
Q Consensus 235 ~~CPiCrks~~dm~~ 249 (307)
|.||.|.+.+.....
T Consensus 1 y~C~~C~~~f~~~~~ 15 (23)
T PF00096_consen 1 YKCPICGKSFSSKSN 15 (23)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCccCCHHH
Confidence 469999999887544
No 165
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=37.84 E-value=16 Score=23.27 Aligned_cols=13 Identities=23% Similarity=0.856 Sum_probs=9.3
Q ss_pred cceeecCcccccc
Q 021794 133 MGEYFCESCKLFD 145 (307)
Q Consensus 133 f~~YfC~~Ckl~d 145 (307)
++.|||++|..+=
T Consensus 1 ~~~~~C~~C~~~~ 13 (35)
T smart00451 1 TGGFYCKLCNVTF 13 (35)
T ss_pred CcCeEccccCCcc
Confidence 4678898886553
No 166
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=37.75 E-value=8.4 Score=37.32 Aligned_cols=53 Identities=15% Similarity=0.159 Sum_probs=44.2
Q ss_pred cccccCCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCccee
Q 021794 124 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 180 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s 180 (307)
..|+-|+...++-||.||-=+|.. .-|||.|.-||--....+-||.+|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~----R~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK----RSTCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc----cccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 568889999999999999888652 28999999999887777888888887764
No 167
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=37.45 E-value=17 Score=31.87 Aligned_cols=16 Identities=38% Similarity=0.843 Sum_probs=14.1
Q ss_pred eccCCCCCCccccccC
Q 021794 291 AQKCPNCKSYNTRLTR 306 (307)
Q Consensus 291 g~kC~~C~SYNT~~~~ 306 (307)
...|++|||-||++++
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 3699999999999875
No 168
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.29 E-value=22 Score=40.17 Aligned_cols=17 Identities=24% Similarity=0.755 Sum_probs=10.4
Q ss_pred eEcCccCC---eecCCcccc
Q 021794 82 IRAPCCNE---IFDCRHCHN 98 (307)
Q Consensus 82 i~aPCC~~---~y~CR~CHd 98 (307)
-+||-||+ +|.|..|..
T Consensus 627 RfCpsCG~~t~~frCP~CG~ 646 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGT 646 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCC
Confidence 46777775 455666654
No 169
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=37.18 E-value=11 Score=41.61 Aligned_cols=46 Identities=28% Similarity=0.623 Sum_probs=0.0
Q ss_pred cccccCCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcc
Q 021794 124 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 178 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C 178 (307)
..|.+||..--.-.|+.|.-. ....|.|+.||+ ++.. .+|.+|+.=
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~~----~~C~~C~~~ 701 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVEE----DECPKCGRE 701 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc-ccCc----ccccccccc
Confidence 458888888777778888655 347888988887 3321 277777653
No 170
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=36.82 E-value=28 Score=34.76 Aligned_cols=49 Identities=16% Similarity=0.316 Sum_probs=35.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.....||||+...-+ +.+.--=|-+|+-.|+..++. ...+||+=..++.
T Consensus 298 ~~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCC---CceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 446789999964222 222323499999999999998 4578999877664
No 171
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.63 E-value=26 Score=37.64 Aligned_cols=21 Identities=24% Similarity=0.759 Sum_probs=13.4
Q ss_pred ccccccCCcccceeecCcccc
Q 021794 123 QQVCVNCGVCMGEYFCESCKL 143 (307)
Q Consensus 123 ~~~C~nCg~~f~~YfC~~Ckl 143 (307)
+..|.+||..+..-.|..|.-
T Consensus 15 akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 15 NRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CccccccCCCCCCCcCCCCCC
Confidence 456777887776555555543
No 172
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=36.56 E-value=25 Score=25.40 Aligned_cols=9 Identities=44% Similarity=1.505 Sum_probs=4.9
Q ss_pred CccccCCCC
Q 021794 151 KQYHCDGCG 159 (307)
Q Consensus 151 ~~yHC~~Cg 159 (307)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455555555
No 173
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=35.81 E-value=16 Score=25.00 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.6
Q ss_pred cceeecCcccccc
Q 021794 133 MGEYFCESCKLFD 145 (307)
Q Consensus 133 f~~YfC~~Ckl~d 145 (307)
|.+|||+-|+.|=
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 6789999998875
No 174
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=35.45 E-value=4 Score=28.42 Aligned_cols=43 Identities=23% Similarity=0.627 Sum_probs=27.1
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHh-----cCCCCCCCCC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-----HHQYACPICS 241 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~-----~~~~~CPiCr 241 (307)
|+||... .....-+.=-.|+-.||..|+..-+. ...+.||.|+
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 7788872 22222122237899999999987433 1357888875
No 175
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=34.99 E-value=44 Score=35.76 Aligned_cols=135 Identities=25% Similarity=0.440 Sum_probs=69.7
Q ss_pred CCCCccccCCCCccc---ccC-Ccceee-----ccCCCcceeccccCCccccCCCCCCCCc-ccccccccCcceeEEcCC
Q 021794 148 TSKKQYHCDGCGICR---IGG-CDNFFH-----CNKCRCCYSMLLKNSHPCVEGAMHHDCP-VCCEYLFETRQDVIVLPC 217 (307)
Q Consensus 148 ~~k~~yHC~~CgiCR---~G~-~~~ffH-----C~~C~~C~s~~l~~~H~CiE~~~~~~CP-IClE~lf~s~~~v~~LpC 217 (307)
..|..-||+.|+-== |+. .+++|| |.+||.=+....+. +++-| ...++ -|.+ |. +..++..=
T Consensus 12 ~~~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff-~k~~~---~~ygt~~c~~--~~--~gevvsa~ 83 (670)
T KOG1044|consen 12 TGKQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFF-TKPEN---RLYGTDDCRA--FV--EGEVVSTL 83 (670)
T ss_pred ccccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccce-ecccc---eeecccchhh--hc--cceeEecc
Confidence 356667777776422 221 345554 55555544433322 34443 22222 3333 21 22344455
Q ss_pred CCcccHHHHHHHHhcCCCCCCCCCcccCchhH-HH--HHhHHHHhcCCCChhhhcCceeEEcCCCCCCc---------cc
Q 021794 218 GHTIHKNCLKEMREHHQYACPICSKSVCDMSK-VW--EKYDREIAATPMPEAYLNKKVWILCNDCGKTS---------NV 285 (307)
Q Consensus 218 GH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~-~~--~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s---------~~ 285 (307)
|-+||..| +.|-+|++++..-.. .+ +...-+.-.|+||-.=......--|-.|+..- ..
T Consensus 84 gktyh~~c---------f~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~ 154 (670)
T KOG1044|consen 84 GKTYHPKC---------FSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDK 154 (670)
T ss_pred cceecccc---------ceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeecc
Confidence 88888876 457788877752111 11 11222333455543312223345577787532 56
Q ss_pred cceeeeccCCCCCC
Q 021794 286 QFHVLAQKCPNCKS 299 (307)
Q Consensus 286 ~fH~lg~kC~~C~S 299 (307)
++|+..-||..|.-
T Consensus 155 qwhv~cfkc~~c~~ 168 (670)
T KOG1044|consen 155 QWHVSCFKCKSCSA 168 (670)
T ss_pred ceeeeeeehhhhcc
Confidence 89999999998864
No 176
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=34.91 E-value=13 Score=37.76 Aligned_cols=49 Identities=29% Similarity=0.565 Sum_probs=0.6
Q ss_pred CCCCCCCccccccc----------ccCcceeEEcCCCCcccHHHHHHHHhc-----CCCCCCCCCcc
Q 021794 192 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPICSKS 243 (307)
Q Consensus 192 ~~~~~~CPIClE~l----------f~s~~~v~~LpCGH~fH~~Cl~~wl~~-----~~~~CPiCrks 243 (307)
|++.--|||=|..| .+..++.+.|.|||.+=. -.|-.. ....||+|+..
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp S------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCcccc
Confidence 57778899987654 334567789999986432 246421 24679999954
No 177
>PLN02436 cellulose synthase A
Probab=34.62 E-value=32 Score=39.11 Aligned_cols=56 Identities=20% Similarity=0.440 Sum_probs=39.7
Q ss_pred cCCCCCCCCcccccccccCcceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 190 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 190 iE~~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
++......|.||.|++-...+.-... -||--.++.|++-=.+.++..||.|+....
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34445669999999874443333333 367779999996666667889999997665
No 178
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=33.75 E-value=17 Score=36.16 Aligned_cols=30 Identities=27% Similarity=0.752 Sum_probs=23.3
Q ss_pred EEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 213 IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 213 ~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
+.+||.|+|+.+|...- ....||.|.-.+.
T Consensus 105 RmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD---SDKICPLCDDRVQ 134 (389)
T ss_pred cccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence 57899999999998653 2357999986655
No 179
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=33.73 E-value=26 Score=23.38 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=15.8
Q ss_pred cccccCCcccceeecCccccc
Q 021794 124 QVCVNCGVCMGEYFCESCKLF 144 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~~Ckl~ 144 (307)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 468888887788999888754
No 180
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=33.60 E-value=8.3 Score=37.35 Aligned_cols=75 Identities=25% Similarity=0.595 Sum_probs=56.5
Q ss_pred ccCCcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcceeccccCCccccCCCCCCCCcccccc
Q 021794 127 VNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEY 204 (307)
Q Consensus 127 ~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~ 204 (307)
+.=|+.-|-.||+.|..| ..+-.-||..|+.|-.-.++.|-||.+|-.|+-.++..-..|..-+...-|-||.++
T Consensus 196 i~~~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 196 IILPTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred eecccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 446778888899999998 567888999999998777779999999999998877432233333445567777764
No 181
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=33.39 E-value=62 Score=24.42 Aligned_cols=50 Identities=18% Similarity=0.441 Sum_probs=34.0
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCc
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 246 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 246 (307)
+.-+|-.|-.+|..+..+..+-.=--+|+..|.+..|. ..||-|+..+..
T Consensus 4 lrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv~ 53 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELVR 53 (57)
T ss_pred cCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCcccc
Confidence 45577788777665442222211135899999999984 689999987764
No 182
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.01 E-value=40 Score=39.08 Aligned_cols=36 Identities=28% Similarity=0.664 Sum_probs=23.4
Q ss_pred ccccCCccc-ceeecCcccccc-CCCCCCccccCCCCcc
Q 021794 125 VCVNCGVCM-GEYFCESCKLFD-DDTSKKQYHCDGCGIC 161 (307)
Q Consensus 125 ~C~nCg~~f-~~YfC~~Ckl~d-dd~~k~~yHC~~CgiC 161 (307)
.|.+||... ..|+|..|..-- .++.. ...|+.||.=
T Consensus 681 fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CGtp 718 (1337)
T PRK14714 681 RCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCDVE 718 (1337)
T ss_pred cCcccCCcCCCceeCccCCCccCCCccc-cccCCCCCCc
Confidence 677787776 467788887642 22223 6679999853
No 183
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=32.53 E-value=37 Score=35.19 Aligned_cols=20 Identities=30% Similarity=0.815 Sum_probs=11.1
Q ss_pred CCccccCCCCCCCCcccccccc
Q 021794 185 NSHPCVEGAMHHDCPVCCEYLF 206 (307)
Q Consensus 185 ~~H~CiE~~~~~~CPIClE~lf 206 (307)
...+|..+- .+||+|.-.|.
T Consensus 44 ~~nrC~r~C--f~CP~C~~~L~ 63 (483)
T PF05502_consen 44 EKNRCSRNC--FDCPICFSPLS 63 (483)
T ss_pred ccceecccc--ccCCCCCCcce
Confidence 345665443 36777776543
No 184
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=32.27 E-value=62 Score=32.57 Aligned_cols=53 Identities=19% Similarity=0.453 Sum_probs=42.4
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEEc--CCCCCCccccceeee
Q 021794 235 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILC--NDCGKTSNVQFHVLA 291 (307)
Q Consensus 235 ~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~IlC--nDC~~~s~~~fH~lg 291 (307)
..||-|++...|.-..-..+++.+...++| -+.+..-| |.|++.....+=+.|
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 359999999999888888899999988888 33456678 899988777666554
No 185
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=32.03 E-value=21 Score=38.66 Aligned_cols=47 Identities=30% Similarity=0.692 Sum_probs=37.0
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc--CCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~--~~~~CPiCrks~~ 245 (307)
...||||++..++. ..+.|-|.|...|+..-+.. ..-.||+|+..+.
T Consensus 21 ~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 21 ILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 56899999987762 67899999999999985433 2356999996665
No 186
>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=31.93 E-value=34 Score=22.72 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=14.6
Q ss_pred eecCccccccCCCCCCccccCCCC
Q 021794 136 YFCESCKLFDDDTSKKQYHCDGCG 159 (307)
Q Consensus 136 YfC~~Ckl~ddd~~k~~yHC~~Cg 159 (307)
|-|..|..--+....++-.|..||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 556666444334456677888888
No 187
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=31.04 E-value=39 Score=32.00 Aligned_cols=46 Identities=24% Similarity=0.666 Sum_probs=34.6
Q ss_pred CcccceeecCccccccCCCCCCccccCCCCcccccCCcceeeccCCCcceec
Q 021794 130 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 181 (307)
Q Consensus 130 g~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~ 181 (307)
|....-.||.+|+++ ..+.-.||.-||.|-.+ ---||.==|.|+..
T Consensus 108 ~~~~~~~~C~~C~~~---rPpRs~HCsvC~~CV~r---fDHHC~WvnnCVG~ 153 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLY---RPPRSSHCSVCNNCVLR---FDHHCPWLNNCIGE 153 (299)
T ss_pred CcccceEEcCcCccc---CCCCcccchhhcccccc---cCCCCCCccceECC
Confidence 445567899999999 44578899999999774 33688777777764
No 188
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=30.27 E-value=37 Score=23.52 Aligned_cols=20 Identities=30% Similarity=0.856 Sum_probs=11.4
Q ss_pred cccCCCCcccccCCcceeeccCCC
Q 021794 153 YHCDGCGICRIGGCDNFFHCNKCR 176 (307)
Q Consensus 153 yHC~~CgiCR~G~~~~ffHC~~C~ 176 (307)
|+|+.|+- +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 56666655 332 566776653
No 189
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=30.02 E-value=44 Score=35.05 Aligned_cols=29 Identities=34% Similarity=0.737 Sum_probs=22.0
Q ss_pred EEcCCCCCCccccceeeeccCCCCCCccccccC
Q 021794 274 ILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTR 306 (307)
Q Consensus 274 IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~~ 306 (307)
..|++|+.... -++.+|+.|||-|+.+++
T Consensus 519 ~~C~~CG~~~~----~~~~~CP~CGs~~~~~~~ 547 (555)
T cd01675 519 DICNDCGYIGE----GEGFKCPKCGSEDVEVIS 547 (555)
T ss_pred ccCCCCCCCCc----CCCCCCcCCCCcCceEEE
Confidence 38999997654 245799999998866553
No 190
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=29.68 E-value=39 Score=23.49 Aligned_cols=21 Identities=43% Similarity=0.947 Sum_probs=10.9
Q ss_pred cccCCCCcccccCCcceeeccCCC
Q 021794 153 YHCDGCGICRIGGCDNFFHCNKCR 176 (307)
Q Consensus 153 yHC~~CgiCR~G~~~~ffHC~~C~ 176 (307)
|.|+.|+. -+- ...|||..|.
T Consensus 1 ~~C~~C~~-~i~--g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIV--GVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCc--CCEEECCCCC
Confidence 45555555 222 2566666654
No 191
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=29.49 E-value=26 Score=25.15 Aligned_cols=13 Identities=46% Similarity=1.142 Sum_probs=10.6
Q ss_pred ccCCCCCCccccc
Q 021794 292 QKCPNCKSYNTRL 304 (307)
Q Consensus 292 ~kC~~C~SYNT~~ 304 (307)
-||+.||.||-..
T Consensus 12 rkCp~CGt~NG~R 24 (44)
T PF14952_consen 12 RKCPKCGTYNGTR 24 (44)
T ss_pred ccCCcCcCccCcc
Confidence 4899999999543
No 192
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.06 E-value=34 Score=34.66 Aligned_cols=38 Identities=24% Similarity=0.467 Sum_probs=30.0
Q ss_pred CCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhc
Q 021794 192 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH 232 (307)
Q Consensus 192 ~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~ 232 (307)
......|.||.+.... ....+.|||.|+..|...++..
T Consensus 67 ~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 3456889999985322 4677899999999999999864
No 193
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=28.93 E-value=24 Score=23.91 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=16.5
Q ss_pred ccccCCcccceeecCccccccCCCCCCccccCCCCc
Q 021794 125 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 160 (307)
Q Consensus 125 ~C~nCg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 160 (307)
.|.+||..+-.+| ++.|..--||.||-
T Consensus 3 ~C~~Cg~~Yh~~~---------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEF---------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTT---------B--SSTTBCTTTTE
T ss_pred CcCCCCCcccccc---------CCCCCCCccCCCCC
Confidence 4666666665444 45677777888885
No 194
>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=28.18 E-value=40 Score=24.14 Aligned_cols=12 Identities=25% Similarity=0.963 Sum_probs=6.7
Q ss_pred CCCCCCCcccCc
Q 021794 235 YACPICSKSVCD 246 (307)
Q Consensus 235 ~~CPiCrks~~d 246 (307)
..||+|++++..
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999999985
No 195
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.09 E-value=43 Score=23.24 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=5.2
Q ss_pred CccccCCCC
Q 021794 151 KQYHCDGCG 159 (307)
Q Consensus 151 ~~yHC~~Cg 159 (307)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 356666665
No 196
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=27.98 E-value=46 Score=22.89 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=19.2
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCcccc
Q 021794 273 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNTR 303 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH~---lg~kC~~C~SYNT~ 303 (307)
...|.+|+...++-..+ ....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 45688888665443222 34688899885443
No 197
>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=27.79 E-value=66 Score=31.53 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=7.3
Q ss_pred CCCCCCCCcc
Q 021794 234 QYACPICSKS 243 (307)
Q Consensus 234 ~~~CPiCrks 243 (307)
...||+|+..
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 3479999953
No 198
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=27.15 E-value=37 Score=28.90 Aligned_cols=36 Identities=25% Similarity=0.571 Sum_probs=24.2
Q ss_pred CCCccccCCCCcccccCCcceeeccCCCcceeccccCCcccc
Q 021794 149 SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 190 (307)
Q Consensus 149 ~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 190 (307)
....-.|.. |++-....-.||..||.|+..- .|.|.
T Consensus 45 ~~~~~~C~~---C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 45 NGELKYCST---CKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CCCCEECcc---cCCcCCCcceeccccccccccc---cccch
Confidence 344444554 5556668899999999998643 46555
No 199
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.03 E-value=43 Score=24.56 Aligned_cols=29 Identities=31% Similarity=0.803 Sum_probs=22.0
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021794 272 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 305 (307)
Q Consensus 272 ~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~ 305 (307)
..+.|..|++.. ..| .-|+.||-|+.+|+
T Consensus 25 ~l~~c~~cg~~~--~~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEPK--LPH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSEE--STT---SBCTTTBBSSSSSS
T ss_pred ceeeeccCCCEe--ccc---EeeCCCCeECCEEE
Confidence 467899999543 334 56999999999986
No 200
>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=26.44 E-value=52 Score=31.99 Aligned_cols=43 Identities=23% Similarity=0.407 Sum_probs=27.0
Q ss_pred CCCCCCcccccccccCcceeEEcCCCC----cccHHHHHHHHhcCCCCCC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGH----TIHKNCLKEMREHHQYACP 238 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH----~fH~~Cl~~wl~~~~~~CP 238 (307)
.+-..|+||+| |.-.+.+-.-|. | .=|++|+.+|-.-.+..||
T Consensus 28 ~tLsfChiCfE-l~iegvpks~ll--HtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFE-LSIEGVPKSNLL--HTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeec-cccccCcccccc--ccccccchHHHHHHHHHHHcCCCC
Confidence 44567999998 554443333221 2 2489999998443467788
No 201
>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=26.35 E-value=36 Score=21.36 Aligned_cols=37 Identities=22% Similarity=0.551 Sum_probs=21.9
Q ss_pred CcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 198 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 198 CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
|+.|.+.+...... +..=|..||.+| ++|..|++++.
T Consensus 2 C~~C~~~i~~~~~~--~~~~~~~~H~~C---------f~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELV--LRALGKVWHPEC---------FKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEE--EEeCCccccccC---------CCCcccCCcCc
Confidence 67787765553122 222267787765 56777777653
No 202
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=25.97 E-value=47 Score=22.73 Aligned_cols=9 Identities=22% Similarity=0.681 Sum_probs=3.1
Q ss_pred eccCCCcce
Q 021794 171 HCNKCRCCY 179 (307)
Q Consensus 171 HC~~C~~C~ 179 (307)
-|..||.-+
T Consensus 21 vC~~CG~Vl 29 (43)
T PF08271_consen 21 VCPNCGLVL 29 (43)
T ss_dssp EETTT-BBE
T ss_pred ECCCCCCEe
Confidence 344444333
No 203
>PF15353 HECA: Headcase protein family homologue
Probab=25.66 E-value=41 Score=28.37 Aligned_cols=16 Identities=25% Similarity=0.891 Sum_probs=13.8
Q ss_pred CCCCcccHHHHHHHHh
Q 021794 216 PCGHTIHKNCLKEMRE 231 (307)
Q Consensus 216 pCGH~fH~~Cl~~wl~ 231 (307)
|-|+.+|.+||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4589999999999954
No 204
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.96 E-value=51 Score=22.11 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=8.6
Q ss_pred cccccccCCccc
Q 021794 122 VQQVCVNCGVCM 133 (307)
Q Consensus 122 v~~~C~nCg~~f 133 (307)
....|.+|+..|
T Consensus 24 ~~vrC~~C~~~f 35 (37)
T PF13719_consen 24 RKVRCPKCGHVF 35 (37)
T ss_pred cEEECCCCCcEe
Confidence 456688888766
No 205
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=24.76 E-value=70 Score=32.06 Aligned_cols=51 Identities=24% Similarity=0.610 Sum_probs=32.2
Q ss_pred CCCCccccccc--------------ccCccee-EEcCCCCcccHHHHHHHHhc--------CCCCCCCCCcccC
Q 021794 195 HHDCPVCCEYL--------------FETRQDV-IVLPCGHTIHKNCLKEMREH--------HQYACPICSKSVC 245 (307)
Q Consensus 195 ~~~CPIClE~l--------------f~s~~~v-~~LpCGH~fH~~Cl~~wl~~--------~~~~CPiCrks~~ 245 (307)
+..||+|+..= .+++-+. .+-||||.--.+=..-|.+. -+..||.|-..+.
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 77899998520 1122222 34489998877777778642 1356999987654
No 206
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=24.73 E-value=34 Score=34.21 Aligned_cols=46 Identities=30% Similarity=0.675 Sum_probs=31.3
Q ss_pred CCCCCCCccccccc----------ccCcceeEEcCCCCc--ccHHHHHHHHhc-----CCCCCCCCCc
Q 021794 192 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHT--IHKNCLKEMREH-----HQYACPICSK 242 (307)
Q Consensus 192 ~~~~~~CPIClE~l----------f~s~~~v~~LpCGH~--fH~~Cl~~wl~~-----~~~~CPiCrk 242 (307)
|+..-.|||=|..| .+..++.++|.|||. +| .|=.. ....||+|+.
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H-----~WG~~e~~g~~~r~CPmC~~ 349 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYH-----NWGVRENTGQRERECPMCRV 349 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEecccccccc-----ccccccccCcccCcCCeeee
Confidence 56677899998765 233467799999976 44 46322 2356999994
No 207
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=24.54 E-value=60 Score=37.02 Aligned_cols=55 Identities=16% Similarity=0.410 Sum_probs=38.6
Q ss_pred CCCCCCCCcccccccccCcceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 191 EGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 191 E~~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
++.....|.||.|++-...+.-... -||=-.++.|++-=.+.++..||.|+....
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 3445668999999864443333333 467779999996656667888999996554
No 208
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=24.19 E-value=22 Score=35.02 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=25.6
Q ss_pred CCCCcccccCCcceeeccCCCcceeccccCCcccc
Q 021794 156 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 190 (307)
Q Consensus 156 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 190 (307)
-+|-.|++.+.-...||..||.|..+ ..|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~r---fDHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHR---FDHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHH---hccceE
Confidence 56788888888888899999999764 358887
No 209
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.80 E-value=37 Score=25.49 Aligned_cols=12 Identities=17% Similarity=0.553 Sum_probs=10.8
Q ss_pred eeEcCccCCeec
Q 021794 81 RIRAPCCNEIFD 92 (307)
Q Consensus 81 ki~aPCC~~~y~ 92 (307)
.++||-|++|||
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 589999999997
No 210
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=23.66 E-value=57 Score=23.24 Aligned_cols=26 Identities=23% Similarity=0.664 Sum_probs=16.9
Q ss_pred EEcCCCCCCccccceeeeccCCCCCCccc
Q 021794 274 ILCNDCGKTSNVQFHVLAQKCPNCKSYNT 302 (307)
Q Consensus 274 IlCnDC~~~s~~~fH~lg~kC~~C~SYNT 302 (307)
|.|+.|.+...+.++ .+|..|..|+-
T Consensus 1 ~~C~~C~~~~i~g~R---~~C~~C~dydL 26 (49)
T cd02345 1 LSCSACRKQDISGIR---FPCQVCRDYSL 26 (49)
T ss_pred CcCCCCCCCCceEee---EECCCCCCcCc
Confidence 468888875444444 47777777764
No 211
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.12 E-value=54 Score=27.43 Aligned_cols=6 Identities=33% Similarity=1.176 Sum_probs=3.5
Q ss_pred ccCCCC
Q 021794 154 HCDGCG 159 (307)
Q Consensus 154 HC~~Cg 159 (307)
+|+.||
T Consensus 90 ~CP~Cg 95 (117)
T PRK00564 90 VCEKCH 95 (117)
T ss_pred cCcCCC
Confidence 466665
No 212
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.09 E-value=97 Score=23.53 Aligned_cols=10 Identities=40% Similarity=1.165 Sum_probs=7.5
Q ss_pred CCCCCCCCCc
Q 021794 233 HQYACPICSK 242 (307)
Q Consensus 233 ~~~~CPiCrk 242 (307)
..|+||-|+.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4688888873
No 213
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=22.92 E-value=13 Score=36.04 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=24.8
Q ss_pred CcCCCcccccCceeEcCccCCeecCCcccc
Q 021794 69 MEYGCQHYRRRCRIRAPCCNEIFDCRHCHN 98 (307)
Q Consensus 69 ~~~GC~HY~R~Cki~aPCC~~~y~CR~CHd 98 (307)
..+-|.||.-.=.++.++|.. |+|+.||+
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 345799999855688999999 99999999
No 214
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=22.53 E-value=49 Score=32.27 Aligned_cols=29 Identities=31% Similarity=0.887 Sum_probs=0.0
Q ss_pred CcccceeecCccccccCCCCCCccccCCCCcc
Q 021794 130 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 161 (307)
Q Consensus 130 g~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiC 161 (307)
|.-..+-||.+|+.| ..-...||..||.|
T Consensus 104 ~~~~~~~~C~~C~~~---KP~RS~HC~~Cn~C 132 (309)
T COG5273 104 GKFGTENFCSTCNIY---KPPRSHHCSICNRC 132 (309)
T ss_pred Cccccceeccccccc---cCCCCccchhhcch
No 215
>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=22.27 E-value=61 Score=22.52 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=5.9
Q ss_pred CCCCccccCCCCc
Q 021794 148 TSKKQYHCDGCGI 160 (307)
Q Consensus 148 ~~k~~yHC~~Cgi 160 (307)
..++-|+|..|++
T Consensus 24 ~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 24 LGKQGYRCSWCGL 36 (53)
T ss_dssp SSSCEEEETTTT-
T ss_pred CCCCeEEECCCCC
Confidence 3445555555443
No 216
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=22.01 E-value=1.2e+02 Score=22.27 Aligned_cols=47 Identities=21% Similarity=0.568 Sum_probs=29.3
Q ss_pred HHhHHHHhcCCCChhhhcCceeEEcCCCCCCc----cccceeeeccCCCCCCcc
Q 021794 252 EKYDREIAATPMPEAYLNKKVWILCNDCGKTS----NVQFHVLAQKCPNCKSYN 301 (307)
Q Consensus 252 ~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s----~~~fH~lg~kC~~C~SYN 301 (307)
+.+|-++...|..++ + +-.+.|-.|.... ...|--+--+|+.|+..|
T Consensus 4 ki~d~L~G~d~~~~~--~-r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPS--N-RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCcccc--C-ceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 346666666663222 2 3345599998643 233445577999999887
No 217
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.85 E-value=54 Score=22.21 Aligned_cols=8 Identities=25% Similarity=0.717 Sum_probs=3.3
Q ss_pred CccccCCC
Q 021794 151 KQYHCDGC 158 (307)
Q Consensus 151 ~~yHC~~C 158 (307)
.+++|+.|
T Consensus 18 ~id~C~~C 25 (41)
T PF13453_consen 18 EIDVCPSC 25 (41)
T ss_pred EEEECCCC
Confidence 34444444
No 218
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=21.76 E-value=73 Score=31.98 Aligned_cols=98 Identities=26% Similarity=0.616 Sum_probs=61.7
Q ss_pred cccccCC-cccc--eeecCccc-----------cccC--CCCCCccccCCCCcccccC-CcceeeccCCCcceecc---c
Q 021794 124 QVCVNCG-VCMG--EYFCESCK-----------LFDD--DTSKKQYHCDGCGICRIGG-CDNFFHCNKCRCCYSML---L 183 (307)
Q Consensus 124 ~~C~nCg-~~f~--~YfC~~Ck-----------l~dd--d~~k~~yHC~~CgiCR~G~-~~~ffHC~~C~~C~s~~---l 183 (307)
..|.+|. +.-| +-||.+|+ -||| .+.+-+-||+.| |--|. .|=||.| +++.+-. -
T Consensus 135 V~Ck~Cd~v~~GKLRV~C~~C~~~s~tv~~~P~cWdDVLks~Ripg~Ces~--~~pg~fAEFfFKC---~ah~~~~k~~a 209 (446)
T KOG0006|consen 135 VWCKNCDDVKRGKLRVYCQKCSSTSVTVKSEPQCWDDVLKSKRIPGVCESC--CTPGLFAEFFFKC---GAHPTSDKETA 209 (446)
T ss_pred EEecchhhccCCceEEEeecccCceEEEecCccchhhhhhcccCccccccc--cCCcchHhheehh---ccCCCccccch
Confidence 4577773 2233 56788886 3777 235678888876 33444 4666655 4444431 1
Q ss_pred cCCccccCCCCCCCCcccccccccCcceeEEcCCC--CcccHHHHHHHH
Q 021794 184 KNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCG--HTIHKNCLKEMR 230 (307)
Q Consensus 184 ~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCG--H~fH~~Cl~~wl 230 (307)
...|.=..|.-...|-.|-+ .++++.+++|. |..+..|+.-|-
T Consensus 210 a~lhli~~N~~ni~C~~Ctd----v~~~vlvf~Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 210 AALHLIATNSRNITCITCTD----VRSPVLVFQCNSRHVTCLDCFRLYC 254 (446)
T ss_pred hHHHHhhcccccceeEEecC----CccceEEEecCCceeehHHhhhhHh
Confidence 11233334555678999986 24578889998 999999999664
No 219
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=21.76 E-value=51 Score=30.82 Aligned_cols=33 Identities=24% Similarity=0.693 Sum_probs=19.6
Q ss_pred ecCCccccccccCcCcCCcCCcccCcccccccccccccCCcccc
Q 021794 91 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVQQVCVNCGVCMG 134 (307)
Q Consensus 91 y~CR~CHde~~~~~~~~~~~~H~l~R~~v~ev~~~C~nCg~~f~ 134 (307)
+.|++|||.... . +...+.--...|++||.+..
T Consensus 26 ~~C~~c~~p~~~---------~--~~~~~~~~~~~C~~C~~C~~ 58 (295)
T TIGR02494 26 LRCKWCSNPESQ---------R--KSPELLFKENRCLGCGKCVE 58 (295)
T ss_pred ccCcccCCcccc---------C--CCceEEEccccCCCCchhhh
Confidence 468889986421 0 11122234578999998764
No 220
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=21.72 E-value=35 Score=25.58 Aligned_cols=27 Identities=30% Similarity=0.950 Sum_probs=20.0
Q ss_pred cCceeEEcCCCCCCccccceeeeccCCCCC
Q 021794 269 NKKVWILCNDCGKTSNVQFHVLAQKCPNCK 298 (307)
Q Consensus 269 ~~~~~IlCnDC~~~s~~~fH~lg~kC~~C~ 298 (307)
+.+..|+|--|+.+ .||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~~---syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGRR---SYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSSE---EEETTTTEETTTB
T ss_pred CCccEeeecccCCe---eeecCCCcccccC
Confidence 44589999999975 4777778899998
No 221
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.37 E-value=79 Score=20.72 Aligned_cols=27 Identities=33% Similarity=0.658 Sum_probs=14.8
Q ss_pred eEEcCCCCCCccccce---eeeccCCCCCC
Q 021794 273 WILCNDCGKTSNVQFH---VLAQKCPNCKS 299 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH---~lg~kC~~C~S 299 (307)
...|.+|+...++..- -....|+.||+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 3456677765543222 12356777777
No 222
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=21.21 E-value=77 Score=23.77 Aligned_cols=27 Identities=19% Similarity=0.116 Sum_probs=20.1
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021794 273 WILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 305 (307)
Q Consensus 273 ~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~~~ 305 (307)
.+.|..|+.. ...|- -|+ ||.|+.+++
T Consensus 27 ~~~c~~cg~~--~~pH~---vc~-cG~Y~gr~v 53 (60)
T PRK01110 27 LSVDKTTGEY--HLPHH---VSP-KGYYKGRKV 53 (60)
T ss_pred eeEcCCCCce--eccce---ecC-CcccCCeEe
Confidence 5779999865 33443 499 999999886
No 223
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.18 E-value=43 Score=33.40 Aligned_cols=20 Identities=45% Similarity=1.007 Sum_probs=15.8
Q ss_pred ccccCCcccceeecCccccc
Q 021794 125 VCVNCGVCMGEYFCESCKLF 144 (307)
Q Consensus 125 ~C~nCg~~f~~YfC~~Ckl~ 144 (307)
.|.-||+++++|.|.-|+|.
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eccccccccccccCCCCCcc
Confidence 46678888888888888775
No 224
>PRK00420 hypothetical protein; Validated
Probab=21.17 E-value=54 Score=27.75 Aligned_cols=30 Identities=33% Similarity=0.724 Sum_probs=21.5
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 194 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 194 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
....||+|.-+||.. ..+...||.|+..+.
T Consensus 22 l~~~CP~Cg~pLf~l----------------------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFEL----------------------KDGEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceec----------------------CCCceECCCCCCeee
Confidence 356899999877752 235678999998665
No 225
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.05 E-value=85 Score=25.29 Aligned_cols=46 Identities=28% Similarity=0.724 Sum_probs=30.4
Q ss_pred CCCCCCCCcccCchhHHHHHhHHHHhcCCCChhhhcCceeEEcCCCCCCccccceeeeccCCCCCCcccc
Q 021794 234 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTR 303 (307)
Q Consensus 234 ~~~CPiCrks~~dm~~~~~~lD~eia~~pmPeey~~~~~~IlCnDC~~~s~~~fH~lg~kC~~C~SYNT~ 303 (307)
.+.|+.|++.+..+ .++|+-.-- ....+.+.+.|.+|..|+.+..-
T Consensus 5 rF~C~~C~~~W~S~-----------------------~v~i~f~~~-~~g~v~~rv~~Q~C~~C~~~~~P 50 (98)
T PF13695_consen 5 RFQCSKCSRGWTSA-----------------------KVWILFHMY-RGGQVNMRVFGQRCKKCNPLERP 50 (98)
T ss_pred EEECCCCCCCCccC-----------------------EEEEEEEEc-CCCeEEEEEECCCCCCCCCCCCc
Confidence 47788888776643 233333322 33668888999999999776543
No 226
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.03 E-value=85 Score=30.58 Aligned_cols=115 Identities=24% Similarity=0.444 Sum_probs=66.8
Q ss_pred cccccccCCcccceeec-Cccccc-cCCCCCCccccCCCCcccccCC---------cceeeccCCCcceec--ccc---C
Q 021794 122 VQQVCVNCGVCMGEYFC-ESCKLF-DDDTSKKQYHCDGCGICRIGGC---------DNFFHCNKCRCCYSM--LLK---N 185 (307)
Q Consensus 122 v~~~C~nCg~~f~~YfC-~~Ckl~-ddd~~k~~yHC~~CgiCR~G~~---------~~ffHC~~C~~C~s~--~l~---~ 185 (307)
.--.|..||+..+.+-= ++=|=+ -+-.+|+.++|..||.=-|--+ .--+-|..||-=.|. -|+ .
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiR 208 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIR 208 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccc
Confidence 34457889998887751 000000 0112488999999998754421 235678888887775 233 3
Q ss_pred CccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccCchhHH
Q 021794 186 SHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKV 250 (307)
Q Consensus 186 ~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~dm~~~ 250 (307)
+|.- .-...||.|--- |.++...+. | ++..-...+|.|+.|.|+|.-|+-+
T Consensus 209 THTG---EKPF~C~hC~kA-FADRSNLRA-------H---mQTHS~~K~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 209 THTG---EKPFSCPHCGKA-FADRSNLRA-------H---MQTHSDVKKHQCPRCGKSFALKSYL 259 (279)
T ss_pred cccC---CCCccCCcccch-hcchHHHHH-------H---HHhhcCCccccCcchhhHHHHHHHH
Confidence 3442 225689999874 544432211 0 1111112469999999999876543
No 227
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.76 E-value=1.5e+02 Score=28.88 Aligned_cols=50 Identities=20% Similarity=0.375 Sum_probs=35.1
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcccC
Q 021794 193 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 245 (307)
Q Consensus 193 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 245 (307)
.....|||=.-.|...-+=....+|||+|-..-+.+.- ...|++|...+.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhh---hccccccCCccc
Confidence 34567998865444322223445999999999888873 368999998775
No 228
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.70 E-value=78 Score=26.17 Aligned_cols=33 Identities=24% Similarity=0.512 Sum_probs=20.0
Q ss_pred cceeeccCCCcceeccccCCccccCCCCCCCCcccccc
Q 021794 167 DNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEY 204 (307)
Q Consensus 167 ~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~ 204 (307)
.++|+|..||. .++...-.+ +..+..|++|..+
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKK----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCC-eEeeeecCC----CcceEECCCCCCc
Confidence 56788888883 233222112 3557889999865
No 229
>PF11405 Inhibitor_I67: Bromelain inhibitor VI; InterPro: IPR022713 Bromelain inhibitor VI is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. ; PDB: 2BI6_H 1BI6_H.
Probab=20.64 E-value=34 Score=23.57 Aligned_cols=16 Identities=31% Similarity=0.912 Sum_probs=12.1
Q ss_pred cccccCCcccceeecC
Q 021794 124 QVCVNCGVCMGEYFCE 139 (307)
Q Consensus 124 ~~C~nCg~~f~~YfC~ 139 (307)
-.|..|...||+|.|-
T Consensus 16 gfcktckaefgkyicl 31 (41)
T PF11405_consen 16 GFCKTCKAEFGKYICL 31 (41)
T ss_dssp TT-SSEEEETTEEEE-
T ss_pred hHHHHHHHHhcceEEE
Confidence 4578899999999874
Done!