Query 041030
Match_columns 249
No_of_seqs 223 out of 1441
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:06:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14369 zf-RING_3: zinc-finge 99.6 1.2E-16 2.6E-21 101.8 3.2 35 22-56 1-35 (35)
2 KOG4628 Predicted E3 ubiquitin 99.6 1.4E-15 3.1E-20 140.9 3.8 81 136-228 203-283 (348)
3 PF13639 zf-RING_2: Ring finge 99.5 2.8E-15 6E-20 99.7 2.5 43 167-219 2-44 (44)
4 PF12678 zf-rbx1: RING-H2 zinc 99.3 4E-13 8.7E-18 99.0 2.0 55 164-219 18-73 (73)
5 COG5540 RING-finger-containing 99.3 8.7E-13 1.9E-17 119.5 3.5 52 165-225 323-374 (374)
6 PHA02929 N1R/p28-like protein; 99.3 4.1E-12 9E-17 113.0 4.5 78 140-223 150-227 (238)
7 PF13920 zf-C3HC4_3: Zinc fing 99.1 1.1E-10 2.5E-15 79.4 3.2 46 165-223 2-48 (50)
8 PLN03208 E3 ubiquitin-protein 99.0 1.2E-10 2.6E-15 100.4 3.7 51 163-225 16-81 (193)
9 cd00162 RING RING-finger (Real 99.0 3E-10 6.6E-15 73.4 3.7 45 167-222 1-45 (45)
10 KOG0317 Predicted E3 ubiquitin 99.0 1.6E-10 3.5E-15 104.3 2.4 51 163-226 237-287 (293)
11 COG5243 HRD1 HRD ubiquitin lig 99.0 3.4E-10 7.4E-15 105.2 3.9 77 141-223 268-345 (491)
12 PF13923 zf-C3HC4_2: Zinc fing 99.0 3.7E-10 8.1E-15 73.1 2.5 39 168-218 1-39 (39)
13 KOG0823 Predicted E3 ubiquitin 98.9 4.3E-10 9.3E-15 98.8 3.0 51 164-226 46-98 (230)
14 PF12861 zf-Apc11: Anaphase-pr 98.9 1.6E-09 3.4E-14 82.0 3.8 60 164-223 20-82 (85)
15 PF15227 zf-C3HC4_4: zinc fing 98.9 1.8E-09 3.8E-14 71.4 2.9 39 168-218 1-42 (42)
16 COG5194 APC11 Component of SCF 98.8 2.1E-09 4.5E-14 79.9 3.2 63 162-225 17-83 (88)
17 smart00184 RING Ring finger. E 98.8 3.7E-09 8.1E-14 65.9 3.0 39 168-218 1-39 (39)
18 smart00504 Ubox Modified RING 98.8 5.4E-09 1.2E-13 73.6 3.8 46 166-224 2-47 (63)
19 PF00097 zf-C3HC4: Zinc finger 98.8 5.8E-09 1.3E-13 67.8 2.8 40 168-218 1-41 (41)
20 PF14634 zf-RING_5: zinc-RING 98.7 1E-08 2.2E-13 68.1 2.8 44 167-220 1-44 (44)
21 KOG0320 Predicted E3 ubiquitin 98.7 8E-09 1.7E-13 87.6 2.4 51 163-224 129-179 (187)
22 KOG0802 E3 ubiquitin ligase [P 98.7 6.1E-09 1.3E-13 102.7 2.0 53 164-224 290-342 (543)
23 PHA02926 zinc finger-like prot 98.7 1E-08 2.2E-13 90.0 2.8 56 164-223 169-230 (242)
24 KOG2930 SCF ubiquitin ligase, 98.7 5.2E-09 1.1E-13 81.4 0.6 75 148-223 29-108 (114)
25 TIGR00599 rad18 DNA repair pro 98.6 2.6E-08 5.6E-13 94.7 3.3 51 164-227 25-75 (397)
26 KOG1493 Anaphase-promoting com 98.5 2.4E-08 5.2E-13 73.7 0.5 63 161-223 16-81 (84)
27 COG5574 PEX10 RING-finger-cont 98.3 2.5E-07 5.3E-12 83.0 1.9 51 164-227 214-266 (271)
28 KOG0828 Predicted E3 ubiquitin 98.3 2.5E-07 5.5E-12 88.9 2.1 61 164-224 570-635 (636)
29 PF04564 U-box: U-box domain; 98.3 5.2E-07 1.1E-11 66.2 3.2 49 165-225 4-52 (73)
30 KOG1734 Predicted RING-contain 98.3 1.9E-07 4.2E-12 83.9 0.9 64 161-226 220-284 (328)
31 PF13445 zf-RING_UBOX: RING-ty 98.3 5.1E-07 1.1E-11 60.1 2.4 40 168-216 1-43 (43)
32 KOG2164 Predicted E3 ubiquitin 98.3 4.1E-07 8.8E-12 87.9 2.6 49 165-225 186-238 (513)
33 smart00744 RINGv The RING-vari 98.3 6.9E-07 1.5E-11 61.0 2.9 43 167-219 1-49 (49)
34 KOG0287 Postreplication repair 98.2 3.6E-07 7.7E-12 84.5 0.2 50 165-227 23-72 (442)
35 KOG0804 Cytoplasmic Zn-finger 98.2 6.1E-07 1.3E-11 85.5 1.4 53 164-227 174-226 (493)
36 TIGR00570 cdk7 CDK-activating 98.1 1.8E-06 4E-11 79.4 3.7 56 165-227 3-58 (309)
37 KOG2177 Predicted E3 ubiquitin 98.1 9.9E-07 2.2E-11 76.6 1.0 43 164-219 12-54 (386)
38 KOG0311 Predicted E3 ubiquitin 98.0 6.1E-07 1.3E-11 83.3 -1.7 51 165-227 43-94 (381)
39 COG5432 RAD18 RING-finger-cont 98.0 2.6E-06 5.6E-11 77.5 2.0 49 165-226 25-73 (391)
40 COG5219 Uncharacterized conser 97.8 4.6E-06 1E-10 85.4 0.8 55 163-223 1467-1523(1525)
41 PF11793 FANCL_C: FANCL C-term 97.7 1.1E-05 2.5E-10 58.9 0.7 54 165-224 2-67 (70)
42 KOG0824 Predicted E3 ubiquitin 97.7 1.6E-05 3.5E-10 72.6 1.4 56 165-232 7-62 (324)
43 KOG1645 RING-finger-containing 97.6 3.2E-05 7E-10 73.2 3.0 50 165-221 4-54 (463)
44 PF14835 zf-RING_6: zf-RING of 97.6 1.1E-05 2.4E-10 58.0 -0.4 44 165-222 7-50 (65)
45 KOG0825 PHD Zn-finger protein 97.6 1.1E-05 2.4E-10 81.3 -0.6 54 165-228 123-176 (1134)
46 KOG4265 Predicted E3 ubiquitin 97.6 4.7E-05 1E-09 71.0 3.0 49 163-224 288-337 (349)
47 KOG0827 Predicted E3 ubiquitin 97.5 3.1E-05 6.8E-10 72.9 1.6 53 166-227 5-60 (465)
48 KOG1039 Predicted E3 ubiquitin 97.2 0.00014 3.1E-09 68.2 1.7 56 164-224 160-222 (344)
49 KOG4159 Predicted E3 ubiquitin 97.1 0.00021 4.6E-09 68.3 2.2 47 165-224 84-130 (398)
50 PF11789 zf-Nse: Zinc-finger o 97.1 0.00022 4.7E-09 50.2 1.4 42 165-217 11-53 (57)
51 KOG4445 Uncharacterized conser 97.0 0.00022 4.7E-09 65.4 0.4 52 164-224 114-187 (368)
52 KOG0297 TNF receptor-associate 97.0 0.00031 6.7E-09 67.1 1.4 51 163-225 19-69 (391)
53 KOG0978 E3 ubiquitin ligase in 96.9 0.00023 5E-09 71.9 0.3 49 165-225 643-691 (698)
54 KOG1785 Tyrosine kinase negati 96.9 0.00033 7.2E-09 66.4 0.9 47 166-224 370-417 (563)
55 KOG2660 Locus-specific chromos 96.8 0.0003 6.6E-09 65.1 0.3 49 164-225 14-63 (331)
56 KOG4172 Predicted E3 ubiquitin 96.8 0.0002 4.4E-09 49.9 -0.7 47 165-223 7-54 (62)
57 KOG3970 Predicted E3 ubiquitin 96.3 0.0036 7.7E-08 55.6 3.4 56 161-226 46-108 (299)
58 KOG1941 Acetylcholine receptor 96.3 0.0013 2.9E-08 62.3 0.7 48 165-220 365-413 (518)
59 PF05883 Baculo_RING: Baculovi 96.1 0.0022 4.7E-08 52.6 0.9 36 165-209 26-67 (134)
60 COG5152 Uncharacterized conser 96.0 0.002 4.3E-08 56.1 0.5 46 165-223 196-241 (259)
61 PF10367 Vps39_2: Vacuolar sor 96.0 0.0028 6E-08 48.6 1.2 33 163-205 76-108 (109)
62 KOG1428 Inhibitor of type V ad 96.0 0.0042 9.2E-08 66.8 2.6 54 161-223 3482-3544(3738)
63 KOG0801 Predicted E3 ubiquitin 95.9 0.0025 5.3E-08 53.9 0.5 29 164-201 176-204 (205)
64 KOG1571 Predicted E3 ubiquitin 95.7 0.0059 1.3E-07 57.3 2.3 44 164-223 304-347 (355)
65 KOG2879 Predicted E3 ubiquitin 95.6 0.013 2.8E-07 53.4 3.9 49 163-223 237-287 (298)
66 PF14570 zf-RING_4: RING/Ubox 95.5 0.0065 1.4E-07 41.3 1.3 45 168-222 1-47 (48)
67 PHA03096 p28-like protein; Pro 95.5 0.0067 1.4E-07 55.7 1.5 52 166-222 179-236 (284)
68 PF12906 RINGv: RING-variant d 95.3 0.014 3.1E-07 39.2 2.4 41 168-218 1-47 (47)
69 KOG1813 Predicted E3 ubiquitin 95.1 0.0064 1.4E-07 55.7 0.3 49 166-227 242-290 (313)
70 KOG4692 Predicted E3 ubiquitin 95.1 0.015 3.2E-07 54.8 2.6 53 163-228 420-472 (489)
71 KOG1814 Predicted E3 ubiquitin 94.8 0.012 2.7E-07 56.1 1.4 47 165-220 184-237 (445)
72 PHA02825 LAP/PHD finger-like p 94.5 0.026 5.6E-07 47.6 2.3 50 164-226 7-62 (162)
73 COG5236 Uncharacterized conser 94.5 0.022 4.8E-07 53.5 2.1 51 162-224 58-109 (493)
74 KOG1002 Nucleotide excision re 94.2 0.017 3.7E-07 56.9 0.8 51 163-225 534-588 (791)
75 KOG0827 Predicted E3 ubiquitin 94.0 0.0039 8.6E-08 59.1 -3.9 52 165-226 196-248 (465)
76 PHA02862 5L protein; Provision 93.9 0.031 6.7E-07 46.5 1.7 51 165-228 2-58 (156)
77 KOG4275 Predicted E3 ubiquitin 93.8 0.014 3E-07 53.6 -0.5 42 165-223 300-342 (350)
78 COG5222 Uncharacterized conser 93.6 0.032 7E-07 51.5 1.4 46 166-223 275-322 (427)
79 KOG4185 Predicted E3 ubiquitin 93.6 0.044 9.6E-07 49.8 2.2 52 165-222 3-54 (296)
80 KOG3039 Uncharacterized conser 93.4 0.087 1.9E-06 47.5 3.7 55 164-227 220-274 (303)
81 KOG1952 Transcription factor N 93.3 0.05 1.1E-06 56.1 2.2 50 163-223 189-247 (950)
82 PF08746 zf-RING-like: RING-li 93.2 0.03 6.4E-07 37.1 0.3 39 168-218 1-43 (43)
83 COG0375 HybF Zn finger protein 93.0 0.059 1.3E-06 43.2 1.9 32 22-56 69-100 (115)
84 KOG2114 Vacuolar assembly/sort 92.6 0.075 1.6E-06 54.9 2.4 43 165-222 840-882 (933)
85 PF07800 DUF1644: Protein of u 92.3 0.15 3.1E-06 43.1 3.4 34 165-210 2-48 (162)
86 KOG4739 Uncharacterized protei 92.2 0.057 1.2E-06 48.2 0.9 51 166-230 4-55 (233)
87 KOG0826 Predicted E3 ubiquitin 91.6 0.12 2.6E-06 48.2 2.3 45 165-222 300-345 (357)
88 KOG2932 E3 ubiquitin ligase in 91.4 0.088 1.9E-06 48.9 1.2 43 166-222 91-133 (389)
89 PF04641 Rtf2: Rtf2 RING-finge 91.1 0.23 4.9E-06 44.9 3.6 53 163-225 111-163 (260)
90 KOG3268 Predicted E3 ubiquitin 90.8 0.15 3.3E-06 43.9 2.0 62 161-227 161-232 (234)
91 KOG1940 Zn-finger protein [Gen 90.5 0.13 2.7E-06 47.2 1.3 47 165-220 158-204 (276)
92 PF14447 Prok-RING_4: Prokaryo 90.1 0.17 3.6E-06 35.4 1.4 34 190-226 20-53 (55)
93 KOG2817 Predicted E3 ubiquitin 89.5 0.27 5.8E-06 46.9 2.7 49 165-222 334-384 (394)
94 PF10571 UPF0547: Uncharacteri 89.0 0.21 4.5E-06 29.6 1.0 23 26-53 3-25 (26)
95 KOG1001 Helicase-like transcri 88.9 0.17 3.7E-06 51.8 1.0 52 166-230 455-507 (674)
96 PRK00398 rpoP DNA-directed RNA 88.9 0.47 1E-05 31.4 2.8 32 23-55 3-34 (46)
97 PF14446 Prok-RING_1: Prokaryo 88.7 0.44 9.4E-06 33.2 2.6 31 165-204 5-36 (54)
98 KOG2034 Vacuolar sorting prote 88.7 0.19 4.1E-06 52.2 1.2 35 163-207 815-849 (911)
99 TIGR00100 hypA hydrogenase nic 88.5 0.38 8.2E-06 38.3 2.6 29 23-54 70-98 (115)
100 KOG3161 Predicted E3 ubiquitin 88.1 0.15 3.3E-06 51.4 0.0 45 165-221 11-55 (861)
101 PF13240 zinc_ribbon_2: zinc-r 86.7 0.27 5.8E-06 28.2 0.5 23 25-52 1-23 (23)
102 PRK03681 hypA hydrogenase nick 86.6 0.56 1.2E-05 37.3 2.5 30 23-54 70-99 (114)
103 PRK12380 hydrogenase nickel in 86.4 0.58 1.3E-05 37.1 2.5 29 23-54 70-98 (113)
104 PF01155 HypA: Hydrogenase exp 85.6 0.47 1E-05 37.6 1.6 29 23-54 70-98 (113)
105 PRK03824 hypA hydrogenase nick 85.5 0.7 1.5E-05 37.8 2.6 33 22-54 69-119 (135)
106 COG5175 MOT2 Transcriptional r 85.4 0.54 1.2E-05 44.3 2.1 57 163-227 12-68 (480)
107 KOG0298 DEAD box-containing he 85.0 0.3 6.5E-06 52.7 0.3 44 165-220 1153-1196(1394)
108 KOG3800 Predicted E3 ubiquitin 84.9 0.71 1.5E-05 42.5 2.6 52 167-225 2-53 (300)
109 PF10272 Tmpp129: Putative tra 84.9 0.51 1.1E-05 44.8 1.8 30 195-224 311-352 (358)
110 PRK00564 hypA hydrogenase nick 84.9 0.61 1.3E-05 37.2 2.0 31 22-54 70-100 (117)
111 COG5220 TFB3 Cdk activating ki 84.7 0.51 1.1E-05 42.5 1.5 49 165-222 10-63 (314)
112 KOG3002 Zn finger protein [Gen 83.8 0.71 1.5E-05 42.8 2.2 42 165-223 48-91 (299)
113 PF03854 zf-P11: P-11 zinc fin 82.7 0.4 8.7E-06 32.6 0.0 32 193-225 16-48 (50)
114 COG2093 DNA-directed RNA polym 82.0 0.6 1.3E-05 33.5 0.7 26 26-56 7-33 (64)
115 PF13248 zf-ribbon_3: zinc-rib 82.0 0.61 1.3E-05 27.4 0.6 24 24-52 3-26 (26)
116 PRK00762 hypA hydrogenase nick 81.9 0.96 2.1E-05 36.5 2.0 31 23-54 70-104 (124)
117 PRK06266 transcription initiat 81.3 0.84 1.8E-05 39.1 1.5 34 21-54 115-148 (178)
118 smart00659 RPOLCX RNA polymera 78.7 2.2 4.7E-05 28.4 2.6 31 23-55 2-32 (44)
119 PF05290 Baculo_IE-1: Baculovi 76.9 1.9 4E-05 35.6 2.2 55 164-227 79-136 (140)
120 PF03604 DNA_RNApol_7kD: DNA d 76.9 3 6.4E-05 25.9 2.6 28 24-53 1-28 (32)
121 PF02891 zf-MIZ: MIZ/SP-RING z 76.5 1.2 2.5E-05 30.3 0.8 43 166-220 3-49 (50)
122 TIGR00373 conserved hypothetic 75.9 1.3 2.8E-05 37.1 1.1 36 21-57 107-142 (158)
123 COG1996 RPC10 DNA-directed RNA 75.6 2.2 4.7E-05 29.2 1.9 32 23-55 6-37 (49)
124 KOG0309 Conserved WD40 repeat- 75.6 1.5 3.3E-05 45.3 1.6 25 192-217 1045-1069(1081)
125 PF07754 DUF1610: Domain of un 75.1 1.8 3.9E-05 25.2 1.2 23 26-49 1-23 (24)
126 smart00834 CxxC_CXXC_SSSS Puta 75.0 3.4 7.4E-05 26.0 2.7 29 23-51 5-35 (41)
127 COG5270 PUA domain (predicted 74.8 1.7 3.7E-05 37.7 1.5 27 21-54 12-38 (202)
128 KOG1609 Protein involved in mR 74.7 1.5 3.2E-05 39.6 1.2 53 165-225 78-136 (323)
129 KOG3053 Uncharacterized conser 74.5 1.1 2.4E-05 40.7 0.4 53 164-224 19-83 (293)
130 KOG3899 Uncharacterized conser 74.4 1.6 3.4E-05 40.5 1.3 31 195-225 325-367 (381)
131 KOG1100 Predicted E3 ubiquitin 73.4 1.4 3.1E-05 38.6 0.8 38 168-222 161-199 (207)
132 smart00531 TFIIE Transcription 71.4 1.9 4.2E-05 35.5 1.0 35 21-55 97-136 (147)
133 KOG1812 Predicted E3 ubiquitin 71.1 1.5 3.3E-05 42.0 0.4 38 165-210 146-183 (384)
134 TIGR02098 MJ0042_CXXC MJ0042 f 70.9 2.7 5.8E-05 26.4 1.4 30 24-53 3-36 (38)
135 PF08772 NOB1_Zn_bind: Nin one 70.8 2.8 6.2E-05 30.9 1.7 30 23-56 9-38 (73)
136 PF14569 zf-UDP: Zinc-binding 70.8 4.7 0.0001 30.2 2.8 55 165-224 9-63 (80)
137 KOG4367 Predicted Zn-finger pr 70.3 2.1 4.5E-05 41.8 1.1 36 163-210 2-37 (699)
138 COG5109 Uncharacterized conser 67.6 3.6 7.9E-05 38.5 2.1 46 165-219 336-383 (396)
139 PF09723 Zn-ribbon_8: Zinc rib 67.6 8.5 0.00018 25.0 3.3 33 22-54 4-38 (42)
140 PF06906 DUF1272: Protein of u 66.6 9.3 0.0002 26.9 3.4 50 166-226 6-55 (57)
141 COG5183 SSM4 Protein involved 66.2 3.1 6.6E-05 43.5 1.4 53 165-227 12-70 (1175)
142 TIGR02605 CxxC_CxxC_SSSS putat 63.6 10 0.00022 25.3 3.2 34 23-56 5-40 (52)
143 smart00132 LIM Zinc-binding do 63.5 6.7 0.00014 23.7 2.1 38 167-223 1-38 (39)
144 KOG1812 Predicted E3 ubiquitin 61.6 4.1 8.9E-05 39.0 1.3 46 165-218 306-351 (384)
145 KOG2066 Vacuolar assembly/sort 61.4 3.8 8.2E-05 42.5 1.1 47 165-218 784-830 (846)
146 KOG0269 WD40 repeat-containing 61.3 7 0.00015 40.5 2.9 39 166-217 780-820 (839)
147 PF08271 TF_Zn_Ribbon: TFIIB z 61.1 8 0.00017 25.1 2.3 32 24-56 1-32 (43)
148 PF01485 IBR: IBR domain; Int 60.2 6 0.00013 26.9 1.6 29 25-53 20-51 (64)
149 COG1439 Predicted nucleic acid 59.5 5.8 0.00013 34.1 1.7 33 15-53 132-164 (177)
150 KOG4718 Non-SMC (structural ma 59.5 4.4 9.5E-05 35.9 1.0 42 165-218 181-222 (235)
151 KOG4362 Transcriptional regula 59.4 2.3 5E-05 43.5 -0.9 49 165-225 21-71 (684)
152 KOG1815 Predicted E3 ubiquitin 58.6 5.1 0.00011 38.9 1.4 36 165-211 70-105 (444)
153 smart00647 IBR In Between Ring 57.9 8.7 0.00019 26.1 2.1 32 23-54 18-52 (64)
154 PRK12496 hypothetical protein; 57.5 6.4 0.00014 33.2 1.7 27 24-53 128-154 (164)
155 COG4391 Uncharacterized protei 57.4 7.3 0.00016 27.9 1.6 21 33-53 39-59 (62)
156 KOG0802 E3 ubiquitin ligase [P 56.6 6.3 0.00014 39.3 1.7 48 164-228 478-525 (543)
157 KOG1829 Uncharacterized conser 55.2 4.7 0.0001 40.7 0.5 25 190-218 532-556 (580)
158 KOG0825 PHD Zn-finger protein 54.5 6.7 0.00015 41.0 1.5 51 164-222 95-153 (1134)
159 PF13901 DUF4206: Domain of un 52.7 6.7 0.00015 34.1 1.0 39 165-219 152-196 (202)
160 PF07191 zinc-ribbons_6: zinc- 52.7 11 0.00023 27.7 1.9 25 22-52 16-40 (70)
161 PF14803 Nudix_N_2: Nudix N-te 52.1 8.6 0.00019 24.2 1.2 26 25-50 2-30 (34)
162 TIGR00155 pqiA_fam integral me 51.6 9.6 0.00021 36.7 2.0 29 25-53 15-44 (403)
163 PF09538 FYDLN_acid: Protein o 51.5 9 0.00019 30.3 1.5 27 26-55 12-39 (108)
164 PF01363 FYVE: FYVE zinc finge 51.2 9.2 0.0002 26.9 1.4 36 164-208 8-44 (69)
165 smart00249 PHD PHD zinc finger 50.9 8.1 0.00017 24.1 1.0 31 167-206 1-31 (47)
166 PF05191 ADK_lid: Adenylate ki 50.7 17 0.00038 23.0 2.5 31 25-55 3-34 (36)
167 PF10263 SprT-like: SprT-like 48.6 13 0.00028 30.2 2.1 35 20-54 120-155 (157)
168 PLN02189 cellulose synthase 47.6 27 0.00058 37.7 4.6 55 165-225 34-89 (1040)
169 PRK15103 paraquat-inducible me 46.8 14 0.0003 35.8 2.3 29 25-53 12-41 (419)
170 PF08792 A2L_zn_ribbon: A2L zi 46.7 14 0.0003 23.0 1.5 28 24-52 4-31 (33)
171 COG3809 Uncharacterized protei 45.4 13 0.00028 28.0 1.4 33 25-57 3-38 (88)
172 smart00661 RPOL9 RNA polymeras 45.3 14 0.00031 24.4 1.5 27 25-51 2-29 (52)
173 smart00154 ZnF_AN1 AN1-like Zi 45.0 12 0.00025 24.1 1.0 25 26-55 1-25 (39)
174 TIGR01206 lysW lysine biosynth 44.3 20 0.00044 24.9 2.2 31 24-54 3-34 (54)
175 PF13717 zinc_ribbon_4: zinc-r 44.2 17 0.00037 22.9 1.6 27 26-52 5-35 (36)
176 PF00628 PHD: PHD-finger; Int 44.0 9.9 0.00021 25.0 0.6 44 167-219 1-49 (51)
177 PRK00432 30S ribosomal protein 43.5 10 0.00023 25.8 0.6 13 43-55 21-33 (50)
178 PF00412 LIM: LIM domain; Int 43.1 17 0.00036 24.2 1.6 39 168-225 1-39 (58)
179 KOG1729 FYVE finger containing 42.5 5.6 0.00012 36.7 -1.1 42 165-215 214-255 (288)
180 KOG3039 Uncharacterized conser 42.0 15 0.00033 33.4 1.6 34 165-210 43-76 (303)
181 PLN02436 cellulose synthase A 41.7 26 0.00057 37.9 3.5 55 165-224 36-90 (1094)
182 PF04710 Pellino: Pellino; In 41.6 7.1 0.00015 37.6 -0.6 54 165-221 277-337 (416)
183 PF13913 zf-C2HC_2: zinc-finge 40.9 11 0.00023 21.8 0.3 13 43-55 3-15 (25)
184 PRK13794 hypothetical protein; 40.6 16 0.00035 35.9 1.7 25 22-53 9-33 (479)
185 KOG3005 GIY-YIG type nuclease 40.1 14 0.0003 33.9 1.0 50 165-223 182-243 (276)
186 PF14255 Cys_rich_CPXG: Cystei 39.9 18 0.00039 24.9 1.3 18 43-60 1-18 (52)
187 PF12773 DZR: Double zinc ribb 39.3 16 0.00035 24.0 1.0 27 23-51 12-38 (50)
188 PRK06393 rpoE DNA-directed RNA 39.2 17 0.00037 26.2 1.2 20 26-52 8-27 (64)
189 TIGR01053 LSD1 zinc finger dom 39.0 26 0.00057 21.5 1.9 24 25-49 3-26 (31)
190 PF04216 FdhE: Protein involve 38.7 5.3 0.00012 36.4 -1.9 49 163-221 170-220 (290)
191 PF13719 zinc_ribbon_5: zinc-r 38.6 20 0.00042 22.6 1.3 28 26-53 5-36 (37)
192 PLN02400 cellulose synthase 37.9 33 0.00072 37.2 3.6 62 165-232 36-97 (1085)
193 PF00527 E7: E7 protein, Early 37.8 17 0.00036 27.8 1.1 24 25-48 54-91 (92)
194 TIGR02300 FYDLN_acid conserved 37.6 21 0.00046 29.2 1.7 28 25-55 11-39 (129)
195 cd00065 FYVE FYVE domain; Zinc 37.3 21 0.00046 23.9 1.4 37 165-209 2-38 (57)
196 PRK08351 DNA-directed RNA poly 36.3 20 0.00043 25.6 1.1 19 26-51 6-24 (61)
197 PF06943 zf-LSD1: LSD1 zinc fi 36.2 35 0.00077 20.0 2.0 23 26-49 1-23 (25)
198 PF10276 zf-CHCC: Zinc-finger 36.2 21 0.00046 23.2 1.2 12 42-53 29-40 (40)
199 KOG2231 Predicted E3 ubiquitin 36.1 30 0.00065 35.6 2.8 57 167-235 2-64 (669)
200 PLN02638 cellulose synthase A 36.0 47 0.001 36.0 4.3 56 165-225 17-72 (1079)
201 PF06844 DUF1244: Protein of u 35.9 20 0.00044 26.0 1.1 13 198-210 11-23 (68)
202 KOG2807 RNA polymerase II tran 34.0 38 0.00082 32.1 2.9 46 165-220 330-375 (378)
203 smart00064 FYVE Protein presen 33.8 30 0.00065 24.1 1.8 38 165-210 10-47 (68)
204 PF12172 DUF35_N: Rubredoxin-l 33.7 23 0.0005 22.0 1.0 22 25-51 13-34 (37)
205 TIGR00155 pqiA_fam integral me 33.6 23 0.00049 34.2 1.4 26 24-53 216-241 (403)
206 PF04423 Rad50_zn_hook: Rad50 32.6 16 0.00035 24.7 0.2 12 213-224 21-32 (54)
207 PF07975 C1_4: TFIIH C1-like d 32.4 16 0.00034 25.1 0.1 33 25-57 1-36 (51)
208 PHA02776 E7 protein; Provision 31.9 25 0.00054 27.6 1.2 26 25-50 60-99 (101)
209 PF07649 C1_3: C1-like domain; 31.7 25 0.00054 20.9 0.9 29 167-204 2-30 (30)
210 KOG2068 MOT2 transcription fac 31.6 44 0.00096 31.5 2.9 55 165-230 249-305 (327)
211 PF07295 DUF1451: Protein of u 31.4 48 0.001 27.6 2.9 30 21-51 110-139 (146)
212 PF03119 DNA_ligase_ZBD: NAD-d 31.4 27 0.00059 20.8 1.0 14 44-57 1-14 (28)
213 TIGR00622 ssl1 transcription f 31.0 55 0.0012 26.2 3.0 53 166-219 56-110 (112)
214 PF08274 PhnA_Zn_Ribbon: PhnA 30.6 23 0.0005 21.6 0.6 24 26-51 5-28 (30)
215 COG1579 Zn-ribbon protein, pos 30.4 17 0.00036 32.8 -0.0 34 21-54 195-233 (239)
216 PF12760 Zn_Tnp_IS1595: Transp 30.3 29 0.00062 22.8 1.1 10 42-51 18-27 (46)
217 COG1675 TFA1 Transcription ini 30.2 16 0.00034 31.5 -0.2 37 18-54 108-144 (176)
218 KOG3113 Uncharacterized conser 29.2 84 0.0018 28.8 4.2 50 165-225 111-160 (293)
219 PRK00420 hypothetical protein; 29.1 39 0.00085 26.9 1.9 29 24-55 24-53 (112)
220 PF14787 zf-CCHC_5: GAG-polypr 29.1 27 0.00059 22.3 0.8 12 43-54 3-14 (36)
221 COG2995 PqiA Uncharacterized p 29.1 36 0.00079 32.9 2.0 39 20-58 15-54 (418)
222 PF05605 zf-Di19: Drought indu 29.1 28 0.00061 23.5 0.9 11 43-53 3-13 (54)
223 PF13453 zf-TFIIB: Transcripti 28.9 26 0.00056 22.4 0.7 29 26-54 2-31 (41)
224 KOG3579 Predicted E3 ubiquitin 28.4 33 0.00072 31.9 1.5 36 165-210 268-305 (352)
225 PLN02915 cellulose synthase A 28.4 55 0.0012 35.4 3.3 56 164-224 14-69 (1044)
226 KOG2879 Predicted E3 ubiquitin 28.2 19 0.00041 33.2 -0.1 28 22-52 259-286 (298)
227 PRK13795 hypothetical protein; 28.1 40 0.00086 34.4 2.2 30 21-58 10-39 (636)
228 COG3813 Uncharacterized protei 27.9 73 0.0016 23.7 3.0 35 190-227 22-56 (84)
229 KOG0824 Predicted E3 ubiquitin 26.8 38 0.00082 31.7 1.6 51 165-228 105-156 (324)
230 PF01396 zf-C4_Topoisom: Topoi 26.7 36 0.00078 21.7 1.1 13 43-55 2-14 (39)
231 COG1198 PriA Primosomal protei 26.6 39 0.00085 35.2 1.9 27 22-54 461-487 (730)
232 COG1645 Uncharacterized Zn-fin 26.0 45 0.00098 27.4 1.8 27 24-53 29-55 (131)
233 PF02148 zf-UBP: Zn-finger in 25.9 36 0.00079 23.7 1.1 11 24-34 50-60 (63)
234 KOG1356 Putative transcription 25.8 29 0.00063 36.6 0.7 33 8-52 221-253 (889)
235 PF14169 YdjO: Cold-inducible 25.4 55 0.0012 23.2 1.9 28 29-56 26-53 (59)
236 PF06044 DRP: Dam-replacing fa 25.3 30 0.00064 31.4 0.6 32 22-53 30-64 (254)
237 PF14353 CpXC: CpXC protein 25.2 39 0.00084 26.8 1.2 16 42-57 1-16 (128)
238 KOG3993 Transcription factor ( 25.1 39 0.00084 33.1 1.4 22 27-54 286-307 (500)
239 PF03811 Zn_Tnp_IS1: InsA N-te 24.9 33 0.00071 21.8 0.6 11 42-52 5-15 (36)
240 PF13832 zf-HC5HC2H_2: PHD-zin 24.8 61 0.0013 24.7 2.3 31 165-206 55-87 (110)
241 PLN02195 cellulose synthase A 24.7 85 0.0018 33.8 3.9 54 165-223 6-59 (977)
242 PRK12495 hypothetical protein; 24.6 37 0.00081 30.3 1.1 30 22-54 41-70 (226)
243 PRK00415 rps27e 30S ribosomal 24.5 55 0.0012 23.2 1.7 32 23-54 11-42 (59)
244 PF06677 Auto_anti-p27: Sjogre 24.2 65 0.0014 21.0 1.9 23 25-49 19-41 (41)
245 PF06827 zf-FPG_IleRS: Zinc fi 24.2 27 0.00058 20.7 0.1 7 24-30 22-28 (30)
246 PRK04338 N(2),N(2)-dimethylgua 24.1 64 0.0014 30.8 2.7 31 21-53 242-272 (382)
247 PF12674 Zn_ribbon_2: Putative 23.5 27 0.00059 26.1 0.0 32 25-56 2-42 (81)
248 COG2888 Predicted Zn-ribbon RN 22.8 56 0.0012 23.3 1.5 28 25-53 11-38 (61)
249 PF09151 DUF1936: Domain of un 22.6 53 0.0011 20.4 1.2 14 43-56 2-15 (36)
250 KOG1815 Predicted E3 ubiquitin 22.1 29 0.00063 33.7 -0.1 42 165-211 226-268 (444)
251 TIGR00308 TRM1 tRNA(guanine-26 22.1 64 0.0014 30.8 2.3 33 21-53 231-263 (374)
252 KOG3183 Predicted Zn-finger pr 22.0 46 0.00099 30.1 1.1 34 190-225 24-68 (250)
253 PF00096 zf-C2H2: Zinc finger, 21.7 31 0.00068 18.6 0.0 11 44-54 2-12 (23)
254 PF04475 DUF555: Protein of un 21.4 64 0.0014 25.3 1.7 19 32-53 40-58 (102)
255 PF09297 zf-NADH-PPase: NADH p 21.3 72 0.0016 19.2 1.6 25 25-50 5-29 (32)
256 KOG2071 mRNA cleavage and poly 21.3 65 0.0014 32.7 2.2 44 163-206 511-555 (579)
257 PF12874 zf-met: Zinc-finger o 20.9 46 0.001 18.3 0.7 10 24-33 1-10 (25)
258 COG4847 Uncharacterized protei 20.9 69 0.0015 25.0 1.8 36 165-210 6-41 (103)
259 PRK04351 hypothetical protein; 20.8 68 0.0015 26.7 1.9 32 23-54 112-144 (149)
260 PHA00616 hypothetical protein 20.4 28 0.0006 23.3 -0.4 12 43-54 2-13 (44)
261 PRK14890 putative Zn-ribbon RN 20.4 68 0.0015 22.8 1.5 27 24-51 8-34 (59)
262 KOG1597 Transcription initiati 20.3 49 0.0011 30.8 1.0 32 25-56 2-35 (308)
263 PF05715 zf-piccolo: Piccolo Z 20.2 73 0.0016 22.7 1.6 12 212-223 2-13 (61)
264 PRK10220 hypothetical protein; 20.1 69 0.0015 25.5 1.7 28 26-55 6-33 (111)
No 1
>PF14369 zf-RING_3: zinc-finger
Probab=99.64 E-value=1.2e-16 Score=101.84 Aligned_cols=35 Identities=29% Similarity=0.869 Sum_probs=30.8
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl 56 (249)
++||||+|+|+|++....+++++||+|+|||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 47999999999999866556677999999999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.56 E-value=1.4e-15 Score=140.90 Aligned_cols=81 Identities=26% Similarity=0.610 Sum_probs=67.2
Q ss_pred CCCCCCHHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCC
Q 041030 136 APTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTC 215 (249)
Q Consensus 136 ~~~pas~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sC 215 (249)
.-..+.+..++++|..+++...... ....|+||||+|+.|++ ++.|||+|.||..||++||...+..|
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~---~~~~CaIClEdY~~Gdk---------lRiLPC~H~FH~~CIDpWL~~~r~~C 270 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDED---ATDTCAICLEDYEKGDK---------LRILPCSHKFHVNCIDPWLTQTRTFC 270 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccC---CCceEEEeecccccCCe---------eeEecCCCchhhccchhhHhhcCccC
Confidence 4456788999999999988765433 12599999999999999 99999999999999999999933559
Q ss_pred ccccccccCCCCC
Q 041030 216 PVCRYELKDSIIG 228 (249)
Q Consensus 216 PvCR~~l~~~~~~ 228 (249)
|+||+++.+..-.
T Consensus 271 PvCK~di~~~~~~ 283 (348)
T KOG4628|consen 271 PVCKRDIRTDSGS 283 (348)
T ss_pred CCCCCcCCCCCCC
Confidence 9999998765443
No 3
>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=99.54 E-value=2.8e-15 Score=99.66 Aligned_cols=43 Identities=49% Similarity=1.292 Sum_probs=40.1
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
.|+||+++|..++. ++.++|+|+||.+||.+|++. +++||+||
T Consensus 2 ~C~IC~~~~~~~~~---------~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEK---------VVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSC---------EEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCcCCChhhcCCCe---------EEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 79999999998877 999999999999999999999 99999997
No 4
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.33 E-value=4e-13 Score=99.01 Aligned_cols=55 Identities=35% Similarity=0.799 Sum_probs=40.2
Q ss_pred CccccccccccccccCCCCCCCC-ccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSD-EVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~-~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
.+..|+||++.|.......+... +..++..+|+|.||..||.+||+. +++||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 35569999999955443222222 233556679999999999999999 99999998
No 5
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.31 E-value=8.7e-13 Score=119.51 Aligned_cols=52 Identities=38% Similarity=0.888 Sum_probs=48.2
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
..+|+|||++|..++. ++.|||+|.||..||.+|+..+++.||+||.++|+.
T Consensus 323 GveCaICms~fiK~d~---------~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp 374 (374)
T COG5540 323 GVECAICMSNFIKNDR---------LRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP 374 (374)
T ss_pred CceEEEEhhhhcccce---------EEEeccCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence 5799999999998887 999999999999999999996699999999999873
No 6
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.26 E-value=4.1e-12 Score=113.01 Aligned_cols=78 Identities=21% Similarity=0.429 Sum_probs=56.5
Q ss_pred CCHHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 140 APVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 140 as~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
.++..++.+|.+......... ..++..|+||++.+...... ..+.++.++|+|.||..||.+|++. +.+||+||
T Consensus 150 ~~~~~i~~lp~vl~~~e~~~~-~~~~~eC~ICle~~~~~~~~----~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR 223 (238)
T PHA02929 150 NYKKFLKTIPSVLSEYEKLYN-RSKDKECAICMEKVYDKEIK----NMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCR 223 (238)
T ss_pred hhHHHHHhcchhhhhhhhhhc-CCCCCCCccCCcccccCccc----cccceecCCCCCcccHHHHHHHHhc-CCCCCCCC
Confidence 378889999988654433322 23468999999998754310 0001344569999999999999999 99999999
Q ss_pred cccc
Q 041030 220 YELK 223 (249)
Q Consensus 220 ~~l~ 223 (249)
..+.
T Consensus 224 ~~~~ 227 (238)
T PHA02929 224 TPFI 227 (238)
T ss_pred CEee
Confidence 9875
No 7
>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=99.05 E-value=1.1e-10 Score=79.44 Aligned_cols=46 Identities=37% Similarity=0.907 Sum_probs=40.5
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
+..|.||++.... +..+||+|. |+..|+..|++. ...||+||+++.
T Consensus 2 ~~~C~iC~~~~~~------------~~~~pCgH~~~C~~C~~~~~~~-~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD------------VVLLPCGHLCFCEECAERLLKR-KKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS------------EEEETTCEEEEEHHHHHHHHHT-TSBBTTTTBB-S
T ss_pred cCCCccCCccCCc------------eEEeCCCChHHHHHHhHHhccc-CCCCCcCChhhc
Confidence 5699999999776 889999999 999999999998 999999999874
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.05 E-value=1.2e-10 Score=100.39 Aligned_cols=51 Identities=27% Similarity=0.654 Sum_probs=42.2
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---------------CCCCccccccccCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---------------STTCPVCRYELKDS 225 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---------------~~sCPvCR~~l~~~ 225 (249)
.++.+|+||++.+.. .+.++|+|+||+.||..|+... ...||+||..+...
T Consensus 16 ~~~~~CpICld~~~d------------PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 16 GGDFDCNICLDQVRD------------PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred CCccCCccCCCcCCC------------cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 357899999999876 6678899999999999998631 35799999999653
No 9
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.01 E-value=3e-10 Score=73.43 Aligned_cols=45 Identities=47% Similarity=1.116 Sum_probs=36.8
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
+|+||++.+.. . +..++|+|.||..|+..|++.++..||+||..+
T Consensus 1 ~C~iC~~~~~~--~---------~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFRE--P---------VVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhC--c---------eEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 59999999832 2 445559999999999999997567799999864
No 10
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.99 E-value=1.6e-10 Score=104.28 Aligned_cols=51 Identities=27% Similarity=0.744 Sum_probs=45.2
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~ 226 (249)
.....|.|||+.... ..-+||||+||+.||..|... +..||+||..+.+..
T Consensus 237 ~a~~kC~LCLe~~~~------------pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 237 EATRKCSLCLENRSN------------PSATPCGHIFCWSCILEWCSE-KAECPLCREKFQPSK 287 (293)
T ss_pred CCCCceEEEecCCCC------------CCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCCcc
Confidence 446899999999888 455999999999999999999 999999999987654
No 11
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.97 E-value=3.4e-10 Score=105.23 Aligned_cols=77 Identities=25% Similarity=0.561 Sum_probs=53.3
Q ss_pred CHHHHHhhhhheeccccccccccCcccccccccc-ccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 141 PVSAVEALKRVRISESTQLTRSNEVQCCPICKEE-FRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 141 s~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~-f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
.|..-+.++++..... .+.+..|.||||+ |..+.+.-.-.-+-..++|||||++|.+|+.-|+.. .++||+||
T Consensus 268 ~kdl~~~~~t~t~eql-----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr 341 (491)
T COG5243 268 TKDLNAMYPTATEEQL-----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICR 341 (491)
T ss_pred hhHHHhhcchhhhhhh-----cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCccc
Confidence 3444444555443332 2447899999999 554422111112233689999999999999999999 99999999
Q ss_pred cccc
Q 041030 220 YELK 223 (249)
Q Consensus 220 ~~l~ 223 (249)
.++.
T Consensus 342 ~p~i 345 (491)
T COG5243 342 RPVI 345 (491)
T ss_pred Cccc
Confidence 9964
No 12
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.95 E-value=3.7e-10 Score=73.12 Aligned_cols=39 Identities=41% Similarity=1.100 Sum_probs=33.8
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
|+||++.+... ++.++|||+|+..||..|++. +.+||+|
T Consensus 1 C~iC~~~~~~~-----------~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDP-----------VVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSE-----------EEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccCc-----------CEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 89999998872 578899999999999999999 9999998
No 13
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=4.3e-10 Score=98.78 Aligned_cols=51 Identities=29% Similarity=0.638 Sum_probs=43.0
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC--CCCCccccccccCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELKDSI 226 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~ 226 (249)
..++|.||||.-++ .+++.|||+||+.||-+||... ++.|||||.++..+.
T Consensus 46 ~~FdCNICLd~akd------------PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 46 GFFDCNICLDLAKD------------PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CceeeeeeccccCC------------CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 47999999999777 5566699999999999999985 446999999886544
No 14
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.88 E-value=1.6e-09 Score=81.95 Aligned_cols=60 Identities=28% Similarity=0.588 Sum_probs=42.9
Q ss_pred CccccccccccccccCCCCCCC-CccceEEeccCCccChhhHHHHHhhC--CCCCcccccccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDS-DEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELK 223 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~-~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~ 223 (249)
++..|.||...|...-....-+ ++-.++.-.|+|.||..||.+||... +..||+||++..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 4789999999998543222222 12123333499999999999999973 568999999764
No 15
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.85 E-value=1.8e-09 Score=71.45 Aligned_cols=39 Identities=36% Similarity=0.928 Sum_probs=31.1
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC---CCCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS---TTCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~---~sCPvC 218 (249)
|+||++.|.. .+.|+|||.|+..||..|++..+ ..||+|
T Consensus 1 CpiC~~~~~~------------Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD------------PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS------------EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC------------ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999998 88999999999999999998742 369988
No 16
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.84 E-value=2.1e-09 Score=79.92 Aligned_cols=63 Identities=21% Similarity=0.453 Sum_probs=50.7
Q ss_pred ccCccccccccccccccCCCCCC---CCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 162 SNEVQCCPICKEEFRVRDDVDDD---SDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 162 ~~~~~~C~ICle~f~~~~~~~~~---~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
......|+||...+..-....+. +.++.++... |+|.||..||.+||.. ++.||++|++..-.
T Consensus 17 di~id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~~ 83 (88)
T COG5194 17 DIPIDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVLA 83 (88)
T ss_pred ccccchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEEe
Confidence 33457999999998776555554 4556777887 9999999999999999 99999999987543
No 17
>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=98.80 E-value=3.7e-09 Score=65.92 Aligned_cols=39 Identities=46% Similarity=1.166 Sum_probs=33.5
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
|+||++.... ++.++|+|.||..|+..|++.++..||+|
T Consensus 1 C~iC~~~~~~------------~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKD------------PVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCC------------cEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899998433 78899999999999999999437789997
No 18
>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=98.78 E-value=5.4e-09 Score=73.60 Aligned_cols=46 Identities=30% Similarity=0.452 Sum_probs=41.4
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
..|+||++.+.. .+.++|||+|+..||..|++. +..||+|+..+..
T Consensus 2 ~~Cpi~~~~~~~------------Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD------------PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC------------CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCCh
Confidence 579999999887 667899999999999999999 9999999988743
No 19
>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=98.75 E-value=5.8e-09 Score=67.76 Aligned_cols=40 Identities=45% Similarity=1.140 Sum_probs=34.3
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHh-hCCCCCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR-HYSTTCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~-~~~~sCPvC 218 (249)
|+||++.+... +..++|+|.||..||..|++ .+...||+|
T Consensus 1 C~iC~~~~~~~-----------~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP-----------VILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE-----------EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCC-----------CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999998873 34788999999999999999 337789998
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.70 E-value=1e-08 Score=68.14 Aligned_cols=44 Identities=27% Similarity=0.699 Sum_probs=37.2
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~ 220 (249)
.|+||++.+..... ...++|+|+|+..||..+... ...||+||+
T Consensus 1 ~C~~C~~~~~~~~~---------~~l~~CgH~~C~~C~~~~~~~-~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERR---------PRLTSCGHIFCEKCLKKLKGK-SVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCC---------eEEcccCCHHHHHHHHhhcCC-CCCCcCCCC
Confidence 59999999944334 888999999999999999855 779999985
No 21
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.68 E-value=8e-09 Score=87.64 Aligned_cols=51 Identities=27% Similarity=0.709 Sum_probs=43.3
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
++.+.|+|||+.+.... .+...|||+||+.||..-++. ...||+||..|..
T Consensus 129 ~~~~~CPiCl~~~sek~----------~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV----------PVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhcc----------ccccccchhHHHHHHHHHHHh-CCCCCCcccccch
Confidence 34689999999998753 345679999999999999999 9999999987644
No 22
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.68 E-value=6.1e-09 Score=102.73 Aligned_cols=53 Identities=36% Similarity=0.901 Sum_probs=45.6
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
.+..|+||+|.+..+..+. +++|+|+|+||..|+..|++. .++||+||..+-.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~-------~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNIT-------PKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLYD 342 (543)
T ss_pred cCCeeeeechhhccccccc-------cceeecccchHHHHHHHHHHH-hCcCCcchhhhhc
Confidence 3789999999998864422 678999999999999999999 9999999995543
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.67 E-value=1e-08 Score=90.00 Aligned_cols=56 Identities=29% Similarity=0.669 Sum_probs=40.0
Q ss_pred CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-----CCCCcccccccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-----STTCPVCRYELK 223 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-----~~sCPvCR~~l~ 223 (249)
.+.+|+||||....... ..++....|+ |+|.||..||..|.+.. ..+||+||..+.
T Consensus 169 kE~eCgICmE~I~eK~~----~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRL----ENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCCccCccccccccc----cccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 46899999998754211 0111244564 99999999999999861 346999999764
No 24
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.66 E-value=5.2e-09 Score=81.37 Aligned_cols=75 Identities=20% Similarity=0.392 Sum_probs=56.7
Q ss_pred hhhheeccccccccccCccccccccccccccCCCCCCC----CccceEEec-cCCccChhhHHHHHhhCCCCCccccccc
Q 041030 148 LKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDS----DEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 148 lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~----~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
+...+.+.-.+.........|+||..-+.+-..+.+.. .++.++... |.|.||..||.+||+. ++.||+|.++-
T Consensus 29 F~lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW 107 (114)
T KOG2930|consen 29 FELKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEW 107 (114)
T ss_pred eEEeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhh-cCcCCCcCcce
Confidence 44445555556666666789999998876554444332 457788888 9999999999999999 99999998764
Q ss_pred c
Q 041030 223 K 223 (249)
Q Consensus 223 ~ 223 (249)
.
T Consensus 108 ~ 108 (114)
T KOG2930|consen 108 V 108 (114)
T ss_pred e
Confidence 3
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.59 E-value=2.6e-08 Score=94.67 Aligned_cols=51 Identities=35% Similarity=0.688 Sum_probs=44.2
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
....|+||++.|.. .+.++|+|.||..||..|+.. ...||+||..+....+
T Consensus 25 ~~l~C~IC~d~~~~------------PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~~~L 75 (397)
T TIGR00599 25 TSLRCHICKDFFDV------------PVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQESKL 75 (397)
T ss_pred cccCCCcCchhhhC------------ccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccccccC
Confidence 37899999999976 567899999999999999998 8899999998865433
No 26
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=2.4e-08 Score=73.74 Aligned_cols=63 Identities=24% Similarity=0.523 Sum_probs=46.2
Q ss_pred cccCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CCCCcccccccc
Q 041030 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--STTCPVCRYELK 223 (249)
Q Consensus 161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~sCPvCR~~l~ 223 (249)
....+.+|-||.-.|....-....+-+....++. |.|.||..||.+|+... ...||+||++..
T Consensus 16 W~~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 16 WDAPDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred EcCCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 3345679999999997654433333333344566 99999999999999984 346999999763
No 27
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=2.5e-07 Score=82.95 Aligned_cols=51 Identities=29% Similarity=0.690 Sum_probs=43.6
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHH-HHhhCCCC-CccccccccCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVP-WLRHYSTT-CPVCRYELKDSII 227 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~-WL~~~~~s-CPvCR~~l~~~~~ 227 (249)
.+..|.||++..+. ...++|||+||..||.. |=+. +.. ||+||+.+.+..+
T Consensus 214 ~d~kC~lC~e~~~~------------ps~t~CgHlFC~~Cl~~~~t~~-k~~~CplCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEV------------PSCTPCGHLFCLSCLLISWTKK-KYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCC------------cccccccchhhHHHHHHHHHhh-ccccCchhhhhccchhh
Confidence 47899999999888 66789999999999999 9777 665 9999998866543
No 28
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=2.5e-07 Score=88.93 Aligned_cols=61 Identities=31% Similarity=0.768 Sum_probs=45.6
Q ss_pred CccccccccccccccCCCCCCC-C----ccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDS-D----EVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~-~----~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
...+|+|||..+..-....+-- . .+-.+.+||.|+||..|+..|....+-.||+||..|++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 3679999999887654322111 1 12355679999999999999999636699999999975
No 29
>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=98.29 E-value=5.2e-07 Score=66.22 Aligned_cols=49 Identities=35% Similarity=0.526 Sum_probs=40.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
.+.|+|+.+-+.+ .+.+++||.|...||..||..++..||+|+..|...
T Consensus 4 ~f~CpIt~~lM~d------------PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 4 EFLCPITGELMRD------------PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GGB-TTTSSB-SS------------EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred ccCCcCcCcHhhC------------ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence 6799999999998 888999999999999999998778999999888654
No 30
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.29 E-value=1.9e-07 Score=83.93 Aligned_cols=64 Identities=23% Similarity=0.546 Sum_probs=47.1
Q ss_pred cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccCCC
Q 041030 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKDSI 226 (249)
Q Consensus 161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~ 226 (249)
+..++..|+||-..+-...+ +++--+-.-+|.|+|+||..||..|--.| +.+||.|+..+....
T Consensus 220 khl~d~vCaVCg~~~~~s~~--eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 220 KHLSDSVCAVCGQQIDVSVD--EEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CCCCcchhHhhcchheeecc--hhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence 34458899999998876552 01100125688999999999999998877 678999988775443
No 31
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.27 E-value=5.1e-07 Score=60.06 Aligned_cols=40 Identities=40% Similarity=0.973 Sum_probs=23.2
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---CCCCc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---STTCP 216 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~~sCP 216 (249)
|+||+| |...+- ..+.|+|||+|+.+||.+|++.+ ...||
T Consensus 1 CpIc~e-~~~~~n--------~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEEN--------PPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS---------EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCC--------CCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 754332 17889999999999999999962 23566
No 32
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=4.1e-07 Score=87.91 Aligned_cols=49 Identities=29% Similarity=0.695 Sum_probs=40.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----CCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~~l~~~ 225 (249)
+..|+|||+.... +..+.|||+||..||..++..+ ..+||+||..|-..
T Consensus 186 ~~~CPICL~~~~~------------p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k 238 (513)
T KOG2164|consen 186 DMQCPICLEPPSV------------PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLK 238 (513)
T ss_pred CCcCCcccCCCCc------------ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence 5799999999887 5556699999999999987773 45899999888653
No 33
>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=98.26 E-value=6.9e-07 Score=60.97 Aligned_cols=43 Identities=28% Similarity=0.862 Sum_probs=33.4
Q ss_pred ccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCcccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCR 219 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR 219 (249)
.|.||++ ....+. ...+||. |.+|..|+.+|+... +.+||+|+
T Consensus 1 ~CrIC~~-~~~~~~---------~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGD---------PLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCC---------eeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4899999 333334 6678985 899999999999773 45899995
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.18 E-value=3.6e-07 Score=84.53 Aligned_cols=50 Identities=34% Similarity=0.709 Sum_probs=45.3
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
...|-||.+-|.. .+.+||+|.||+-||...|.. +..||.|+.++....+
T Consensus 23 lLRC~IC~eyf~i------------p~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 23 LLRCGICFEYFNI------------PMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHHhHHHHHhcC------------ceeccccchHHHHHHHHHhcc-CCCCCceecccchhhh
Confidence 6799999999998 788999999999999999999 9999999998865544
No 35
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.17 E-value=6.1e-07 Score=85.48 Aligned_cols=53 Identities=34% Similarity=0.952 Sum_probs=42.6
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+..+|+||||.+-.... +++.+.|.|.||..|+..|... +|||||+-..+...
T Consensus 174 ELPTCpVCLERMD~s~~--------gi~t~~c~Hsfh~~cl~~w~~~---scpvcR~~q~p~~v 226 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTT--------GILTILCNHSFHCSCLMKWWDS---SCPVCRYCQSPSVV 226 (493)
T ss_pred cCCCcchhHhhcCcccc--------ceeeeecccccchHHHhhcccC---cChhhhhhcCcchh
Confidence 46799999999876553 2677779999999999999554 99999998774433
No 36
>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=98.13 E-value=1.8e-06 Score=79.45 Aligned_cols=56 Identities=25% Similarity=0.460 Sum_probs=41.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+..|+||+..-...... . +...+|||.||..||...+..+...||+|+..|.....
T Consensus 3 ~~~CP~Ck~~~y~np~~------k-l~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f 58 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSL------K-LMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF 58 (309)
T ss_pred CCCCCcCCCCCccCccc------c-cccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence 56899999975443320 0 22237999999999999776657789999998876543
No 37
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=9.9e-07 Score=76.57 Aligned_cols=43 Identities=42% Similarity=0.891 Sum_probs=38.9
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
+...|+||++.|.. .+.++|+|.||..||..|+.. ...||.||
T Consensus 12 ~~~~C~iC~~~~~~------------p~~l~C~H~~c~~C~~~~~~~-~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFRE------------PVLLPCGHNFCRACLTRSWEG-PLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhc------------CccccccchHhHHHHHHhcCC-CcCCcccC
Confidence 47899999999998 567999999999999999884 77899999
No 38
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=6.1e-07 Score=83.30 Aligned_cols=51 Identities=33% Similarity=0.634 Sum_probs=44.2
Q ss_pred ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+..|+|||+-++. .+..+ |.|.||.+||..-+..++++||.||+.+.....
T Consensus 43 ~v~c~icl~llk~------------tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs 94 (381)
T KOG0311|consen 43 QVICPICLSLLKK------------TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS 94 (381)
T ss_pred hhccHHHHHHHHh------------hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence 7899999999987 44454 999999999999999999999999998865443
No 39
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.00 E-value=2.6e-06 Score=77.54 Aligned_cols=49 Identities=33% Similarity=0.615 Sum_probs=43.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~ 226 (249)
...|-||.+.|.. ...++|||.||+-||...|.. +..||+||.+.....
T Consensus 25 ~lrC~IC~~~i~i------------p~~TtCgHtFCslCIR~hL~~-qp~CP~Cr~~~~esr 73 (391)
T COG5432 25 MLRCRICDCRISI------------PCETTCGHTFCSLCIRRHLGT-QPFCPVCREDPCESR 73 (391)
T ss_pred HHHhhhhhheeec------------ceecccccchhHHHHHHHhcC-CCCCccccccHHhhh
Confidence 5799999999998 667899999999999999999 999999999875443
No 40
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.84 E-value=4.6e-06 Score=85.44 Aligned_cols=55 Identities=25% Similarity=0.711 Sum_probs=40.4
Q ss_pred cCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-CCCCcccccccc
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-STTCPVCRYELK 223 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-~~sCPvCR~~l~ 223 (249)
.+-..|+||...+..-+. .-.-.+-+ |+|.||..|+.+|++.+ ++.||+||.+++
T Consensus 1467 sG~eECaICYsvL~~vdr------~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDR------SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhc------cCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 346899999998763111 00022334 99999999999999985 668999998875
No 41
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.69 E-value=1.1e-05 Score=58.86 Aligned_cols=54 Identities=19% Similarity=0.419 Sum_probs=24.8
Q ss_pred ccccccccccccccCCCCCCCCccceEEe--ccCCccChhhHHHHHhhC----------CCCCccccccccC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--PCKHLYHSDCIVPWLRHY----------STTCPVCRYELKD 224 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~WL~~~----------~~sCPvCR~~l~~ 224 (249)
+..|.||++.+...... ..++-- .|+..||..|+..||..- ...||.|+.+|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~------p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEI------PDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----------B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCc------CceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 46899999987632210 002222 399999999999999852 1259999998853
No 42
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=1.6e-05 Score=72.64 Aligned_cols=56 Identities=25% Similarity=0.419 Sum_probs=45.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGD 232 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~~~~~ 232 (249)
...|+||+..-.. .+.|+|+|.||..||.--...+...|+|||++++...+.-...
T Consensus 7 ~~eC~IC~nt~n~------------Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~~psl 62 (324)
T KOG0824|consen 7 KKECLICYNTGNC------------PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDFEPSL 62 (324)
T ss_pred CCcceeeeccCCc------------CccccccchhhhhhhcchhhcCCCCCceecCCCCcchhcchhh
Confidence 4589999998776 6679999999999998866664778999999998877654433
No 43
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.64 E-value=3.2e-05 Score=73.19 Aligned_cols=50 Identities=34% Similarity=0.859 Sum_probs=40.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCcccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYE 221 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~ 221 (249)
..+|+||++.++..... ..+.+.|+|.|-.+||.+||.+. ...||.|..+
T Consensus 4 g~tcpiclds~~~~g~h-------r~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNH-------RIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred cccCceeeeeeeecCce-------EEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 57999999999887652 26777799999999999999642 4579999654
No 44
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.61 E-value=1.1e-05 Score=57.98 Aligned_cols=44 Identities=27% Similarity=0.680 Sum_probs=23.4
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
...|++|.+-+... |....|.|+|++.||..-+.. .||+|+.+.
T Consensus 7 lLrCs~C~~~l~~p-----------v~l~~CeH~fCs~Ci~~~~~~---~CPvC~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDILKEP-----------VCLGGCEHIFCSSCIRDCIGS---ECPVCHTPA 50 (65)
T ss_dssp TTS-SSS-S--SS------------B---SSS--B-TTTGGGGTTT---B-SSS--B-
T ss_pred hcCCcHHHHHhcCC-----------ceeccCccHHHHHHhHHhcCC---CCCCcCChH
Confidence 57899999998872 334459999999999885544 599998765
No 45
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.60 E-value=1.1e-05 Score=81.33 Aligned_cols=54 Identities=26% Similarity=0.507 Sum_probs=47.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG 228 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~ 228 (249)
...|+||+..|.++.. ....+|+|+||..||..|-+. .++||+||.++....+.
T Consensus 123 ~~~CP~Ci~s~~DqL~---------~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~v~V~ 176 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLE---------ESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGEVKVL 176 (1134)
T ss_pred hhhhhHHHHHHHHHhh---------ccccccccccHHHHhhhhhhh-cccCchhhhhhheeeee
Confidence 5789999999988876 667789999999999999999 99999999998654443
No 46
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=4.7e-05 Score=71.00 Aligned_cols=49 Identities=33% Similarity=0.744 Sum_probs=41.9
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
+....|-|||.+-.+ ++.|||.|+ -|+.|.+..--+ ++.||+||+.+..
T Consensus 288 ~~gkeCVIClse~rd------------t~vLPCRHLCLCs~Ca~~Lr~q-~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSESRD------------TVVLPCRHLCLCSGCAKSLRYQ-TNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCCcc------------eEEecchhhehhHhHHHHHHHh-hcCCCccccchHh
Confidence 346899999999888 899999998 588998886656 8899999998854
No 47
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=3.1e-05 Score=72.89 Aligned_cols=53 Identities=23% Similarity=0.764 Sum_probs=39.4
Q ss_pred cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CCCCccccccccCCCC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--STTCPVCRYELKDSII 227 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~~ 227 (249)
..|.||.+-+-.... +.-+. |||+||..|+..|+... +..||+||-.++...+
T Consensus 5 A~C~Ic~d~~p~~~~---------l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~ 60 (465)
T KOG0827|consen 5 AECHICIDGRPNDHE---------LGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHV 60 (465)
T ss_pred ceeeEeccCCccccc---------cccccchhhHHHHHHHHHHHccCCccCCCCceeecccceee
Confidence 589999555544444 66666 99999999999999984 3479999965654433
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=0.00014 Score=68.18 Aligned_cols=56 Identities=30% Similarity=0.640 Sum_probs=40.9
Q ss_pred CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC------CCCCccccccccC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY------STTCPVCRYELKD 224 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~------~~sCPvCR~~l~~ 224 (249)
.+..|.||++....... .+.....|| |.|.||..||..|-... .++||.||....-
T Consensus 160 ~~k~CGICme~i~ek~~-----~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 160 SEKECGICMETINEKAA-----SERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred ccccceehhhhccccch-----hhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 37899999998766431 122245566 99999999999998442 3689999986543
No 49
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.14 E-value=0.00021 Score=68.25 Aligned_cols=47 Identities=30% Similarity=0.668 Sum_probs=43.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
++.|.||+.-|.. .+.+||||.||..||.+-+.. +..||.||.++..
T Consensus 84 ef~c~vc~~~l~~------------pv~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 84 EFECCVCSRALYP------------PVVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE 130 (398)
T ss_pred hhhhhhhHhhcCC------------CccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence 8999999998887 667799999999999998888 9999999999985
No 50
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.10 E-value=0.00022 Score=50.17 Aligned_cols=42 Identities=26% Similarity=0.621 Sum_probs=28.8
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh-CCCCCcc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH-YSTTCPV 217 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~-~~~sCPv 217 (249)
...|+|.+..|+.. |+...|+|+|-++.|..||+. +...||+
T Consensus 11 ~~~CPiT~~~~~~P-----------V~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFEDP-----------VKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-SSE-----------EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhhCC-----------cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 67999999999973 555679999999999999943 1557998
No 51
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=96.97 E-value=0.00022 Score=65.41 Aligned_cols=52 Identities=29% Similarity=0.620 Sum_probs=43.5
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----------------------CCCCcccccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----------------------STTCPVCRYE 221 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----------------------~~sCPvCR~~ 221 (249)
+.-+|.|||--|..+.. ..+++|-|+||..|+.++|+.- ...|||||..
T Consensus 114 p~gqCvICLygfa~~~~---------ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~ 184 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPA---------FTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRER 184 (368)
T ss_pred CCCceEEEEEeecCCCc---------eeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhh
Confidence 35799999999999988 8999999999999998776540 2369999998
Q ss_pred ccC
Q 041030 222 LKD 224 (249)
Q Consensus 222 l~~ 224 (249)
|..
T Consensus 185 i~~ 187 (368)
T KOG4445|consen 185 IKI 187 (368)
T ss_pred ccc
Confidence 864
No 52
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.96 E-value=0.00031 Score=67.06 Aligned_cols=51 Identities=33% Similarity=0.750 Sum_probs=43.2
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
+++..|+||...+..... ...|+|.||..||..|+.. +..||.|+..+...
T Consensus 19 ~~~l~C~~C~~vl~~p~~-----------~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~ 69 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPVQ-----------TTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQA 69 (391)
T ss_pred cccccCccccccccCCCC-----------CCCCCCcccccccchhhcc-CcCCcccccccchh
Confidence 347899999999998422 2579999999999999999 99999998887543
No 53
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00023 Score=71.89 Aligned_cols=49 Identities=16% Similarity=0.599 Sum_probs=41.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
-..|++|...++. ++..-|+|+||..||.+-+......||.|...+.+-
T Consensus 643 ~LkCs~Cn~R~Kd------------~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD------------AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred ceeCCCccCchhh------------HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 4799999999887 555669999999999999888678899998877543
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=96.88 E-value=0.00033 Score=66.44 Aligned_cols=47 Identities=36% Similarity=0.868 Sum_probs=40.4
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKD 224 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~ 224 (249)
..|-||-|.=++ |+.-||||+.|..|+..|-..- .++||.||.+|..
T Consensus 370 eLCKICaendKd------------vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 370 ELCKICAENDKD------------VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHHHHhhccCCC------------cccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 689999988665 8888999999999999997542 6789999999964
No 55
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.84 E-value=0.0003 Score=65.07 Aligned_cols=49 Identities=24% Similarity=0.631 Sum_probs=41.9
Q ss_pred CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
...+|.+|.--|.+ +.++. |-|.||+.||...|.. +++||.|...+-..
T Consensus 14 ~~itC~LC~GYliD------------ATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 14 PHITCRLCGGYLID------------ATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKT 63 (331)
T ss_pred cceehhhccceeec------------chhHHHHHHHHHHHHHHHHHHH-hccCCccceeccCc
Confidence 46799999999988 44455 9999999999999999 99999998877443
No 56
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.83 E-value=0.0002 Score=49.89 Aligned_cols=47 Identities=26% Similarity=0.556 Sum_probs=35.3
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
+.+|.||+|.-.+. +.--|||+ .|.+|-.+.++.++..||+||..+.
T Consensus 7 ~dECTICye~pvds------------VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVDS------------VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcchH------------HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 36899999986653 22349998 4788877755544999999999874
No 57
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.31 E-value=0.0036 Score=55.55 Aligned_cols=56 Identities=27% Similarity=0.593 Sum_probs=45.0
Q ss_pred cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCccccccccCCC
Q 041030 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPVCRYELKDSI 226 (249)
Q Consensus 161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPvCR~~l~~~~ 226 (249)
+++....|..|.-.+..|+. +.|-|-|+||++|+..|-..- .-.||-|.++|-+..
T Consensus 46 DsDY~pNC~LC~t~La~gdt----------~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~ 108 (299)
T KOG3970|consen 46 DSDYNPNCRLCNTPLASGDT----------TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI 108 (299)
T ss_pred hcCCCCCCceeCCccccCcc----------eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence 34557899999999998875 456799999999999997762 337999999996543
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.27 E-value=0.0013 Score=62.25 Aligned_cols=48 Identities=29% Similarity=0.842 Sum_probs=39.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRY 220 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~ 220 (249)
+.-|..|=+.+....+. .--|||.|+||..|+...|.+. -.+||-||.
T Consensus 365 ~L~Cg~CGe~~Glk~e~--------LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNER--------LQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCccc--------ccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 57899999998776542 6779999999999999998762 458999993
No 59
>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=96.08 E-value=0.0022 Score=52.56 Aligned_cols=36 Identities=22% Similarity=0.557 Sum_probs=30.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccC------CccChhhHHHHHh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK------HLYHSDCIVPWLR 209 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~------H~FH~~CI~~WL~ 209 (249)
...|.||++.+..... |+.++|+ |+||.+|+.+|-.
T Consensus 26 ~~EC~IC~~~I~~~~G---------vV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDG---------VVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCC---------EEEEecCCeehHHHHHHHHHHHHHHh
Confidence 5799999999988333 7788886 9999999999943
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.04 E-value=0.002 Score=56.15 Aligned_cols=46 Identities=24% Similarity=0.528 Sum_probs=40.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
.+.|.||.++|+. .+...|||.||..|...-++. ...|-+|-.+.-
T Consensus 196 PF~C~iCKkdy~s------------pvvt~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t~ 241 (259)
T COG5152 196 PFLCGICKKDYES------------PVVTECGHSFCSLCAIRKYQK-GDECGVCGKATY 241 (259)
T ss_pred ceeehhchhhccc------------hhhhhcchhHHHHHHHHHhcc-CCcceecchhhc
Confidence 5799999999997 566779999999999998888 889999976543
No 61
>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=96.02 E-value=0.0028 Score=48.61 Aligned_cols=33 Identities=27% Similarity=0.686 Sum_probs=27.9
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHH
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIV 205 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~ 205 (249)
.++..|+||-..+..+ . ....||+|+||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~-~---------f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNS-V---------FVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCc-e---------EEEeCCCeEEeccccc
Confidence 3478899999999874 3 7888999999999974
No 62
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.98 E-value=0.0042 Score=66.82 Aligned_cols=54 Identities=24% Similarity=0.639 Sum_probs=41.6
Q ss_pred cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---------CCCCcccccccc
Q 041030 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---------STTCPVCRYELK 223 (249)
Q Consensus 161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---------~~sCPvCR~~l~ 223 (249)
+.+.+..|-||+-+-....- ..+|.|+|+||..|...-|... --+||+|+.+|.
T Consensus 3482 kQD~DDmCmICFTE~L~AAP---------~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAP---------AIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hcccCceEEEEehhhhCCCc---------ceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 34557899999987665555 7889999999999998766652 128999998774
No 63
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0025 Score=53.94 Aligned_cols=29 Identities=38% Similarity=0.835 Sum_probs=26.8
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccCh
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHS 201 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~ 201 (249)
+.-+|.||||+++.+.. +..|||..+||+
T Consensus 176 dkGECvICLEdL~~Gdt---------IARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDT---------IARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccCCCc---------eeccceEEEeec
Confidence 35699999999999999 999999999997
No 64
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.0059 Score=57.26 Aligned_cols=44 Identities=30% Similarity=0.790 Sum_probs=34.7
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
....|.||+++.+. .+.+||||+-+ |+.-- +. ..+||+||+.+.
T Consensus 304 ~p~lcVVcl~e~~~------------~~fvpcGh~cc--ct~cs-~~-l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 304 QPDLCVVCLDEPKS------------AVFVPCGHVCC--CTLCS-KH-LPQCPVCRQRIR 347 (355)
T ss_pred CCCceEEecCCccc------------eeeecCCcEEE--chHHH-hh-CCCCchhHHHHH
Confidence 35799999999988 77899999966 66543 33 567999999774
No 65
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.63 E-value=0.013 Score=53.37 Aligned_cols=49 Identities=29% Similarity=0.589 Sum_probs=37.7
Q ss_pred cCccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhC-CCCCcccccccc
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHY-STTCPVCRYELK 223 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~ 223 (249)
..+.+|++|-+.-.. ..++ +|+|+||.-||..=+..- ..+||.|-.+..
T Consensus 237 t~~~~C~~Cg~~Pti------------P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTI------------PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCC------------CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 347899999988665 4444 499999999998855431 468999988776
No 66
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.55 E-value=0.0065 Score=41.34 Aligned_cols=45 Identities=31% Similarity=0.616 Sum_probs=22.2
Q ss_pred cccccccccccCCCCCCCCccceEEec--cCCccChhhHHHHHhhCCCCCccccccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELP--CKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
|++|.+++.... ...+| |++..+..|-..-++.+...||-||.++
T Consensus 1 cp~C~e~~d~~d----------~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETD----------KDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCC----------TT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCC----------CccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 789999983322 23455 8999999998887764478999999875
No 67
>PHA03096 p28-like protein; Provisional
Probab=95.45 E-value=0.0067 Score=55.71 Aligned_cols=52 Identities=19% Similarity=0.296 Sum_probs=36.6
Q ss_pred cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CC---CCccccccc
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--ST---TCPVCRYEL 222 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~---sCPvCR~~l 222 (249)
..|.||++....... .++....|+ |.|.|+..||..|.... .. .||+|+.-+
T Consensus 179 k~c~ic~e~~~~k~~-----~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYI-----IKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI 236 (284)
T ss_pred hhcccchhhhhhhcc-----ccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence 589999998775321 122367787 99999999999998873 22 355555443
No 68
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.29 E-value=0.014 Score=39.25 Aligned_cols=41 Identities=32% Similarity=0.840 Sum_probs=27.2
Q ss_pred cccccccccccCCCCCCCCccceEEecc--CC---ccChhhHHHHHhhC-CCCCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPC--KH---LYHSDCIVPWLRHY-STTCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC--~H---~FH~~CI~~WL~~~-~~sCPvC 218 (249)
|-||++.-.... ....|| +- ..|.+|+..|+... +.+|++|
T Consensus 1 CrIC~~~~~~~~----------~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE----------PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-----------EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC----------ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 678988866543 345675 44 78999999999962 5679887
No 69
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.10 E-value=0.0064 Score=55.75 Aligned_cols=49 Identities=22% Similarity=0.458 Sum_probs=41.9
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+.|-||...|.. .++..|+|.||..|...=++. ...|.+|-+..-..+.
T Consensus 242 f~c~icr~~f~~------------pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 242 FKCFICRKYFYR------------PVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFN 290 (313)
T ss_pred cccccccccccc------------chhhcCCceeehhhhcccccc-CCcceecccccccccc
Confidence 579999999998 666789999999999998888 8899999887655443
No 70
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.08 E-value=0.015 Score=54.75 Aligned_cols=53 Identities=28% Similarity=0.542 Sum_probs=44.0
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG 228 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~ 228 (249)
.++..|+||.-.-.. ++-.||+|.-|++||.+-|-. .+.|=.|+..+.+...+
T Consensus 420 sEd~lCpICyA~pi~------------Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~~~ld 472 (489)
T KOG4692|consen 420 SEDNLCPICYAGPIN------------AVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVIDVILD 472 (489)
T ss_pred cccccCcceecccch------------hhccCCCCchHHHHHHHHHhc-CCeeeEecceeeehhcc
Confidence 457899999876444 567899999999999999998 99999999988765444
No 71
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.012 Score=56.11 Aligned_cols=47 Identities=26% Similarity=0.526 Sum_probs=38.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPVCRY 220 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPvCR~ 220 (249)
..+|.||+++.....- ...+||+|+||+.|+..++..- .-.||-+..
T Consensus 184 lf~C~ICf~e~~G~~c---------~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHC---------FKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehhhcCcce---------eeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 6899999999877666 8899999999999999998772 225776643
No 72
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.50 E-value=0.026 Score=47.60 Aligned_cols=50 Identities=24% Similarity=0.681 Sum_probs=36.9
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccC--C---ccChhhHHHHHhhC-CCCCccccccccCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK--H---LYHSDCIVPWLRHY-STTCPVCRYELKDSI 226 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~--H---~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~ 226 (249)
.+..|-||.++-. .. .-||. . .-|.+|+..|+... ..+|++|++++....
T Consensus 7 ~~~~CRIC~~~~~--~~-----------~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~ 62 (162)
T PHA02825 7 MDKCCWICKDEYD--VV-----------TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK 62 (162)
T ss_pred CCCeeEecCCCCC--Cc-----------cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEE
Confidence 4679999988732 11 24754 4 56999999999985 557999999886543
No 73
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.48 E-value=0.022 Score=53.52 Aligned_cols=51 Identities=29% Similarity=0.610 Sum_probs=41.7
Q ss_pred ccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccC
Q 041030 162 SNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKD 224 (249)
Q Consensus 162 ~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~ 224 (249)
.++...|-||-+.+.- +..+||+|.-|--|..+.-..+ .+.||+||.+-..
T Consensus 58 DEen~~C~ICA~~~TY------------s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~ 109 (493)
T COG5236 58 DEENMNCQICAGSTTY------------SARYPCGHQICHACAVRLRALYMQKGCPLCRTETEA 109 (493)
T ss_pred ccccceeEEecCCceE------------EEeccCCchHHHHHHHHHHHHHhccCCCccccccce
Confidence 3557899999998876 7789999999999998755444 7799999998643
No 74
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.23 E-value=0.017 Score=56.91 Aligned_cols=51 Identities=25% Similarity=0.634 Sum_probs=41.1
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----CCCCccccccccCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRYELKDS 225 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~~l~~~ 225 (249)
.+...|.+|-+.-++ ..+..|.|.||.-||..+.... +-+||+|-..|.-+
T Consensus 534 k~~~~C~lc~d~aed------------~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 534 KGEVECGLCHDPAED------------YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred cCceeecccCChhhh------------hHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 346899999998776 6678899999999998887653 55899997766544
No 75
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.98 E-value=0.0039 Score=59.06 Aligned_cols=52 Identities=33% Similarity=0.652 Sum_probs=44.3
Q ss_pred cccccccccccccc-CCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030 165 VQCCPICKEEFRVR-DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226 (249)
Q Consensus 165 ~~~C~ICle~f~~~-~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~ 226 (249)
...|+||.+.++.. +. ...+-|+|.||.+||.+||.. ...||.||.+|+...
T Consensus 196 v~sl~I~~~slK~~y~k---------~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDK---------ISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPKNG 248 (465)
T ss_pred HhhhHhhHHHHHHHHHH---------HHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhhhh
Confidence 36899999998765 33 566779999999999999999 999999999997543
No 76
>PHA02862 5L protein; Provisional
Probab=93.92 E-value=0.031 Score=46.45 Aligned_cols=51 Identities=18% Similarity=0.455 Sum_probs=37.5
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCccccccccCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCRYELKDSIIG 228 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~~~ 228 (249)
+..|=||+++-.. . .-||. ..-|.+|+.+|++.. +.+|++|++++.....-
T Consensus 2 ~diCWIC~~~~~e--~-----------~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~y 58 (156)
T PHA02862 2 SDICWICNDVCDE--R-----------NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTY 58 (156)
T ss_pred CCEEEEecCcCCC--C-----------cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEcc
Confidence 3589999997322 1 24653 688999999999873 55799999998655443
No 77
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.82 E-value=0.014 Score=53.60 Aligned_cols=42 Identities=29% Similarity=0.651 Sum_probs=32.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCcc-ChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLY-HSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~F-H~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
...|+|||+.-.+ -+-|+|||+. |.+|-.. -+.||+||+.+.
T Consensus 300 ~~LC~ICmDaP~D------------CvfLeCGHmVtCt~CGkr-----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPRD------------CVFLECGHMVTCTKCGKR-----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCcc------------eEEeecCcEEeehhhccc-----cccCchHHHHHH
Confidence 5789999998776 6789999974 6666433 458999998764
No 78
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.63 E-value=0.032 Score=51.52 Aligned_cols=46 Identities=33% Similarity=0.728 Sum_probs=36.6
Q ss_pred cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccc-ccccc
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVC-RYELK 223 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvC-R~~l~ 223 (249)
..|+.|..-+.. .+.++ |+|.||.+||..-|...-..||.| |.++.
T Consensus 275 LkCplc~~Llrn------------p~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvl 322 (427)
T COG5222 275 LKCPLCHCLLRN------------PMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVL 322 (427)
T ss_pred ccCcchhhhhhC------------cccCccccchHHHHHHhhhhhhccccCCCcccccch
Confidence 789999988877 45567 999999999997665537789999 55554
No 79
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.55 E-value=0.044 Score=49.80 Aligned_cols=52 Identities=27% Similarity=0.612 Sum_probs=42.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
-..|-||-++|..+.. ++..+.|.|||.|+..|+.+-+..+...||.||...
T Consensus 3 ~~~c~~c~~~~s~~~~------~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDG------DHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCc------ccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 3589999999987632 233677889999999999998887666799999985
No 80
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.38 E-value=0.087 Score=47.50 Aligned_cols=55 Identities=22% Similarity=0.416 Sum_probs=45.5
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
..+.|+||.+.+....- +++.-||||+|..+|+.+.+.. -..||||-.++....+
T Consensus 220 ~ryiCpvtrd~LtNt~~--------ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTP--------CAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccc--------eEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccce
Confidence 46899999999987654 2444569999999999999988 9999999888876554
No 81
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.25 E-value=0.05 Score=56.13 Aligned_cols=50 Identities=32% Similarity=0.721 Sum_probs=38.4
Q ss_pred cCccccccccccccccCCCCCCCCccceEEec---cCCccChhhHHHHHhhC------CCCCcccccccc
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPWLRHY------STTCPVCRYELK 223 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~WL~~~------~~sCPvCR~~l~ 223 (249)
.....|.||.+.+....- ++. |-|+||..||..|-... .-.||.|.....
T Consensus 189 ~~~yeCmIC~e~I~~t~~-----------~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAP-----------VWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred cCceEEEEeeeeccccCC-----------ceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 457899999999987654 344 77999999999998763 125999985443
No 82
>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=93.15 E-value=0.03 Score=37.09 Aligned_cols=39 Identities=33% Similarity=0.792 Sum_probs=23.4
Q ss_pred cccccccccccCCCCCCCCccceEEe--ccCCccChhhHHHHHhhCCC--CCccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMEL--PCKHLYHSDCIVPWLRHYST--TCPVC 218 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~WL~~~~~--sCPvC 218 (249)
|.+|.+-+..|. +=- .|+-.+|..|+..+++. .. .||.|
T Consensus 1 C~~C~~iv~~G~-----------~C~~~~C~~r~H~~C~~~y~r~-~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQ-----------RCSNRDCNVRLHDDCFKKYFRH-RSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSE-----------E-SS--S--EE-HHHHHHHTTT--SS-B-TTT
T ss_pred CcccchhHeeec-----------cCCCCccCchHHHHHHHHHHhc-CCCCCCcCC
Confidence 678888877763 222 38889999999999998 44 69987
No 83
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=93.01 E-value=0.059 Score=43.18 Aligned_cols=32 Identities=19% Similarity=0.616 Sum_probs=26.2
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl 56 (249)
-..||..|+..+.+-.. +..||.|+|..++-+
T Consensus 69 ~~~~C~~C~~~~~~e~~---~~~CP~C~s~~~~i~ 100 (115)
T COG0375 69 AECWCLDCGQEVELEEL---DYRCPKCGSINLRII 100 (115)
T ss_pred cEEEeccCCCeecchhh---eeECCCCCCCceEEe
Confidence 35899999999887654 678999999998754
No 84
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.63 E-value=0.075 Score=54.91 Aligned_cols=43 Identities=30% Similarity=0.790 Sum_probs=34.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
...|..|--.+... ++..-|+|.||..|+. .. ...||-|+.++
T Consensus 840 ~skCs~C~~~LdlP-----------~VhF~CgHsyHqhC~e---~~-~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLDLP-----------FVHFLCGHSYHQHCLE---DK-EDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCccccc-----------eeeeecccHHHHHhhc---cC-cccCCccchhh
Confidence 46999999888874 5556699999999987 33 67899998855
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=92.34 E-value=0.15 Score=43.09 Aligned_cols=34 Identities=29% Similarity=0.600 Sum_probs=23.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccC-------------CccChhhHHHHHhh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-------------HLYHSDCIVPWLRH 210 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-------------H~FH~~CI~~WL~~ 210 (249)
+..|+||||---. ++.|-|. -.=|+.|+++.-+.
T Consensus 2 d~~CpICme~PHN------------AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka 48 (162)
T PF07800_consen 2 DVTCPICMEHPHN------------AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKA 48 (162)
T ss_pred CccCceeccCCCc------------eEEEEeccccCCccccccCCccchhHHHHHHHHH
Confidence 6799999998665 4455553 23478899887554
No 86
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.25 E-value=0.057 Score=48.22 Aligned_cols=51 Identities=20% Similarity=0.540 Sum_probs=37.3
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCC-CCccccccccCCCCCCC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST-TCPVCRYELKDSIIGSG 230 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~-sCPvCR~~l~~~~~~~~ 230 (249)
.+|..|.-.-. +.. ...+.|.|+||..|...- +. .||+||..+....++..
T Consensus 4 VhCn~C~~~~~-~~~---------f~LTaC~HvfC~~C~k~~----~~~~C~lCkk~ir~i~l~~s 55 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDP---------FFLTACRHVFCEPCLKAS----SPDVCPLCKKSIRIIQLNRS 55 (233)
T ss_pred EEeccccccCC-CCc---------eeeeechhhhhhhhcccC----Cccccccccceeeeeecccc
Confidence 46777766544 444 777889999999997542 33 89999999877666554
No 87
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=91.59 E-value=0.12 Score=48.24 Aligned_cols=45 Identities=22% Similarity=0.558 Sum_probs=36.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
...|+||+....... .+. =|-+||..||...+.. ++.|||=-.++
T Consensus 300 ~~~CpvClk~r~Npt------------vl~vSGyVfCY~Ci~~Yv~~-~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKKRQNPT------------VLEVSGYVFCYPCIFSYVVN-YGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhccCCCc------------eEEecceEEeHHHHHHHHHh-cCCCCccCCcc
Confidence 679999999887743 233 6999999999999999 99999965543
No 88
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=91.35 E-value=0.088 Score=48.89 Aligned_cols=43 Identities=23% Similarity=0.669 Sum_probs=30.0
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
-.|--|--.+.. . -+.+||+|+||.+|... .. -+.||.|--.|
T Consensus 91 HfCd~Cd~PI~I--Y---------GRmIPCkHvFCl~CAr~--~~-dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIAI--Y---------GRMIPCKHVFCLECARS--DS-DKICPLCDDRV 133 (389)
T ss_pred EeecccCCccee--e---------ecccccchhhhhhhhhc--Cc-cccCcCcccHH
Confidence 356666555554 2 56779999999999754 23 45899996555
No 89
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.13 E-value=0.23 Score=44.86 Aligned_cols=53 Identities=21% Similarity=0.582 Sum_probs=41.0
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
...+.|||...+|..... -|...+|||+|...+|..- .. ...||+|-.++...
T Consensus 111 ~~~~~CPvt~~~~~~~~~--------fv~l~~cG~V~s~~alke~-k~-~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHK--------FVYLRPCGCVFSEKALKEL-KK-SKKCPVCGKPFTEE 163 (260)
T ss_pred CceeECCCCCcccCCcee--------EEEEcCCCCEeeHHHHHhh-cc-cccccccCCccccC
Confidence 457899999999954433 1556689999999999986 33 56799998887644
No 90
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.76 E-value=0.15 Score=43.91 Aligned_cols=62 Identities=21% Similarity=0.496 Sum_probs=39.3
Q ss_pred cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---C-------CCCccccccccCCCC
Q 041030 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---S-------TTCPVCRYELKDSII 227 (249)
Q Consensus 161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~-------~sCPvCR~~l~~~~~ 227 (249)
+.++.-.|-||..--..|.. .++.---.+|+.-||.-|+..||..- + ..||.|-.++.-..+
T Consensus 161 kdd~~~~cgicyayqldGTi-----pDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTI-----PDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred cchhhhcccceeeeecCCcc-----ccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 33445567777654444332 11223345699999999999999862 1 259999887755443
No 91
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=90.46 E-value=0.13 Score=47.18 Aligned_cols=47 Identities=34% Similarity=0.652 Sum_probs=40.2
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~ 220 (249)
...|+||.+.+..+... +..++|+|.-|..|....... +-.||+|..
T Consensus 158 ~~ncPic~e~l~~s~~~--------~~~~~CgH~~h~~cf~e~~~~-~y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFED--------AGVLKCGHYMHSRCFEEMICE-GYTCPICSK 204 (276)
T ss_pred cCCCchhHHHhcccccc--------CCccCcccchHHHHHHHHhcc-CCCCCcccc
Confidence 44699999988877652 788999999999999998888 689999977
No 92
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=90.14 E-value=0.17 Score=35.42 Aligned_cols=34 Identities=26% Similarity=0.504 Sum_probs=26.8
Q ss_pred eEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030 190 IMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226 (249)
Q Consensus 190 v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~ 226 (249)
-+.+||+|+-+..|..-| . -+.||+|-+.+....
T Consensus 20 ~~~~pCgH~I~~~~f~~~--r-YngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 20 GTVLPCGHLICDNCFPGE--R-YNGCPFCGTPFEFDD 53 (55)
T ss_pred cccccccceeeccccChh--h-ccCCCCCCCcccCCC
Confidence 567899999999997665 3 558999988876544
No 93
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.49 E-value=0.27 Score=46.93 Aligned_cols=49 Identities=31% Similarity=0.515 Sum_probs=41.8
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC--CCCccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS--TTCPVCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~--~sCPvCR~~l 222 (249)
.+.|||=.+.-...+- .+.|.|||+-.++-|.+-.+.|. ..||.|=.+.
T Consensus 334 vF~CPVlKeqtsdeNP---------Pm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 334 VFICPVLKEQTSDENP---------PMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eeecccchhhccCCCC---------CeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 5899999998887777 89999999999999999888765 6799995443
No 94
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=88.97 E-value=0.21 Score=29.63 Aligned_cols=23 Identities=30% Similarity=0.830 Sum_probs=18.7
Q ss_pred eccCCCeeEeccCCCCCccCCCCCccce
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
|-+|...|.+.. .+||+||-.|.
T Consensus 3 CP~C~~~V~~~~-----~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPESA-----KFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchhhc-----CcCCCCCCCCc
Confidence 778999986654 59999998884
No 95
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=88.92 E-value=0.17 Score=51.76 Aligned_cols=52 Identities=25% Similarity=0.639 Sum_probs=40.3
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCC-CCccccccccCCCCCCC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST-TCPVCRYELKDSIIGSG 230 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~-sCPvCR~~l~~~~~~~~ 230 (249)
..|.||++ .. . ....+|+|.||.+|+..-+..-+. .||+||..+....+-+.
T Consensus 455 ~~c~ic~~-~~---~---------~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~ 507 (674)
T KOG1001|consen 455 HWCHICCD-LD---S---------FFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSA 507 (674)
T ss_pred cccccccc-cc---c---------ceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhc
Confidence 79999999 22 2 667789999999999987766333 59999998876665543
No 96
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.85 E-value=0.47 Score=31.42 Aligned_cols=32 Identities=19% Similarity=0.615 Sum_probs=26.2
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCccceee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
.|=|-+|...+.+.... ..+.||+|++.++..
T Consensus 3 ~y~C~~CG~~~~~~~~~-~~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 3 EYKCARCGREVELDEYG-TGVRCPYCGYRILFK 34 (46)
T ss_pred EEECCCCCCEEEECCCC-CceECCCCCCeEEEc
Confidence 58899999999887542 268999999999854
No 97
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.72 E-value=0.44 Score=33.23 Aligned_cols=31 Identities=42% Similarity=0.933 Sum_probs=27.8
Q ss_pred ccccccccccccccCCCCCCCCccceEEec-cCCccChhhH
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCI 204 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI 204 (249)
...|.+|-+.|..++. +++-| |+-.||.+|-
T Consensus 5 ~~~C~~Cg~~~~~~dD---------iVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDD---------IVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCC---------EEECCCCCCcccHHHH
Confidence 5689999999998887 88888 9999999994
No 98
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.67 E-value=0.19 Score=52.24 Aligned_cols=35 Identities=23% Similarity=0.747 Sum_probs=28.8
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHH
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPW 207 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~W 207 (249)
+....|.||...+.... ..+-||||.||++||.+-
T Consensus 815 ep~d~C~~C~~~ll~~p----------F~vf~CgH~FH~~Cl~~~ 849 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKP----------FYVFPCGHCFHRDCLIRH 849 (911)
T ss_pred cCccchHHhcchhhcCc----------ceeeeccchHHHHHHHHH
Confidence 35789999999887643 677899999999999664
No 99
>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=88.51 E-value=0.38 Score=38.29 Aligned_cols=29 Identities=17% Similarity=0.430 Sum_probs=23.2
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
..||..|...+.+... ...||.|++..++
T Consensus 70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~ 98 (115)
T TIGR00100 70 ECECEDCSEEVSPEID---LYRCPKCHGIMLQ 98 (115)
T ss_pred EEEcccCCCEEecCCc---CccCcCCcCCCcE
Confidence 4899999988877543 5779999998764
No 100
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.06 E-value=0.15 Score=51.39 Aligned_cols=45 Identities=24% Similarity=0.570 Sum_probs=35.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE 221 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~ 221 (249)
-..|.||+..|...... .+.|.|||.-|..|+..-. +.+|| |+++
T Consensus 11 ~l~c~ic~n~f~~~~~~--------Pvsl~cghtic~~c~~~ly---n~scp-~~~D 55 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLE--------PVSLQCGHTICGHCVQLLY---NASCP-TKRD 55 (861)
T ss_pred HhhchHHHHHHHHHhcC--------cccccccchHHHHHHHhHh---hccCC-CCcc
Confidence 46899999999876532 7788899999999998754 55999 6554
No 101
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.68 E-value=0.27 Score=28.25 Aligned_cols=23 Identities=30% Similarity=0.907 Sum_probs=17.2
Q ss_pred eeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
+|.+|...|.-. ..+||.|+..|
T Consensus 1 ~Cp~CG~~~~~~-----~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDD-----AKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCc-----CcchhhhCCcC
Confidence 588898887532 56999998754
No 102
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=86.60 E-value=0.56 Score=37.31 Aligned_cols=30 Identities=23% Similarity=0.738 Sum_probs=22.5
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
..||..|+..+-+... ....||.|++.-++
T Consensus 70 ~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~ 99 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ--RVRRCPQCHGDMLR 99 (114)
T ss_pred EEEcccCCCeeecCCc--cCCcCcCcCCCCcE
Confidence 4899999988776533 12569999988765
No 103
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=86.35 E-value=0.58 Score=37.14 Aligned_cols=29 Identities=24% Similarity=0.778 Sum_probs=22.2
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
.+||..|.....+... ...||.|++.-++
T Consensus 70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~ 98 (113)
T PRK12380 70 QAWCWDCSQVVEIHQH---DAQCPHCHGERLR 98 (113)
T ss_pred EEEcccCCCEEecCCc---CccCcCCCCCCcE
Confidence 4899999977776533 4569999987654
No 104
>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=85.64 E-value=0.47 Score=37.56 Aligned_cols=29 Identities=17% Similarity=0.431 Sum_probs=21.8
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
..||..|.....+... ...||.|++..++
T Consensus 70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~ 98 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF---DFSCPRCGSPDVE 98 (113)
T ss_dssp EEEETTTS-EEECHHC---CHH-SSSSSS-EE
T ss_pred cEECCCCCCEEecCCC---CCCCcCCcCCCcE
Confidence 4899999999988765 4789999998764
No 105
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.46 E-value=0.7 Score=37.82 Aligned_cols=33 Identities=18% Similarity=0.527 Sum_probs=23.0
Q ss_pred CeeeeccCCCeeEecc--CC----------------CCCccCCCCCcccee
Q 041030 22 HYFWCQSCQRTTRFRS--TD----------------PSELFCPHCSAQLYL 54 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~--~~----------------~s~~~CP~C~~gFlE 54 (249)
..|||.+|.....+.. .. .....||.|++.-++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 119 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFE 119 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcE
Confidence 4599999998877651 00 124669999987654
No 106
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=85.37 E-value=0.54 Score=44.35 Aligned_cols=57 Identities=25% Similarity=0.590 Sum_probs=36.9
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+++..|+.|+|++...++- ..-.|||-..|..|-.---+.-+..||-||..+..+.+
T Consensus 12 deed~cplcie~mditdkn--------f~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv 68 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKN--------FFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENV 68 (480)
T ss_pred cccccCcccccccccccCC--------cccCCcccHHHHHHHHHHHhhccCCChHhhhhccccce
Confidence 3355699999998776542 34456887666666322211115589999998877654
No 107
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=84.97 E-value=0.3 Score=52.67 Aligned_cols=44 Identities=30% Similarity=0.656 Sum_probs=37.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~ 220 (249)
...|.||++.+..... ...|+|.|+..|+..|+.. +..||.|+.
T Consensus 1153 ~~~c~ic~dil~~~~~-----------I~~cgh~~c~~c~~~~l~~-~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGG-----------IAGCGHEPCCRCDELWLYA-SSRCPICKS 1196 (1394)
T ss_pred ccchHHHHHHHHhcCC-----------eeeechhHhhhHHHHHHHH-hccCcchhh
Confidence 4699999999985332 3559999999999999999 999999973
No 108
>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=84.92 E-value=0.71 Score=42.52 Aligned_cols=52 Identities=25% Similarity=0.565 Sum_probs=38.6
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
.|++|+......-.- ..+.-+|+|.-|..|++.-+..|...||.|-..|...
T Consensus 2 ~Cp~CKt~~Y~np~l-------k~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDL-------KLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN 53 (300)
T ss_pred CCcccccceecCccc-------eeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence 599999876554330 0222369999999999999999788999997766543
No 109
>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=84.90 E-value=0.51 Score=44.77 Aligned_cols=30 Identities=23% Similarity=0.804 Sum_probs=23.8
Q ss_pred cCCccChhhHHHHHhhC------------CCCCccccccccC
Q 041030 195 CKHLYHSDCIVPWLRHY------------STTCPVCRYELKD 224 (249)
Q Consensus 195 C~H~FH~~CI~~WL~~~------------~~sCPvCR~~l~~ 224 (249)
|.=++|.+|+.+|+..+ +-.||+||..+.-
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 56678899999999873 3479999998753
No 110
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.85 E-value=0.61 Score=37.23 Aligned_cols=31 Identities=13% Similarity=0.359 Sum_probs=22.2
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
-.+||..|+....+... ....||.|++..++
T Consensus 70 ~~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~ 100 (117)
T PRK00564 70 VELECKDCSHVFKPNAL--DYGVCEKCHSKNVI 100 (117)
T ss_pred CEEEhhhCCCccccCCc--cCCcCcCCCCCceE
Confidence 34899999977665432 12359999998775
No 111
>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=84.70 E-value=0.51 Score=42.55 Aligned_cols=49 Identities=31% Similarity=0.647 Sum_probs=39.4
Q ss_pred ccccccccccccccCCCCCCCCccceEEe--c-cCCccChhhHHHHHhhCCCCCc--cccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--P-CKHLYHSDCIVPWLRHYSTTCP--VCRYEL 222 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--p-C~H~FH~~CI~~WL~~~~~sCP--vCR~~l 222 (249)
+..|+||..+....-. ++.| | |-|..|..|+++-|..|...|| -|-.-|
T Consensus 10 d~~CPvCksDrYLnPd---------ik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPD---------IKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCC---------eEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 6799999998776544 4443 6 9999999999999999888999 775533
No 112
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=83.85 E-value=0.71 Score=42.81 Aligned_cols=42 Identities=31% Similarity=0.725 Sum_probs=34.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEecc--CCccChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPC--KHLYHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC--~H~FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
-.+|+||.+.+... .++| ||+-|..|-.+ . .+.||.||.++.
T Consensus 48 lleCPvC~~~l~~P-------------i~QC~nGHlaCssC~~~---~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPP-------------IFQCDNGHLACSSCRTK---V-SNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCccc-------------ceecCCCcEehhhhhhh---h-cccCCccccccc
Confidence 68999999999863 4567 79999999764 4 667999999886
No 113
>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=82.68 E-value=0.4 Score=32.59 Aligned_cols=32 Identities=28% Similarity=0.729 Sum_probs=22.7
Q ss_pred ecc-CCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 193 LPC-KHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 193 LpC-~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
+.| .|+.|..|+...|.. ...||+|..+||+.
T Consensus 16 i~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 16 IKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPTK 48 (50)
T ss_dssp EE-SS-EEEHHHHHHT-SS-SSEETTTTEE----
T ss_pred eeecchhHHHHHHHHHhcc-ccCCCcccCcCccc
Confidence 346 599999999999999 99999999999864
No 114
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=82.02 E-value=0.6 Score=33.47 Aligned_cols=26 Identities=35% Similarity=0.755 Sum_probs=18.8
Q ss_pred eccCCCeeEeccCCCCCccCCCCCcc-ceeec
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQ-LYLEL 56 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~g-FlEEl 56 (249)
|..|.|.+.- ..-+||.|++. |.||-
T Consensus 7 C~~Ck~l~~~-----d~e~CP~Cgs~~~te~W 33 (64)
T COG2093 7 CKNCKRLTPE-----DTEICPVCGSTDLTEEW 33 (64)
T ss_pred HhhccccCCC-----CCccCCCCCCcccchhh
Confidence 8888876542 23589999998 77763
No 115
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.98 E-value=0.61 Score=27.36 Aligned_cols=24 Identities=33% Similarity=0.944 Sum_probs=17.0
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
..|-+|...+.. .+.+||+|+..+
T Consensus 3 ~~Cp~Cg~~~~~-----~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDP-----DAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCc-----ccccChhhCCCC
Confidence 468899985432 257999998753
No 116
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.90 E-value=0.96 Score=36.48 Aligned_cols=31 Identities=16% Similarity=0.327 Sum_probs=21.0
Q ss_pred eeeeccCCCeeEeccCCC--C--CccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDP--S--ELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~--s--~~~CP~C~~gFlE 54 (249)
..|| .|+....+..... . ...||.|++.-++
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 104 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAH 104 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCCE
Confidence 4899 9998866542111 0 1469999988765
No 117
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.32 E-value=0.84 Score=39.11 Aligned_cols=34 Identities=24% Similarity=0.598 Sum_probs=25.8
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
...|.|-+|.+.+..-.--..+..||.|++.+++
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 4789999999777664322346999999998876
No 118
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.74 E-value=2.2 Score=28.36 Aligned_cols=31 Identities=19% Similarity=0.631 Sum_probs=25.9
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCccceee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
.|=|-.|.+.+.+... ..+.||.|++..|--
T Consensus 2 ~Y~C~~Cg~~~~~~~~--~~irC~~CG~rIlyK 32 (44)
T smart00659 2 IYICGECGRENEIKSK--DVVRCRECGYRILYK 32 (44)
T ss_pred EEECCCCCCEeecCCC--CceECCCCCceEEEE
Confidence 4889999999998743 469999999999864
No 119
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=76.91 E-value=1.9 Score=35.56 Aligned_cols=55 Identities=24% Similarity=0.435 Sum_probs=38.9
Q ss_pred CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CCCCccccccccCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--STTCPVCRYELKDSII 227 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~~ 227 (249)
.-.+|.||.|...+..- .+--. ||-.-|..|-...++.. +..||+|++.+.+...
T Consensus 79 ~lYeCnIC~etS~ee~F---------LKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEERF---------LKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhhc---------CCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 47899999998665432 21112 89888988877744542 6689999999877654
No 120
>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=76.88 E-value=3 Score=25.93 Aligned_cols=28 Identities=18% Similarity=0.746 Sum_probs=21.6
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
|-|-.|...|.+... ..+.||.|+...|
T Consensus 1 Y~C~~Cg~~~~~~~~--~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKPG--DPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BSTS--STSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCCC--CcEECCcCCCeEE
Confidence 679999999998765 2489999998776
No 121
>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=76.52 E-value=1.2 Score=30.33 Aligned_cols=43 Identities=28% Similarity=0.639 Sum_probs=22.4
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----CCCCccccc
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRY 220 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~ 220 (249)
..|+|....+... ++...|.|+-+.+ +..||... .-.||+|.+
T Consensus 3 L~CPls~~~i~~P-----------~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP-----------VRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SSE-----------EEETT--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEeC-----------ccCCcCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence 4789988888763 6667799996543 45566652 225999976
No 122
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=75.88 E-value=1.3 Score=37.14 Aligned_cols=36 Identities=28% Similarity=0.497 Sum_probs=25.4
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCccceeecc
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELD 57 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEld 57 (249)
...|.|-+|.+.+..-.--..+..||.|++.+. ++|
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~-~~d 142 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAMLD-YLD 142 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCEee-ecc
Confidence 478999999977765421133689999998854 444
No 123
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=75.59 E-value=2.2 Score=29.18 Aligned_cols=32 Identities=19% Similarity=0.688 Sum_probs=25.3
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCccceee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
.|=|-.|.+.|.+-. ....+-||+|++..|--
T Consensus 6 ~Y~C~~Cg~~~~~~~-~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 6 EYKCARCGREVELDQ-ETRGIRCPYCGSRILVK 37 (49)
T ss_pred EEEhhhcCCeeehhh-ccCceeCCCCCcEEEEe
Confidence 599999999996432 23479999999998854
No 124
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=75.58 E-value=1.5 Score=45.26 Aligned_cols=25 Identities=32% Similarity=0.921 Sum_probs=21.5
Q ss_pred EeccCCccChhhHHHHHhhCCCCCcc
Q 041030 192 ELPCKHLYHSDCIVPWLRHYSTTCPV 217 (249)
Q Consensus 192 ~LpC~H~FH~~CI~~WL~~~~~sCPv 217 (249)
-.-|+|+-|.+|...|+.. ..+||.
T Consensus 1045 Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred hccccccccHHHHHHHHhc-CCcCCC
Confidence 3459999999999999999 778874
No 125
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=75.06 E-value=1.8 Score=25.23 Aligned_cols=23 Identities=35% Similarity=0.842 Sum_probs=16.2
Q ss_pred eccCCCeeEeccCCCCCccCCCCC
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCS 49 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~ 49 (249)
|..|++.+.-+.. .....||.|+
T Consensus 1 C~sC~~~i~~r~~-~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQ-AVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCccc-CceEeCCCCC
Confidence 7788877764432 3468999997
No 126
>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=75.02 E-value=3.4 Score=26.01 Aligned_cols=29 Identities=24% Similarity=0.638 Sum_probs=21.3
Q ss_pred eeeeccCCCeeEeccC--CCCCccCCCCCcc
Q 041030 23 YFWCQSCQRTTRFRST--DPSELFCPHCSAQ 51 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~--~~s~~~CP~C~~g 51 (249)
.|-|-.|...+.+... +...+.||.|++.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 5899999997665432 2345899999983
No 127
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=74.81 E-value=1.7 Score=37.67 Aligned_cols=27 Identities=22% Similarity=0.727 Sum_probs=20.7
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
+.-|||..|+-++. ...|+-|+++|-+
T Consensus 12 ~~iyWCe~cNlPl~-------~~~c~~cg~~~~~ 38 (202)
T COG5270 12 FPIYWCEKCNLPLL-------GRRCSVCGSKVEE 38 (202)
T ss_pred cceeehhhCCCccc-------cccccccCCcceE
Confidence 57899999996554 3489999977654
No 128
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=74.72 E-value=1.5 Score=39.61 Aligned_cols=53 Identities=25% Similarity=0.639 Sum_probs=38.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~ 225 (249)
...|-||.++....... ..+.||. ...|..|+..|+... +..|-+|.......
T Consensus 78 ~~~cRIc~~~~~~~~~~--------~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGL--------LLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEeccccccccc--------ccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 46899999987654310 2456763 677999999999952 66799998866544
No 129
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.51 E-value=1.1 Score=40.65 Aligned_cols=53 Identities=25% Similarity=0.574 Sum_probs=36.5
Q ss_pred CccccccccccccccCCCCCCCCccceEEecc-----CCccChhhHHHHHhhC-------CCCCccccccccC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPC-----KHLYHSDCIVPWLRHY-------STTCPVCRYELKD 224 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC-----~H~FH~~CI~~WL~~~-------~~sCPvCR~~l~~ 224 (249)
.+..|=||+..=++... ..=+=|| .|.-|..|+..|+... .-+||.|+.++-.
T Consensus 19 ~eR~CWiCF~TdeDn~~--------a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii 83 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRL--------AAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII 83 (293)
T ss_pred cceeEEEEeccCcccch--------hhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence 36789999876444221 0123355 4889999999999883 1169999998743
No 130
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.44 E-value=1.6 Score=40.51 Aligned_cols=31 Identities=26% Similarity=0.657 Sum_probs=24.3
Q ss_pred cCCccChhhHHHHHhhC------------CCCCccccccccCC
Q 041030 195 CKHLYHSDCIVPWLRHY------------STTCPVCRYELKDS 225 (249)
Q Consensus 195 C~H~FH~~CI~~WL~~~------------~~sCPvCR~~l~~~ 225 (249)
|.-++|.+|+.+|+... +-+||+||+.+.-.
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~ 367 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR 367 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence 56788899999998752 55899999987543
No 131
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.41 E-value=1.4 Score=38.64 Aligned_cols=38 Identities=32% Similarity=0.739 Sum_probs=26.8
Q ss_pred cccccccccccCCCCCCCCccceEEeccCC-ccChhhHHHHHhhCCCCCccccccc
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKH-LYHSDCIVPWLRHYSTTCPVCRYEL 222 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H-~FH~~CI~~WL~~~~~sCPvCR~~l 222 (249)
|-+|.+.=.. |..+||.| .+|..|-.. -..||+|+...
T Consensus 161 Cr~C~~~~~~------------VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGEREAT------------VLLLPCRHLCLCGICDES-----LRICPICRSPK 199 (207)
T ss_pred ceecCcCCce------------EEeecccceEeccccccc-----CccCCCCcChh
Confidence 7777665333 99999976 577788654 23599998754
No 132
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.42 E-value=1.9 Score=35.52 Aligned_cols=35 Identities=26% Similarity=0.625 Sum_probs=24.5
Q ss_pred cCeeeeccCCCeeEecc-----CCCCCccCCCCCccceee
Q 041030 21 FHYFWCQSCQRTTRFRS-----TDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~-----~~~s~~~CP~C~~gFlEE 55 (249)
...|.|-+|...+..-. ..+....||+|++.+++.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 36788999998876531 112238999999888764
No 133
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.08 E-value=1.5 Score=41.96 Aligned_cols=38 Identities=29% Similarity=0.541 Sum_probs=27.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH 210 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~ 210 (249)
...|.||+.+....+. +....-|+|.||.+|..+.+..
T Consensus 146 ~~~C~iC~~e~~~~~~--------~f~~~~C~H~fC~~C~k~~iev 183 (384)
T KOG1812|consen 146 KEECGICFVEDPEAED--------MFSVLKCGHRFCKDCVKQHIEV 183 (384)
T ss_pred cccCccCccccccHhh--------hHHHhcccchhhhHHhHHHhhh
Confidence 6799999955444322 1444569999999999988875
No 134
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=70.92 E-value=2.7 Score=26.39 Aligned_cols=30 Identities=20% Similarity=0.602 Sum_probs=22.4
Q ss_pred eeeccCCCeeEeccCC----CCCccCCCCCccce
Q 041030 24 FWCQSCQRTTRFRSTD----PSELFCPHCSAQLY 53 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~----~s~~~CP~C~~gFl 53 (249)
+=|-+|...+++.... ...+.||+|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3488999999887531 22489999998875
No 135
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=70.76 E-value=2.8 Score=30.92 Aligned_cols=30 Identities=23% Similarity=0.679 Sum_probs=14.8
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl 56 (249)
-++||.|-...... +-.|||.|+..=|..+
T Consensus 9 vlrC~aCf~~t~~~----~k~FCp~CGn~TL~rv 38 (73)
T PF08772_consen 9 VLRCHACFKITKDM----TKQFCPKCGNATLKRV 38 (73)
T ss_dssp EEE-SSS--EES-S----S--S-SSS--S--EEE
T ss_pred eEEccccccCcCCC----CceeCcccCCCcceEE
Confidence 47999999877633 3489999999988765
No 136
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=70.76 E-value=4.7 Score=30.22 Aligned_cols=55 Identities=18% Similarity=0.388 Sum_probs=25.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
...|.||=+++...... +.+ |.-.-|+---+..|..==.+.|++.||.|+..+..
T Consensus 9 ~qiCqiCGD~VGl~~~G--e~F---VAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 9 GQICQICGDDVGLTENG--EVF---VACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKR 63 (80)
T ss_dssp S-B-SSS--B--B-SSS--SB-----S-SSS-----HHHHHHHHHTS-SB-TTT--B---
T ss_pred CcccccccCccccCCCC--CEE---EEEcccCCccchhHHHHHhhcCcccccccCCCccc
Confidence 67999999998765431 112 45556888899999988778889999999987763
No 137
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=70.29 E-value=2.1 Score=41.79 Aligned_cols=36 Identities=31% Similarity=0.613 Sum_probs=31.0
Q ss_pred cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH 210 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~ 210 (249)
+++..|+||..-|+. ...|||+|..|..|...-+..
T Consensus 2 eeelkc~vc~~f~~e------------piil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFYRE------------PIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhccC------------ceEeecccHHHHHHHHhhccc
Confidence 357899999999988 788999999999999876655
No 138
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.61 E-value=3.6 Score=38.55 Aligned_cols=46 Identities=24% Similarity=0.483 Sum_probs=38.2
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC--CCCCcccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCR 219 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR 219 (249)
-+.|||=.+.-..... .+.|.|||+--++-+...-+.| ...||.|=
T Consensus 336 ~FiCPVlKe~~t~ENp---------P~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 336 LFICPVLKELCTDENP---------PVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeeccccHhhhcccCC---------CeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 5899999888777666 8899999999999998876665 55799993
No 139
>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=67.58 E-value=8.5 Score=24.99 Aligned_cols=33 Identities=15% Similarity=0.424 Sum_probs=21.8
Q ss_pred CeeeeccCCCee--EeccCCCCCccCCCCCcccee
Q 041030 22 HYFWCQSCQRTT--RFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 22 ~~yWCy~C~r~V--r~~~~~~s~~~CP~C~~gFlE 54 (249)
..|-|-.|.... .....++..+.||.|++.=++
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 358899999543 222233456999999994443
No 140
>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=66.56 E-value=9.3 Score=26.87 Aligned_cols=50 Identities=20% Similarity=0.403 Sum_probs=35.9
Q ss_pred cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~ 226 (249)
..|-.|-.++...... +.+-.=...|+.+|...-|.. .||.|-.+|...+
T Consensus 6 pnCE~C~~dLp~~s~~--------A~ICSfECTFC~~C~e~~l~~---~CPNCgGelv~RP 55 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPE--------AYICSFECTFCADCAETMLNG---VCPNCGGELVRRP 55 (57)
T ss_pred CCccccCCCCCCCCCc--------ceEEeEeCcccHHHHHHHhcC---cCcCCCCccccCC
Confidence 3677787887776521 444444578999999987644 8999998887644
No 141
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=66.23 E-value=3.1 Score=43.49 Aligned_cols=53 Identities=32% Similarity=0.770 Sum_probs=38.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCccccccccCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCRYELKDSII 227 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~~ 227 (249)
...|-||..+=..+.. ---||+ ..-|.+|+.+|+.-+ ...|-+|.+++.=+.+
T Consensus 12 ~~~CRICr~e~~~d~p----------LfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 12 KRSCRICRTEDIRDDP----------LFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred chhceeecCCCCCCCc----------CcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 5799999876444332 223665 468999999999874 5579999998865444
No 142
>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=63.63 E-value=10 Score=25.29 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=22.7
Q ss_pred eeeeccCCCeeEecc--CCCCCccCCCCCccceeec
Q 041030 23 YFWCQSCQRTTRFRS--TDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~--~~~s~~~CP~C~~gFlEEl 56 (249)
.|-|-.|.....+.. .+...+.||.|++.=++.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 588999999554432 2233578999999544443
No 143
>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=63.55 E-value=6.7 Score=23.67 Aligned_cols=38 Identities=21% Similarity=0.605 Sum_probs=24.8
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
.|..|.+.+..+.. +.. .=+..||..|. .|..|+..|.
T Consensus 1 ~C~~C~~~i~~~~~---------~~~-~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGEL---------VLR-ALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcE---------EEE-eCCccccccCC---------CCcccCCcCc
Confidence 37788888776522 222 24789998774 5778877653
No 144
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.60 E-value=4.1 Score=38.99 Aligned_cols=46 Identities=26% Similarity=0.564 Sum_probs=32.5
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
-.+|++|.-.++.... =..++-.|+|-|+..|...|... +..|..|
T Consensus 306 wr~CpkC~~~ie~~~G-------Cnhm~CrC~~~fcy~C~~~~~~~-~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEG-------CNHMTCRCGHQFCYMCGGDWKTH-NGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCC-------cceEEeeccccchhhcCcchhhC-CccccCc
Confidence 4589999887665543 00333349999999999999887 6666444
No 145
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.44 E-value=3.8 Score=42.54 Aligned_cols=47 Identities=19% Similarity=0.431 Sum_probs=32.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
+..|.-|.+..-..... =-.++.+.|+|+||+.|+.--... ++ |-.|
T Consensus 784 e~rc~~c~~~~l~~~~~-----~~~~~v~~c~h~yhk~c~~~~~~~-~~-~~~~ 830 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAA-----FDSVVVFHCGHMYHKECLMMESLR-NA-CNIE 830 (846)
T ss_pred hhhhhhhcccccccCcc-----cceeeEEEccchhhhcccccHHHh-cc-cChh
Confidence 45899999987644310 012788899999999999876555 43 5555
No 146
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=61.26 E-value=7 Score=40.49 Aligned_cols=39 Identities=21% Similarity=0.516 Sum_probs=29.9
Q ss_pred cccccccccccccCCCCCCCCccceEEe-c-cCCccChhhHHHHHhhCCCCCcc
Q 041030 166 QCCPICKEEFRVRDDVDDDSDEVMIMEL-P-CKHLYHSDCIVPWLRHYSTTCPV 217 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~~~~~~~~v~~L-p-C~H~FH~~CI~~WL~~~~~sCPv 217 (249)
..|.+|-..+.. +-.. + |+|.=|.+|+.+|+.. +.-||.
T Consensus 780 ~~CtVC~~vi~G------------~~~~c~~C~H~gH~sh~~sw~~~-~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIRG------------VDVWCQVCGHGGHDSHLKSWFFK-ASPCAK 820 (839)
T ss_pred cCceeecceeee------------eEeecccccccccHHHHHHHHhc-CCCCcc
Confidence 467777666543 3333 3 9999999999999999 888876
No 147
>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=61.15 E-value=8 Score=25.06 Aligned_cols=32 Identities=25% Similarity=0.583 Sum_probs=20.7
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl 56 (249)
|-|-.|.....+......+++|+.| |--|||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~C-G~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNC-GLVLEEN 32 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT--BBEE-T
T ss_pred CCCcCCcCCceEEcCCCCeEECCCC-CCEeecc
Confidence 5688898876444444557999999 4455553
No 148
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=60.21 E-value=6 Score=26.91 Aligned_cols=29 Identities=24% Similarity=0.742 Sum_probs=17.4
Q ss_pred eecc--CCCeeEeccCCCCC-ccCCCCCccce
Q 041030 25 WCQS--CQRTTRFRSTDPSE-LFCPHCSAQLY 53 (249)
Q Consensus 25 WCy~--C~r~Vr~~~~~~s~-~~CP~C~~gFl 53 (249)
||-. |...+......... +.|+.|+..|=
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC 51 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFC 51 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEEC
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCc
Confidence 9988 99999988765443 89999988773
No 149
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=59.50 E-value=5.8 Score=34.13 Aligned_cols=33 Identities=27% Similarity=0.662 Sum_probs=23.8
Q ss_pred ceeccccCeeeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 15 TRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 15 ~~~~rt~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
..+.+. ..|=||-|.+.+... .-+||.|||..+
T Consensus 132 I~~v~~-w~~rC~GC~~~f~~~-----~~~Cp~CG~~~~ 164 (177)
T COG1439 132 IKKVRK-WRLRCHGCKRIFPEP-----KDFCPICGSPLK 164 (177)
T ss_pred cceEee-eeEEEecCceecCCC-----CCcCCCCCCceE
Confidence 444444 358899999988722 359999999954
No 150
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=59.45 E-value=4.4 Score=35.94 Aligned_cols=42 Identities=29% Similarity=0.683 Sum_probs=35.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
-..|.+|..-.-.+ ++-=.|+-.||..|+...+.. ...||.|
T Consensus 181 lk~Cn~Ch~LvIqg-----------~rCg~c~i~~h~~c~qty~q~-~~~cphc 222 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQG-----------IRCGSCNIQYHRGCIQTYLQR-RDICPHC 222 (235)
T ss_pred HHHHhHhHHHhhee-----------eccCcccchhhhHHHHHHhcc-cCcCCch
Confidence 46899999987764 444559999999999999999 9999999
No 151
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=59.40 E-value=2.3 Score=43.53 Aligned_cols=49 Identities=22% Similarity=0.656 Sum_probs=38.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC--CCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~ 225 (249)
...|+||+..+.. ...+.|-|.|+..|+..-|... ...||+|+..+...
T Consensus 21 ~lEc~ic~~~~~~------------p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVKE------------PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hccCCceeEEeec------------cchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 6799999999887 4467799999999998755551 34799999766543
No 152
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.61 E-value=5.1 Score=38.92 Aligned_cols=36 Identities=28% Similarity=0.588 Sum_probs=31.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY 211 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~ 211 (249)
..+|-||.+.+.. . ...+.|+|.|+..|....+...
T Consensus 70 ~~~c~ic~~~~~~--~---------~~~~~c~H~~c~~cw~~yl~~k 105 (444)
T KOG1815|consen 70 DVQCGICVESYDG--E---------IIGLGCGHPFCPPCWTGYLGTK 105 (444)
T ss_pred cccCCcccCCCcc--h---------hhhcCCCcHHHHHHHHHHhhhe
Confidence 6799999999876 3 6678899999999999988873
No 153
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=57.90 E-value=8.7 Score=26.12 Aligned_cols=32 Identities=19% Similarity=0.649 Sum_probs=24.6
Q ss_pred eeeec--cCCCeeEecc-CCCCCccCCCCCcccee
Q 041030 23 YFWCQ--SCQRTTRFRS-TDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy--~C~r~Vr~~~-~~~s~~~CP~C~~gFlE 54 (249)
.-||- .|...|.... .....+.||.|+-.|--
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECC
Confidence 34999 9999988863 33446999999988864
No 154
>PRK12496 hypothetical protein; Provisional
Probab=57.48 E-value=6.4 Score=33.20 Aligned_cols=27 Identities=15% Similarity=0.428 Sum_probs=20.4
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
|.|.-|.+....... .-+||.||+..-
T Consensus 128 ~~C~gC~~~~~~~~~---~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYP---DDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCC---CCcCCCCCChhh
Confidence 789999988764322 459999998753
No 155
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.36 E-value=7.3 Score=27.86 Aligned_cols=21 Identities=29% Similarity=0.588 Sum_probs=15.7
Q ss_pred eEeccCCCCCccCCCCCccce
Q 041030 33 TRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 33 Vr~~~~~~s~~~CP~C~~gFl 53 (249)
|.+.-.+..+++||+|+--|.
T Consensus 39 V~L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 39 VFLDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEEcCCCCcEecCccccEEE
Confidence 555545567899999998774
No 156
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.59 E-value=6.3 Score=39.26 Aligned_cols=48 Identities=29% Similarity=0.706 Sum_probs=39.4
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG 228 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~ 228 (249)
....|.||++.. . .+..+|. |.-|...|+.. +..||+|+..+.....+
T Consensus 478 ~~~~~~~~~~~~-~------------~~~~~~~---~~~~l~~~~~~-~~~~pl~~~~~~~~~~~ 525 (543)
T KOG0802|consen 478 PNDVCAICYQEM-S------------ARITPCS---HALCLRKWLYV-QEVCPLCHTYMKEDDFL 525 (543)
T ss_pred ccCcchHHHHHH-H------------hcccccc---chhHHHhhhhh-ccccCCCchhhhccccc
Confidence 367999999998 2 5667788 99999999999 99999998887654443
No 157
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=55.21 E-value=4.7 Score=40.68 Aligned_cols=25 Identities=28% Similarity=0.739 Sum_probs=18.6
Q ss_pred eEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030 190 IMELPCKHLYHSDCIVPWLRHYSTTCPVC 218 (249)
Q Consensus 190 v~~LpC~H~FH~~CI~~WL~~~~~sCPvC 218 (249)
.+-..|+++||+.|... . +.-||-|
T Consensus 532 ~rC~~C~avfH~~C~~r---~-s~~CPrC 556 (580)
T KOG1829|consen 532 RRCSTCLAVFHKKCLRR---K-SPCCPRC 556 (580)
T ss_pred eeHHHHHHHHHHHHHhc---c-CCCCCch
Confidence 44556999999999543 2 4559999
No 158
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=54.54 E-value=6.7 Score=40.95 Aligned_cols=51 Identities=18% Similarity=0.260 Sum_probs=36.3
Q ss_pred CccccccccccccccCCCCCCCCccceEEec---cCCccChhhHHHHHhhC-----CCCCccccccc
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPWLRHY-----STTCPVCRYEL 222 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~WL~~~-----~~sCPvCR~~l 222 (249)
+...|.||+-+|...... .-.+| |+|.||..||..|+..- +..|+.|..-|
T Consensus 95 ~s~Ss~~C~~E~S~~~ds--------~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDS--------SNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred cccccchhheecCCcccc--------cCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 457888888888773221 22344 99999999999998762 44678886644
No 159
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=52.69 E-value=6.7 Score=34.09 Aligned_cols=39 Identities=31% Similarity=0.939 Sum_probs=26.3
Q ss_pred cccccccccc-----ccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCcccc
Q 041030 165 VQCCPICKEE-----FRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 165 ~~~C~ICle~-----f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
+..|-||-++ |+.. .+..-+ |+-+||+.|.. ...||-|-
T Consensus 152 GfiCe~C~~~~~IfPF~~~----------~~~~C~~C~~v~H~~C~~------~~~CpkC~ 196 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQID----------TTVRCPKCKSVFHKSCFR------KKSCPKCA 196 (202)
T ss_pred CCCCccCCCCCCCCCCCCC----------CeeeCCcCccccchhhcC------CCCCCCcH
Confidence 5678888652 2221 145555 99999999964 24699994
No 160
>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=52.67 E-value=11 Score=27.73 Aligned_cols=25 Identities=32% Similarity=0.941 Sum_probs=15.7
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
..|.|-.|+..+.+. .+||.|+..+
T Consensus 16 ~~~~C~~C~~~~~~~------a~CPdC~~~L 40 (70)
T PF07191_consen 16 GHYHCEACQKDYKKE------AFCPDCGQPL 40 (70)
T ss_dssp TEEEETTT--EEEEE------EE-TTT-SB-
T ss_pred CEEECccccccceec------ccCCCcccHH
Confidence 569999999887763 5899998653
No 161
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=52.09 E-value=8.6 Score=24.16 Aligned_cols=26 Identities=31% Similarity=0.772 Sum_probs=10.8
Q ss_pred eeccCCCeeEeccC--CC-CCccCCCCCc
Q 041030 25 WCQSCQRTTRFRST--DP-SELFCPHCSA 50 (249)
Q Consensus 25 WCy~C~r~Vr~~~~--~~-s~~~CP~C~~ 50 (249)
||-+|...+..+-. +. .-.+||.|+.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 57777776654422 22 2367777764
No 162
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=51.59 E-value=9.6 Score=36.71 Aligned_cols=29 Identities=21% Similarity=0.616 Sum_probs=22.5
Q ss_pred eeccCCCeeEeccCC-CCCccCCCCCccce
Q 041030 25 WCQSCQRTTRFRSTD-PSELFCPHCSAQLY 53 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~-~s~~~CP~C~~gFl 53 (249)
=|+.|+.-++++.-+ .....||+|+....
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 399999998887533 23478999999885
No 163
>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=51.52 E-value=9 Score=30.31 Aligned_cols=27 Identities=26% Similarity=0.743 Sum_probs=20.5
Q ss_pred eccCCCe-eEeccCCCCCccCCCCCccceee
Q 041030 26 CQSCQRT-TRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 26 Cy~C~r~-Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
|.+|... +-|... -++||+|+..|.-+
T Consensus 12 Cp~CG~kFYDLnk~---PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 12 CPSCGAKFYDLNKD---PIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCcchhccCCCC---CccCCCCCCccCcc
Confidence 8899754 556543 47899999999876
No 164
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=51.17 E-value=9.2 Score=26.92 Aligned_cols=36 Identities=22% Similarity=0.463 Sum_probs=18.2
Q ss_pred CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHH
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWL 208 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL 208 (249)
+...|.+|...|..-.. -..-. ||++|+.+|.....
T Consensus 8 ~~~~C~~C~~~F~~~~r---------rhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRR---------RHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BSSS----------EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCCcee---------eEccCCCCCEECCchhCCEE
Confidence 36799999999976432 22223 99999999976544
No 165
>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 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=50.65 E-value=17 Score=22.96 Aligned_cols=31 Identities=23% Similarity=0.504 Sum_probs=24.3
Q ss_pred eeccCCCeeEeccCC-CCCccCCCCCccceee
Q 041030 25 WCQSCQRTTRFRSTD-PSELFCPHCSAQLYLE 55 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~-~s~~~CP~C~~gFlEE 55 (249)
-|-.|.+..++...+ ..+.+|..|++.+++.
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBEBEE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCeeEeC
Confidence 488999999886543 4468999999988874
No 167
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=48.62 E-value=13 Score=30.17 Aligned_cols=35 Identities=20% Similarity=0.423 Sum_probs=24.8
Q ss_pred ccCeeeeccCCCeeEeccC-CCCCccCCCCCcccee
Q 041030 20 TFHYFWCQSCQRTTRFRST-DPSELFCPHCSAQLYL 54 (249)
Q Consensus 20 t~~~yWCy~C~r~Vr~~~~-~~s~~~CP~C~~gFlE 54 (249)
....|.|..|+..+..... ......|+.|++.|+.
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 3467899999988754432 2345789999988764
No 168
>PLN02189 cellulose synthase
Probab=47.57 E-value=27 Score=37.72 Aligned_cols=55 Identities=24% Similarity=0.422 Sum_probs=40.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
...|.||-+++...... +..+.-. |+---|..|-.-=.+.|+++||.|++.+..-
T Consensus 34 ~~~C~iCgd~vg~~~~g------~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~ 89 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDG------DLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRL 89 (1040)
T ss_pred CccccccccccCcCCCC------CEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhc
Confidence 56999999998754321 1133334 8888999999766666789999999988743
No 169
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=46.75 E-value=14 Score=35.81 Aligned_cols=29 Identities=21% Similarity=0.610 Sum_probs=22.5
Q ss_pred eeccCCCeeEeccCCC-CCccCCCCCccce
Q 041030 25 WCQSCQRTTRFRSTDP-SELFCPHCSAQLY 53 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~-s~~~CP~C~~gFl 53 (249)
=|+.|+.-+++..-++ ....||+|+...-
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLT 41 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCc
Confidence 3999999998875332 2478999999884
No 170
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=46.72 E-value=14 Score=23.03 Aligned_cols=28 Identities=14% Similarity=0.395 Sum_probs=20.4
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
+=|-.|+...-+.. ..+..+|+.|+.-|
T Consensus 4 ~~C~~C~~~~i~~~-~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNK-EDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEe-cCCeEEcccCCcEe
Confidence 44778999877742 34468999998766
No 171
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.40 E-value=13 Score=28.00 Aligned_cols=33 Identities=27% Similarity=0.549 Sum_probs=22.0
Q ss_pred eeccCCCeeEeccCCCCC-ccCCCCCcccee--ecc
Q 041030 25 WCQSCQRTTRFRSTDPSE-LFCPHCSAQLYL--ELD 57 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~-~~CP~C~~gFlE--Eld 57 (249)
-|-.|+-.+..+....-+ -.||+|.|-.|. |||
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLDrGELd 38 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLDRGELD 38 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeecchhHH
Confidence 388898765544322222 489999999986 554
No 172
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.32 E-value=14 Score=24.37 Aligned_cols=27 Identities=15% Similarity=0.549 Sum_probs=18.2
Q ss_pred eeccCCCeeEeccCCC-CCccCCCCCcc
Q 041030 25 WCQSCQRTTRFRSTDP-SELFCPHCSAQ 51 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~-s~~~CP~C~~g 51 (249)
||-.|...+....... ...+||.|+-.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 6888888776553322 25889999843
No 173
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=44.97 E-value=12 Score=24.11 Aligned_cols=25 Identities=24% Similarity=0.705 Sum_probs=19.6
Q ss_pred eccCCCeeEeccCCCCCccCCCCCccceee
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
|+.|++.+-+.+ ..|.+|+.-|=.+
T Consensus 1 C~~C~~~~~l~~-----f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTG-----FKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccC-----eECCccCCccccc
Confidence 788998877752 5799999998654
No 174
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=44.28 E-value=20 Score=24.86 Aligned_cols=31 Identities=23% Similarity=0.636 Sum_probs=23.5
Q ss_pred eeeccCCCeeEeccCC-CCCccCCCCCcccee
Q 041030 24 FWCQSCQRTTRFRSTD-PSELFCPHCSAQLYL 54 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~-~s~~~CP~C~~gFlE 54 (249)
+=|-.|...|.+.... -..+.||.|+..|--
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 4589999999987532 224899999988754
No 175
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.19 E-value=17 Score=22.88 Aligned_cols=27 Identities=19% Similarity=0.594 Sum_probs=18.4
Q ss_pred eccCCCeeEeccC----CCCCccCCCCCccc
Q 041030 26 CQSCQRTTRFRST----DPSELFCPHCSAQL 52 (249)
Q Consensus 26 Cy~C~r~Vr~~~~----~~s~~~CP~C~~gF 52 (249)
|-+|+....+... ....+.|+.|+.-|
T Consensus 5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 7788888777642 12347888888665
No 176
>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=43.99 E-value=9.9 Score=25.00 Aligned_cols=44 Identities=32% Similarity=0.678 Sum_probs=26.4
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh-----CCCCCcccc
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH-----YSTTCPVCR 219 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~-----~~~sCPvCR 219 (249)
.|.||......+.. +.=-.|+..||..|+..=... +.-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~---------i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDM---------IQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSE---------EEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCe---------EEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 37888883332221 333349999999998654331 033577775
No 177
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.48 E-value=10 Score=25.76 Aligned_cols=13 Identities=38% Similarity=1.045 Sum_probs=10.3
Q ss_pred ccCCCCCccceee
Q 041030 43 LFCPHCSAQLYLE 55 (249)
Q Consensus 43 ~~CP~C~~gFlEE 55 (249)
.+||.|+++|+..
T Consensus 21 ~fCP~Cg~~~m~~ 33 (50)
T PRK00432 21 KFCPRCGSGFMAE 33 (50)
T ss_pred CcCcCCCcchhec
Confidence 5999999986643
No 178
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=43.14 E-value=17 Score=24.24 Aligned_cols=39 Identities=21% Similarity=0.570 Sum_probs=27.5
Q ss_pred cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
|+.|.+.+..... ....-+..||.+|. .|=.|+..|...
T Consensus 1 C~~C~~~I~~~~~----------~~~~~~~~~H~~Cf---------~C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGTEI----------VIKAMGKFWHPECF---------KCSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSSSE----------EEEETTEEEETTTS---------BETTTTCBTTTS
T ss_pred CCCCCCCccCcEE----------EEEeCCcEEEcccc---------ccCCCCCccCCC
Confidence 6778888875443 22247899998874 699998887544
No 179
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=42.45 E-value=5.6 Score=36.75 Aligned_cols=42 Identities=21% Similarity=0.465 Sum_probs=32.3
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTC 215 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sC 215 (249)
...|.+|+++++.+.. .....|.-+||..|+-.|++.+...+
T Consensus 214 ~rvC~~CF~el~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 (288)
T KOG1729|consen 214 IRVCDICFEELEKGAR---------GDREDSLPVFHGKCYPNWLTTGAAST 255 (288)
T ss_pred ceecHHHHHHHhcccc---------cchhhccccccccccccccccccccc
Confidence 4599999999987554 45555666999999999999844343
No 180
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.02 E-value=15 Score=33.39 Aligned_cols=34 Identities=18% Similarity=0.438 Sum_probs=29.5
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH 210 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~ 210 (249)
-..|+.||+.+.. .+..|=||+|+.+||.+++..
T Consensus 43 FdcCsLtLqPc~d------------Pvit~~GylfdrEaILe~ila 76 (303)
T KOG3039|consen 43 FDCCSLTLQPCRD------------PVITPDGYLFDREAILEYILA 76 (303)
T ss_pred cceeeeecccccC------------CccCCCCeeeeHHHHHHHHHH
Confidence 5689999999998 677889999999999987654
No 181
>PLN02436 cellulose synthase A
Probab=41.67 E-value=26 Score=37.93 Aligned_cols=55 Identities=24% Similarity=0.410 Sum_probs=39.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
...|.||-+++...... +.. |.---|+---|..|..-=.+.|+++||.|++.+..
T Consensus 36 ~~iCqICGD~Vg~t~dG--e~F---VACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 36 GQTCQICGDEIELTVDG--EPF---VACNECAFPVCRPCYEYERREGNQACPQCKTRYKR 90 (1094)
T ss_pred CccccccccccCcCCCC--CEE---EeeccCCCccccchhhhhhhcCCccCcccCCchhh
Confidence 56999999998654321 111 33333888899999976666678899999998873
No 182
>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=41.60 E-value=7.1 Score=37.61 Aligned_cols=54 Identities=22% Similarity=0.436 Sum_probs=0.0
Q ss_pred ccccccccccccccCCCCC--CCCccceEEeccCCccChhhHHHHHhhC-----CCCCcccccc
Q 041030 165 VQCCPICKEEFRVRDDVDD--DSDEVMIMELPCKHLYHSDCIVPWLRHY-----STTCPVCRYE 221 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~--~~~~~~v~~LpC~H~FH~~CI~~WL~~~-----~~sCPvCR~~ 221 (249)
-.+|+|=|..+........ ....+..+-|.|||++-. ..|-... ...||+||..
T Consensus 277 rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 277 RPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp ----------------------------------------------------------------
T ss_pred CCCCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCcccc
Confidence 4689998887765443221 113466788899998764 4675431 3479999874
No 183
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.95 E-value=11 Score=21.85 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=10.8
Q ss_pred ccCCCCCccceee
Q 041030 43 LFCPHCSAQLYLE 55 (249)
Q Consensus 43 ~~CP~C~~gFlEE 55 (249)
+.||.|+..|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 5799999999764
No 184
>PRK13794 hypothetical protein; Provisional
Probab=40.58 E-value=16 Score=35.91 Aligned_cols=25 Identities=24% Similarity=0.652 Sum_probs=19.8
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
+-|||-.|+-+|.- -.|..|+..+.
T Consensus 9 ~~~wc~~cn~p~~~-------~~c~~cg~~~~ 33 (479)
T PRK13794 9 HLKWCDNCNVPVLG-------KKCAICGSETR 33 (479)
T ss_pred EEEEcCCCCCeecC-------CchhHhCCCee
Confidence 67999999977762 35999999733
No 185
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=40.06 E-value=14 Score=33.90 Aligned_cols=50 Identities=26% Similarity=0.526 Sum_probs=34.5
Q ss_pred ccccccccccc-cccCCCCCCCCccceEEec---cCCccChhhHHHHHhhC--------CCCCcccccccc
Q 041030 165 VQCCPICKEEF-RVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPWLRHY--------STTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f-~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~WL~~~--------~~sCPvCR~~l~ 223 (249)
...|.+|.+++ +.+.. ...-+ |.-++|..|+..-+..- ...||.|++-+.
T Consensus 182 ~~~celc~~ei~e~~~~---------~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 182 NVECELCEKEILETDWS---------RATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred chhhHHHHHHhccccce---------eccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 36999999999 44333 22222 89999999999844331 447999988553
No 186
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=39.92 E-value=18 Score=24.93 Aligned_cols=18 Identities=28% Similarity=0.671 Sum_probs=14.8
Q ss_pred ccCCCCCccceeecccCC
Q 041030 43 LFCPHCSAQLYLELDVSR 60 (249)
Q Consensus 43 ~~CP~C~~gFlEEld~~~ 60 (249)
+.||+|+..|.=.+|...
T Consensus 1 i~CPyCge~~~~~iD~s~ 18 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSA 18 (52)
T ss_pred CCCCCCCCeeEEEEecCC
Confidence 479999999988888654
No 187
>PF12773 DZR: Double zinc ribbon
Probab=39.35 E-value=16 Score=24.04 Aligned_cols=27 Identities=30% Similarity=0.753 Sum_probs=15.8
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcc
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
.-||-.|...+. .......+||.|+..
T Consensus 12 ~~fC~~CG~~l~--~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP--PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh--hccCCCCCCcCCcCC
Confidence 346777776666 111224677777764
No 188
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=39.19 E-value=17 Score=26.21 Aligned_cols=20 Identities=35% Similarity=0.765 Sum_probs=15.0
Q ss_pred eccCCCeeEeccCCCCCccCCCCCccc
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
|-.|.+-+. +-.||.|++..
T Consensus 8 C~~C~~i~~-------~~~Cp~Cgs~~ 27 (64)
T PRK06393 8 CKKCKRLTP-------EKTCPVHGDEK 27 (64)
T ss_pred HhhCCcccC-------CCcCCCCCCCc
Confidence 778887661 34999999954
No 189
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=39.02 E-value=26 Score=21.49 Aligned_cols=24 Identities=17% Similarity=0.559 Sum_probs=19.6
Q ss_pred eeccCCCeeEeccCCCCCccCCCCC
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCS 49 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~ 49 (249)
+|+.|+..+..+.... -+-|..|+
T Consensus 3 ~C~~C~t~L~yP~gA~-~vrCs~C~ 26 (31)
T TIGR01053 3 VCGGCRTLLMYPRGAS-SVRCALCQ 26 (31)
T ss_pred CcCCCCcEeecCCCCC-eEECCCCC
Confidence 7999999999887644 48899886
No 190
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=38.66 E-value=5.3 Score=36.43 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=23.5
Q ss_pred cCccccccccccccccCCCCCCCCccceEEe--ccCCccChhhHHHHHhhCCCCCcccccc
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMEL--PCKHLYHSDCIVPWLRHYSTTCPVCRYE 221 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~WL~~~~~sCPvCR~~ 221 (249)
+....||||=..-..+.. ...- .=.+.+|+-|-..|--. +..||.|-.+
T Consensus 170 w~~g~CPvCGs~P~~s~l---------~~~~~~G~R~L~Cs~C~t~W~~~-R~~Cp~Cg~~ 220 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVL---------RGGEREGKRYLHCSLCGTEWRFV-RIKCPYCGNT 220 (290)
T ss_dssp TT-SS-TTT---EEEEEE---------E------EEEEEETTT--EEE---TTS-TTT---
T ss_pred ccCCcCCCCCCcCceEEE---------ecCCCCccEEEEcCCCCCeeeec-CCCCcCCCCC
Confidence 345799999887655432 1110 13577888899999888 8899999543
No 191
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.56 E-value=20 Score=22.65 Aligned_cols=28 Identities=25% Similarity=0.664 Sum_probs=19.7
Q ss_pred eccCCCeeEeccC----CCCCccCCCCCccce
Q 041030 26 CQSCQRTTRFRST----DPSELFCPHCSAQLY 53 (249)
Q Consensus 26 Cy~C~r~Vr~~~~----~~s~~~CP~C~~gFl 53 (249)
|-+|+...++... ....+-||.|+.-|.
T Consensus 5 CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 7788888877653 133588888887774
No 192
>PLN02400 cellulose synthase
Probab=37.86 E-value=33 Score=37.19 Aligned_cols=62 Identities=21% Similarity=0.367 Sum_probs=43.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGD 232 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~~~~~ 232 (249)
...|.||=+++..... .... |...-|+---|..|-.==.+.|+++||.|++.+.... ||+..
T Consensus 36 gqiCqICGD~VG~t~d--Ge~F---VAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR~K-gsprV 97 (1085)
T PLN02400 36 GQICQICGDDVGVTET--GDVF---VACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRHK-GSPRV 97 (1085)
T ss_pred CceeeecccccCcCCC--CCEE---EEEccCCCccccchhheecccCCccCcccCCcccccc-CCCCC
Confidence 5699999999876543 1122 5555588889999985444556889999999987543 44443
No 193
>PF00527 E7: E7 protein, Early protein; InterPro: IPR000148 This family includes the E7 oncoprotein from various papillomaviruses []. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2F8B_A 2EWL_A 2B9D_A.
Probab=37.78 E-value=17 Score=27.84 Aligned_cols=24 Identities=29% Similarity=0.769 Sum_probs=14.1
Q ss_pred eeccCCCeeEeccCC--------------CCCccCCCC
Q 041030 25 WCQSCQRTTRFRSTD--------------PSELFCPHC 48 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~--------------~s~~~CP~C 48 (249)
.|+.|++.||+.-.. +-.++||.|
T Consensus 54 ~C~~C~~~lrl~V~as~~~Ir~lq~LLl~~L~lvCp~C 91 (92)
T PF00527_consen 54 CCGRCGKRLRLVVVASHEGIRTLQQLLLGDLSLVCPPC 91 (92)
T ss_dssp EBTTT--EEEEEEEC-HHHHHHHHHHHHCT-EE--CCC
T ss_pred ECCCCCCEEEEEEEeChhhHHHHHHHhhcCceEeCCCC
Confidence 599999999986422 235799988
No 194
>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=37.55 E-value=21 Score=29.15 Aligned_cols=28 Identities=14% Similarity=0.183 Sum_probs=20.4
Q ss_pred eeccCCCe-eEeccCCCCCccCCCCCccceee
Q 041030 25 WCQSCQRT-TRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 25 WCy~C~r~-Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
-|..|... .-|... -++||+|+..|..+
T Consensus 11 ~Cp~cg~kFYDLnk~---p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDLNRR---PAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCccccccCCC---CccCCCcCCccCcc
Confidence 38899754 555443 58999999988655
No 195
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=37.34 E-value=21 Score=23.91 Aligned_cols=37 Identities=16% Similarity=0.368 Sum_probs=25.3
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR 209 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~ 209 (249)
...|.+|-..|.....+ ..--.||++|+..|......
T Consensus 2 ~~~C~~C~~~F~~~~rk--------~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 2 ASSCMGCGKPFTLTRRR--------HHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcCcccCccccCCccc--------cccCcCcCCcChHHcCCeee
Confidence 35899999988874431 22223999999999765443
No 196
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=36.29 E-value=20 Score=25.59 Aligned_cols=19 Identities=37% Similarity=0.936 Sum_probs=14.0
Q ss_pred eccCCCeeEeccCCCCCccCCCCCcc
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
|-+|.+-+. +-.||.|++.
T Consensus 6 C~~C~~i~~-------~~~CP~Cgs~ 24 (61)
T PRK08351 6 CRHCHYITT-------EDRCPVCGSR 24 (61)
T ss_pred hhhCCcccC-------CCcCCCCcCC
Confidence 778887661 2379999984
No 197
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=36.25 E-value=35 Score=20.03 Aligned_cols=23 Identities=22% Similarity=0.728 Sum_probs=18.3
Q ss_pred eccCCCeeEeccCCCCCccCCCCC
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCS 49 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~ 49 (249)
|..|+..+..+...+ .+-|..|+
T Consensus 1 C~~Cr~~L~yp~GA~-sVrCa~C~ 23 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAP-SVRCACCH 23 (25)
T ss_pred CCCCCceEEcCCCCC-CeECCccC
Confidence 788999988887644 48898886
No 198
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=36.20 E-value=21 Score=23.24 Aligned_cols=12 Identities=25% Similarity=0.866 Sum_probs=10.1
Q ss_pred CccCCCCCccce
Q 041030 42 ELFCPHCSAQLY 53 (249)
Q Consensus 42 ~~~CP~C~~gFl 53 (249)
.+.||+|+-.|+
T Consensus 29 ~~~CpYCg~~yv 40 (40)
T PF10276_consen 29 PVVCPYCGTRYV 40 (40)
T ss_dssp EEEETTTTEEEE
T ss_pred eEECCCCCCEEC
Confidence 489999998875
No 199
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.11 E-value=30 Score=35.61 Aligned_cols=57 Identities=28% Similarity=0.542 Sum_probs=42.0
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCC-ccChhhHHHHHhhC-----CCCCccccccccCCCCCCCCCCCC
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKH-LYHSDCIVPWLRHY-----STTCPVCRYELKDSIIGSGGDNIM 235 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H-~FH~~CI~~WL~~~-----~~sCPvCR~~l~~~~~~~~~~~~~ 235 (249)
.|+||-..... ++.=.|+| .-+..|.++..... .+.||+||.++.....+.......
T Consensus 2 ~c~ic~~s~~~------------~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~~s~~~~~~~~~ 64 (669)
T KOG2231|consen 2 SCAICAFSPDF------------VGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVETKSNGDSSDAVG 64 (669)
T ss_pred CcceeecCccc------------cccccccccccchhhhhhhhhhcccccccccCcccccceeeecccccccccc
Confidence 58999887765 44455999 99999998865553 345899999998877775554443
No 200
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=36.03 E-value=47 Score=36.04 Aligned_cols=56 Identities=20% Similarity=0.338 Sum_probs=40.6
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
...|.||=+++...... +.. |.---|+---|..|-.==.+.|+++||.|++.+..-
T Consensus 17 ~qiCqICGD~vg~~~~G--e~F---VAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr~ 72 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDG--EPF---VACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKRH 72 (1079)
T ss_pred CceeeecccccCcCCCC--CEE---EEeccCCCccccchhhhhhhcCCccCCccCCchhhh
Confidence 56999999998765431 112 444448888999998655556688999999988743
No 201
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=35.88 E-value=20 Score=26.04 Aligned_cols=13 Identities=23% Similarity=0.856 Sum_probs=9.5
Q ss_pred ccChhhHHHHHhh
Q 041030 198 LYHSDCIVPWLRH 210 (249)
Q Consensus 198 ~FH~~CI~~WL~~ 210 (249)
-||..|+.+|+..
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999875
No 202
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=34.03 E-value=38 Score=32.07 Aligned_cols=46 Identities=24% Similarity=0.468 Sum_probs=32.0
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~ 220 (249)
...|-.|.++...+.. ++--.|++.||.+|=+--=.. -..||-|-.
T Consensus 330 ~~~Cf~C~~~~~~~~~---------y~C~~Ck~~FCldCDv~iHes-Lh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGR---------YRCESCKNVFCLDCDVFIHES-LHNCPGCEH 375 (378)
T ss_pred CcceeeeccccCCCCc---------EEchhccceeeccchHHHHhh-hhcCCCcCC
Confidence 4569999777766554 555559999999996543222 335999963
No 203
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=33.69 E-value=23 Score=22.02 Aligned_cols=22 Identities=32% Similarity=0.854 Sum_probs=11.3
Q ss_pred eeccCCCeeEeccCCCCCccCCCCCcc
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
-|-.|.+.+..+ ..+||.|++.
T Consensus 13 rC~~Cg~~~~pP-----r~~Cp~C~s~ 34 (37)
T PF12172_consen 13 RCRDCGRVQFPP-----RPVCPHCGSD 34 (37)
T ss_dssp E-TTT--EEES-------SEETTTT--
T ss_pred EcCCCCCEecCC-----CcCCCCcCcc
Confidence 477777765543 3699999875
No 205
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=33.61 E-value=23 Score=34.19 Aligned_cols=26 Identities=38% Similarity=0.797 Sum_probs=19.1
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
-=|++|+..+.. .....||+|+....
T Consensus 216 ~~C~~Cd~~~~~----~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 216 RSCSACHTTILP----AQEPVCPRCSTPLY 241 (403)
T ss_pred CcCCCCCCccCC----CCCcCCcCCCCccc
Confidence 349999986632 23578999999874
No 206
>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=32.58 E-value=16 Score=24.71 Aligned_cols=12 Identities=33% Similarity=0.963 Sum_probs=6.3
Q ss_pred CCCccccccccC
Q 041030 213 TTCPVCRYELKD 224 (249)
Q Consensus 213 ~sCPvCR~~l~~ 224 (249)
..||||.++|..
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 389999998854
No 207
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=32.40 E-value=16 Score=25.13 Aligned_cols=33 Identities=27% Similarity=0.697 Sum_probs=15.1
Q ss_pred eeccCCCeeEeccC---CCCCccCCCCCccceeecc
Q 041030 25 WCQSCQRTTRFRST---DPSELFCPHCSAQLYLELD 57 (249)
Q Consensus 25 WCy~C~r~Vr~~~~---~~s~~~CP~C~~gFlEEld 57 (249)
+||-|++.+..... +.+...||.|..-|=-+-|
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcC
Confidence 47888876654321 1234788888887765544
No 208
>PHA02776 E7 protein; Provisional
Probab=31.94 E-value=25 Score=27.59 Aligned_cols=26 Identities=23% Similarity=0.692 Sum_probs=19.1
Q ss_pred eeccCCCeeEeccCC--------------CCCccCCCCCc
Q 041030 25 WCQSCQRTTRFRSTD--------------PSELFCPHCSA 50 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~--------------~s~~~CP~C~~ 50 (249)
-|+.|.+.||+.-.. .-.++||.|..
T Consensus 60 ~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~ 99 (101)
T PHA02776 60 CCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAP 99 (101)
T ss_pred ECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCC
Confidence 499999999986321 23479999965
No 209
>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=31.66 E-value=25 Score=20.89 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=10.6
Q ss_pred ccccccccccccCCCCCCCCccceEEeccCCccChhhH
Q 041030 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCI 204 (249)
Q Consensus 167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI 204 (249)
.|.+|.+....+.. ..=..|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~---------Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWF---------YRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--E---------EE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCce---------EECccCCCccChhcC
Confidence 57888887765222 555669999999886
No 210
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=31.59 E-value=44 Score=31.47 Aligned_cols=55 Identities=27% Similarity=0.479 Sum_probs=38.1
Q ss_pred ccccccccccccccCCCCCCCCccceEEec--cCCccChhhHHHHHhhCCCCCccccccccCCCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP--CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSG 230 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~~~ 230 (249)
...|+||-+..-... ..-+| |++.-|..|...-... +.+||.||........-++
T Consensus 249 ~~s~p~~~~~~~~~d----------~~~lP~~~~~~~~l~~~~t~~~~-~~~~~~~rk~~~~~t~~s~ 305 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTD----------SNFLPCPCGFRLCLFCHKTISDG-DGRCPGCRKPYERNTKKSE 305 (327)
T ss_pred CCCCCCCCCcccccc----------cccccccccccchhhhhhccccc-CCCCCccCCccccCccccc
Confidence 368999999773322 23355 7887777787776666 8899999977765444333
No 211
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=31.44 E-value=48 Score=27.57 Aligned_cols=30 Identities=17% Similarity=0.453 Sum_probs=24.1
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCcc
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
-.+|-|-+|...+.+... ..-+-||.|++.
T Consensus 110 ~G~l~C~~Cg~~~~~~~~-~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHP-ERLPPCPKCGHT 139 (146)
T ss_pred CceEecccCCCEEEecCC-CcCCCCCCCCCC
Confidence 356999999999999753 335899999975
No 212
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=31.36 E-value=27 Score=20.80 Aligned_cols=14 Identities=36% Similarity=0.738 Sum_probs=7.7
Q ss_pred cCCCCCccceeecc
Q 041030 44 FCPHCSAQLYLELD 57 (249)
Q Consensus 44 ~CP~C~~gFlEEld 57 (249)
.||.|++..+.+-+
T Consensus 1 ~CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 1 TCPVCGSKLVREEG 14 (28)
T ss_dssp B-TTT--BEEE-CC
T ss_pred CcCCCCCEeEcCCC
Confidence 49999999996543
No 213
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.04 E-value=55 Score=26.15 Aligned_cols=53 Identities=25% Similarity=0.384 Sum_probs=32.9
Q ss_pred cccccccccccccCCCC-C-CCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030 166 QCCPICKEEFRVRDDVD-D-DSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219 (249)
Q Consensus 166 ~~C~ICle~f~~~~~~~-~-~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR 219 (249)
..|--|+..|....... + ...+...+--.|++.|+.+|=.-|-.. -..||-|-
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~-Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES-LHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh-ccCCcCCC
Confidence 36888888886431100 0 000111333349999999998887776 67799985
No 214
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=30.57 E-value=23 Score=21.64 Aligned_cols=24 Identities=25% Similarity=0.771 Sum_probs=10.9
Q ss_pred eccCCCeeEeccCCCCCccCCCCCcc
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
|-.|.....+.. ..-.+||.|+..
T Consensus 5 Cp~C~se~~y~D--~~~~vCp~C~~e 28 (30)
T PF08274_consen 5 CPLCGSEYTYED--GELLVCPECGHE 28 (30)
T ss_dssp -TTT-----EE---SSSEEETTTTEE
T ss_pred CCCCCCcceecc--CCEEeCCccccc
Confidence 556666665543 235788888764
No 215
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=30.43 E-value=17 Score=32.81 Aligned_cols=34 Identities=24% Similarity=0.558 Sum_probs=22.6
Q ss_pred cCeeeeccCCCeeEecc-----CCCCCccCCCCCcccee
Q 041030 21 FHYFWCQSCQRTTRFRS-----TDPSELFCPHCSAQLYL 54 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~-----~~~s~~~CP~C~~gFlE 54 (249)
....=|.-|...+...- ..++-++||+||.=.+-
T Consensus 195 l~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 195 LEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred ecCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 45577999997764321 13556999999865443
No 216
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.34 E-value=29 Score=22.77 Aligned_cols=10 Identities=40% Similarity=1.311 Sum_probs=8.7
Q ss_pred CccCCCCCcc
Q 041030 42 ELFCPHCSAQ 51 (249)
Q Consensus 42 ~~~CP~C~~g 51 (249)
.++||+|++.
T Consensus 18 g~~CP~Cg~~ 27 (46)
T PF12760_consen 18 GFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCe
Confidence 4889999987
No 217
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.18 E-value=16 Score=31.46 Aligned_cols=37 Identities=22% Similarity=0.548 Sum_probs=26.7
Q ss_pred ccccCeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 18 TRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 18 ~rt~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
......|-|-+|...+.+-..-.....||.||+...+
T Consensus 108 ~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred hccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 3445779999999777765333456899999987653
No 218
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.18 E-value=84 Score=28.82 Aligned_cols=50 Identities=14% Similarity=0.339 Sum_probs=35.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~ 225 (249)
.+.|+|=--+|..... -+...+|||+|-..-+.+. . ..+|++|...+..+
T Consensus 111 ~fiCPvtgleMng~~~--------F~~l~~CGcV~SerAlKei--k-as~C~~C~a~y~~~ 160 (293)
T KOG3113|consen 111 RFICPVTGLEMNGKYR--------FCALRCCGCVFSERALKEI--K-ASVCHVCGAAYQED 160 (293)
T ss_pred eeecccccceecceEE--------EEEEeccceeccHHHHHHh--h-hccccccCCccccc
Confidence 4788887666654322 1566789999999887764 2 66899998887544
No 219
>PRK00420 hypothetical protein; Validated
Probab=29.14 E-value=39 Score=26.93 Aligned_cols=29 Identities=17% Similarity=0.418 Sum_probs=20.7
Q ss_pred eeeccCCCeeE-eccCCCCCccCCCCCccceee
Q 041030 24 FWCQSCQRTTR-FRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 24 yWCy~C~r~Vr-~~~~~~s~~~CP~C~~gFlEE 55 (249)
.-|-.|.-++- +..+ ..+||.|+...+.+
T Consensus 24 ~~CP~Cg~pLf~lk~g---~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFELKDG---EVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceecCCC---ceECCCCCCeeeec
Confidence 56889996643 3444 79999999965543
No 220
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.14 E-value=27 Score=22.33 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=8.3
Q ss_pred ccCCCCCcccee
Q 041030 43 LFCPHCSAQLYL 54 (249)
Q Consensus 43 ~~CP~C~~gFlE 54 (249)
-.||+|+.||-=
T Consensus 3 ~~CprC~kg~Hw 14 (36)
T PF14787_consen 3 GLCPRCGKGFHW 14 (36)
T ss_dssp -C-TTTSSSCS-
T ss_pred ccCcccCCCcch
Confidence 479999999973
No 221
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=29.11 E-value=36 Score=32.94 Aligned_cols=39 Identities=23% Similarity=0.484 Sum_probs=28.8
Q ss_pred ccCeeeeccCCCeeEeccCC-CCCccCCCCCccceeeccc
Q 041030 20 TFHYFWCQSCQRTTRFRSTD-PSELFCPHCSAQLYLELDV 58 (249)
Q Consensus 20 t~~~yWCy~C~r~Vr~~~~~-~s~~~CP~C~~gFlEEld~ 58 (249)
..+.-=|-+|+.-+.++.-+ .....||+|+--.-.--+.
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~~~~~~ 54 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLTRGGDW 54 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCCccccCCCC
Confidence 56778899999999988532 2348999999877654333
No 222
>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=29.07 E-value=28 Score=23.50 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=7.3
Q ss_pred ccCCCCCccce
Q 041030 43 LFCPHCSAQLY 53 (249)
Q Consensus 43 ~~CP~C~~gFl 53 (249)
..||+|+.+|-
T Consensus 3 f~CP~C~~~~~ 13 (54)
T PF05605_consen 3 FTCPYCGKGFS 13 (54)
T ss_pred cCCCCCCCccC
Confidence 56777777554
No 223
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.88 E-value=26 Score=22.41 Aligned_cols=29 Identities=17% Similarity=0.401 Sum_probs=17.0
Q ss_pred eccCCCeeEeccCC-CCCccCCCCCcccee
Q 041030 26 CQSCQRTTRFRSTD-PSELFCPHCSAQLYL 54 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~-~s~~~CP~C~~gFlE 54 (249)
|-.|+......... -.--.||.|+|-|+.
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIWFD 31 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEEcc
Confidence 55666543322211 122479999999985
No 224
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.44 E-value=33 Score=31.87 Aligned_cols=36 Identities=19% Similarity=0.561 Sum_probs=28.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEec--cCCccChhhHHHHHhh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP--CKHLYHSDCIVPWLRH 210 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~WL~~ 210 (249)
-..|.+|.|.+++-. .++-| =.|.||.-|-.+-++.
T Consensus 268 pLcCTLC~ERLEDTH----------FVQCPSVp~HKFCFPCSResIK~ 305 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTH----------FVQCPSVPSHKFCFPCSRESIKQ 305 (352)
T ss_pred ceeehhhhhhhccCc----------eeecCCCcccceecccCHHHHHh
Confidence 479999999999854 33444 3899999999988877
No 225
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=28.39 E-value=55 Score=35.43 Aligned_cols=56 Identities=20% Similarity=0.404 Sum_probs=41.2
Q ss_pred CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224 (249)
Q Consensus 164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~ 224 (249)
....|.||=+++...... +.. |.---|+---|..|..-=.+.|+++||.|++.+..
T Consensus 14 ~~~~c~iCGd~vg~~~~G--e~F---VAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDG--QPF---VACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred CcchhhccccccCcCCCC--CEE---EEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 367999999998765431 112 44444888899999966666668899999998874
No 226
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.16 E-value=19 Score=33.19 Aligned_cols=28 Identities=25% Similarity=0.717 Sum_probs=21.6
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
.--|||-|-++-++++- ...||.|++.-
T Consensus 259 ~HiyCY~Ci~ts~~~~a---sf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 259 GHIYCYYCIATSRLWDA---SFTCPLCGENV 286 (298)
T ss_pred cceeehhhhhhhhcchh---hcccCccCCCC
Confidence 34689999988877643 47999999754
No 227
>PRK13795 hypothetical protein; Provisional
Probab=28.08 E-value=40 Score=34.43 Aligned_cols=30 Identities=20% Similarity=0.634 Sum_probs=22.0
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCccceeeccc
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDV 58 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEld~ 58 (249)
.+-|||-.|+-+|. .-.|..|+.+. .++..
T Consensus 10 ~~~~wc~~cn~p~~-------~~~c~~c~~~~-~~~~~ 39 (636)
T PRK13795 10 DHIYWCEKCNVPLL-------GKKCGICGKEG-FKVRL 39 (636)
T ss_pred eeEEEcccCCCeec-------cccccccCCCc-eEeec
Confidence 36799999997776 24699999965 44433
No 228
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.94 E-value=73 Score=23.67 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=26.2
Q ss_pred eEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030 190 IMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227 (249)
Q Consensus 190 v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~ 227 (249)
+++-.-.|.||.+|..--| +..||.|-.+|....+
T Consensus 22 A~ICtfEcTFCadCae~~l---~g~CPnCGGelv~RP~ 56 (84)
T COG3813 22 ARICTFECTFCADCAENRL---HGLCPNCGGELVARPI 56 (84)
T ss_pred eeEEEEeeehhHhHHHHhh---cCcCCCCCchhhcCcC
Confidence 4444457899999998754 4599999988876554
No 229
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.82 E-value=38 Score=31.68 Aligned_cols=51 Identities=24% Similarity=0.544 Sum_probs=40.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG 228 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~ 228 (249)
...|-||.-.+.... +.. |.|.|+..|-..|... .+-||.||....+-.-|
T Consensus 105 ~~~~~~~~g~l~vpt------------~~qg~w~qf~~~~p~~~~~~-~~~~~d~~~~~~pv~aG 156 (324)
T KOG0824|consen 105 HDICYICYGKLTVPT------------RIQGCWHQFCYVCPKSNFAM-GNDCPDCRGKISPVLAG 156 (324)
T ss_pred ccceeeeeeeEEecc------------cccCceeeeeecCCchhhhh-hhccchhhcCcCceecc
Confidence 568999998888743 233 9999999999999999 99999998866554444
No 230
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=26.74 E-value=36 Score=21.72 Aligned_cols=13 Identities=38% Similarity=0.848 Sum_probs=9.6
Q ss_pred ccCCCCCccceee
Q 041030 43 LFCPHCSAQLYLE 55 (249)
Q Consensus 43 ~~CP~C~~gFlEE 55 (249)
..||.|++.+++-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 5799999665554
No 231
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.56 E-value=39 Score=35.21 Aligned_cols=27 Identities=19% Similarity=0.514 Sum_probs=20.1
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
+..-||.|...-.++ ..||.|+|.=|.
T Consensus 461 ~~L~CH~Cg~~~~~p------~~Cp~Cgs~~L~ 487 (730)
T COG1198 461 GQLRCHYCGYQEPIP------QSCPECGSEHLR 487 (730)
T ss_pred CeeEeCCCCCCCCCC------CCCCCCCCCeeE
Confidence 667899999774432 589999999554
No 232
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=26.04 E-value=45 Score=27.36 Aligned_cols=27 Identities=26% Similarity=0.604 Sum_probs=20.5
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
+-|-.|..+.---.+ +++||.|+--++
T Consensus 29 ~hCp~Cg~PLF~KdG---~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPKCGTPLFRKDG---EVFCPVCGYREV 55 (131)
T ss_pred hhCcccCCcceeeCC---eEECCCCCceEE
Confidence 669999988654444 799999996555
No 233
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=25.87 E-value=36 Score=23.71 Aligned_cols=11 Identities=27% Similarity=1.044 Sum_probs=10.0
Q ss_pred eeeccCCCeeE
Q 041030 24 FWCQSCQRTTR 34 (249)
Q Consensus 24 yWCy~C~r~Vr 34 (249)
.|||.|+..|.
T Consensus 50 i~C~~C~~~v~ 60 (63)
T PF02148_consen 50 IWCYACDDYVY 60 (63)
T ss_dssp EEETTTTEEEE
T ss_pred EEEcCCCcEEe
Confidence 79999999886
No 234
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=25.83 E-value=29 Score=36.56 Aligned_cols=33 Identities=27% Similarity=0.545 Sum_probs=25.1
Q ss_pred CeeeeCCceeccccCeeeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030 8 PRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQL 52 (249)
Q Consensus 8 ~~~~~~~~~~~rt~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF 52 (249)
.+..|+|+|+| |++|+.+.+.. .-+|+.|+.++
T Consensus 221 ~k~a~~g~~~m-------C~~C~~tlfn~-----hw~C~~C~~~~ 253 (889)
T KOG1356|consen 221 WKRAVKGIREM-------CDRCETTLFNI-----HWRCPRCGFGV 253 (889)
T ss_pred hhhcccCcchh-------hhhhcccccce-----eEEccccCCee
Confidence 34457899886 99999987732 35899999884
No 235
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=25.39 E-value=55 Score=23.23 Aligned_cols=28 Identities=21% Similarity=0.360 Sum_probs=19.5
Q ss_pred CCCeeEeccCCCCCccCCCCCccceeec
Q 041030 29 CQRTTRFRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 29 C~r~Vr~~~~~~s~~~CP~C~~gFlEEl 56 (249)
|+-=+|-.-.....+.||.|++..+++.
T Consensus 26 C~gWmR~nFs~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 26 CNGWMRDNFSFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred CCcccccccccCCCccCCCcCCccccce
Confidence 6655554433344599999999999874
No 236
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=25.26 E-value=30 Score=31.39 Aligned_cols=32 Identities=16% Similarity=0.619 Sum_probs=13.2
Q ss_pred CeeeeccCCCe-eEecc--CCCCCccCCCCCccce
Q 041030 22 HYFWCQSCQRT-TRFRS--TDPSELFCPHCSAQLY 53 (249)
Q Consensus 22 ~~yWCy~C~r~-Vr~~~--~~~s~~~CP~C~~gFl 53 (249)
+.++|-.|... +.--. .+..|.+||.|...|-
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp HH---TTT--SS-EE--------EEE-TTT--EEE
T ss_pred HCCcCCCCCChhHhhccCCCccceeECCCCchHHh
Confidence 45789999987 33222 2245899999999884
No 237
>PF14353 CpXC: CpXC protein
Probab=25.16 E-value=39 Score=26.75 Aligned_cols=16 Identities=38% Similarity=0.908 Sum_probs=13.5
Q ss_pred CccCCCCCccceeecc
Q 041030 42 ELFCPHCSAQLYLELD 57 (249)
Q Consensus 42 ~~~CP~C~~gFlEEld 57 (249)
++.||.|+..|--|+.
T Consensus 1 ~itCP~C~~~~~~~v~ 16 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVW 16 (128)
T ss_pred CcCCCCCCCeeEEEEE
Confidence 3689999999998874
No 238
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=25.13 E-value=39 Score=33.10 Aligned_cols=22 Identities=27% Similarity=0.692 Sum_probs=18.6
Q ss_pred ccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 27 QSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 27 y~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
|.|-|-|++ +.-||.|+..|-.
T Consensus 286 HrC~RIV~v------EYrCPEC~KVFsC 307 (500)
T KOG3993|consen 286 HRCPRIVHV------EYRCPECDKVFSC 307 (500)
T ss_pred ccCCeeEEe------eecCCcccccccC
Confidence 677788886 6889999999986
No 239
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.92 E-value=33 Score=21.78 Aligned_cols=11 Identities=27% Similarity=1.032 Sum_probs=9.1
Q ss_pred CccCCCCCccc
Q 041030 42 ELFCPHCSAQL 52 (249)
Q Consensus 42 ~~~CP~C~~gF 52 (249)
++.||+|++.=
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 68999999864
No 240
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=24.83 E-value=61 Score=24.74 Aligned_cols=31 Identities=23% Similarity=0.410 Sum_probs=21.8
Q ss_pred ccccccccccccccCCCCCCCCccceEEec--cCCccChhhHHH
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP--CKHLYHSDCIVP 206 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~ 206 (249)
...|.||..... .. +.--. |...||..|...
T Consensus 55 ~~~C~iC~~~~G--~~---------i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKSGG--AC---------IKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CCcCcCCCCCCc--ee---------EEcCCCCCCcCCCHHHHHH
Confidence 569999999832 22 33333 888999999855
No 241
>PLN02195 cellulose synthase A
Probab=24.71 E-value=85 Score=33.84 Aligned_cols=54 Identities=17% Similarity=0.320 Sum_probs=39.7
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~ 223 (249)
...|.||=+.+...... ... |.---|+---|..|-.==.+.|+++||.|++.+.
T Consensus 6 ~~~c~~cgd~~~~~~~g--~~f---vaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNG--EAF---VACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCC--CeE---EEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 56899999988765321 111 4444488889999986655667889999998887
No 242
>PRK12495 hypothetical protein; Provisional
Probab=24.63 E-value=37 Score=30.28 Aligned_cols=30 Identities=20% Similarity=0.492 Sum_probs=23.1
Q ss_pred CeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
-.++|-.|..+|-.-.+ .++||.|...+-+
T Consensus 41 sa~hC~~CG~PIpa~pG---~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG---QEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccCCCC---eeECCCCCCcccc
Confidence 45899999999873333 7899999976665
No 243
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=24.51 E-value=55 Score=23.23 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=25.7
Q ss_pred eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
.-=|-.|.....+=+.+.+.+.|+.|+..+.+
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 34599999988877777778999999987763
No 244
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=24.20 E-value=65 Score=21.03 Aligned_cols=23 Identities=22% Similarity=0.781 Sum_probs=11.8
Q ss_pred eeccCCCeeEeccCCCCCccCCCCC
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCS 49 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~ 49 (249)
.|..|.-+.- +.. .-.++||.|+
T Consensus 19 ~Cp~C~~PL~-~~k-~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLM-RDK-DGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeE-Eec-CCCEECCCCC
Confidence 4677754422 211 1257777774
No 245
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=24.17 E-value=27 Score=20.70 Aligned_cols=7 Identities=43% Similarity=1.412 Sum_probs=2.6
Q ss_pred eeeccCC
Q 041030 24 FWCQSCQ 30 (249)
Q Consensus 24 yWCy~C~ 30 (249)
|||-.|+
T Consensus 22 ~~C~rCq 28 (30)
T PF06827_consen 22 YLCPRCQ 28 (30)
T ss_dssp EE-TTTC
T ss_pred eECcCCc
Confidence 4444443
No 246
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=24.15 E-value=64 Score=30.78 Aligned_cols=31 Identities=16% Similarity=0.443 Sum_probs=22.5
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
..-|+|+.|...-.+.. ...-.||.|++.+.
T Consensus 242 g~~~~C~~c~~~~~~~~--~~~~~C~~c~~~~~ 272 (382)
T PRK04338 242 GYVYYCPKCLYREEVEG--LPPEECPVCGGKFG 272 (382)
T ss_pred eeEEECCCCCcEEEecC--CCCCCCCCCCCcce
Confidence 45789999998766543 22357999988654
No 247
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=23.49 E-value=27 Score=26.10 Aligned_cols=32 Identities=25% Similarity=0.605 Sum_probs=24.2
Q ss_pred eeccCCCeeEecc-------CCCCCccCCCC--Cccceeec
Q 041030 25 WCQSCQRTTRFRS-------TDPSELFCPHC--SAQLYLEL 56 (249)
Q Consensus 25 WCy~C~r~Vr~~~-------~~~s~~~CP~C--~~gFlEEl 56 (249)
+|.+|.+++.... ...++-.|-+| +|.|++++
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~~~ 42 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQDI 42 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceeecC
Confidence 6999999987654 22467799999 68899843
No 248
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.80 E-value=56 Score=23.29 Aligned_cols=28 Identities=29% Similarity=0.581 Sum_probs=15.3
Q ss_pred eeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
-|-+|.+.+..... .....||.|+...|
T Consensus 11 ~CtSCg~~i~p~e~-~v~F~CPnCGe~~I 38 (61)
T COG2888 11 VCTSCGREIAPGET-AVKFPCPNCGEVEI 38 (61)
T ss_pred eeccCCCEeccCCc-eeEeeCCCCCceee
Confidence 56677765544322 22456777775444
No 249
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.55 E-value=53 Score=20.44 Aligned_cols=14 Identities=21% Similarity=0.740 Sum_probs=10.4
Q ss_pred ccCCCCCccceeec
Q 041030 43 LFCPHCSAQLYLEL 56 (249)
Q Consensus 43 ~~CP~C~~gFlEEl 56 (249)
-+||.|+-|.|+-+
T Consensus 2 hlcpkcgvgvl~pv 15 (36)
T PF09151_consen 2 HLCPKCGVGVLEPV 15 (36)
T ss_dssp -B-TTTSSSBEEEE
T ss_pred ccCCccCceEEEEe
Confidence 37999999999854
No 250
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.14 E-value=29 Score=33.69 Aligned_cols=42 Identities=24% Similarity=0.426 Sum_probs=29.0
Q ss_pred ccccccccccccccCCCCCCCCccc-eEEeccCCccChhhHHHHHhhC
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVM-IMELPCKHLYHSDCIVPWLRHY 211 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~-v~~LpC~H~FH~~CI~~WL~~~ 211 (249)
...|+.|....+.... -..+ -...+|+|.||..|+..|-..+
T Consensus 226 tk~CP~c~~~iek~~g-----c~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 226 TKECPKCKVPIEKDGG-----CNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred CccCCCcccchhccCC-----ccccccccCCcCCeeceeeeccccccc
Confidence 4459999999887552 0011 1222499999999999998773
No 251
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=22.08 E-value=64 Score=30.77 Aligned_cols=33 Identities=12% Similarity=0.343 Sum_probs=20.8
Q ss_pred cCeeeeccCCCeeEeccCCCCCccCCCCCccce
Q 041030 21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
..-|+|+.|.....+.........||.|++.+.
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~~ 263 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGEYH 263 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCcce
Confidence 357899999654333221233467999998654
No 252
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=21.99 E-value=46 Score=30.10 Aligned_cols=34 Identities=18% Similarity=0.459 Sum_probs=22.7
Q ss_pred eEEeccCCccChh--------hHHHHHhhC---CCCCccccccccCC
Q 041030 190 IMELPCKHLYHSD--------CIVPWLRHY---STTCPVCRYELKDS 225 (249)
Q Consensus 190 v~~LpC~H~FH~~--------CI~~WL~~~---~~sCPvCR~~l~~~ 225 (249)
+.---|+++||.+ | +|...+ ..+||+|-+.++..
T Consensus 24 f~Cd~C~~~FC~eHrsye~H~C--p~~~~~~~~v~icp~cs~pv~~~ 68 (250)
T KOG3183|consen 24 FKCDGCSGIFCLEHRSYESHHC--PKGLRIDVQVPICPLCSKPVPTK 68 (250)
T ss_pred eeeCCccchhhhccchHhhcCC--CcccccceeecccCCCCCCCCCC
Confidence 3344488888765 4 444442 45799999988776
No 253
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.67 E-value=31 Score=18.59 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=8.3
Q ss_pred cCCCCCcccee
Q 041030 44 FCPHCSAQLYL 54 (249)
Q Consensus 44 ~CP~C~~gFlE 54 (249)
.|+.|+..|-.
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 58888888763
No 254
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=21.42 E-value=64 Score=25.30 Aligned_cols=19 Identities=21% Similarity=0.609 Sum_probs=13.5
Q ss_pred eeEeccCCCCCccCCCCCccce
Q 041030 32 TTRFRSTDPSELFCPHCSAQLY 53 (249)
Q Consensus 32 ~Vr~~~~~~s~~~CP~C~~gFl 53 (249)
+|.+..+ ...||.|+..|-
T Consensus 40 ~VeIevG---~~~cP~Cge~~~ 58 (102)
T PF04475_consen 40 YVEIEVG---DTICPKCGEELD 58 (102)
T ss_pred eEEEecC---cccCCCCCCccC
Confidence 4555555 689999997664
No 255
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.33 E-value=72 Score=19.15 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=12.6
Q ss_pred eeccCCCeeEeccCCCCCccCCCCCc
Q 041030 25 WCQSCQRTTRFRSTDPSELFCPHCSA 50 (249)
Q Consensus 25 WCy~C~r~Vr~~~~~~s~~~CP~C~~ 50 (249)
||=.|......... ....+||.|+.
T Consensus 5 fC~~CG~~t~~~~~-g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPG-GWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SS-SS-EEESSSS-
T ss_pred ccCcCCccccCCCC-cCEeECCCCcC
Confidence 67778777666543 23478888875
No 256
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=21.31 E-value=65 Score=32.67 Aligned_cols=44 Identities=30% Similarity=0.572 Sum_probs=26.8
Q ss_pred cCccccccccccccccCCCCCCC-CccceEEeccCCccChhhHHH
Q 041030 163 NEVQCCPICKEEFRVRDDVDDDS-DEVMIMELPCKHLYHSDCIVP 206 (249)
Q Consensus 163 ~~~~~C~ICle~f~~~~~~~~~~-~~~~v~~LpC~H~FH~~CI~~ 206 (249)
+....|+||.|.|+.--..+++. .=.-.+.+.=|-+||..|+..
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e 555 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSE 555 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccch
Confidence 34679999999998632211111 001133443699999999855
No 257
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.89 E-value=46 Score=18.30 Aligned_cols=10 Identities=30% Similarity=1.195 Sum_probs=6.9
Q ss_pred eeeccCCCee
Q 041030 24 FWCQSCQRTT 33 (249)
Q Consensus 24 yWCy~C~r~V 33 (249)
|||-.|++..
T Consensus 1 ~~C~~C~~~f 10 (25)
T PF12874_consen 1 FYCDICNKSF 10 (25)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCCc
Confidence 6777777554
No 258
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.88 E-value=69 Score=24.98 Aligned_cols=36 Identities=17% Similarity=0.229 Sum_probs=29.9
Q ss_pred ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh
Q 041030 165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH 210 (249)
Q Consensus 165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~ 210 (249)
...|.||-..+..|+. ..-++ +-..|.+|+..=...
T Consensus 6 ewkC~VCg~~iieGqk---------FTF~~-kGsVH~eCl~~s~~~ 41 (103)
T COG4847 6 EWKCYVCGGTIIEGQK---------FTFTK-KGSVHYECLAESKRK 41 (103)
T ss_pred eeeEeeeCCEeeeccE---------EEEee-CCcchHHHHHHHHhc
Confidence 5689999999999987 77777 888999999875443
No 259
>PRK04351 hypothetical protein; Provisional
Probab=20.85 E-value=68 Score=26.68 Aligned_cols=32 Identities=31% Similarity=0.651 Sum_probs=21.1
Q ss_pred eeeeccCCCe-eEeccCCCCCccCCCCCcccee
Q 041030 23 YFWCQSCQRT-TRFRSTDPSELFCPHCSAQLYL 54 (249)
Q Consensus 23 ~yWCy~C~r~-Vr~~~~~~s~~~CP~C~~gFlE 54 (249)
.|-|-.|+.. .|.+..+.....|-.|+|.|+.
T Consensus 112 ~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRKRRINTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeeeeecCCCcEEeCCCCcEeee
Confidence 3445445544 3445556667999999998875
No 260
>PHA00616 hypothetical protein
Probab=20.42 E-value=28 Score=23.25 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=10.2
Q ss_pred ccCCCCCcccee
Q 041030 43 LFCPHCSAQLYL 54 (249)
Q Consensus 43 ~~CP~C~~gFlE 54 (249)
.-||.|+..|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 369999999986
No 261
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.41 E-value=68 Score=22.77 Aligned_cols=27 Identities=26% Similarity=0.613 Sum_probs=14.0
Q ss_pred eeeccCCCeeEeccCCCCCccCCCCCcc
Q 041030 24 FWCQSCQRTTRFRSTDPSELFCPHCSAQ 51 (249)
Q Consensus 24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~g 51 (249)
.-|-+|.+.+..... .....||.|+..
T Consensus 8 ~~CtSCg~~i~~~~~-~~~F~CPnCG~~ 34 (59)
T PRK14890 8 PKCTSCGIEIAPREK-AVKFLCPNCGEV 34 (59)
T ss_pred ccccCCCCcccCCCc-cCEeeCCCCCCe
Confidence 456666655543321 224566666654
No 262
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.29 E-value=49 Score=30.85 Aligned_cols=32 Identities=19% Similarity=0.538 Sum_probs=22.3
Q ss_pred eeccCCCeeE--eccCCCCCccCCCCCccceeec
Q 041030 25 WCQSCQRTTR--FRSTDPSELFCPHCSAQLYLEL 56 (249)
Q Consensus 25 WCy~C~r~Vr--~~~~~~s~~~CP~C~~gFlEEl 56 (249)
||+.|.+.-- +......|.+|+.||--|-+.+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~ 35 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRI 35 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeecccc
Confidence 7899988643 2233355899999987776543
No 263
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.23 E-value=73 Score=22.70 Aligned_cols=12 Identities=33% Similarity=1.060 Sum_probs=9.8
Q ss_pred CCCCcccccccc
Q 041030 212 STTCPVCRYELK 223 (249)
Q Consensus 212 ~~sCPvCR~~l~ 223 (249)
+..||+|+.++.
T Consensus 2 k~~CPlCkt~~n 13 (61)
T PF05715_consen 2 KSLCPLCKTTLN 13 (61)
T ss_pred CccCCcccchhh
Confidence 567999999883
No 264
>PRK10220 hypothetical protein; Provisional
Probab=20.13 E-value=69 Score=25.52 Aligned_cols=28 Identities=18% Similarity=0.643 Sum_probs=16.5
Q ss_pred eccCCCeeEeccCCCCCccCCCCCccceee
Q 041030 26 CQSCQRTTRFRSTDPSELFCPHCSAQLYLE 55 (249)
Q Consensus 26 Cy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE 55 (249)
|-+|+........ ...+||-|+..+-.+
T Consensus 6 CP~C~seytY~d~--~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYEDN--GMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEcCC--CeEECCcccCcCCcc
Confidence 6666666555433 246777777666543
Done!