Query 021640
Match_columns 309
No_of_seqs 331 out of 1820
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:33:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021640.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021640hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4628 Predicted E3 ubiquitin 99.6 7.3E-16 1.6E-20 145.5 8.5 82 157-238 203-286 (348)
2 PF14369 zf-RING_3: zinc-finge 99.5 6.8E-15 1.5E-19 94.4 2.8 32 6-37 1-35 (35)
3 PF13639 zf-RING_2: Ring finge 99.5 7.7E-15 1.7E-19 99.2 0.9 44 183-226 1-44 (44)
4 COG5243 HRD1 HRD ubiquitin lig 99.3 2.1E-12 4.5E-17 121.3 6.1 54 180-233 285-348 (491)
5 PF12678 zf-rbx1: RING-H2 zinc 99.2 3.9E-12 8.4E-17 95.4 2.2 45 182-226 19-73 (73)
6 PHA02929 N1R/p28-like protein; 99.2 4.9E-12 1.1E-16 114.7 3.2 69 162-230 151-227 (238)
7 COG5540 RING-finger-containing 99.2 8.1E-12 1.8E-16 114.6 1.6 51 181-231 322-373 (374)
8 KOG1002 Nucleotide excision re 99.1 1.2E-11 2.7E-16 120.5 1.7 200 6-234 375-590 (791)
9 KOG0823 Predicted E3 ubiquitin 98.9 1.5E-09 3.2E-14 96.9 4.3 55 180-237 45-102 (230)
10 PLN03208 E3 ubiquitin-protein 98.9 1.1E-09 2.5E-14 95.8 3.2 52 180-234 16-83 (193)
11 KOG0317 Predicted E3 ubiquitin 98.8 1.6E-09 3.5E-14 99.3 2.8 51 180-233 237-287 (293)
12 PF13920 zf-C3HC4_3: Zinc fing 98.8 1.8E-09 3.9E-14 74.8 1.8 46 182-230 2-48 (50)
13 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.7E-09 3.6E-14 71.1 1.4 39 185-225 1-39 (39)
14 cd00162 RING RING-finger (Real 98.8 1.7E-09 3.7E-14 71.7 1.2 44 184-229 1-45 (45)
15 PF12861 zf-Apc11: Anaphase-pr 98.8 1.6E-09 3.6E-14 82.6 1.0 54 178-231 17-83 (85)
16 KOG0802 E3 ubiquitin ligase [P 98.7 2.7E-09 6E-14 108.2 0.7 50 181-230 290-341 (543)
17 PF15227 zf-C3HC4_4: zinc fing 98.6 1.9E-08 4.1E-13 67.3 1.2 38 185-225 1-42 (42)
18 PF14634 zf-RING_5: zinc-RING 98.6 2.2E-08 4.7E-13 67.6 1.3 44 184-227 1-44 (44)
19 KOG0320 Predicted E3 ubiquitin 98.5 1.8E-08 3.9E-13 86.5 0.5 52 181-233 130-181 (187)
20 PF00097 zf-C3HC4: Zinc finger 98.5 3.2E-08 7E-13 65.4 1.6 39 185-225 1-41 (41)
21 smart00504 Ubox Modified RING 98.5 3.4E-08 7.3E-13 71.2 1.8 48 183-233 2-49 (63)
22 PHA02926 zinc finger-like prot 98.5 3.2E-08 6.9E-13 87.9 0.8 51 180-230 168-230 (242)
23 smart00184 RING Ring finger. E 98.5 4.9E-08 1.1E-12 62.3 0.9 38 185-225 1-39 (39)
24 TIGR00599 rad18 DNA repair pro 98.4 7.8E-08 1.7E-12 93.4 1.9 51 179-232 23-73 (397)
25 COG5194 APC11 Component of SCF 98.4 9.3E-08 2E-12 71.5 1.0 51 183-233 21-84 (88)
26 KOG1493 Anaphase-promoting com 98.3 1.3E-07 2.8E-12 70.2 -0.0 51 181-231 19-82 (84)
27 KOG1734 Predicted RING-contain 98.3 1.7E-07 3.7E-12 85.2 -0.1 58 181-238 223-289 (328)
28 smart00744 RINGv The RING-vari 98.2 5.6E-07 1.2E-11 62.2 0.7 42 184-226 1-49 (49)
29 COG5574 PEX10 RING-finger-cont 98.1 7.7E-07 1.7E-11 80.9 0.5 50 181-233 214-265 (271)
30 KOG2164 Predicted E3 ubiquitin 98.1 1E-06 2.2E-11 86.6 1.0 51 182-235 186-241 (513)
31 KOG0287 Postreplication repair 98.0 6.3E-07 1.4E-11 83.9 -1.2 49 180-231 21-69 (442)
32 PF13445 zf-RING_UBOX: RING-ty 98.0 1.7E-06 3.6E-11 58.1 0.8 34 185-219 1-35 (43)
33 KOG0828 Predicted E3 ubiquitin 97.9 1.8E-06 3.9E-11 84.3 0.1 51 181-231 570-635 (636)
34 PF04564 U-box: U-box domain; 97.9 4.4E-06 9.5E-11 62.5 1.3 49 182-233 4-53 (73)
35 COG5432 RAD18 RING-finger-cont 97.9 3.1E-06 6.8E-11 77.9 0.5 48 179-229 22-69 (391)
36 PF11793 FANCL_C: FANCL C-term 97.9 3.3E-06 7.1E-11 62.7 0.4 50 182-231 2-67 (70)
37 COG5219 Uncharacterized conser 97.8 2.4E-06 5.3E-11 88.7 -1.1 51 178-230 1465-1523(1525)
38 KOG2930 SCF ubiquitin ligase, 97.8 5.5E-06 1.2E-10 65.1 0.0 51 182-232 46-110 (114)
39 TIGR00570 cdk7 CDK-activating 97.8 1E-05 2.3E-10 75.9 1.7 53 182-234 3-58 (309)
40 PF14835 zf-RING_6: zf-RING of 97.7 1.1E-05 2.3E-10 58.4 1.3 55 180-238 5-59 (65)
41 KOG0804 Cytoplasmic Zn-finger 97.7 9.8E-06 2.1E-10 78.6 1.3 48 181-230 174-222 (493)
42 KOG2177 Predicted E3 ubiquitin 97.7 7.9E-06 1.7E-10 74.3 0.2 45 179-226 10-54 (386)
43 KOG4445 Uncharacterized conser 97.6 1.8E-05 3.8E-10 73.3 0.3 54 182-235 115-191 (368)
44 KOG0311 Predicted E3 ubiquitin 97.5 1.2E-05 2.7E-10 75.8 -2.4 58 172-231 33-91 (381)
45 KOG3970 Predicted E3 ubiquitin 97.4 1.8E-05 3.8E-10 70.5 -1.5 75 182-257 50-132 (299)
46 KOG4265 Predicted E3 ubiquitin 97.4 5E-05 1.1E-09 72.0 1.3 47 181-230 289-336 (349)
47 KOG0825 PHD Zn-finger protein 97.4 2.5E-05 5.5E-10 80.0 -1.3 49 182-230 123-171 (1134)
48 KOG0827 Predicted E3 ubiquitin 97.4 4.6E-05 1E-09 72.8 0.2 47 183-229 5-55 (465)
49 KOG0824 Predicted E3 ubiquitin 97.3 9.1E-05 2E-09 68.8 1.2 48 182-232 7-55 (324)
50 KOG1039 Predicted E3 ubiquitin 97.2 0.00013 2.8E-09 69.9 0.9 49 181-229 160-220 (344)
51 KOG1785 Tyrosine kinase negati 97.1 0.00022 4.9E-09 68.4 1.8 49 183-234 370-420 (563)
52 KOG0297 TNF receptor-associate 96.8 0.00088 1.9E-08 65.6 2.8 54 179-234 18-71 (391)
53 KOG0801 Predicted E3 ubiquitin 96.7 0.00068 1.5E-08 57.7 1.5 40 170-209 164-204 (205)
54 PF11789 zf-Nse: Zinc-finger o 96.7 0.00086 1.9E-08 47.8 1.6 41 182-224 11-53 (57)
55 KOG1645 RING-finger-containing 96.6 0.00074 1.6E-08 65.1 1.1 46 182-227 4-53 (463)
56 KOG4172 Predicted E3 ubiquitin 96.6 0.00023 4.9E-09 49.7 -1.9 46 182-230 7-54 (62)
57 KOG4159 Predicted E3 ubiquitin 96.5 0.00078 1.7E-08 65.8 0.6 49 180-231 82-130 (398)
58 KOG1941 Acetylcholine receptor 96.4 0.00083 1.8E-08 64.5 0.3 47 182-228 365-414 (518)
59 PF12906 RINGv: RING-variant d 96.4 0.0021 4.6E-08 43.9 1.8 40 185-225 1-47 (47)
60 COG5152 Uncharacterized conser 96.1 0.0012 2.5E-08 58.1 -0.5 44 183-229 197-240 (259)
61 KOG0978 E3 ubiquitin ligase in 96.1 0.0011 2.3E-08 68.5 -1.2 48 181-231 642-690 (698)
62 KOG2660 Locus-specific chromos 96.0 0.00089 1.9E-08 63.0 -1.8 47 181-229 14-60 (331)
63 KOG1428 Inhibitor of type V ad 95.9 0.0026 5.5E-08 69.4 0.7 50 180-229 3484-3543(3738)
64 PF10367 Vps39_2: Vacuolar sor 95.8 0.0057 1.2E-07 48.2 2.1 33 180-213 76-108 (109)
65 PF05883 Baculo_RING: Baculovi 95.4 0.0037 8.1E-08 51.9 -0.3 35 182-216 26-66 (134)
66 PHA02862 5L protein; Provision 95.3 0.0059 1.3E-07 51.2 0.5 45 183-231 3-54 (156)
67 KOG1813 Predicted E3 ubiquitin 95.2 0.0072 1.6E-07 56.2 1.0 44 183-229 242-285 (313)
68 KOG4692 Predicted E3 ubiquitin 95.2 0.012 2.6E-07 56.0 2.3 51 181-234 421-471 (489)
69 KOG1814 Predicted E3 ubiquitin 94.9 0.0051 1.1E-07 59.6 -0.9 47 181-227 183-237 (445)
70 PHA02825 LAP/PHD finger-like p 94.8 0.0099 2.2E-07 50.7 0.7 49 180-232 6-61 (162)
71 KOG3039 Uncharacterized conser 94.6 0.029 6.2E-07 51.1 3.1 71 165-235 194-275 (303)
72 KOG2879 Predicted E3 ubiquitin 94.5 0.021 4.6E-07 52.7 2.2 48 181-230 238-287 (298)
73 PF04641 Rtf2: Rtf2 RING-finge 94.5 0.059 1.3E-06 49.9 5.0 91 142-233 58-164 (260)
74 PF08746 zf-RING-like: RING-li 94.4 0.01 2.2E-07 39.7 -0.3 41 185-225 1-43 (43)
75 PF14447 Prok-RING_4: Prokaryo 94.3 0.034 7.4E-07 39.1 2.3 46 183-233 8-53 (55)
76 KOG1571 Predicted E3 ubiquitin 94.3 0.025 5.4E-07 54.1 2.0 43 182-230 305-347 (355)
77 COG0375 HybF Zn finger protein 94.2 0.029 6.4E-07 45.5 2.0 33 6-38 69-101 (115)
78 KOG1952 Transcription factor N 94.0 0.016 3.5E-07 60.6 0.3 47 181-227 190-244 (950)
79 KOG0827 Predicted E3 ubiquitin 93.8 0.0033 7.2E-08 60.4 -4.8 51 182-232 196-247 (465)
80 KOG4739 Uncharacterized protei 93.7 0.032 6.9E-07 50.7 1.5 48 184-234 5-52 (233)
81 KOG0826 Predicted E3 ubiquitin 93.5 0.058 1.3E-06 51.0 2.9 46 182-229 300-345 (357)
82 PF14570 zf-RING_4: RING/Ubox 93.2 0.035 7.6E-07 38.0 0.7 44 185-229 1-47 (48)
83 KOG4275 Predicted E3 ubiquitin 92.9 0.033 7.1E-07 51.9 0.2 42 182-230 300-342 (350)
84 KOG1940 Zn-finger protein [Gen 92.6 0.039 8.5E-07 51.4 0.4 45 183-227 159-204 (276)
85 KOG3268 Predicted E3 ubiquitin 92.3 0.046 9.9E-07 47.5 0.4 52 182-233 165-231 (234)
86 TIGR00100 hypA hydrogenase nic 91.6 0.15 3.2E-06 41.5 2.6 32 6-37 69-100 (115)
87 KOG4185 Predicted E3 ubiquitin 91.4 0.11 2.3E-06 48.7 1.9 47 183-229 4-54 (296)
88 PRK03681 hypA hydrogenase nick 91.1 0.17 3.7E-06 41.0 2.5 32 6-37 69-101 (114)
89 PF01155 HypA: Hydrogenase exp 90.5 0.14 3.1E-06 41.4 1.5 32 6-37 69-100 (113)
90 KOG2114 Vacuolar assembly/sort 90.3 0.1 2.3E-06 54.8 0.8 43 182-229 840-882 (933)
91 PRK12380 hydrogenase nickel in 90.3 0.23 5E-06 40.2 2.6 32 6-37 69-100 (113)
92 PF14446 Prok-RING_1: Prokaryo 90.2 0.16 3.4E-06 35.7 1.3 33 182-214 5-38 (54)
93 COG5236 Uncharacterized conser 90.1 0.12 2.6E-06 49.3 0.9 47 180-229 59-107 (493)
94 PHA03096 p28-like protein; Pro 90.1 0.076 1.6E-06 49.9 -0.5 36 183-218 179-219 (284)
95 PF03854 zf-P11: P-11 zinc fin 90.0 0.099 2.1E-06 35.6 0.2 44 184-232 4-48 (50)
96 PF10272 Tmpp129: Putative tra 89.5 0.38 8.3E-06 46.5 3.9 29 203-231 311-352 (358)
97 PRK00564 hypA hydrogenase nick 89.3 0.28 6E-06 40.0 2.3 32 6-37 70-102 (117)
98 PRK00398 rpoP DNA-directed RNA 89.1 0.41 8.9E-06 32.2 2.7 32 6-37 2-35 (46)
99 KOG2932 E3 ubiquitin ligase in 89.1 0.15 3.2E-06 48.0 0.6 43 183-229 91-133 (389)
100 KOG3002 Zn finger protein [Gen 89.0 0.2 4.3E-06 47.4 1.4 42 182-230 48-91 (299)
101 PF10571 UPF0547: Uncharacteri 88.8 0.25 5.3E-06 29.5 1.3 23 10-34 3-25 (26)
102 PF07754 DUF1610: Domain of un 88.7 0.24 5.3E-06 28.9 1.2 21 10-30 1-23 (24)
103 PRK03824 hypA hydrogenase nick 87.9 0.4 8.8E-06 40.0 2.5 32 6-37 69-121 (135)
104 KOG1001 Helicase-like transcri 87.6 0.11 2.4E-06 54.3 -1.3 51 183-237 455-507 (674)
105 COG5222 Uncharacterized conser 86.6 0.26 5.7E-06 46.2 0.7 42 183-227 275-318 (427)
106 PF07800 DUF1644: Protein of u 86.2 0.42 9E-06 40.9 1.7 33 182-217 2-47 (162)
107 KOG0802 E3 ubiquitin ligase [P 86.0 0.36 7.8E-06 49.4 1.4 51 181-238 478-528 (543)
108 PRK00762 hypA hydrogenase nick 85.5 0.52 1.1E-05 38.8 1.9 31 6-37 69-106 (124)
109 COG5183 SSM4 Protein involved 85.2 0.31 6.8E-06 51.2 0.5 52 182-234 12-70 (1175)
110 PRK06266 transcription initiat 85.1 0.58 1.3E-05 41.0 2.1 32 5-36 115-149 (178)
111 KOG2034 Vacuolar sorting prote 85.0 0.26 5.7E-06 52.2 -0.1 38 178-216 813-850 (911)
112 KOG2817 Predicted E3 ubiquitin 84.6 0.45 9.8E-06 46.2 1.3 49 179-227 331-382 (394)
113 KOG0309 Conserved WD40 repeat- 84.6 0.32 7E-06 50.7 0.3 40 184-224 1030-1069(1081)
114 PF13240 zinc_ribbon_2: zinc-r 84.1 0.58 1.3E-05 27.0 1.1 23 9-33 1-23 (23)
115 KOG1100 Predicted E3 ubiquitin 84.0 0.72 1.6E-05 41.4 2.2 39 184-229 160-199 (207)
116 KOG0298 DEAD box-containing he 83.8 0.36 7.7E-06 53.1 0.2 44 182-227 1153-1196(1394)
117 TIGR00373 conserved hypothetic 83.1 0.7 1.5E-05 39.6 1.7 32 5-37 107-141 (158)
118 COG1996 RPC10 DNA-directed RNA 82.6 0.74 1.6E-05 31.7 1.3 33 5-37 4-38 (49)
119 PF03604 DNA_RNApol_7kD: DNA d 81.7 1.6 3.6E-05 27.2 2.5 27 8-34 1-28 (32)
120 smart00659 RPOLCX RNA polymera 81.7 1.3 2.8E-05 29.7 2.2 31 7-37 2-33 (44)
121 KOG1609 Protein involved in mR 81.5 0.5 1.1E-05 44.2 0.2 51 182-232 78-136 (323)
122 COG2093 DNA-directed RNA polym 80.9 0.84 1.8E-05 32.9 1.2 27 9-37 6-33 (64)
123 PF05290 Baculo_IE-1: Baculovi 79.7 0.7 1.5E-05 38.4 0.5 50 181-232 79-134 (140)
124 COG5175 MOT2 Transcriptional r 79.4 0.68 1.5E-05 44.2 0.4 51 180-230 12-64 (480)
125 KOG3800 Predicted E3 ubiquitin 77.4 1.1 2.3E-05 42.0 1.0 52 184-235 2-56 (300)
126 PF13248 zf-ribbon_3: zinc-rib 75.3 1.6 3.5E-05 25.7 1.1 23 8-32 3-25 (26)
127 smart00834 CxxC_CXXC_SSSS Puta 75.1 2.4 5.3E-05 27.2 2.0 26 6-31 4-34 (41)
128 TIGR02605 CxxC_CxxC_SSSS putat 75.1 3.3 7.2E-05 28.2 2.8 31 7-37 5-40 (52)
129 COG5270 PUA domain (predicted 73.8 2 4.2E-05 37.8 1.6 27 6-37 13-39 (202)
130 smart00249 PHD PHD zinc finger 73.0 2.3 5E-05 27.4 1.5 32 184-215 1-32 (47)
131 KOG3053 Uncharacterized conser 71.2 0.93 2E-05 41.7 -1.0 50 180-229 18-81 (293)
132 COG5220 TFB3 Cdk activating ki 71.1 1.5 3.3E-05 40.0 0.4 46 182-227 10-61 (314)
133 KOG4362 Transcriptional regula 70.1 1.3 2.8E-05 46.2 -0.3 46 181-229 20-68 (684)
134 smart00132 LIM Zinc-binding do 70.1 3.7 7.9E-05 25.4 1.9 37 184-229 1-37 (39)
135 PRK14890 putative Zn-ribbon RN 69.6 3.8 8.2E-05 29.3 2.0 32 1-32 1-34 (59)
136 KOG1829 Uncharacterized conser 69.4 1.4 3E-05 45.3 -0.3 42 182-226 511-557 (580)
137 PF13901 DUF4206: Domain of un 69.3 3 6.6E-05 37.1 1.9 41 182-227 152-197 (202)
138 KOG1812 Predicted E3 ubiquitin 68.3 2.3 4.9E-05 41.7 1.0 37 182-218 146-183 (384)
139 KOG4367 Predicted Zn-finger pr 67.5 1.8 3.8E-05 42.8 0.0 35 180-217 2-36 (699)
140 PF00628 PHD: PHD-finger; Int 67.2 4 8.6E-05 27.5 1.8 44 184-227 1-50 (51)
141 PF02891 zf-MIZ: MIZ/SP-RING z 66.1 2.5 5.3E-05 29.1 0.5 42 183-227 3-49 (50)
142 KOG3899 Uncharacterized conser 65.5 1.5 3.3E-05 41.1 -0.8 31 203-233 325-368 (381)
143 KOG0825 PHD Zn-finger protein 65.0 2.2 4.9E-05 45.0 0.2 53 182-234 96-158 (1134)
144 PF00412 LIM: LIM domain; Int 64.6 8.1 0.00018 26.4 3.0 40 185-233 1-40 (58)
145 KOG4317 Predicted Zn-finger pr 64.2 4.3 9.3E-05 38.5 1.8 27 1-32 2-28 (383)
146 PF09723 Zn-ribbon_8: Zinc rib 64.1 8.6 0.00019 25.3 2.8 29 7-35 5-38 (42)
147 KOG4718 Non-SMC (structural ma 62.8 3.1 6.8E-05 37.3 0.7 48 182-231 181-228 (235)
148 KOG2068 MOT2 transcription fac 62.0 8.9 0.00019 36.6 3.6 49 183-232 250-300 (327)
149 smart00154 ZnF_AN1 AN1-like Zi 61.1 5.3 0.00012 26.0 1.4 25 10-36 1-25 (39)
150 PF09538 FYDLN_acid: Protein o 61.0 5.4 0.00012 32.1 1.7 31 6-36 8-39 (108)
151 KOG1812 Predicted E3 ubiquitin 59.9 4.9 0.00011 39.4 1.5 44 182-225 306-351 (384)
152 KOG2066 Vacuolar assembly/sort 57.8 4.6 9.9E-05 42.7 0.9 44 182-226 784-831 (846)
153 PF14968 CCDC84: Coiled coil p 56.3 3.6 7.7E-05 39.6 -0.1 31 5-39 56-86 (336)
154 KOG3005 GIY-YIG type nuclease 56.2 4 8.8E-05 37.9 0.2 47 183-229 183-242 (276)
155 TIGR02098 MJ0042_CXXC MJ0042 f 54.9 7.4 0.00016 24.7 1.3 27 8-34 3-36 (38)
156 KOG1815 Predicted E3 ubiquitin 54.5 5.6 0.00012 39.7 0.9 36 181-218 69-104 (444)
157 PF13717 zinc_ribbon_4: zinc-r 53.6 7.2 0.00016 24.9 1.0 25 9-33 4-35 (36)
158 KOG3113 Uncharacterized conser 53.0 13 0.00028 34.3 2.9 51 182-234 111-162 (293)
159 TIGR02300 FYDLN_acid conserved 50.6 10 0.00022 31.3 1.7 31 6-36 8-39 (129)
160 KOG3161 Predicted E3 ubiquitin 50.4 3.7 8E-05 42.5 -1.1 43 182-227 11-54 (861)
161 COG1675 TFA1 Transcription ini 50.3 7.1 0.00015 34.2 0.8 29 6-34 112-143 (176)
162 PF01363 FYVE: FYVE zinc finge 49.7 12 0.00026 26.8 1.9 37 181-217 8-45 (69)
163 PF07191 zinc-ribbons_6: zinc- 49.4 5.8 0.00013 29.4 0.1 40 183-230 2-41 (70)
164 PF10122 Mu-like_Com: Mu-like 48.0 4.8 0.0001 27.9 -0.5 27 6-32 3-33 (51)
165 COG5109 Uncharacterized conser 47.1 9.3 0.0002 36.4 1.1 49 178-226 332-383 (396)
166 PF05605 zf-Di19: Drought indu 47.1 10 0.00023 26.1 1.1 11 23-33 2-12 (54)
167 PRK06393 rpoE DNA-directed RNA 46.7 11 0.00024 27.4 1.2 19 10-32 8-26 (64)
168 PF08792 A2L_zn_ribbon: A2L zi 45.1 13 0.00028 23.3 1.2 26 8-33 4-31 (33)
169 PF08772 NOB1_Zn_bind: Nin one 45.0 18 0.00038 27.0 2.1 31 8-39 10-40 (73)
170 KOG3993 Transcription factor ( 45.0 11 0.00023 37.3 1.2 23 11-36 286-308 (500)
171 TIGR02159 PA_CoA_Oxy4 phenylac 44.8 14 0.0003 31.3 1.8 19 23-41 105-123 (146)
172 PRK10220 hypothetical protein; 44.0 14 0.0003 29.7 1.5 28 9-36 5-33 (111)
173 PF13719 zinc_ribbon_5: zinc-r 42.5 14 0.00031 23.5 1.1 25 10-34 5-36 (37)
174 PF04710 Pellino: Pellino; In 42.5 6.5 0.00014 38.5 -0.7 30 197-229 303-338 (416)
175 KOG2807 RNA polymerase II tran 42.2 18 0.0004 34.6 2.2 46 182-227 330-375 (378)
176 PF02318 FYVE_2: FYVE-type zin 41.8 17 0.00037 29.3 1.8 47 181-228 53-103 (118)
177 PF00130 C1_1: Phorbol esters/ 40.9 36 0.00078 22.9 3.1 36 180-215 9-46 (53)
178 PRK08351 DNA-directed RNA poly 40.8 16 0.00035 26.3 1.3 20 9-32 5-24 (61)
179 smart00661 RPOL9 RNA polymeras 40.2 17 0.00037 24.5 1.3 27 9-37 2-32 (52)
180 KOG0269 WD40 repeat-containing 39.7 12 0.00027 39.5 0.7 41 183-224 780-820 (839)
181 PF03107 C1_2: C1 domain; Int 39.4 16 0.00036 22.1 1.0 22 8-30 1-22 (30)
182 KOG0824 Predicted E3 ubiquitin 39.4 62 0.0013 30.8 5.2 47 181-229 104-150 (324)
183 PF15135 UPF0515: Uncharacteri 38.8 14 0.00031 34.0 0.9 27 10-36 135-168 (278)
184 COG3813 Uncharacterized protei 38.6 14 0.0003 27.5 0.7 14 23-36 41-54 (84)
185 PF04216 FdhE: Protein involve 38.4 11 0.00025 35.2 0.3 45 182-227 172-219 (290)
186 PF06220 zf-U1: U1 zinc finger 38.0 13 0.00029 24.0 0.5 13 6-18 2-14 (38)
187 PRK13794 hypothetical protein; 37.8 17 0.00037 36.7 1.4 23 6-32 9-31 (479)
188 KOG2169 Zn-finger transcriptio 37.6 33 0.00071 36.0 3.5 82 141-229 260-355 (636)
189 PF05191 ADK_lid: Adenylate ki 37.3 27 0.00059 22.3 1.8 28 8-35 2-33 (36)
190 TIGR00686 phnA alkylphosphonat 37.2 19 0.00042 28.9 1.3 27 10-36 5-32 (109)
191 PF08271 TF_Zn_Ribbon: TFIIB z 37.0 22 0.00048 23.3 1.4 28 8-36 1-31 (43)
192 cd04718 BAH_plant_2 BAH, or Br 37.0 26 0.00057 29.8 2.2 27 207-233 2-32 (148)
193 KOG3842 Adaptor protein Pellin 36.4 39 0.00085 32.3 3.4 44 183-229 291-351 (429)
194 PF12760 Zn_Tnp_IS1595: Transp 36.3 21 0.00045 23.8 1.2 18 20-37 15-32 (46)
195 PF14353 CpXC: CpXC protein 36.1 22 0.00047 28.9 1.5 17 23-39 1-17 (128)
196 PF14255 Cys_rich_CPXG: Cystei 35.9 29 0.00062 24.2 1.9 18 24-41 1-18 (52)
197 PF07975 C1_4: TFIIH C1-like d 35.6 22 0.00047 24.7 1.2 24 203-226 27-50 (51)
198 KOG1729 FYVE finger containing 35.4 12 0.00026 35.3 -0.1 37 183-219 215-251 (288)
199 PF06906 DUF1272: Protein of u 35.2 34 0.00074 24.2 2.2 46 183-230 6-52 (57)
200 PRK12495 hypothetical protein; 35.0 21 0.00046 32.3 1.4 30 5-34 40-69 (226)
201 PF07191 zinc-ribbons_6: zinc- 34.5 23 0.00049 26.3 1.2 22 7-31 17-38 (70)
202 TIGR00155 pqiA_fam integral me 34.4 24 0.00052 34.9 1.8 24 9-33 217-240 (403)
203 cd04476 RPA1_DBD_C RPA1_DBD_C: 34.1 26 0.00057 29.7 1.8 24 10-33 37-61 (166)
204 smart00647 IBR In Between Ring 34.0 28 0.00061 24.1 1.7 31 6-36 17-53 (64)
205 PF02148 zf-UBP: Zn-finger in 33.9 17 0.00036 25.9 0.4 17 3-19 45-61 (63)
206 smart00109 C1 Protein kinase C 33.8 25 0.00054 22.8 1.3 24 7-30 11-34 (49)
207 KOG3579 Predicted E3 ubiquitin 33.7 23 0.0005 33.3 1.4 37 182-219 268-306 (352)
208 cd00350 rubredoxin_like Rubred 33.5 41 0.00089 20.8 2.2 25 8-32 2-26 (33)
209 TIGR00155 pqiA_fam integral me 32.8 25 0.00054 34.7 1.6 27 9-35 15-45 (403)
210 PF14803 Nudix_N_2: Nudix N-te 32.1 20 0.00044 22.6 0.6 22 9-30 2-29 (34)
211 PF08274 PhnA_Zn_Ribbon: PhnA 31.9 16 0.00034 22.5 0.0 23 10-32 5-28 (30)
212 PF13453 zf-TFIIB: Transcripti 31.0 25 0.00054 22.8 0.9 26 10-35 2-31 (41)
213 PF13913 zf-C2HC_2: zinc-finge 31.0 14 0.0003 21.5 -0.3 13 24-36 3-15 (25)
214 PF01485 IBR: IBR domain; Int 30.5 29 0.00063 23.9 1.3 28 7-34 18-51 (64)
215 PF06677 Auto_anti-p27: Sjogre 30.4 42 0.00092 22.1 1.9 22 9-30 19-41 (41)
216 KOG1815 Predicted E3 ubiquitin 29.6 26 0.00057 34.9 1.2 37 183-219 227-268 (444)
217 TIGR00354 polC DNA polymerase, 29.4 35 0.00076 37.3 2.1 37 4-40 1009-1045(1095)
218 TIGR01384 TFS_arch transcripti 29.3 30 0.00064 27.0 1.2 24 9-32 2-25 (104)
219 PF03811 Zn_Tnp_IS1: InsA N-te 29.3 25 0.00054 22.5 0.6 10 23-32 5-14 (36)
220 smart00064 FYVE Protein presen 29.0 19 0.0004 25.8 0.0 36 182-217 10-46 (68)
221 COG2888 Predicted Zn-ribbon RN 28.8 33 0.00071 24.6 1.2 24 9-32 11-36 (61)
222 KOG2932 E3 ubiquitin ligase in 28.7 34 0.00073 32.6 1.7 15 7-21 90-104 (389)
223 PRK14715 DNA polymerase II lar 28.4 36 0.00078 38.5 2.0 36 4-40 1539-1574(1627)
224 COG4391 Uncharacterized protei 28.3 27 0.00058 25.2 0.7 13 22-34 47-59 (62)
225 TIGR00622 ssl1 transcription f 28.2 53 0.0012 26.6 2.5 44 183-226 56-110 (112)
226 COG3809 Uncharacterized protei 28.2 34 0.00075 25.9 1.3 25 10-34 4-32 (88)
227 PF06827 zf-FPG_IleRS: Zinc fi 27.9 24 0.00051 21.2 0.4 21 10-30 4-28 (30)
228 PRK06260 threonine synthase; V 27.8 51 0.0011 32.2 2.9 32 6-37 2-33 (397)
229 PF03119 DNA_ligase_ZBD: NAD-d 27.6 35 0.00076 20.5 1.1 15 25-39 1-15 (28)
230 PF09297 zf-NADH-PPase: NADH p 27.3 42 0.0009 20.5 1.4 24 8-31 4-29 (32)
231 PF01396 zf-C4_Topoisom: Topoi 26.7 38 0.00081 21.9 1.2 16 23-38 1-16 (39)
232 PF12773 DZR: Double zinc ribb 26.4 47 0.001 22.1 1.7 26 7-32 12-38 (50)
233 cd00065 FYVE FYVE domain; Zinc 26.1 31 0.00066 23.6 0.7 35 183-217 3-38 (57)
234 PRK04023 DNA polymerase II lar 25.9 44 0.00096 36.8 2.1 37 4-40 1034-1070(1121)
235 TIGR01206 lysW lysine biosynth 25.9 43 0.00093 23.5 1.4 27 8-34 3-33 (54)
236 PF06844 DUF1244: Protein of u 25.5 17 0.00036 26.6 -0.8 12 206-217 11-22 (68)
237 PRK07591 threonine synthase; V 25.4 56 0.0012 32.3 2.7 31 6-37 17-47 (421)
238 PF07282 OrfB_Zn_ribbon: Putat 25.3 37 0.0008 24.3 1.0 21 10-30 31-53 (69)
239 PRK04338 N(2),N(2)-dimethylgua 24.9 57 0.0012 31.9 2.6 29 6-34 243-272 (382)
240 KOG0957 PHD finger protein [Ge 24.9 50 0.0011 33.5 2.2 44 182-225 544-595 (707)
241 PRK15103 paraquat-inducible me 24.9 41 0.0009 33.4 1.6 25 10-34 13-41 (419)
242 PF14311 DUF4379: Domain of un 24.7 62 0.0013 22.2 2.1 20 10-29 31-55 (55)
243 PRK08197 threonine synthase; V 24.1 64 0.0014 31.5 2.8 36 1-37 1-36 (394)
244 PHA00616 hypothetical protein 24.1 20 0.00043 24.1 -0.5 12 24-35 2-13 (44)
245 PF07649 C1_3: C1-like domain; 23.9 25 0.00054 21.1 -0.1 29 184-212 2-30 (30)
246 PF13771 zf-HC5HC2H: PHD-like 23.9 31 0.00067 25.9 0.4 33 182-214 36-68 (90)
247 PF00096 zf-C2H2: Zinc finger, 23.7 20 0.00044 19.6 -0.5 10 25-34 2-11 (23)
248 PF13832 zf-HC5HC2H_2: PHD-zin 23.6 23 0.0005 27.8 -0.3 31 182-214 55-87 (110)
249 PRK00464 nrdR transcriptional 23.6 45 0.00098 28.5 1.4 16 24-39 1-16 (154)
250 PF04502 DUF572: Family of unk 23.5 43 0.00093 32.0 1.4 32 7-38 40-92 (324)
251 PRK00420 hypothetical protein; 23.5 62 0.0013 26.2 2.1 28 8-35 24-52 (112)
252 PF07503 zf-HYPF: HypF finger; 23.4 15 0.00033 23.4 -1.2 23 10-32 2-30 (35)
253 PRK14714 DNA polymerase II lar 23.3 51 0.0011 37.2 2.1 37 4-40 1250-1286(1337)
254 KOG4443 Putative transcription 23.3 38 0.00083 35.3 1.1 45 182-227 18-70 (694)
255 PF06044 DRP: Dam-replacing fa 23.2 32 0.00069 31.7 0.4 26 8-33 32-63 (254)
256 KOG1244 Predicted transcriptio 23.2 29 0.00063 32.5 0.2 81 150-230 249-333 (336)
257 COG5257 GCD11 Translation init 23.2 53 0.0011 31.9 1.9 27 6-33 56-82 (415)
258 KOG2593 Transcription initiati 23.2 39 0.00085 33.5 1.1 38 2-39 123-169 (436)
259 COG1645 Uncharacterized Zn-fin 22.8 56 0.0012 27.2 1.8 28 7-34 28-55 (131)
260 COG4847 Uncharacterized protei 22.6 34 0.00074 26.8 0.4 33 183-216 7-39 (103)
261 KOG4517 Uncharacterized conser 22.6 40 0.00087 27.1 0.8 33 5-37 45-81 (117)
262 PRK15103 paraquat-inducible me 22.5 53 0.0011 32.7 1.8 23 9-33 223-245 (419)
263 KOG3799 Rab3 effector RIM1 and 22.3 35 0.00076 28.6 0.5 49 180-228 63-116 (169)
264 KOG4185 Predicted E3 ubiquitin 21.7 17 0.00037 33.9 -1.7 47 182-228 207-265 (296)
265 COG1867 TRM1 N2,N2-dimethylgua 21.7 50 0.0011 32.3 1.4 26 6-32 239-266 (380)
266 PHA00626 hypothetical protein 21.7 70 0.0015 22.7 1.8 27 10-36 3-36 (59)
267 PF14787 zf-CCHC_5: GAG-polypr 21.5 48 0.001 21.3 0.8 11 24-34 3-13 (36)
268 KOG2231 Predicted E3 ubiquitin 21.5 48 0.001 34.9 1.3 49 184-235 2-57 (669)
269 KOG1356 Putative transcription 21.5 37 0.0008 36.5 0.5 50 166-216 213-262 (889)
270 CHL00174 accD acetyl-CoA carbo 21.4 37 0.0008 32.2 0.5 26 9-34 40-68 (296)
271 PRK13795 hypothetical protein; 21.4 58 0.0013 34.1 2.0 24 6-33 11-34 (636)
272 KOG2071 mRNA cleavage and poly 21.3 68 0.0015 33.1 2.4 35 181-215 512-556 (579)
273 PF04423 Rad50_zn_hook: Rad50 21.3 34 0.00074 23.5 0.2 11 221-231 22-32 (54)
274 PF03966 Trm112p: Trm112p-like 21.2 39 0.00084 24.4 0.4 12 22-33 52-63 (68)
275 COG1885 Uncharacterized protei 21.2 60 0.0013 26.0 1.5 21 17-37 43-63 (115)
276 PF09986 DUF2225: Uncharacteri 21.0 41 0.0009 30.1 0.7 52 181-235 4-64 (214)
277 PRK05654 acetyl-CoA carboxylas 21.0 38 0.00082 32.0 0.5 25 9-33 29-56 (292)
278 PF13465 zf-H2C2_2: Zinc-finge 20.8 27 0.00058 20.3 -0.4 12 23-34 14-25 (26)
279 KOG2462 C2H2-type Zn-finger pr 20.6 41 0.00089 31.5 0.6 49 182-230 161-226 (279)
280 KOG1597 Transcription initiati 20.4 48 0.001 31.3 1.0 29 9-37 2-35 (308)
281 COG1066 Sms Predicted ATP-depe 20.4 91 0.002 31.2 2.9 38 1-40 1-40 (456)
282 KOG2893 Zn finger protein [Gen 20.4 35 0.00076 31.3 0.1 27 7-33 10-44 (341)
283 PRK14873 primosome assembly pr 20.3 65 0.0014 34.0 2.1 27 7-37 410-436 (665)
284 PRK03564 formate dehydrogenase 20.2 75 0.0016 30.3 2.3 44 182-227 187-234 (309)
285 COG1198 PriA Primosomal protei 20.1 95 0.0021 33.2 3.2 30 6-38 461-490 (730)
286 PF11261 IRF-2BP1_2: Interfero 20.1 40 0.00087 23.4 0.3 24 6-29 2-30 (54)
No 1
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.62 E-value=7.3e-16 Score=145.51 Aligned_cols=82 Identities=27% Similarity=0.724 Sum_probs=69.6
Q ss_pred CCCCcchhhhhcCCceeeeccccccc-ccccccccccccCCceEEccccceeccccchhhhccCCC-cCcccccccCCCC
Q 021640 157 GPPPAARSAIDAMPTVRITQRHLRSD-SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNS-CPVCRQELPLQGS 234 (309)
Q Consensus 157 ~~ppa~~~~i~~lp~~~~~~~~~~~~-~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~s-CP~CR~~l~~~~~ 234 (309)
....+.+..++++|..+++....+.. ..|+||+|+|+.|++++.|||+|.||..||++||.++.+ ||+||+++.....
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG 282 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence 44568899999999999987664433 499999999999999999999999999999999998865 9999998876665
Q ss_pred CCCc
Q 021640 235 SSSR 238 (309)
Q Consensus 235 ~~~~ 238 (309)
....
T Consensus 283 ~~~~ 286 (348)
T KOG4628|consen 283 SEPV 286 (348)
T ss_pred CCCc
Confidence 5433
No 2
>PF14369 zf-RING_3: zinc-finger
Probab=99.51 E-value=6.8e-15 Score=94.39 Aligned_cols=32 Identities=44% Similarity=1.047 Sum_probs=27.6
Q ss_pred CceecccCCCceeecC---CCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE~ 37 (309)
++||||+|++.|++.. .+++||+|++||||||
T Consensus 1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 4899999999999863 3445999999999997
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=99.48 E-value=7.7e-15 Score=99.18 Aligned_cols=44 Identities=48% Similarity=1.294 Sum_probs=40.6
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
++|+||+++|..++.++.++|+|+||.+||..|++.+++||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 36999999999889999999999999999999999999999997
No 4
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.31 E-value=2.1e-12 Score=121.28 Aligned_cols=54 Identities=31% Similarity=0.929 Sum_probs=45.3
Q ss_pred ccccccccccccc-ccC---------CceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 180 RSDSHCPVCQDKF-ELG---------SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 180 ~~~~~C~IC~~~~-~~~---------~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
.++..|.||++++ ..+ .+.++|||||++|.+|++-|++++++||+||.++.-+.
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~ 348 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQ 348 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcccccc
Confidence 4567999999994 333 25789999999999999999999999999999964443
No 5
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.22 E-value=3.9e-12 Score=95.38 Aligned_cols=45 Identities=42% Similarity=1.059 Sum_probs=36.2
Q ss_pred ccccccccccccc----------CCceEEccccceeccccchhhhccCCCcCccc
Q 021640 182 DSHCPVCQDKFEL----------GSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 182 ~~~C~IC~~~~~~----------~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
++.|+||++.|.. .-.+...+|+|.||..||.+||+.+++||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 4569999999932 12455667999999999999999999999997
No 6
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.22 E-value=4.9e-12 Score=114.73 Aligned_cols=69 Identities=28% Similarity=0.636 Sum_probs=55.3
Q ss_pred chhhhhcCCceeeecccc---cccccccccccccccCCc-----eEEccccceeccccchhhhccCCCcCccccccc
Q 021640 162 ARSAIDAMPTVRITQRHL---RSDSHCPVCQDKFELGSE-----ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 162 ~~~~i~~lp~~~~~~~~~---~~~~~C~IC~~~~~~~~~-----~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
.+..++.+|.+...-+.+ ..+.+|+||++.+..++. ++.++|+|.||..||.+|+..+.+||+||..+.
T Consensus 151 ~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 151 YKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred hHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 889999999887654332 346789999999765431 245579999999999999999999999998774
No 7
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.16 E-value=8.1e-12 Score=114.62 Aligned_cols=51 Identities=35% Similarity=0.977 Sum_probs=47.0
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccC
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPL 231 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~ 231 (309)
..-+|+||++.|..++.++.|||.|.||..||.+|+. -++.||+||.+||+
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 4578999999999999999999999999999999999 56789999999986
No 8
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=99.14 E-value=1.2e-11 Score=120.47 Aligned_cols=200 Identities=17% Similarity=0.324 Sum_probs=138.0
Q ss_pred CceecccCCCceeecC--CCccCCCCCCCceEEecCCCC--CCCCCcCCCCCchhhHhhhhhHHHHHHHHhhhhcCCCCC
Q 021640 6 NTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQELDDMVS--VSPLDFFGLDNDEERDQRLGLMEAFSAFVRHRMADRHSH 81 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~~~~~~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (309)
++|||.+|.+.+..+. +-..|++|.+.-+.+..-.+. .-|++-||.++.+..+.. -....+..+|.+
T Consensus 375 syyfc~~cdc~~~~~~ftdr~~c~~c~h~~m~h~~~~n~~mlk~IqkfG~eGpGk~af~-~~h~llk~Imlr-------- 445 (791)
T KOG1002|consen 375 SYYFCTKCDCASLDWKFTDRMHCDHCSHNIMQHTCFFNHFMLKPIQKFGVEGPGKEAFN-NIHTLLKNIMLR-------- 445 (791)
T ss_pred hhhhhhhccccccceeecccccCCcccchhhhhhhhhcccccccchhhcccCchHHHHH-HHHHHHHHHHHH--------
Confidence 6899999999998887 467999999999988866654 457788898888776543 223345567765
Q ss_pred CccCCCCCCCCCCCCCCCeEEeccCCCcccCCCCccccccCCCCC-------CCCCCCCCCCCccCcchHHHHHHHHhcC
Q 021640 82 DIRGRYDSTPEHGQGFGPLLIFGGQIPLRLSGNSGFEAIFGGAPG-------LGFARGNTGDYFIGPGLEELFEQLSANG 154 (309)
Q Consensus 82 ~~r~r~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~g-------~~~~~~~~~dy~~~~~l~~l~~~l~~~~ 154 (309)
|++-+.+++.+++|.++.-+..-|...+.+.++.+|..+.. .|. -+.+|. .+..|+..|.+..
T Consensus 446 ----rTkl~RAdDLgLPPRiv~vRrD~fn~eE~D~YeSLY~dSkrkfntyieeGv---vlNNYA---nIF~LitRmRQ~a 515 (791)
T KOG1002|consen 446 ----RTKLERADDLGLPPRIVTVRRDFFNEEEKDLYESLYKDSKRKFNTYIEEGV---VLNNYA---NIFTLITRMRQAA 515 (791)
T ss_pred ----HhhcccccccCCCccceeeehhhhhhHHHHHHHHHHHhhHHhhhhHHhhhh---hhhhHH---HHHHHHHHHHHhc
Confidence 56667778889999988777777777777888888866421 011 123443 4567777777754
Q ss_pred CCCCCCcchhhhhcCCceeeecccccccccccccccccccCCceEEccccceeccccchhhhc-----cCCCcCcccccc
Q 021640 155 RRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-----QHNSCPVCRQEL 229 (309)
Q Consensus 155 ~~~~ppa~~~~i~~lp~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-----~~~sCP~CR~~l 229 (309)
.++-.. ..++...|+. .-.++..|.+|.+.-+ ..+...|.|.||.-||..++. .+-+||+|...|
T Consensus 516 DHP~LV-l~S~~~n~~~------enk~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 516 DHPDLV-LYSANANLPD------ENKGEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred cCccee-eehhhcCCCc------cccCceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence 432211 1122333321 1134578999998753 457788999999999988886 245799999888
Q ss_pred cCCCC
Q 021640 230 PLQGS 234 (309)
Q Consensus 230 ~~~~~ 234 (309)
..+..
T Consensus 586 siDls 590 (791)
T KOG1002|consen 586 SIDLS 590 (791)
T ss_pred ccccc
Confidence 76643
No 9
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=1.5e-09 Score=96.88 Aligned_cols=55 Identities=24% Similarity=0.650 Sum_probs=43.2
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccC---CCcCcccccccCCCCCCC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH---NSCPVCRQELPLQGSSSS 237 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~---~sCP~CR~~l~~~~~~~~ 237 (309)
...-+|.|||+.-+ ..+++.|+|.||+.||.+||..+ +.|||||..|..++...-
T Consensus 45 ~~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPl 102 (230)
T KOG0823|consen 45 GGFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPL 102 (230)
T ss_pred CCceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEee
Confidence 34578999998764 34677799999999999999854 459999999876665433
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.87 E-value=1.1e-09 Score=95.82 Aligned_cols=52 Identities=25% Similarity=0.645 Sum_probs=41.8
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhcc----------------CCCcCcccccccCCCC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ----------------HNSCPVCRQELPLQGS 234 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~----------------~~sCP~CR~~l~~~~~ 234 (309)
.+..+|+||++.++. .+.++|+|.||+.||..|+.. ...||+||..+.....
T Consensus 16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 356789999998854 477889999999999999852 2469999999865544
No 11
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.83 E-value=1.6e-09 Score=99.30 Aligned_cols=51 Identities=25% Similarity=0.823 Sum_probs=44.1
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
+....|.+|++... ....+||||+||+.||..|+..+..||+||..+.+.+
T Consensus 237 ~a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 237 EATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK 287 (293)
T ss_pred CCCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence 34578999998764 4579999999999999999999999999999886654
No 12
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.81 E-value=1.8e-09 Score=74.80 Aligned_cols=46 Identities=30% Similarity=0.929 Sum_probs=39.3
Q ss_pred cccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
+..|.||++.. ..+..+||+|. |+..|+..|++....||+||+++.
T Consensus 2 ~~~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 46899999876 45789999999 999999999999999999999874
No 13
>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=98.80 E-value=1.7e-09 Score=71.11 Aligned_cols=39 Identities=36% Similarity=1.002 Sum_probs=33.3
Q ss_pred ccccccccccCCceEEccccceeccccchhhhccCCCcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~C 225 (309)
|+||++.+.. .++.++|+|.|+..||..|++.+..||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999998864 45789999999999999999998899998
No 14
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.79 E-value=1.7e-09 Score=71.66 Aligned_cols=44 Identities=36% Similarity=1.131 Sum_probs=36.6
Q ss_pred cccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQEL 229 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l 229 (309)
.|+||++.+. +.+..++|+|.||..|+..|++. ...||+|+..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4999999883 44556669999999999999997 66799999764
No 15
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.78 E-value=1.6e-09 Score=82.65 Aligned_cols=54 Identities=31% Similarity=0.810 Sum_probs=40.9
Q ss_pred ccccccccccccccccc--------CC--ceEEccccceeccccchhhhccC---CCcCcccccccC
Q 021640 178 HLRSDSHCPVCQDKFEL--------GS--EARQMPCNHIYHSDCIVPWLVQH---NSCPVCRQELPL 231 (309)
Q Consensus 178 ~~~~~~~C~IC~~~~~~--------~~--~~~~lpC~H~fh~~Ci~~Wl~~~---~sCP~CR~~l~~ 231 (309)
.+..++.|.||...|.. ++ .++.-.|+|.||..||.+||... ..||+||+++..
T Consensus 17 d~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 17 DVANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred ecCCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 34457899999999852 11 23444599999999999999853 579999998753
No 16
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=2.7e-09 Score=108.22 Aligned_cols=50 Identities=34% Similarity=1.024 Sum_probs=44.8
Q ss_pred ccccccccccccccCCc--eEEccccceeccccchhhhccCCCcCccccccc
Q 021640 181 SDSHCPVCQDKFELGSE--ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~--~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
.+..|+||+|++..+.+ +++|+|+|+||..|+..|+++.++||+||..+.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY 341 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence 46799999999987655 799999999999999999999999999999553
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.57 E-value=1.9e-08 Score=67.29 Aligned_cols=38 Identities=34% Similarity=0.977 Sum_probs=29.3
Q ss_pred ccccccccccCCceEEccccceeccccchhhhccC----CCcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----NSCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----~sCP~C 225 (309)
|+||++.|. +.+.|+|+|.|+..||..|++.. ..||+|
T Consensus 1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999996 45899999999999999999854 359987
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.56 E-value=2.2e-08 Score=67.56 Aligned_cols=44 Identities=30% Similarity=0.841 Sum_probs=38.4
Q ss_pred cccccccccccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
.|.||++.|........++|+|+|+..||..+......||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 49999999965667889999999999999999866678999985
No 19
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.53 E-value=1.8e-08 Score=86.49 Aligned_cols=52 Identities=29% Similarity=0.714 Sum_probs=42.7
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
+..-|+|||+.+... ..+-+.|||+||..||+.-|+....||+|++.|..+.
T Consensus 130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 346799999998743 2244679999999999999999999999999876553
No 20
>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=98.53 E-value=3.2e-08 Score=65.36 Aligned_cols=39 Identities=38% Similarity=1.086 Sum_probs=33.2
Q ss_pred ccccccccccCCceEEccccceeccccchhhhc--cCCCcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV--QHNSCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~--~~~sCP~C 225 (309)
|+||++.+... +..++|+|.||..||..|++ ....||+|
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 89999988643 35899999999999999999 44569998
No 21
>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=98.53 E-value=3.4e-08 Score=71.16 Aligned_cols=48 Identities=25% Similarity=0.501 Sum_probs=41.6
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
..|+||++.+..+ +.++|||+|+..||..|++.+.+||+|+..+..++
T Consensus 2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 4699999998754 77899999999999999999889999998885443
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.49 E-value=3.2e-08 Score=87.93 Aligned_cols=51 Identities=25% Similarity=0.673 Sum_probs=38.1
Q ss_pred cccccccccccccccCC------ceEEccccceeccccchhhhccC------CCcCccccccc
Q 021640 180 RSDSHCPVCQDKFELGS------EARQMPCNHIYHSDCIVPWLVQH------NSCPVCRQELP 230 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~------~~~~lpC~H~fh~~Ci~~Wl~~~------~sCP~CR~~l~ 230 (309)
..+.+|+||+|..-.+. -....+|+|.||..||..|...+ .+||+||..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 34689999998863221 12344699999999999999753 35999998764
No 23
>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=98.46 E-value=4.9e-08 Score=62.28 Aligned_cols=38 Identities=37% Similarity=1.209 Sum_probs=32.8
Q ss_pred ccccccccccCCceEEccccceeccccchhhhc-cCCCcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~C 225 (309)
|+||++.. .....++|+|.||..||..|+. ....||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 78999873 5678899999999999999998 55679987
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.43 E-value=7.8e-08 Score=93.37 Aligned_cols=51 Identities=31% Similarity=0.702 Sum_probs=43.3
Q ss_pred ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232 (309)
Q Consensus 179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~ 232 (309)
++....|+||++.|... +.++|+|.||..||..|+.....||+|+..+...
T Consensus 23 Le~~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 45668999999999644 5789999999999999999888899999877543
No 25
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.39 E-value=9.3e-08 Score=71.48 Aligned_cols=51 Identities=33% Similarity=0.770 Sum_probs=37.7
Q ss_pred cccccccccc-----------ccCCceE--EccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 183 SHCPVCQDKF-----------ELGSEAR--QMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 183 ~~C~IC~~~~-----------~~~~~~~--~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
+.|+||...+ ..+++.. ---|.|.||..||..||..++.||++|+++...+
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~ 84 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD 84 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence 5677776655 2333322 2339999999999999999999999999875443
No 26
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=1.3e-07 Score=70.19 Aligned_cols=51 Identities=33% Similarity=0.877 Sum_probs=36.9
Q ss_pred cccccccccccccc--------CCc-eEEc-cccceeccccchhhhccCC---CcCcccccccC
Q 021640 181 SDSHCPVCQDKFEL--------GSE-ARQM-PCNHIYHSDCIVPWLVQHN---SCPVCRQELPL 231 (309)
Q Consensus 181 ~~~~C~IC~~~~~~--------~~~-~~~l-pC~H~fh~~Ci~~Wl~~~~---sCP~CR~~l~~ 231 (309)
.+..|.||.-.|.. ++. ..++ -|.|.||..||.+||.... .||+||+++..
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 34589999988842 222 2222 2999999999999998543 59999998643
No 27
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=1.7e-07 Score=85.22 Aligned_cols=58 Identities=31% Similarity=0.841 Sum_probs=46.4
Q ss_pred ccccccccccccccCC-------ceEEccccceeccccchhhhc--cCCCcCcccccccCCCCCCCc
Q 021640 181 SDSHCPVCQDKFELGS-------EARQMPCNHIYHSDCIVPWLV--QHNSCPVCRQELPLQGSSSSR 238 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~-------~~~~lpC~H~fh~~Ci~~Wl~--~~~sCP~CR~~l~~~~~~~~~ 238 (309)
++..|+||-..+.... +.-+|.|+|+||..||.-|-. ++++||.|++.+..+...++.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnp 289 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNP 289 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCc
Confidence 4568999998875544 667899999999999999986 566899999988766554443
No 28
>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=98.16 E-value=5.6e-07 Score=62.20 Aligned_cols=42 Identities=24% Similarity=0.819 Sum_probs=33.8
Q ss_pred cccccccccccCCceEEcccc-----ceeccccchhhhccC--CCcCccc
Q 021640 184 HCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQH--NSCPVCR 226 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~~--~sCP~CR 226 (309)
.|.||++ ...++....+||. |.+|..||.+|+..+ .+||+|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4899998 4445567789985 899999999999654 4799995
No 29
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=7.7e-07 Score=80.94 Aligned_cols=50 Identities=24% Similarity=0.736 Sum_probs=41.9
Q ss_pred ccccccccccccccCCceEEccccceeccccchh-hhccCCC-cCcccccccCCC
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVP-WLVQHNS-CPVCRQELPLQG 233 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~-Wl~~~~s-CP~CR~~l~~~~ 233 (309)
.+..|.||++.. +....++|+|+||..||.. |-.++.- ||+||+.+..++
T Consensus 214 ~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 214 ADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred cccceeeeeccc---CCcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 367899999876 4568999999999999999 8877776 999999876554
No 30
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=1e-06 Score=86.65 Aligned_cols=51 Identities=29% Similarity=0.785 Sum_probs=40.8
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccC-----CCcCcccccccCCCCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-----NSCPVCRQELPLQGSS 235 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-----~sCP~CR~~l~~~~~~ 235 (309)
+..|+||++.... +..+.|||+||..||..++... ..||+||..|..++..
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~ 241 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLL 241 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcccccee
Confidence 6789999987643 4677799999999999988754 4699999988765543
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.04 E-value=6.3e-07 Score=83.94 Aligned_cols=49 Identities=27% Similarity=0.634 Sum_probs=43.1
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL 231 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~ 231 (309)
+....|.||.+.|..+ .++||+|.||.-||..+|..+..||.|+.++.+
T Consensus 21 D~lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE 69 (442)
T ss_pred HHHHHHhHHHHHhcCc---eeccccchHHHHHHHHHhccCCCCCceecccch
Confidence 4457899999999765 789999999999999999999999999877643
No 32
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.01 E-value=1.7e-06 Score=58.11 Aligned_cols=34 Identities=26% Similarity=0.877 Sum_probs=21.7
Q ss_pred cccccccccc-CCceEEccccceeccccchhhhccC
Q 021640 185 CPVCQDKFEL-GSEARQMPCNHIYHSDCIVPWLVQH 219 (309)
Q Consensus 185 C~IC~~~~~~-~~~~~~lpC~H~fh~~Ci~~Wl~~~ 219 (309)
|+||++ |.. ....+.|+|+|+|+.+||.+++...
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~ 35 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS 35 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence 899999 754 3346889999999999999999854
No 33
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.95 E-value=1.8e-06 Score=84.34 Aligned_cols=51 Identities=35% Similarity=0.918 Sum_probs=39.8
Q ss_pred ccccccccccccccCC--------------ceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640 181 SDSHCPVCQDKFELGS--------------EARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL 231 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~--------------~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~ 231 (309)
....|+||+..+..-. .-..+||.|+||..|+..|+.. +-.||+||..|++
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 3568999998863211 2345699999999999999994 4489999999874
No 34
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.89 E-value=4.4e-06 Score=62.47 Aligned_cols=49 Identities=27% Similarity=0.494 Sum_probs=37.8
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccCCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPLQG 233 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~~~ 233 (309)
...|+|+.+.|.. .+.+||||.|...||..||.. +.+||+|+..+...+
T Consensus 4 ~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~ 53 (73)
T PF04564_consen 4 EFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD 53 (73)
T ss_dssp GGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred ccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence 4689999999964 488999999999999999998 788999998876543
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.89 E-value=3.1e-06 Score=77.85 Aligned_cols=48 Identities=31% Similarity=0.684 Sum_probs=41.8
Q ss_pred ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
+...+.|-||.+.|..+ ..++|+|.||.-||...|..+.-||+||.+.
T Consensus 22 LDs~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 22 LDSMLRCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred chhHHHhhhhhheeecc---eecccccchhHHHHHHHhcCCCCCccccccH
Confidence 34557899999999765 7888999999999999999999999999643
No 36
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.88 E-value=3.3e-06 Score=62.75 Aligned_cols=50 Identities=20% Similarity=0.594 Sum_probs=23.5
Q ss_pred cccccccccccc-cCCc--eEEc--cccceeccccchhhhcc----C-------CCcCcccccccC
Q 021640 182 DSHCPVCQDKFE-LGSE--ARQM--PCNHIYHSDCIVPWLVQ----H-------NSCPVCRQELPL 231 (309)
Q Consensus 182 ~~~C~IC~~~~~-~~~~--~~~l--pC~H~fh~~Ci~~Wl~~----~-------~sCP~CR~~l~~ 231 (309)
+..|.||+..+. .++. ++.- .|++.||..||..||.. + ..||.|+++|..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 357999998865 3222 1221 38999999999999973 1 249999998753
No 37
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.84 E-value=2.4e-06 Score=88.73 Aligned_cols=51 Identities=25% Similarity=0.950 Sum_probs=38.8
Q ss_pred cccccccccccccccccCCceEEcc------ccceeccccchhhhccC--CCcCccccccc
Q 021640 178 HLRSDSHCPVCQDKFELGSEARQMP------CNHIYHSDCIVPWLVQH--NSCPVCRQELP 230 (309)
Q Consensus 178 ~~~~~~~C~IC~~~~~~~~~~~~lp------C~H~fh~~Ci~~Wl~~~--~sCP~CR~~l~ 230 (309)
+..+-.+|+||...+..-+ +.|| |+|.||..||.+|++.. ++||+||.+++
T Consensus 1465 ~fsG~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1465 KFSGHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hcCCcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3456689999998764211 3333 99999999999999864 56999998775
No 38
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=5.5e-06 Score=65.05 Aligned_cols=51 Identities=31% Similarity=0.725 Sum_probs=37.7
Q ss_pred cccccccccccc------------cCCc--eEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640 182 DSHCPVCQDKFE------------LGSE--ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232 (309)
Q Consensus 182 ~~~C~IC~~~~~------------~~~~--~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~ 232 (309)
.+.|+||..-+. ..++ +.---|.|.||..||..||+.++.||+|.++....
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQ 110 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEe
Confidence 467888876541 1122 22233999999999999999999999998876543
No 39
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.76 E-value=1e-05 Score=75.91 Aligned_cols=53 Identities=25% Similarity=0.488 Sum_probs=37.5
Q ss_pred cccccccccccccCCce--EEccccceeccccchhhhc-cCCCcCcccccccCCCC
Q 021640 182 DSHCPVCQDKFELGSEA--RQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPLQGS 234 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~--~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~~~~ 234 (309)
+..|+||+.+--..... ...+|+|.||..||...+. ....||+|+..+.....
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f 58 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF 58 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence 35799999863222222 2337999999999999554 44579999988765543
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.75 E-value=1.1e-05 Score=58.37 Aligned_cols=55 Identities=27% Similarity=0.540 Sum_probs=26.6
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCCCCc
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSR 238 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~~~ 238 (309)
+....|++|.+.+.. .+....|.|+|+..||..-+.. .||+|+.+...++...++
T Consensus 5 e~lLrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~~Nr 59 (65)
T PF14835_consen 5 EELLRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQINR 59 (65)
T ss_dssp HHTTS-SSS-S--SS---B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS----H
T ss_pred HHhcCCcHHHHHhcC--CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHHhhh
Confidence 445789999998863 3455669999999999886553 499999887766655443
No 41
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.74 E-value=9.8e-06 Score=78.57 Aligned_cols=48 Identities=33% Similarity=0.895 Sum_probs=38.2
Q ss_pred ccccccccccccccCC-ceEEccccceeccccchhhhccCCCcCccccccc
Q 021640 181 SDSHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
+..+|+||||.+.... .++...|.|.||..|+..| ...+||+||....
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS 222 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence 4578999999986433 2355569999999999999 4568999998665
No 42
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=7.9e-06 Score=74.35 Aligned_cols=45 Identities=33% Similarity=0.816 Sum_probs=39.1
Q ss_pred ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCccc
Q 021640 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
+.+...|+||++.|... +.++|+|.||..||..++.....||.||
T Consensus 10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 34568999999999866 8999999999999999988445699999
No 43
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.57 E-value=1.8e-05 Score=73.27 Aligned_cols=54 Identities=26% Similarity=0.728 Sum_probs=44.7
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhcc-----------------------CCCcCcccccccCCCCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-----------------------HNSCPVCRQELPLQGSS 235 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-----------------------~~sCP~CR~~l~~~~~~ 235 (309)
...|.|||.-|..++...+++|.|+||..|+..+|.. ...|||||..|..+..+
T Consensus 115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~s 191 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENS 191 (368)
T ss_pred CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccc
Confidence 5689999999999988999999999999999888751 12499999988655443
No 44
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=1.2e-05 Score=75.82 Aligned_cols=58 Identities=26% Similarity=0.565 Sum_probs=43.4
Q ss_pred eeeecccccccccccccccccccCCceEEccccceeccccchhhhcc-CCCcCcccccccC
Q 021640 172 VRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ-HNSCPVCRQELPL 231 (309)
Q Consensus 172 ~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~-~~sCP~CR~~l~~ 231 (309)
..+.-..+..+..|+|||+.++.. ....-|.|.||.+||..-++. +++||.||+.+..
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~t--mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKKT--MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHhh--cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 344445566778999999988643 233339999999999888875 5679999987743
No 45
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=1.8e-05 Score=70.55 Aligned_cols=75 Identities=20% Similarity=0.505 Sum_probs=56.4
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhcc--------CCCcCcccccccCCCCCCCcccCCCCCCCCCCCCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--------HNSCPVCRQELPLQGSSSSRIHQSSSGQSRSTSFG 253 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--------~~sCP~CR~~l~~~~~~~~~~~~~~~~~~~~~~~~ 253 (309)
...|..|...+..++. .+|.|.|+||++|+..|-.. ...||.|..+|.+.....+........+...++++
T Consensus 50 ~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qvNWa 128 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQVNWA 128 (299)
T ss_pred CCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhhhHH
Confidence 4579999999988864 45669999999999999863 34699999999888777666555555555555665
Q ss_pred CCCC
Q 021640 254 SNGS 257 (309)
Q Consensus 254 ~~~~ 257 (309)
.++-
T Consensus 129 RagL 132 (299)
T KOG3970|consen 129 RAGL 132 (299)
T ss_pred hhcc
Confidence 5443
No 46
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.42 E-value=5e-05 Score=72.01 Aligned_cols=47 Identities=32% Similarity=0.790 Sum_probs=39.6
Q ss_pred ccccccccccccccCCceEEccccce-eccccchhhhccCCCcCccccccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
+..+|.||+.+- ..+.+|||.|. .|..|-+.-.-+++.||+||+.+.
T Consensus 289 ~gkeCVIClse~---rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICLSES---RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred CCCeeEEEecCC---cceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 357899999775 46789999998 789998887667889999999874
No 47
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.38 E-value=2.5e-05 Score=80.02 Aligned_cols=49 Identities=24% Similarity=0.591 Sum_probs=43.3
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
...|++|+..+..+......+|.|+||..||..|-+.-++||+||.++.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 3579999999987776677789999999999999999999999998763
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=4.6e-05 Score=72.76 Aligned_cols=47 Identities=30% Similarity=0.886 Sum_probs=35.4
Q ss_pred ccccccccccccCCceEEcc-ccceeccccchhhhccC---CCcCcccccc
Q 021640 183 SHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLVQH---NSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~~~---~sCP~CR~~l 229 (309)
..|.||.+-+-....+.-.. |||+||..|+..|+..- ..||+|+-.+
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 47999966655544555444 99999999999999853 4699998333
No 49
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=9.1e-05 Score=68.76 Aligned_cols=48 Identities=21% Similarity=0.460 Sum_probs=38.8
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCC-CcCcccccccCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQ 232 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~ 232 (309)
..+|+||+.... ..+.|+|+|.||.-||+--..... +|++||.+++..
T Consensus 7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 468999997754 458999999999999987666544 699999988654
No 50
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.16 E-value=0.00013 Score=69.88 Aligned_cols=49 Identities=31% Similarity=0.733 Sum_probs=36.1
Q ss_pred ccccccccccccccCC----ceEE-ccccceeccccchhhh--cc-----CCCcCcccccc
Q 021640 181 SDSHCPVCQDKFELGS----EARQ-MPCNHIYHSDCIVPWL--VQ-----HNSCPVCRQEL 229 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~----~~~~-lpC~H~fh~~Ci~~Wl--~~-----~~sCP~CR~~l 229 (309)
.+..|.||++...... .... .+|.|.||..||..|- .+ ...||.||...
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 4578999999865332 0123 4499999999999998 34 46799999654
No 51
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.09 E-value=0.00022 Score=68.41 Aligned_cols=49 Identities=24% Similarity=0.798 Sum_probs=39.8
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhcc--CCCcCcccccccCCCC
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--HNSCPVCRQELPLQGS 234 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~~~~ 234 (309)
..|.||-|. ...+++-||+|..|..|+..|-.. .++||.||.+|.....
T Consensus 370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~ 420 (563)
T KOG1785|consen 370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEP 420 (563)
T ss_pred HHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccc
Confidence 469999754 356888999999999999999853 5789999999865544
No 52
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.75 E-value=0.00088 Score=65.61 Aligned_cols=54 Identities=31% Similarity=0.750 Sum_probs=44.2
Q ss_pred ccccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234 (309)
Q Consensus 179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~ 234 (309)
++.+..|+||...+..+ +....|+|.||..||..|+..+..||.|+..+.....
T Consensus 18 ~~~~l~C~~C~~vl~~p--~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDP--VQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE 71 (391)
T ss_pred CcccccCccccccccCC--CCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence 56778999999988754 2225799999999999999999999999887754443
No 53
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.00068 Score=57.71 Aligned_cols=40 Identities=28% Similarity=0.740 Sum_probs=32.2
Q ss_pred Cceeeecccccc-cccccccccccccCCceEEccccceecc
Q 021640 170 PTVRITQRHLRS-DSHCPVCQDKFELGSEARQMPCNHIYHS 209 (309)
Q Consensus 170 p~~~~~~~~~~~-~~~C~IC~~~~~~~~~~~~lpC~H~fh~ 209 (309)
|.+.+..+.+.. ..+|.||+|+++.++.+.+|||..+||+
T Consensus 164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 444455554443 4689999999999999999999999997
No 54
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.68 E-value=0.00086 Score=47.75 Aligned_cols=41 Identities=24% Similarity=0.763 Sum_probs=28.9
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccC--CCcCc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--NSCPV 224 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~ 224 (309)
...|+|.+..|+ +.++...|+|+|-+..|..||.++ ..||+
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 478999999987 456777899999999999999543 35998
No 55
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.61 E-value=0.00074 Score=65.12 Aligned_cols=46 Identities=30% Similarity=0.941 Sum_probs=35.7
Q ss_pred cccccccccccccCC--ceEEccccceeccccchhhhccC--CCcCcccc
Q 021640 182 DSHCPVCQDKFELGS--EARQMPCNHIYHSDCIVPWLVQH--NSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~--~~~~lpC~H~fh~~Ci~~Wl~~~--~sCP~CR~ 227 (309)
..+|+||++.++..- .+..+.|+|.|-.+||.+||.+. ..||.|..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ 53 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG 53 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence 468999999986533 35566699999999999999632 24999963
No 56
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.58 E-value=0.00023 Score=49.73 Aligned_cols=46 Identities=22% Similarity=0.642 Sum_probs=33.3
Q ss_pred cccccccccccccCCceEEccccce-eccccchhhhc-cCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLV-QHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~-~~~sCP~CR~~l~ 230 (309)
+++|.||+|--. ..+...|+|. .|.+|-..-++ .+..||+||.++.
T Consensus 7 ~dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 378999987543 3355669997 67788655444 7889999998763
No 57
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.52 E-value=0.00078 Score=65.79 Aligned_cols=49 Identities=35% Similarity=0.710 Sum_probs=41.6
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL 231 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~ 231 (309)
..+..|.||+..+.. .+.+||+|.||..||..-+.....||.||..+..
T Consensus 82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCccccccccc
Confidence 567899999988854 4677999999999999977777789999998875
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.45 E-value=0.00083 Score=64.46 Aligned_cols=47 Identities=32% Similarity=0.834 Sum_probs=39.1
Q ss_pred cccccccccccccC-CceEEccccceeccccchhhhccCC--CcCccccc
Q 021640 182 DSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQE 228 (309)
Q Consensus 182 ~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~ 228 (309)
+..|..|-+.+... +..-.|||.|+||..|+...|.++. +||-||+-
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence 57899999988543 4577899999999999999997654 69999953
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.35 E-value=0.0021 Score=43.87 Aligned_cols=40 Identities=25% Similarity=0.792 Sum_probs=27.2
Q ss_pred ccccccccccCCceEEcccc--c---eeccccchhhhcc--CCCcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCN--H---IYHSDCIVPWLVQ--HNSCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~--H---~fh~~Ci~~Wl~~--~~sCP~C 225 (309)
|-||++.-.... ....||. - ..|..||..|+.. ..+|++|
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 789998865543 5677853 3 8999999999984 4569987
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.12 E-value=0.0012 Score=58.08 Aligned_cols=44 Identities=23% Similarity=0.570 Sum_probs=38.2
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
-.|.||.++|+.+ +.+.|+|.||..|...-++....|-+|-+..
T Consensus 197 F~C~iCKkdy~sp---vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 197 FLCGICKKDYESP---VVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred eeehhchhhccch---hhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 4799999999654 7788999999999999888889999997654
No 61
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.05 E-value=0.0011 Score=68.52 Aligned_cols=48 Identities=21% Similarity=0.684 Sum_probs=38.1
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhc-cCCCcCcccccccC
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELPL 231 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~~ 231 (309)
+-..|++|-.-++ .++...|+|+||..||.+-+. ++..||.|-..+-.
T Consensus 642 ~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 642 ELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred hceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 4578999996664 345666999999999999987 56679999887643
No 62
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.04 E-value=0.00089 Score=63.03 Aligned_cols=47 Identities=23% Similarity=0.612 Sum_probs=38.5
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
...+|.+|...|.+.. .+.-|-|.||+.||...|...++||+|...|
T Consensus 14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~~~CP~C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEESKYCPTCDIVI 60 (331)
T ss_pred cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence 4568999999886442 3334999999999999999999999997655
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.91 E-value=0.0026 Score=69.40 Aligned_cols=50 Identities=30% Similarity=0.712 Sum_probs=39.7
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhccC----------CCcCcccccc
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH----------NSCPVCRQEL 229 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~----------~sCP~CR~~l 229 (309)
+.++.|.||..+--....+++|-|+|+||..|...-|++. .+||+|+.++
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 4578999999876555678899999999999997655532 3699998766
No 64
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=95.78 E-value=0.0057 Score=48.20 Aligned_cols=33 Identities=30% Similarity=0.692 Sum_probs=28.1
Q ss_pred cccccccccccccccCCceEEccccceeccccch
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIV 213 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~ 213 (309)
..+..|+||...+.. ......||+|+||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 345689999999876 578889999999999985
No 65
>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=95.38 E-value=0.0037 Score=51.88 Aligned_cols=35 Identities=17% Similarity=0.534 Sum_probs=29.9
Q ss_pred cccccccccccccCCceEEcccc------ceeccccchhhh
Q 021640 182 DSHCPVCQDKFELGSEARQMPCN------HIYHSDCIVPWL 216 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~------H~fh~~Ci~~Wl 216 (309)
..+|.||++.+...+.++.++|+ |.||.+|+.+|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 46899999999875578888886 999999999994
No 66
>PHA02862 5L protein; Provisional
Probab=95.27 E-value=0.0059 Score=51.19 Aligned_cols=45 Identities=20% Similarity=0.675 Sum_probs=34.0
Q ss_pred ccccccccccccCCceEEcccc-----ceeccccchhhhcc--CCCcCcccccccC
Q 021640 183 SHCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQ--HNSCPVCRQELPL 231 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~ 231 (309)
..|-||+++-+. . .-||. ...|.+|+..|+.. +.+|+.|+.+...
T Consensus 3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 579999987432 2 46764 57999999999974 3469999987643
No 67
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.24 E-value=0.0072 Score=56.23 Aligned_cols=44 Identities=23% Similarity=0.507 Sum_probs=38.6
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
..|-||...|..+ ++..|+|.||..|-..-++....|.+|-+..
T Consensus 242 f~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 242 FKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred ccccccccccccc---hhhcCCceeehhhhccccccCCcceeccccc
Confidence 3599999999755 7888999999999999888889999998765
No 68
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.17 E-value=0.012 Score=56.00 Aligned_cols=51 Identities=25% Similarity=0.503 Sum_probs=42.6
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~ 234 (309)
++..|+||... +-.++..||+|.=|..||.+-|...+.|=.|+..+.....
T Consensus 421 Ed~lCpICyA~---pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~~l 471 (489)
T KOG4692|consen 421 EDNLCPICYAG---PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDVIL 471 (489)
T ss_pred ccccCcceecc---cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeeehhc
Confidence 56789999744 3567889999999999999999999999999988764333
No 69
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.94 E-value=0.0051 Score=59.58 Aligned_cols=47 Identities=19% Similarity=0.489 Sum_probs=38.0
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccC--------CCcCcccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH--------NSCPVCRQ 227 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~--------~sCP~CR~ 227 (309)
....|.||+++..-....+.|||+|+||+.|+..++..+ -.||-+..
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 357899999997665889999999999999999998732 24877654
No 70
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.85 E-value=0.0099 Score=50.68 Aligned_cols=49 Identities=27% Similarity=0.754 Sum_probs=35.7
Q ss_pred cccccccccccccccCCceEEccccc-----eeccccchhhhccC--CCcCcccccccCC
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNH-----IYHSDCIVPWLVQH--NSCPVCRQELPLQ 232 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H-----~fh~~Ci~~Wl~~~--~sCP~CR~~l~~~ 232 (309)
..+..|-||.++-. . -..||.. ..|.+|+..|+..+ .+|++|+.+....
T Consensus 6 ~~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 34678999998743 1 2357543 67999999999854 4699999876443
No 71
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.62 E-value=0.029 Score=51.08 Aligned_cols=71 Identities=17% Similarity=0.317 Sum_probs=53.5
Q ss_pred hhhcCCceeeecccc----------cccccccccccccccCCceEEc-cccceeccccchhhhccCCCcCcccccccCCC
Q 021640 165 AIDAMPTVRITQRHL----------RSDSHCPVCQDKFELGSEARQM-PCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 165 ~i~~lp~~~~~~~~~----------~~~~~C~IC~~~~~~~~~~~~l-pC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
.++.|-.++++.... .....|+||.+.+........| ||+|+|+.+|+.+.+.....||+|-.++...+
T Consensus 194 klkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 194 KLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD 273 (303)
T ss_pred chhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence 455666666654332 1247899999999876655544 59999999999999999999999988887665
Q ss_pred CC
Q 021640 234 SS 235 (309)
Q Consensus 234 ~~ 235 (309)
..
T Consensus 274 iI 275 (303)
T KOG3039|consen 274 II 275 (303)
T ss_pred eE
Confidence 43
No 72
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.021 Score=52.65 Aligned_cols=48 Identities=31% Similarity=0.687 Sum_probs=37.2
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhcc--CCCcCccccccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ--HNSCPVCRQELP 230 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~--~~sCP~CR~~l~ 230 (309)
.+.+|++|.+.-..+ -...+|+|+||.-||..=+.- ..+||.|-.++.
T Consensus 238 ~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 467999999775543 356669999999999886653 357999988775
No 73
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.48 E-value=0.059 Score=49.89 Aligned_cols=91 Identities=18% Similarity=0.372 Sum_probs=59.5
Q ss_pred chHHHHHHHHhcCCCCCCCcchhh---hhcCCceeeeccc------------ccccccccccccccccCCceEE-ccccc
Q 021640 142 GLEELFEQLSANGRRGPPPAARSA---IDAMPTVRITQRH------------LRSDSHCPVCQDKFELGSEARQ-MPCNH 205 (309)
Q Consensus 142 ~l~~l~~~l~~~~~~~~ppa~~~~---i~~lp~~~~~~~~------------~~~~~~C~IC~~~~~~~~~~~~-lpC~H 205 (309)
..+.||+.|......+..+..-.. ++.|-.+.++... ......|+|...+|......+. -||||
T Consensus 58 nKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~ 137 (260)
T PF04641_consen 58 NKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGC 137 (260)
T ss_pred cHHHHHHHHHhcCcCCCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCC
Confidence 568889998886543222332223 3444445555431 2345789999999955444444 47999
Q ss_pred eeccccchhhhccCCCcCcccccccCCC
Q 021640 206 IYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 206 ~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
+|-..+|..- .....||+|-.++...+
T Consensus 138 V~s~~alke~-k~~~~Cp~c~~~f~~~D 164 (260)
T PF04641_consen 138 VFSEKALKEL-KKSKKCPVCGKPFTEED 164 (260)
T ss_pred EeeHHHHHhh-cccccccccCCccccCC
Confidence 9999999886 23557999988776444
No 74
>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=94.36 E-value=0.01 Score=39.74 Aligned_cols=41 Identities=27% Similarity=0.784 Sum_probs=23.8
Q ss_pred ccccccccccCCceEEccccceeccccchhhhccCC--CcCcc
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVC 225 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~C 225 (309)
|.+|.+....|.......|.-.+|..|+..+++... .||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 778888887664333334999999999999998665 69987
No 75
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.34 E-value=0.034 Score=39.10 Aligned_cols=46 Identities=24% Similarity=0.689 Sum_probs=33.9
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
..|..|... +.+-.++||+|+.+..|..-+ +-+.||+|-+.+...+
T Consensus 8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD 53 (55)
T ss_pred eeEEEcccc---ccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence 456666643 345579999999999997654 6677999988876543
No 76
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.26 E-value=0.025 Score=54.10 Aligned_cols=43 Identities=35% Similarity=0.756 Sum_probs=31.8
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
.+.|.||+++.. ..+.+||||+-+ |..-- +...+||+||..+.
T Consensus 305 p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 305 PDLCVVCLDEPK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred CCceEEecCCcc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 578999998875 478999999966 65442 22335999998763
No 77
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=94.19 E-value=0.029 Score=45.50 Aligned_cols=33 Identities=24% Similarity=0.575 Sum_probs=29.0
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEec
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELD 38 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~ 38 (309)
...||..|+..+.....++.||.|+|..++-+.
T Consensus 69 ~~~~C~~C~~~~~~e~~~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 69 AECWCLDCGQEVELEELDYRCPKCGSINLRIIG 101 (115)
T ss_pred cEEEeccCCCeecchhheeECCCCCCCceEEec
Confidence 568999999999888888889999999888764
No 78
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=94.02 E-value=0.016 Score=60.61 Aligned_cols=47 Identities=23% Similarity=0.781 Sum_probs=35.1
Q ss_pred ccccccccccccccCCceE-EccccceeccccchhhhccCC-------CcCcccc
Q 021640 181 SDSHCPVCQDKFELGSEAR-QMPCNHIYHSDCIVPWLVQHN-------SCPVCRQ 227 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~-~lpC~H~fh~~Ci~~Wl~~~~-------sCP~CR~ 227 (309)
...+|.||.+.+.....+- ...|.|+||..||..|.+... .||.|..
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 4578999999986544322 233999999999999997421 3999983
No 79
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.77 E-value=0.0033 Score=60.36 Aligned_cols=51 Identities=27% Similarity=0.681 Sum_probs=43.6
Q ss_pred cccccccccccccC-CceEEccccceeccccchhhhccCCCcCcccccccCC
Q 021640 182 DSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232 (309)
Q Consensus 182 ~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~ 232 (309)
...|+||.+.++.. +++..+-|+|.+|.+||.+||.....||.|+.+|+..
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN 247 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence 45799999998755 5677888999999999999999988899999888543
No 80
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.74 E-value=0.032 Score=50.67 Aligned_cols=48 Identities=19% Similarity=0.532 Sum_probs=35.3
Q ss_pred cccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~ 234 (309)
.|..|..--. ++...++.|.|+||..|...-. ...||+|++.|.....
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~l 52 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQL 52 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeeeeec
Confidence 5887775544 6778888999999999986532 2289999998754433
No 81
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=93.49 E-value=0.058 Score=51.01 Aligned_cols=46 Identities=24% Similarity=0.481 Sum_probs=35.5
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
...|+||+.....+. +..--|-+||..||..++..++.|||=-.++
T Consensus 300 ~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhccCCCc--eEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 457999998876542 2333599999999999999999999865443
No 82
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.19 E-value=0.035 Score=38.04 Aligned_cols=44 Identities=25% Similarity=0.702 Sum_probs=21.4
Q ss_pred ccccccccccCCceEEcc--ccceeccccchhhhc-cCCCcCcccccc
Q 021640 185 CPVCQDKFELGSEARQMP--CNHIYHSDCIVPWLV-QHNSCPVCRQEL 229 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~Wl~-~~~sCP~CR~~l 229 (309)
|++|.+++.. .....+| |++.++..|...-++ ....||-||++.
T Consensus 1 cp~C~e~~d~-~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDE-TDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--C-CCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCccccccc-CCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899999833 2334555 889999999887775 467899999753
No 83
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.86 E-value=0.033 Score=51.87 Aligned_cols=42 Identities=29% Similarity=0.720 Sum_probs=31.9
Q ss_pred cccccccccccccCCceEEcccccee-ccccchhhhccCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIY-HSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~f-h~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
...|.||++.- ...+.|+|||.. |..|-.. -+.||+||+.|.
T Consensus 300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence 56899998754 567899999974 5667544 237999998764
No 84
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=92.59 E-value=0.039 Score=51.37 Aligned_cols=45 Identities=29% Similarity=0.821 Sum_probs=37.9
Q ss_pred ccccccccccccCC-ceEEccccceeccccchhhhccCCCcCcccc
Q 021640 183 SHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 183 ~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
..|+||.+.+.... .+..++|+|.-|..|+......+.+||+|.+
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 34999998875544 5678899999999999998888889999988
No 85
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.27 E-value=0.046 Score=47.49 Aligned_cols=52 Identities=23% Similarity=0.641 Sum_probs=36.5
Q ss_pred cccccccccccccCC----ceEEccccceeccccchhhhcc----C-------CCcCcccccccCCC
Q 021640 182 DSHCPVCQDKFELGS----EARQMPCNHIYHSDCIVPWLVQ----H-------NSCPVCRQELPLQG 233 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~----~~~~lpC~H~fh~~Ci~~Wl~~----~-------~sCP~CR~~l~~~~ 233 (309)
...|.||+..--.|. ..--..|+.-||.-|+..||+. . ..||.|..++..+.
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm 231 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM 231 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence 356999986543332 2234459999999999999973 1 24999998876553
No 86
>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=91.56 E-value=0.15 Score=41.46 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=26.4
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
...||..|...+.+......||.|++..++=+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHGIMLQVR 100 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcCCCcEEe
Confidence 57899999988887666788999999876655
No 87
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.40 E-value=0.11 Score=48.72 Aligned_cols=47 Identities=23% Similarity=0.691 Sum_probs=38.2
Q ss_pred ccccccccccccCC---ceEEccccceeccccchhhhccCC-CcCcccccc
Q 021640 183 SHCPVCQDKFELGS---EARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~---~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l 229 (309)
..|-||-++|...+ ..+.|.|+|.|+..|+.+-+.... .||.||...
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 57999999997763 356777999999999988776543 599999885
No 88
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=91.07 E-value=0.17 Score=41.05 Aligned_cols=32 Identities=25% Similarity=0.680 Sum_probs=25.3
Q ss_pred CceecccCCCceeecCCC-ccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGED-AVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~-~~CP~C~~gFvEE~ 37 (309)
..+||..|...+...... ..||.|++.-++=+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~ 101 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIV 101 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCCcEEc
Confidence 579999999888776544 67999998876554
No 89
>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=90.48 E-value=0.14 Score=41.37 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=24.4
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
..+||..|.....+......||.|++..++=+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~ 100 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFDFSCPRCGSPDVEII 100 (113)
T ss_dssp -EEEETTTS-EEECHHCCHH-SSSSSS-EEEE
T ss_pred CcEECCCCCCEEecCCCCCCCcCCcCCCcEEc
Confidence 57899999999998877789999999977554
No 90
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.33 E-value=0.1 Score=54.83 Aligned_cols=43 Identities=33% Similarity=0.828 Sum_probs=33.5
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
...|..|--.+..+ .+..-|+|.||.+|+. .....||-|+.++
T Consensus 840 ~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCccccc--eeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 35799998877654 5666799999999998 3455799998744
No 91
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=90.30 E-value=0.23 Score=40.23 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=25.6
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
..+||..|..........+.||.|++.-++=+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCHGERLRVD 100 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCCCCCcEEc
Confidence 57899999988877666677999998766544
No 92
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.20 E-value=0.16 Score=35.73 Aligned_cols=33 Identities=39% Similarity=0.887 Sum_probs=28.1
Q ss_pred cccccccccccccCCceEEcc-ccceeccccchh
Q 021640 182 DSHCPVCQDKFELGSEARQMP-CNHIYHSDCIVP 214 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~ 214 (309)
...|.+|-+.|+.++.+++-| |+-.||.+|...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 457999999998888888888 999999999543
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.13 E-value=0.12 Score=49.29 Aligned_cols=47 Identities=28% Similarity=0.739 Sum_probs=36.9
Q ss_pred cccccccccccccccCCceEEccccceeccccchhh--hccCCCcCcccccc
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPW--LVQHNSCPVCRQEL 229 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~W--l~~~~sCP~CR~~l 229 (309)
+++..|-||-+.. ..+.++||+|..|.-|-... |-..+.||+||.+.
T Consensus 59 Een~~C~ICA~~~---TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGST---TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCCc---eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 4567899999876 35689999999999997543 33577899999865
No 94
>PHA03096 p28-like protein; Provisional
Probab=90.09 E-value=0.076 Score=49.87 Aligned_cols=36 Identities=17% Similarity=0.469 Sum_probs=27.5
Q ss_pred ccccccccccccCC----ceEEcc-ccceeccccchhhhcc
Q 021640 183 SHCPVCQDKFELGS----EARQMP-CNHIYHSDCIVPWLVQ 218 (309)
Q Consensus 183 ~~C~IC~~~~~~~~----~~~~lp-C~H~fh~~Ci~~Wl~~ 218 (309)
..|.||++...... .-..|+ |.|.||..||..|...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~ 219 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE 219 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence 68999999865321 223455 9999999999999864
No 95
>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=90.02 E-value=0.099 Score=35.61 Aligned_cols=44 Identities=25% Similarity=0.687 Sum_probs=25.4
Q ss_pred cccccccccccCCceEEccc-cceeccccchhhhccCCCcCcccccccCC
Q 021640 184 HCPVCQDKFELGSEARQMPC-NHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC-~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~ 232 (309)
.|.-|+-.. . ....| .|+.+..|+...|.+...||+|.++||.+
T Consensus 4 nCKsCWf~~--k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFAN--K---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S----S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred cChhhhhcC--C---CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 466666332 1 24447 59999999999999999999999999864
No 96
>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=89.53 E-value=0.38 Score=46.55 Aligned_cols=29 Identities=24% Similarity=0.923 Sum_probs=22.2
Q ss_pred ccceeccccchhhhcc-------------CCCcCcccccccC
Q 021640 203 CNHIYHSDCIVPWLVQ-------------HNSCPVCRQELPL 231 (309)
Q Consensus 203 C~H~fh~~Ci~~Wl~~-------------~~sCP~CR~~l~~ 231 (309)
|.-..|.+|+-+|+.. +-.||+||+.+..
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 5677888999999863 2359999998754
No 97
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.31 E-value=0.28 Score=40.00 Aligned_cols=32 Identities=22% Similarity=0.312 Sum_probs=24.7
Q ss_pred CceecccCCCceeecCCC-ccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGED-AVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~-~~CP~C~~gFvEE~ 37 (309)
..+||..|...+...... ..||.|++..++=+
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNVIIT 102 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCceEEe
Confidence 578999999887765433 45999999877654
No 98
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.12 E-value=0.41 Score=32.20 Aligned_cols=32 Identities=28% Similarity=0.533 Sum_probs=26.2
Q ss_pred CceecccCCCceeecC--CCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~ 37 (309)
..|-|-.|...+.... ..+.||+|++-++...
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 4688999999998766 3689999999888544
No 99
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=89.07 E-value=0.15 Score=48.01 Aligned_cols=43 Identities=23% Similarity=0.724 Sum_probs=29.6
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
-.|--|-..+. -.-+.+||+|+||.+|-.. ...+.||.|-..|
T Consensus 91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred EeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 35666754433 3457889999999999643 3456899996443
No 100
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=88.97 E-value=0.2 Score=47.45 Aligned_cols=42 Identities=31% Similarity=0.706 Sum_probs=33.4
Q ss_pred cccccccccccccCCceEEccc--cceeccccchhhhccCCCcCccccccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPC--NHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC--~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
-.+|+||.+.+..+ .+.| ||+.|..|-. +..+.||.||.++.
T Consensus 48 lleCPvC~~~l~~P----i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPP----IFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCccc----ceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 46899999998765 5667 6999999865 35678999998875
No 101
>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=88.84 E-value=0.25 Score=29.46 Aligned_cols=23 Identities=26% Similarity=0.545 Sum_probs=18.9
Q ss_pred cccCCCceeecCCCccCCCCCCCce
Q 021640 10 CYRCRRPVRLQGEDAVCLYCSGGFV 34 (309)
Q Consensus 10 Ch~C~r~v~~~~~~~~CP~C~~gFv 34 (309)
|-.|...|.. ...+||+|+..|.
T Consensus 3 CP~C~~~V~~--~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPE--SAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchh--hcCcCCCCCCCCc
Confidence 7789998844 5789999999885
No 102
>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=88.72 E-value=0.24 Score=28.93 Aligned_cols=21 Identities=29% Similarity=0.732 Sum_probs=17.3
Q ss_pred cccCCCceeecC--CCccCCCCC
Q 021640 10 CYRCRRPVRLQG--EDAVCLYCS 30 (309)
Q Consensus 10 Ch~C~r~v~~~~--~~~~CP~C~ 30 (309)
|..|++.|.... -.+.||.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 788999997765 457999997
No 103
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=87.88 E-value=0.4 Score=40.03 Aligned_cols=32 Identities=16% Similarity=0.244 Sum_probs=24.3
Q ss_pred CceecccCCCceeec---------------------CCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQ---------------------GEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~---------------------~~~~~CP~C~~gFvEE~ 37 (309)
..|||..|....... ...+.||.|++.-++=+
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 679999999887765 23467999998766544
No 104
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=87.60 E-value=0.11 Score=54.33 Aligned_cols=51 Identities=25% Similarity=0.544 Sum_probs=41.1
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCC--CcCcccccccCCCCCCC
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQELPLQGSSSS 237 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~~~~ 237 (309)
..|.||++ .+.+...+|+|.||..|+..-+.... .||+||..+..+.....
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~ 507 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSA 507 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhc
Confidence 68999998 36778889999999999988887543 49999988866665543
No 105
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.59 E-value=0.26 Score=46.17 Aligned_cols=42 Identities=29% Similarity=0.774 Sum_probs=32.8
Q ss_pred ccccccccccccCCceEEcc-ccceeccccchhhhc-cCCCcCcccc
Q 021640 183 SHCPVCQDKFELGSEARQMP-CNHIYHSDCIVPWLV-QHNSCPVCRQ 227 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lp-C~H~fh~~Ci~~Wl~-~~~sCP~CR~ 227 (309)
+.|+.|...+... .+++ |+|.||..||..-|. ....||.|..
T Consensus 275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 6799998877543 4455 899999999987665 4567999954
No 106
>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=86.23 E-value=0.42 Score=40.89 Aligned_cols=33 Identities=27% Similarity=0.674 Sum_probs=22.1
Q ss_pred cccccccccccccCCceEEcccc-------------ceeccccchhhhc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCN-------------HIYHSDCIVPWLV 217 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~-------------H~fh~~Ci~~Wl~ 217 (309)
+..|+||+|-- ..+++|-|. -.-|..||+++-+
T Consensus 2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 46899999653 556666653 2347789887654
No 107
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.04 E-value=0.36 Score=49.38 Aligned_cols=51 Identities=27% Similarity=0.746 Sum_probs=41.7
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCCCCCCc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSSSSR 238 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~~~~ 238 (309)
....|.||+++. ..+..+|. |..|+.+|+..+.+||+|++.+..++.....
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~~~ 528 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFLSKN 528 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhcccccCcc
Confidence 457899999987 44677788 9999999999999999999988766655443
No 108
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.54 E-value=0.52 Score=38.80 Aligned_cols=31 Identities=16% Similarity=0.257 Sum_probs=22.8
Q ss_pred CceecccCCCceeecCC-------CccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGE-------DAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~-------~~~CP~C~~gFvEE~ 37 (309)
..+|| .|.....+... ...||.|++.-++=+
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 57899 99988665421 256999998877655
No 109
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=85.16 E-value=0.31 Score=51.19 Aligned_cols=52 Identities=19% Similarity=0.648 Sum_probs=38.4
Q ss_pred cccccccccccccCCceEEcccc-----ceeccccchhhhccCC--CcCcccccccCCCC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCN-----HIYHSDCIVPWLVQHN--SCPVCRQELPLQGS 234 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~-----H~fh~~Ci~~Wl~~~~--sCP~CR~~l~~~~~ 234 (309)
+..|.||..+-.. +....-||+ .+.|.+|+.+|+.-+. .|-+|+.++.-++-
T Consensus 12 ~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 12 KRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred chhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 4689999987433 445556776 4689999999998554 49999988755443
No 110
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.12 E-value=0.58 Score=40.95 Aligned_cols=32 Identities=13% Similarity=0.274 Sum_probs=25.6
Q ss_pred CCceecccCCCceeecC---CCccCCCCCCCceEE
Q 021640 5 RNTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQE 36 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE 36 (309)
...|.|-.|...+...- .++.||.|++-++|.
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 37899999998886542 579999999987763
No 111
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.98 E-value=0.26 Score=52.20 Aligned_cols=38 Identities=24% Similarity=0.680 Sum_probs=30.1
Q ss_pred cccccccccccccccccCCceEEccccceeccccchhhh
Q 021640 178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL 216 (309)
Q Consensus 178 ~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl 216 (309)
.++..+.|.+|...+.. ..-.+.||+|.||++||.+-.
T Consensus 813 v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 813 VLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred EecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence 34567899999988754 366788899999999997654
No 112
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.61 E-value=0.45 Score=46.20 Aligned_cols=49 Identities=20% Similarity=0.430 Sum_probs=40.5
Q ss_pred ccccccccccccccccCCceEEccccceeccccchhhhccCC---CcCcccc
Q 021640 179 LRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQ 227 (309)
Q Consensus 179 ~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR~ 227 (309)
..+.-.|+|=.+.-.....+..|.|||+..++-|.+..+.+. .||+|=.
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 345678999998888878899999999999999999776554 4999943
No 113
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=84.57 E-value=0.32 Score=50.71 Aligned_cols=40 Identities=28% Similarity=0.785 Sum_probs=30.1
Q ss_pred cccccccccccCCceEEccccceeccccchhhhccCCCcCc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPV 224 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~ 224 (309)
.|+||--.+ .+.......|+|+-|.+|...|++....||.
T Consensus 1030 ~C~~C~l~V-~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAV-RGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeeEeeEe-eccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 455554332 3445566779999999999999999999985
No 114
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.14 E-value=0.58 Score=26.98 Aligned_cols=23 Identities=17% Similarity=0.621 Sum_probs=18.2
Q ss_pred ecccCCCceeecCCCccCCCCCCCc
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGGF 33 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~gF 33 (309)
||.+|-.+|.. ...+||.|+..|
T Consensus 1 ~Cp~CG~~~~~--~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED--DAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC--cCcchhhhCCcC
Confidence 68999999853 577899998653
No 115
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.96 E-value=0.72 Score=41.39 Aligned_cols=39 Identities=26% Similarity=0.737 Sum_probs=27.9
Q ss_pred cccccccccccCCceEEccccce-eccccchhhhccCCCcCcccccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHI-YHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~-fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
.|-+|.+. ...|..+||.|+ +|..|=.. -..||+|+...
T Consensus 160 ~Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 160 SCRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPK 199 (207)
T ss_pred cceecCcC---CceEEeecccceEeccccccc----CccCCCCcChh
Confidence 38888644 456899999987 66778543 34599998644
No 116
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=83.75 E-value=0.36 Score=53.15 Aligned_cols=44 Identities=25% Similarity=0.637 Sum_probs=37.0
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
-..|.||++.+... ..+.-|+|.++..|+..|+..+..||+|+.
T Consensus 1153 ~~~c~ic~dil~~~--~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQ--GGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred ccchHHHHHHHHhc--CCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence 35899999998632 245559999999999999999999999973
No 117
>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=83.14 E-value=0.7 Score=39.62 Aligned_cols=32 Identities=13% Similarity=0.170 Sum_probs=24.6
Q ss_pred CCceecccCCCceeecC---CCccCCCCCCCceEEe
Q 021640 5 RNTHWCYRCRRPVRLQG---EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~---~~~~CP~C~~gFvEE~ 37 (309)
...|.|-.|...+...- .+++||.|++-+ +++
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L-~~~ 141 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAML-DYL 141 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCEe-eec
Confidence 47899999998876532 579999999874 444
No 118
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.64 E-value=0.74 Score=31.70 Aligned_cols=33 Identities=27% Similarity=0.530 Sum_probs=25.7
Q ss_pred CCceecccCCCceeecC--CCccCCCCCCCceEEe
Q 021640 5 RNTHWCYRCRRPVRLQG--EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~--~~~~CP~C~~gFvEE~ 37 (309)
+..|-|-.|.+.|.... .++.||+|++-.+-..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSRILVKE 38 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcEEEEec
Confidence 46799999999997432 6789999998765443
No 119
>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=81.72 E-value=1.6 Score=27.25 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=20.6
Q ss_pred eecccCCCceeecC-CCccCCCCCCCce
Q 021640 8 HWCYRCRRPVRLQG-EDAVCLYCSGGFV 34 (309)
Q Consensus 8 ywCh~C~r~v~~~~-~~~~CP~C~~gFv 34 (309)
|-|-.|...|.+.. +.+.||+|+.-.+
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeEE
Confidence 67999999999876 5578999998654
No 120
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=81.69 E-value=1.3 Score=29.74 Aligned_cols=31 Identities=16% Similarity=0.351 Sum_probs=25.9
Q ss_pred ceecccCCCceeecC-CCccCCCCCCCceEEe
Q 021640 7 THWCYRCRRPVRLQG-EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~-~~~~CP~C~~gFvEE~ 37 (309)
.|-|-.|..++.+.. ..+.||+|++-.+--.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRILYKK 33 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence 488999999999875 5689999999877554
No 121
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=81.46 E-value=0.5 Score=44.20 Aligned_cols=51 Identities=20% Similarity=0.569 Sum_probs=37.1
Q ss_pred cccccccccccccCCc-eEEcccc-----ceeccccchhhhcc--CCCcCcccccccCC
Q 021640 182 DSHCPVCQDKFELGSE-ARQMPCN-----HIYHSDCIVPWLVQ--HNSCPVCRQELPLQ 232 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~-~~~lpC~-----H~fh~~Ci~~Wl~~--~~sCP~CR~~l~~~ 232 (309)
...|-||.++...... ....||. +..|..|+..|+.. ...|.+|.......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence 4689999987643221 4677764 67899999999984 45699998765443
No 122
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=80.94 E-value=0.84 Score=32.91 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=20.3
Q ss_pred ecccCCCceeecCCCccCCCCCCC-ceEEe
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGG-FVQEL 37 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~g-FvEE~ 37 (309)
=|+.|.+-+.. +.-+||.|++. |.||-
T Consensus 6 AC~~Ck~l~~~--d~e~CP~Cgs~~~te~W 33 (64)
T COG2093 6 ACKNCKRLTPE--DTEICPVCGSTDLTEEW 33 (64)
T ss_pred HHhhccccCCC--CCccCCCCCCcccchhh
Confidence 38999876632 34589999998 87775
No 123
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=79.70 E-value=0.7 Score=38.43 Aligned_cols=50 Identities=18% Similarity=0.418 Sum_probs=34.7
Q ss_pred ccccccccccccccCCceEEcc---ccceeccccchhhhc---cCCCcCcccccccCC
Q 021640 181 SDSHCPVCQDKFELGSEARQMP---CNHIYHSDCIVPWLV---QHNSCPVCRQELPLQ 232 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lp---C~H~fh~~Ci~~Wl~---~~~sCP~CR~~l~~~ 232 (309)
...+|.||.|.-.+. -..-| ||-..|..|...-++ .+..||+|+..+...
T Consensus 79 ~lYeCnIC~etS~ee--~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 79 KLYECNICKETSAEE--RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred CceeccCcccccchh--hcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 457899999875432 22333 898899888655444 456799999887543
No 124
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=79.43 E-value=0.68 Score=44.20 Aligned_cols=51 Identities=20% Similarity=0.544 Sum_probs=33.8
Q ss_pred cccccccccccccccCCc-eEEccccceeccccchhhhc-cCCCcCccccccc
Q 021640 180 RSDSHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLV-QHNSCPVCRQELP 230 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~-~~~sCP~CR~~l~ 230 (309)
++++.|+.|++.+...++ ..-.||+-..|.-|...--+ .+..||-||....
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 345669999999876654 34456887766666433222 3457999997653
No 125
>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=77.37 E-value=1.1 Score=42.01 Aligned_cols=52 Identities=21% Similarity=0.423 Sum_probs=35.8
Q ss_pred cccccccccccCC--ceEEccccceeccccchhhhccCC-CcCcccccccCCCCC
Q 021640 184 HCPVCQDKFELGS--EARQMPCNHIYHSDCIVPWLVQHN-SCPVCRQELPLQGSS 235 (309)
Q Consensus 184 ~C~IC~~~~~~~~--~~~~lpC~H~fh~~Ci~~Wl~~~~-sCP~CR~~l~~~~~~ 235 (309)
.|++|+.+.-..- ....-+|+|..|.+|++.-+..+. .||.|-..|-.....
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr 56 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR 56 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence 5999986532222 223336999999999999887654 599997766544443
No 126
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=75.33 E-value=1.6 Score=25.72 Aligned_cols=23 Identities=17% Similarity=0.638 Sum_probs=17.5
Q ss_pred eecccCCCceeecCCCccCCCCCCC
Q 021640 8 HWCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 8 ywCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
-+|.+|...| ..++.+||+|+..
T Consensus 3 ~~Cp~Cg~~~--~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEI--DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcC--CcccccChhhCCC
Confidence 3688999854 4467899999864
No 127
>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=75.13 E-value=2.4 Score=27.19 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=19.8
Q ss_pred CceecccCCCceeecC-----CCccCCCCCC
Q 021640 6 NTHWCYRCRRPVRLQG-----EDAVCLYCSG 31 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~-----~~~~CP~C~~ 31 (309)
-.|-|..|...+.... ....||.|++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 3588999999776433 3468999998
No 128
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=75.12 E-value=3.3 Score=28.21 Aligned_cols=31 Identities=23% Similarity=0.447 Sum_probs=22.5
Q ss_pred ceecccCCCceeecC-----CCccCCCCCCCceEEe
Q 021640 7 THWCYRCRRPVRLQG-----EDAVCLYCSGGFVQEL 37 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~-----~~~~CP~C~~gFvEE~ 37 (309)
.|.|-.|........ ....||.|++.=++.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 588999999665543 2358999999655554
No 129
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=73.76 E-value=2 Score=37.79 Aligned_cols=27 Identities=30% Similarity=0.805 Sum_probs=20.6
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
.-|||..||-.+. .-.|+-|+++| +++
T Consensus 13 ~iyWCe~cNlPl~----~~~c~~cg~~~-~~l 39 (202)
T COG5270 13 PIYWCEKCNLPLL----GRRCSVCGSKV-EEL 39 (202)
T ss_pred ceeehhhCCCccc----cccccccCCcc-eEE
Confidence 4699999997653 46899999665 555
No 130
>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 KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.23 E-value=0.93 Score=41.72 Aligned_cols=50 Identities=28% Similarity=0.634 Sum_probs=33.8
Q ss_pred cccccccccccccccCCce-EEcccc-----ceeccccchhhhccC--------CCcCcccccc
Q 021640 180 RSDSHCPVCQDKFELGSEA-RQMPCN-----HIYHSDCIVPWLVQH--------NSCPVCRQEL 229 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~-~~lpC~-----H~fh~~Ci~~Wl~~~--------~sCP~CR~~l 229 (309)
+.+..|-||+..=++.... -.-||. |-.|..||..|+..+ -+||-|+.+.
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 4467899998664332111 234663 789999999999633 2599999764
No 132
>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=71.14 E-value=1.5 Score=39.97 Aligned_cols=46 Identities=28% Similarity=0.715 Sum_probs=33.9
Q ss_pred cccccccccccccCCceE--Ecc-ccceeccccchhhhccCC-CcC--cccc
Q 021640 182 DSHCPVCQDKFELGSEAR--QMP-CNHIYHSDCIVPWLVQHN-SCP--VCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~--~lp-C~H~fh~~Ci~~Wl~~~~-sCP--~CR~ 227 (309)
+..|+||..+--..-.++ .-| |-|..|.+|++.-+.+.. .|| -|-+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 458999997643333333 335 999999999999998776 599 7754
No 133
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=70.10 E-value=1.3 Score=46.16 Aligned_cols=46 Identities=20% Similarity=0.696 Sum_probs=36.6
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCC---CcCcccccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCRQEL 229 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR~~l 229 (309)
...+|+||+..+... ..+.|.|.|+..|+..-+...+ .||+|+..+
T Consensus 20 k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 20 KILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 457899999988755 6777999999999877666544 599998655
No 134
>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=70.09 E-value=3.7 Score=25.41 Aligned_cols=37 Identities=22% Similarity=0.641 Sum_probs=24.1
Q ss_pred cccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
.|..|.+.+...+... ..=+..||..|+ .|..|...|
T Consensus 1 ~C~~C~~~i~~~~~~~-~~~~~~~H~~Cf--------~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVL-RALGKVWHPECF--------KCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEE-EeCCccccccCC--------CCcccCCcC
Confidence 3778888776542222 223678998886 688887765
No 135
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=69.61 E-value=3.8 Score=29.29 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=23.7
Q ss_pred CCCCCCceecccCCCceeecC--CCccCCCCCCC
Q 021640 1 MSSGRNTHWCYRCRRPVRLQG--EDAVCLYCSGG 32 (309)
Q Consensus 1 mss~~~~ywCh~C~r~v~~~~--~~~~CP~C~~g 32 (309)
|+.......|-.|.+.|.... ..+.||.|+.-
T Consensus 1 ~~~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 1 ISEMMEPPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CcccccCccccCCCCcccCCCccCEeeCCCCCCe
Confidence 455556778999999997654 45789999764
No 136
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=69.38 E-value=1.4 Score=45.29 Aligned_cols=42 Identities=29% Similarity=0.763 Sum_probs=27.8
Q ss_pred cccccccccc-----cccCCceEEccccceeccccchhhhccCCCcCccc
Q 021640 182 DSHCPVCQDK-----FELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 182 ~~~C~IC~~~-----~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
...|.||... |+.....+...|+++||..|+.. .+.-||.|-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~ 557 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCE 557 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence 4678888432 33333445566999999999644 344499994
No 137
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.34 E-value=3 Score=37.11 Aligned_cols=41 Identities=27% Similarity=0.848 Sum_probs=28.5
Q ss_pred cccccccccc-----cccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDK-----FELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~-----~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
+..|-||.+. |+.....+.-.|+.+||..|..+ ..||-|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-----~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-----KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-----CCCCCcHh
Confidence 5678888753 34433344445999999999762 66999953
No 138
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.31 E-value=2.3 Score=41.75 Aligned_cols=37 Identities=16% Similarity=0.416 Sum_probs=26.9
Q ss_pred cccccccccccccC-CceEEccccceeccccchhhhcc
Q 021640 182 DSHCPVCQDKFELG-SEARQMPCNHIYHSDCIVPWLVQ 218 (309)
Q Consensus 182 ~~~C~IC~~~~~~~-~~~~~lpC~H~fh~~Ci~~Wl~~ 218 (309)
..+|.||..++... .....+-|+|.||.+|+...+..
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev 183 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV 183 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence 46899999444333 33345569999999999988773
No 139
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=67.54 E-value=1.8 Score=42.76 Aligned_cols=35 Identities=29% Similarity=0.654 Sum_probs=28.2
Q ss_pred cccccccccccccccCCceEEccccceeccccchhhhc
Q 021640 180 RSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLV 217 (309)
Q Consensus 180 ~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~ 217 (309)
+++..|+||..-|.. .++|||+|..|..|-..-+.
T Consensus 2 eeelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYRE---PIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhccC---ceEeecccHHHHHHHHhhcc
Confidence 456789999988854 58999999999998765544
No 140
>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=67.23 E-value=4 Score=27.49 Aligned_cols=44 Identities=34% Similarity=0.717 Sum_probs=29.9
Q ss_pred cccccccccccCCceEEccccceeccccchhhhcc------CCCcCcccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ------HNSCPVCRQ 227 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~------~~sCP~CR~ 227 (309)
.|.||......++.+.--.|...||..|+..=+.. .-.||.|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 48899885444444444459999999999776541 235888864
No 141
>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=66.07 E-value=2.5 Score=29.08 Aligned_cols=42 Identities=24% Similarity=0.705 Sum_probs=20.7
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccC---C--CcCcccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH---N--SCPVCRQ 227 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~---~--sCP~CR~ 227 (309)
..|+|....+.. .++...|.|.-+.+ +..||... . .||+|.+
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence 468888877764 46777799975433 34565532 2 4999976
No 142
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.50 E-value=1.5 Score=41.08 Aligned_cols=31 Identities=19% Similarity=0.793 Sum_probs=23.5
Q ss_pred ccceeccccchhhhc-------------cCCCcCcccccccCCC
Q 021640 203 CNHIYHSDCIVPWLV-------------QHNSCPVCRQELPLQG 233 (309)
Q Consensus 203 C~H~fh~~Ci~~Wl~-------------~~~sCP~CR~~l~~~~ 233 (309)
|...+|.+|+.+|+. .+-+||+||+.+..-+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 667788899988875 2446999999876443
No 143
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=65.01 E-value=2.2 Score=44.97 Aligned_cols=53 Identities=15% Similarity=0.266 Sum_probs=37.7
Q ss_pred cccccccccccccCC-ceEEcc---ccceeccccchhhhcc------CCCcCcccccccCCCC
Q 021640 182 DSHCPVCQDKFELGS-EARQMP---CNHIYHSDCIVPWLVQ------HNSCPVCRQELPLQGS 234 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~-~~~~lp---C~H~fh~~Ci~~Wl~~------~~sCP~CR~~l~~~~~ 234 (309)
...|.||..++..+. ....+| |.|.||..||..|+.+ +-.|+.|...|.....
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR 158 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR 158 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh
Confidence 467888888887622 233445 9999999999999963 3358999877754433
No 144
>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=64.64 E-value=8.1 Score=26.43 Aligned_cols=40 Identities=18% Similarity=0.453 Sum_probs=27.9
Q ss_pred ccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccCCC
Q 021640 185 CPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQG 233 (309)
Q Consensus 185 C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~ 233 (309)
|..|.+.+...+ .....-+..||..|+ .|-.|+..|....
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCcE-EEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 677888876443 332346788999886 6889988875443
No 145
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=64.18 E-value=4.3 Score=38.52 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=20.6
Q ss_pred CCCCCCceecccCCCceeecCCCccCCCCCCC
Q 021640 1 MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 1 mss~~~~ywCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
|+++ ..-+||.|+.+-+ +++||+|+--
T Consensus 2 ~pts-~~~~C~ic~vq~~----~YtCPRCn~~ 28 (383)
T KOG4317|consen 2 MPTS-SFLACGICGVQKR----EYTCPRCNLL 28 (383)
T ss_pred CCCC-ceeeccccccccc----cccCCCCCcc
Confidence 4444 7889999998764 4899999754
No 146
>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=64.07 E-value=8.6 Score=25.29 Aligned_cols=29 Identities=17% Similarity=0.399 Sum_probs=20.2
Q ss_pred ceecccCCCceeecC-----CCccCCCCCCCceE
Q 021640 7 THWCYRCRRPVRLQG-----EDAVCLYCSGGFVQ 35 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~-----~~~~CP~C~~gFvE 35 (309)
.|-|-.|........ ....||.|++.=++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 588999996654322 34799999995444
No 147
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=62.81 E-value=3.1 Score=37.27 Aligned_cols=48 Identities=29% Similarity=0.620 Sum_probs=38.5
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccccC
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPL 231 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~ 231 (309)
...|.+|..-.-.+ ++.-.|+-.||..|+...+.+...||.|-.-++.
T Consensus 181 lk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w~h 228 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGDLWTH 228 (235)
T ss_pred HHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhcccCc
Confidence 46899999876544 4566699999999999999998899999654443
No 148
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=61.96 E-value=8.9 Score=36.64 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=35.0
Q ss_pred ccccccccccccCCceEEcc--ccceeccccchhhhccCCCcCcccccccCC
Q 021640 183 SHCPVCQDKFELGSEARQMP--CNHIYHSDCIVPWLVQHNSCPVCRQELPLQ 232 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~ 232 (309)
..|+||.+..... ..-.+| |++..|..|+..-...+.+||.||+.....
T Consensus 250 ~s~p~~~~~~~~~-d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLT-DSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCccccc-ccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 6899999876322 233444 778778888887777888999999655433
No 149
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.13 E-value=5.3 Score=25.98 Aligned_cols=25 Identities=36% Similarity=0.687 Sum_probs=20.4
Q ss_pred cccCCCceeecCCCccCCCCCCCceEE
Q 021640 10 CYRCRRPVRLQGEDAVCLYCSGGFVQE 36 (309)
Q Consensus 10 Ch~C~r~v~~~~~~~~CP~C~~gFvEE 36 (309)
|+.|++.+.+. .+.|.+|+.-|-.+
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc--CeECCccCCccccc
Confidence 78899887664 68899999998754
No 150
>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=61.04 E-value=5.4 Score=32.07 Aligned_cols=31 Identities=23% Similarity=0.416 Sum_probs=23.4
Q ss_pred CceecccCCCceeecC-CCccCCCCCCCceEE
Q 021640 6 NTHWCYRCRRPVRLQG-EDAVCLYCSGGFVQE 36 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~-~~~~CP~C~~gFvEE 36 (309)
.-.-|..|.....--+ .-++||+|+.-|.-+
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3445999988876544 557899999988777
No 151
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.91 E-value=4.9 Score=39.41 Aligned_cols=44 Identities=27% Similarity=0.645 Sum_probs=31.9
Q ss_pred cccccccccccccCCceEEc--cccceeccccchhhhccCCCcCcc
Q 021640 182 DSHCPVCQDKFELGSEARQM--PCNHIYHSDCIVPWLVQHNSCPVC 225 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~l--pC~H~fh~~Ci~~Wl~~~~sCP~C 225 (309)
-..|++|.-.++.......+ .|+|.|+..|...|......|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 46799998776554433333 389999999999998877766554
No 152
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.77 E-value=4.6 Score=42.71 Aligned_cols=44 Identities=18% Similarity=0.563 Sum_probs=32.5
Q ss_pred cccccccccccccC----CceEEccccceeccccchhhhccCCCcCccc
Q 021640 182 DSHCPVCQDKFELG----SEARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 182 ~~~C~IC~~~~~~~----~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
+..|.-|.+..... ..++.+-|+|.||..|+.--..+.+ |-.|-
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhh
Confidence 45899998875422 4677888999999999987766655 65553
No 153
>PF14968 CCDC84: Coiled coil protein 84
Probab=56.27 E-value=3.6 Score=39.61 Aligned_cols=31 Identities=35% Similarity=0.806 Sum_probs=26.2
Q ss_pred CCceecccCCCceeecCCCccCCCCCCCceEEecC
Q 021640 5 RNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDD 39 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~ 39 (309)
+.+|||+-|...|.....-+.| +|.||+|..
T Consensus 56 ~~~fWC~fC~~ev~~~~s~~~~----~~ai~HLaS 86 (336)
T PF14968_consen 56 RNRFWCVFCDCEVREHDSSFAC----GGAIEHLAS 86 (336)
T ss_pred cceeEeeCccchhhhccchhhh----ccHHhhcCC
Confidence 4789999999999877676777 899999954
No 154
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=56.23 E-value=4 Score=37.85 Aligned_cols=47 Identities=26% Similarity=0.660 Sum_probs=32.7
Q ss_pred ccccccccccccCCceE-Ecc---ccceeccccchhhhc---------cCCCcCcccccc
Q 021640 183 SHCPVCQDKFELGSEAR-QMP---CNHIYHSDCIVPWLV---------QHNSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~-~lp---C~H~fh~~Ci~~Wl~---------~~~sCP~CR~~l 229 (309)
..|.+|.+++...+..+ .-+ |.-++|..|+..-+. ....||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 58999999994333222 222 889999999988443 134599998754
No 155
>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=54.89 E-value=7.4 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.444 Sum_probs=20.4
Q ss_pred eecccCCCceeecC-------CCccCCCCCCCce
Q 021640 8 HWCYRCRRPVRLQG-------EDAVCLYCSGGFV 34 (309)
Q Consensus 8 ywCh~C~r~v~~~~-------~~~~CP~C~~gFv 34 (309)
+=|-+|...+.+.. ..+.||.|+.-|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 45888999888764 2379999998774
No 156
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.48 E-value=5.6 Score=39.69 Aligned_cols=36 Identities=22% Similarity=0.619 Sum_probs=30.2
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhcc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ 218 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~ 218 (309)
...+|-||.+.+.. ....+.|+|.|+..|+...|.+
T Consensus 69 ~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 69 GDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred ccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 45789999998754 5678889999999999998874
No 157
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.65 E-value=7.2 Score=24.85 Aligned_cols=25 Identities=20% Similarity=0.542 Sum_probs=18.4
Q ss_pred ecccCCCceeecC-------CCccCCCCCCCc
Q 021640 9 WCYRCRRPVRLQG-------EDAVCLYCSGGF 33 (309)
Q Consensus 9 wCh~C~r~v~~~~-------~~~~CP~C~~gF 33 (309)
-|.+|+....+.. ..+.|+.|+.-|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4888888877653 347899998765
No 158
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.03 E-value=13 Score=34.33 Aligned_cols=51 Identities=14% Similarity=0.272 Sum_probs=33.4
Q ss_pred cccccccccccccCCc-eEEccccceeccccchhhhccCCCcCcccccccCCCC
Q 021640 182 DSHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPLQGS 234 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~ 234 (309)
...|+|---+|...-. +..-+|||+|-..-+.+. ...+|++|...+..++.
T Consensus 111 ~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dv 162 (293)
T KOG3113|consen 111 RFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDV 162 (293)
T ss_pred eeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCe
Confidence 3579988776643332 234459999987766553 35679999876654443
No 159
>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=50.63 E-value=10 Score=31.33 Aligned_cols=31 Identities=19% Similarity=0.181 Sum_probs=23.5
Q ss_pred CceecccCCCceeecC-CCccCCCCCCCceEE
Q 021640 6 NTHWCYRCRRPVRLQG-EDAVCLYCSGGFVQE 36 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~-~~~~CP~C~~gFvEE 36 (309)
...-|..|.....--+ .-++||+|+.-|..+
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 3456999988876544 668999999987665
No 160
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.44 E-value=3.7 Score=42.49 Aligned_cols=43 Identities=23% Similarity=0.595 Sum_probs=31.3
Q ss_pred cccccccccccccCC-ceEEccccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
...|.||+..|.... ..+-|-|+|..|..|+..- -+.+|| |+.
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 457999988875543 4456669999999999764 345788 543
No 161
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=50.26 E-value=7.1 Score=34.17 Aligned_cols=29 Identities=17% Similarity=0.340 Sum_probs=23.1
Q ss_pred CceecccCCCceeecC---CCccCCCCCCCce
Q 021640 6 NTHWCYRCRRPVRLQG---EDAVCLYCSGGFV 34 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~---~~~~CP~C~~gFv 34 (309)
..|-|-.|.-.+.... .+++||.|++-.+
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~ 143 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE 143 (176)
T ss_pred CceeCCCCCCcccHHHHHHhCCCCCCCCchhh
Confidence 6788999988887653 5799999998743
No 162
>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=49.75 E-value=12 Score=26.84 Aligned_cols=37 Identities=24% Similarity=0.494 Sum_probs=18.8
Q ss_pred ccccccccccccccCCceE-Eccccceeccccchhhhc
Q 021640 181 SDSHCPVCQDKFELGSEAR-QMPCNHIYHSDCIVPWLV 217 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~-~lpC~H~fh~~Ci~~Wl~ 217 (309)
+...|.+|...|..-..-. --.||++|+..|....+.
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEc
Confidence 3468999999996532222 223999999999876654
No 163
>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=49.41 E-value=5.8 Score=29.37 Aligned_cols=40 Identities=30% Similarity=0.645 Sum_probs=21.1
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCccccccc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
..|+.|..++.... +|.++..|-.. +.....||-|..+|.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHHH
Confidence 46999988765432 67777777655 344556899887763
No 164
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=47.96 E-value=4.8 Score=27.90 Aligned_cols=27 Identities=19% Similarity=0.415 Sum_probs=20.4
Q ss_pred CceecccCCCceeecC----CCccCCCCCCC
Q 021640 6 NTHWCYRCRRPVRLQG----EDAVCLYCSGG 32 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~----~~~~CP~C~~g 32 (309)
.-+-|-.|++-+.... -+++||+|+-=
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 3467999999887642 46899999753
No 165
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.14 E-value=9.3 Score=36.36 Aligned_cols=49 Identities=20% Similarity=0.437 Sum_probs=37.8
Q ss_pred cccccccccccccccccCCceEEccccceeccccchhhhccCC---CcCccc
Q 021640 178 HLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHN---SCPVCR 226 (309)
Q Consensus 178 ~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~---sCP~CR 226 (309)
+....-.|++-.+.-.......-|.|+|+.-..-+..-.+... .||.|=
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 4556678999888877777888999999999888877544332 499993
No 166
>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=47.10 E-value=10 Score=26.09 Aligned_cols=11 Identities=45% Similarity=1.198 Sum_probs=7.1
Q ss_pred CccCCCCCCCc
Q 021640 23 DAVCLYCSGGF 33 (309)
Q Consensus 23 ~~~CP~C~~gF 33 (309)
.+.||+|+.+|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 45677777653
No 167
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=46.70 E-value=11 Score=27.44 Aligned_cols=19 Identities=21% Similarity=0.649 Sum_probs=15.2
Q ss_pred cccCCCceeecCCCccCCCCCCC
Q 021640 10 CYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 10 Ch~C~r~v~~~~~~~~CP~C~~g 32 (309)
|..|.+-+ .+-+||.|++.
T Consensus 8 C~~C~~i~----~~~~Cp~Cgs~ 26 (64)
T PRK06393 8 CKKCKRLT----PEKTCPVHGDE 26 (64)
T ss_pred HhhCCccc----CCCcCCCCCCC
Confidence 88888877 34599999994
No 168
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=45.13 E-value=13 Score=23.34 Aligned_cols=26 Identities=23% Similarity=0.733 Sum_probs=19.4
Q ss_pred eecccCCCceee-cC-CCccCCCCCCCc
Q 021640 8 HWCYRCRRPVRL-QG-EDAVCLYCSGGF 33 (309)
Q Consensus 8 ywCh~C~r~v~~-~~-~~~~CP~C~~gF 33 (309)
.-|..|+..... .. ...+|+.|+.-|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 458889999877 33 446999998765
No 169
>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=45.04 E-value=18 Score=27.05 Aligned_cols=31 Identities=13% Similarity=0.323 Sum_probs=14.8
Q ss_pred eecccCCCceeecCCCccCCCCCCCceEEecC
Q 021640 8 HWCYRCRRPVRLQGEDAVCLYCSGGFVQELDD 39 (309)
Q Consensus 8 ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~ 39 (309)
++||.|-..... ..-.+||.|+..=+.-+.-
T Consensus 10 lrC~aCf~~t~~-~~k~FCp~CGn~TL~rvsv 40 (73)
T PF08772_consen 10 LRCHACFKITKD-MTKQFCPKCGNATLKRVSV 40 (73)
T ss_dssp EE-SSS--EES--SS--S-SSS--S--EEEE-
T ss_pred EEccccccCcCC-CCceeCcccCCCcceEEEE
Confidence 569999877652 4567999999998888743
No 170
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=44.98 E-value=11 Score=37.31 Aligned_cols=23 Identities=30% Similarity=0.533 Sum_probs=18.5
Q ss_pred ccCCCceeecCCCccCCCCCCCceEE
Q 021640 11 YRCRRPVRLQGEDAVCLYCSGGFVQE 36 (309)
Q Consensus 11 h~C~r~v~~~~~~~~CP~C~~gFvEE 36 (309)
|.|-|-|++ |+.||.|+.-|--=
T Consensus 286 HrC~RIV~v---EYrCPEC~KVFsCP 308 (500)
T KOG3993|consen 286 HRCPRIVHV---EYRCPECDKVFSCP 308 (500)
T ss_pred ccCCeeEEe---eecCCcccccccCc
Confidence 677777766 89999999998643
No 171
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=44.83 E-value=14 Score=31.27 Aligned_cols=19 Identities=11% Similarity=0.104 Sum_probs=16.5
Q ss_pred CccCCCCCCCceEEecCCC
Q 021640 23 DAVCLYCSGGFVQELDDMV 41 (309)
Q Consensus 23 ~~~CP~C~~gFvEE~~~~~ 41 (309)
.+.||+|++.-.+.+..+.
T Consensus 105 ~~~cp~c~s~~t~~~s~fg 123 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFG 123 (146)
T ss_pred CCcCCCCCCCCcEeecCCC
Confidence 4799999999999997764
No 172
>PRK10220 hypothetical protein; Provisional
Probab=44.00 E-value=14 Score=29.74 Aligned_cols=28 Identities=14% Similarity=0.456 Sum_probs=19.7
Q ss_pred ecccCCCceeecC-CCccCCCCCCCceEE
Q 021640 9 WCYRCRRPVRLQG-EDAVCLYCSGGFVQE 36 (309)
Q Consensus 9 wCh~C~r~v~~~~-~~~~CP~C~~gFvEE 36 (309)
=|-+|+-+..-.. ..++||.|++.+..+
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 3788887765544 447888888877655
No 173
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=42.52 E-value=14 Score=23.53 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=17.4
Q ss_pred cccCCCceeecC-------CCccCCCCCCCce
Q 021640 10 CYRCRRPVRLQG-------EDAVCLYCSGGFV 34 (309)
Q Consensus 10 Ch~C~r~v~~~~-------~~~~CP~C~~gFv 34 (309)
|-+|.....+.. ..+.||.|+.-|.
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 777877776654 2468888887763
No 174
>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=42.50 E-value=6.5 Score=38.50 Aligned_cols=30 Identities=27% Similarity=0.567 Sum_probs=0.0
Q ss_pred ceEEccccceeccccchhhhcc------CCCcCcccccc
Q 021640 197 EARQMPCNHIYHSDCIVPWLVQ------HNSCPVCRQEL 229 (309)
Q Consensus 197 ~~~~lpC~H~fh~~Ci~~Wl~~------~~sCP~CR~~l 229 (309)
.-+-|.|+|++-. ..|-.. ..+||+||..=
T Consensus 303 P~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g 338 (416)
T PF04710_consen 303 PWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVG 338 (416)
T ss_dssp ---------------------------------------
T ss_pred ceeeccccceeee---cccccccccccccccCCCccccC
Confidence 3445669998764 457542 34699999753
No 175
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=42.24 E-value=18 Score=34.59 Aligned_cols=46 Identities=24% Similarity=0.539 Sum_probs=32.9
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
...|-.|.++.......+.-.|+++||.+|=.---+.-..||-|..
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 3459999887776666666679999999995433233345999964
No 176
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=41.85 E-value=17 Score=29.35 Aligned_cols=47 Identities=23% Similarity=0.565 Sum_probs=30.6
Q ss_pred ccccccccccccc--cCCceEEccccceeccccchhhhccCC--CcCccccc
Q 021640 181 SDSHCPVCQDKFE--LGSEARQMPCNHIYHSDCIVPWLVQHN--SCPVCRQE 228 (309)
Q Consensus 181 ~~~~C~IC~~~~~--~~~~~~~lpC~H~fh~~Ci~~Wl~~~~--sCP~CR~~ 228 (309)
+...|.+|...|. .+......-|+|.+|..|-.. ..... .|-+|.+.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQKQ 103 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHHH
Confidence 4568999998764 233566666999999999765 22222 39998653
No 177
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=40.92 E-value=36 Score=22.88 Aligned_cols=36 Identities=19% Similarity=0.330 Sum_probs=25.5
Q ss_pred ccccccccccccc--ccCCceEEccccceeccccchhh
Q 021640 180 RSDSHCPVCQDKF--ELGSEARQMPCNHIYHSDCIVPW 215 (309)
Q Consensus 180 ~~~~~C~IC~~~~--~~~~~~~~lpC~H~fh~~Ci~~W 215 (309)
.....|.+|.+.+ ......+-.-|+-.+|..|+...
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 4456899999988 34445666779999999998663
No 178
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=40.76 E-value=16 Score=26.33 Aligned_cols=20 Identities=20% Similarity=0.569 Sum_probs=14.7
Q ss_pred ecccCCCceeecCCCccCCCCCCC
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
=|..|.+-+ .+-.||.|++.
T Consensus 5 AC~~C~~i~----~~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYIT----TEDRCPVCGSR 24 (61)
T ss_pred hhhhCCccc----CCCcCCCCcCC
Confidence 378888766 23489999994
No 179
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.18 E-value=17 Score=24.46 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=19.2
Q ss_pred ecccCCCceeecCC----CccCCCCCCCceEEe
Q 021640 9 WCYRCRRPVRLQGE----DAVCLYCSGGFVQEL 37 (309)
Q Consensus 9 wCh~C~r~v~~~~~----~~~CP~C~~gFvEE~ 37 (309)
||-.|...+..... .++||.|+ +++.+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEEC
Confidence 79999887765532 47899998 44555
No 180
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=39.67 E-value=12 Score=39.48 Aligned_cols=41 Identities=22% Similarity=0.560 Sum_probs=29.3
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccCCCcCc
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPV 224 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~ 224 (309)
..|.+|-..+ .|..+-.--|+|.=|.+|+.+|+..+.-||.
T Consensus 780 ~~CtVC~~vi-~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVI-RGVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred cCceeeccee-eeeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 3677776543 2222333349999999999999998888876
No 181
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=39.45 E-value=16 Score=22.06 Aligned_cols=22 Identities=32% Similarity=0.644 Sum_probs=16.7
Q ss_pred eecccCCCceeecCCCccCCCCC
Q 021640 8 HWCYRCRRPVRLQGEDAVCLYCS 30 (309)
Q Consensus 8 ywCh~C~r~v~~~~~~~~CP~C~ 30 (309)
|||-.|.+.+.... -+.|-.|.
T Consensus 1 ~~C~~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE-eEEeCCCC
Confidence 68999988886544 66787776
No 182
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.36 E-value=62 Score=30.75 Aligned_cols=47 Identities=26% Similarity=0.582 Sum_probs=37.6
Q ss_pred ccccccccccccccCCceEEccccceeccccchhhhccCCCcCcccccc
Q 021640 181 SDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQHNSCPVCRQEL 229 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l 229 (309)
....|-||...+.... +.--|.|.|+..|...|....+.||.|+...
T Consensus 104 ~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 104 DHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred CccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCc
Confidence 4568999998876543 2333999999999999999999999998643
No 183
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=38.79 E-value=14 Score=34.00 Aligned_cols=27 Identities=22% Similarity=0.488 Sum_probs=21.0
Q ss_pred cccCCCceeecC-------CCccCCCCCCCceEE
Q 021640 10 CYRCRRPVRLQG-------EDAVCLYCSGGFVQE 36 (309)
Q Consensus 10 Ch~C~r~v~~~~-------~~~~CP~C~~gFvEE 36 (309)
|+.|++...+.. .++.||.|+..|---
T Consensus 135 Cr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 135 CRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccccccccCCCccccccceeeeecccccccchhh
Confidence 888888866543 578999999988643
No 184
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.63 E-value=14 Score=27.55 Aligned_cols=14 Identities=29% Similarity=0.805 Sum_probs=11.5
Q ss_pred CccCCCCCCCceEE
Q 021640 23 DAVCLYCSGGFVQE 36 (309)
Q Consensus 23 ~~~CP~C~~gFvEE 36 (309)
+..||+|+|+||.-
T Consensus 41 ~g~CPnCGGelv~R 54 (84)
T COG3813 41 HGLCPNCGGELVAR 54 (84)
T ss_pred cCcCCCCCchhhcC
Confidence 56899999998854
No 185
>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=38.43 E-value=11 Score=35.16 Aligned_cols=45 Identities=27% Similarity=0.467 Sum_probs=21.1
Q ss_pred cccccccccccccCCceEEc---cccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDKFELGSEARQM---PCNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~l---pC~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
...|+||-..-..+. ++.- -=.|.+|.-|-..|--....||.|-.
T Consensus 172 ~g~CPvCGs~P~~s~-l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSV-LRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEE-EE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CCcCCCCCCcCceEE-EecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 368999986642221 1111 02567888999999888889999954
No 186
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=38.01 E-value=13 Score=23.98 Aligned_cols=13 Identities=15% Similarity=0.593 Sum_probs=5.8
Q ss_pred CceecccCCCcee
Q 021640 6 NTHWCYRCRRPVR 18 (309)
Q Consensus 6 ~~ywCh~C~r~v~ 18 (309)
.+|||--|+..|.
T Consensus 2 ~ryyCdyC~~~~~ 14 (38)
T PF06220_consen 2 PRYYCDYCKKYLT 14 (38)
T ss_dssp -S-B-TTT--B-S
T ss_pred cCeecccccceec
Confidence 5799999999883
No 187
>PRK13794 hypothetical protein; Provisional
Probab=37.82 E-value=17 Score=36.69 Aligned_cols=23 Identities=30% Similarity=0.852 Sum_probs=18.9
Q ss_pred CceecccCCCceeecCCCccCCCCCCC
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
.-|||-.||..|.-. .|..|+..
T Consensus 9 ~~~wc~~cn~p~~~~----~c~~cg~~ 31 (479)
T PRK13794 9 HLKWCDNCNVPVLGK----KCAICGSE 31 (479)
T ss_pred EEEEcCCCCCeecCC----chhHhCCC
Confidence 469999999988543 49999996
No 188
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=37.63 E-value=33 Score=36.02 Aligned_cols=82 Identities=22% Similarity=0.479 Sum_probs=40.4
Q ss_pred cchHHHHHHHHhcCCCCCC-Ccchhh----hhcCCceeeecccccccccccccccccccCCceEEccccceecc--ccch
Q 021640 141 PGLEELFEQLSANGRRGPP-PAARSA----IDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHS--DCIV 213 (309)
Q Consensus 141 ~~l~~l~~~l~~~~~~~~p-pa~~~~----i~~lp~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~--~Ci~ 213 (309)
.+-+.|++++......... ..+... +...+.-.+..-.+.-...|+|+...+ .+||.+..|+ .|.+
T Consensus 260 ~t~~~llq~~~~~~~~~~~~~~s~~~~~~~l~~~~d~~i~tt~~~vSL~CPl~~~Rm-------~~P~r~~~CkHlQcFD 332 (636)
T KOG2169|consen 260 LTSKDLLQRLKQNGKINRNLSQSDALIKKKLTAGPDSEIATTSLRVSLNCPLSKMRM-------SLPARGHTCKHLQCFD 332 (636)
T ss_pred cCHHHHHHHHhccCCccCchhHhHHHhhcccccCCcccceeccceeEecCCccccee-------ecCCcccccccceecc
Confidence 3568888888775543322 122222 222222222222223356798887654 4445544444 4553
Q ss_pred h-hhcc----CC--CcCcccccc
Q 021640 214 P-WLVQ----HN--SCPVCRQEL 229 (309)
Q Consensus 214 ~-Wl~~----~~--sCP~CR~~l 229 (309)
. |+.. .. .||+|.+..
T Consensus 333 ~~~~lq~n~~~pTW~CPVC~~~~ 355 (636)
T KOG2169|consen 333 ALSYLQMNEQKPTWRCPVCQKAA 355 (636)
T ss_pred hhhhHHhccCCCeeeCccCCccc
Confidence 3 3332 12 399998654
No 189
>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=37.29 E-value=27 Score=22.28 Aligned_cols=28 Identities=32% Similarity=0.689 Sum_probs=21.2
Q ss_pred eecccCCCceeecC----CCccCCCCCCCceE
Q 021640 8 HWCYRCRRPVRLQG----EDAVCLYCSGGFVQ 35 (309)
Q Consensus 8 ywCh~C~r~v~~~~----~~~~CP~C~~gFvE 35 (309)
.-|-.|.+...+.. .+.+|..|++.+|+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 45888888777643 57899999997765
No 190
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=37.19 E-value=19 Score=28.88 Aligned_cols=27 Identities=15% Similarity=0.504 Sum_probs=16.9
Q ss_pred cccCCCceeecC-CCccCCCCCCCceEE
Q 021640 10 CYRCRRPVRLQG-EDAVCLYCSGGFVQE 36 (309)
Q Consensus 10 Ch~C~r~v~~~~-~~~~CP~C~~gFvEE 36 (309)
|-+|+-+..-.. ..++||.|++.+-++
T Consensus 5 CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEecCCeeECcccccccccc
Confidence 667776654443 446777777766544
No 191
>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=37.02 E-value=22 Score=23.27 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=16.7
Q ss_pred eecccCCCceee-c--CCCccCCCCCCCceEE
Q 021640 8 HWCYRCRRPVRL-Q--GEDAVCLYCSGGFVQE 36 (309)
Q Consensus 8 ywCh~C~r~v~~-~--~~~~~CP~C~~gFvEE 36 (309)
|.|-.|...... . ..+++|+.| |--|||
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~C-G~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNC-GLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT--BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCC-CCEeec
Confidence 568888876422 1 267899999 333444
No 192
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=36.97 E-value=26 Score=29.76 Aligned_cols=27 Identities=33% Similarity=0.620 Sum_probs=20.2
Q ss_pred eccccchhhhccCC----CcCcccccccCCC
Q 021640 207 YHSDCIVPWLVQHN----SCPVCRQELPLQG 233 (309)
Q Consensus 207 fh~~Ci~~Wl~~~~----sCP~CR~~l~~~~ 233 (309)
||..||.+=|..-. .||.|...-..+.
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~ 32 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQS 32 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCCCCc
Confidence 89999999987543 4999987544333
No 193
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=36.42 E-value=39 Score=32.32 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=25.0
Q ss_pred ccccccccccccC-----------CceEEccccceeccccchhhhccC------CCcCcccccc
Q 021640 183 SHCPVCQDKFELG-----------SEARQMPCNHIYHSDCIVPWLVQH------NSCPVCRQEL 229 (309)
Q Consensus 183 ~~C~IC~~~~~~~-----------~~~~~lpC~H~fh~~Ci~~Wl~~~------~sCP~CR~~l 229 (309)
.+|++=+..+..+ ..-+-|.|+|+-.. ..|=.+. ..||+||..-
T Consensus 291 PQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~---H~WG~~e~~g~~~r~CPmC~~~g 351 (429)
T KOG3842|consen 291 PQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGY---HNWGVRENTGQRERECPMCRVVG 351 (429)
T ss_pred CCCCcccceeecccccccccccccCCeEEEeccccccc---cccccccccCcccCcCCeeeeec
Confidence 4566666555332 23456779986321 2465433 3499998643
No 194
>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=36.33 E-value=21 Score=23.79 Aligned_cols=18 Identities=22% Similarity=0.283 Sum_probs=12.5
Q ss_pred cCCCccCCCCCCCceEEe
Q 021640 20 QGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 20 ~~~~~~CP~C~~gFvEE~ 37 (309)
+...++||+|++-=+-.|
T Consensus 15 W~~g~~CP~Cg~~~~~~~ 32 (46)
T PF12760_consen 15 WPDGFVCPHCGSTKHYRL 32 (46)
T ss_pred CCCCCCCCCCCCeeeEEe
Confidence 346689999999733334
No 195
>PF14353 CpXC: CpXC protein
Probab=36.08 E-value=22 Score=28.93 Aligned_cols=17 Identities=24% Similarity=0.419 Sum_probs=14.7
Q ss_pred CccCCCCCCCceEEecC
Q 021640 23 DAVCLYCSGGFVQELDD 39 (309)
Q Consensus 23 ~~~CP~C~~gFvEE~~~ 39 (309)
+++||.|+.-|--++.+
T Consensus 1 ~itCP~C~~~~~~~v~~ 17 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWT 17 (128)
T ss_pred CcCCCCCCCeeEEEEEe
Confidence 47899999999999854
No 196
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.88 E-value=29 Score=24.17 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=14.6
Q ss_pred ccCCCCCCCceEEecCCC
Q 021640 24 AVCLYCSGGFVQELDDMV 41 (309)
Q Consensus 24 ~~CP~C~~gFvEE~~~~~ 41 (309)
+.||+|+..|-=.++...
T Consensus 1 i~CPyCge~~~~~iD~s~ 18 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSA 18 (52)
T ss_pred CCCCCCCCeeEEEEecCC
Confidence 479999999888886654
No 197
>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=35.55 E-value=22 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.661 Sum_probs=11.9
Q ss_pred ccceeccccchhhhccCCCcCccc
Q 021640 203 CNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 203 C~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
|++.|+.+|=.---+.-..||-|-
T Consensus 27 C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 27 CKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp TT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CCCccccCcChhhhccccCCcCCC
Confidence 888898888433223334688873
No 198
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=35.38 E-value=12 Score=35.29 Aligned_cols=37 Identities=22% Similarity=0.641 Sum_probs=27.0
Q ss_pred ccccccccccccCCceEEccccceeccccchhhhccC
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH 219 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~ 219 (309)
..|.+|+++|..+.....+-|..+||..|+..|+...
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred eecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 4788888888765555566666688888888887644
No 199
>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=35.21 E-value=34 Score=24.21 Aligned_cols=46 Identities=28% Similarity=0.593 Sum_probs=32.5
Q ss_pred ccccccccccccCC-ceEEccccceeccccchhhhccCCCcCccccccc
Q 021640 183 SHCPVCQDKFELGS-EARQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 230 (309)
Q Consensus 183 ~~C~IC~~~~~~~~-~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR~~l~ 230 (309)
..|-.|-.++.... .+.+-.=...|+.+|....| ++.||-|--+|.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccc
Confidence 46888888876554 33333334579999998865 678999987764
No 200
>PRK12495 hypothetical protein; Provisional
Probab=35.01 E-value=21 Score=32.27 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=24.4
Q ss_pred CCceecccCCCceeecCCCccCCCCCCCce
Q 021640 5 RNTHWCYRCRRPVRLQGEDAVCLYCSGGFV 34 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~~~~~CP~C~~gFv 34 (309)
+..++|-.|...|-......+||.|+.-+-
T Consensus 40 msa~hC~~CG~PIpa~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQEFCPTCQQPVT 69 (226)
T ss_pred cchhhcccccCcccCCCCeeECCCCCCccc
Confidence 356899999999986667789999996544
No 201
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=34.48 E-value=23 Score=26.28 Aligned_cols=22 Identities=23% Similarity=0.635 Sum_probs=9.4
Q ss_pred ceecccCCCceeecCCCccCCCCCC
Q 021640 7 THWCYRCRRPVRLQGEDAVCLYCSG 31 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~~~~~CP~C~~ 31 (309)
.|.|-.|+..+.. ...||.|+.
T Consensus 17 ~~~C~~C~~~~~~---~a~CPdC~~ 38 (70)
T PF07191_consen 17 HYHCEACQKDYKK---EAFCPDCGQ 38 (70)
T ss_dssp EEEETTT--EEEE---EEE-TTT-S
T ss_pred EEECcccccccee---cccCCCccc
Confidence 5556556555433 345666654
No 202
>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=34.39 E-value=24 Score=34.88 Aligned_cols=24 Identities=25% Similarity=0.658 Sum_probs=18.8
Q ss_pred ecccCCCceeecCCCccCCCCCCCc
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGGF 33 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~gF 33 (309)
=||.|...+. ..+...||+|+.-.
T Consensus 217 ~C~~Cd~~~~-~~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTIL-PAQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCccC-CCCCcCCcCCCCcc
Confidence 3999999663 34667899999876
No 203
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=34.12 E-value=26 Score=29.71 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=20.3
Q ss_pred cccCCCceeecC-CCccCCCCCCCc
Q 021640 10 CYRCRRPVRLQG-EDAVCLYCSGGF 33 (309)
Q Consensus 10 Ch~C~r~v~~~~-~~~~CP~C~~gF 33 (309)
|-.|++.|.... ....|+.|+.-+
T Consensus 37 C~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 37 CPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccCcccEeCCCCcEECCCCCCcC
Confidence 999999998766 668999998764
No 204
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=34.02 E-value=28 Score=24.05 Aligned_cols=31 Identities=19% Similarity=0.605 Sum_probs=23.5
Q ss_pred Cceecc--cCCCceeecC----CCccCCCCCCCceEE
Q 021640 6 NTHWCY--RCRRPVRLQG----EDAVCLYCSGGFVQE 36 (309)
Q Consensus 6 ~~ywCh--~C~r~v~~~~----~~~~CP~C~~gFvEE 36 (309)
..-||- .|...|.... ..++||.|+..|.-.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 456999 9999887751 457999999888643
No 205
>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=33.89 E-value=17 Score=25.94 Aligned_cols=17 Identities=29% Similarity=0.708 Sum_probs=13.4
Q ss_pred CCCCceecccCCCceee
Q 021640 3 SGRNTHWCYRCRRPVRL 19 (309)
Q Consensus 3 s~~~~ywCh~C~r~v~~ 19 (309)
......|||.|+..|..
T Consensus 45 ~~~~~i~C~~C~~~v~~ 61 (63)
T PF02148_consen 45 LSTGSIWCYACDDYVYD 61 (63)
T ss_dssp TTTTCEEETTTTEEEES
T ss_pred CCCCeEEEcCCCcEEeC
Confidence 44567899999998864
No 206
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=33.84 E-value=25 Score=22.79 Aligned_cols=24 Identities=21% Similarity=0.562 Sum_probs=18.7
Q ss_pred ceecccCCCceeecCCCccCCCCC
Q 021640 7 THWCYRCRRPVRLQGEDAVCLYCS 30 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~~~~~CP~C~ 30 (309)
.-||..|+..|....+.+.|+.|+
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~ 34 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCK 34 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCC
Confidence 458999999986543578999884
No 207
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.74 E-value=23 Score=33.31 Aligned_cols=37 Identities=22% Similarity=0.400 Sum_probs=27.6
Q ss_pred cccccccccccccCCceEEcc--ccceeccccchhhhccC
Q 021640 182 DSHCPVCQDKFELGSEARQMP--CNHIYHSDCIVPWLVQH 219 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~Wl~~~ 219 (309)
-+.|.+|.|.+++. ..+..| =.|.||..|-..-++++
T Consensus 268 pLcCTLC~ERLEDT-HFVQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 268 PLCCTLCHERLEDT-HFVQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred ceeehhhhhhhccC-ceeecCCCcccceecccCHHHHHhh
Confidence 37899999998764 333333 37999999998888754
No 208
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.47 E-value=41 Score=20.77 Aligned_cols=25 Identities=20% Similarity=0.279 Sum_probs=17.5
Q ss_pred eecccCCCceeecCCCccCCCCCCC
Q 021640 8 HWCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 8 ywCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
|-|-.|-=.......+..||.|+.+
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 4577777665554466799999864
No 209
>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=32.81 E-value=25 Score=34.73 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=20.6
Q ss_pred ecccCCCceeecC----CCccCCCCCCCceE
Q 021640 9 WCYRCRRPVRLQG----EDAVCLYCSGGFVQ 35 (309)
Q Consensus 9 wCh~C~r~v~~~~----~~~~CP~C~~gFvE 35 (309)
=||.|..-++... +...||+|+.-...
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCcC
Confidence 3999998876543 45689999998743
No 210
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.08 E-value=20 Score=22.65 Aligned_cols=22 Identities=32% Similarity=0.788 Sum_probs=9.4
Q ss_pred ecccCCCceeecC------CCccCCCCC
Q 021640 9 WCYRCRRPVRLQG------EDAVCLYCS 30 (309)
Q Consensus 9 wCh~C~r~v~~~~------~~~~CP~C~ 30 (309)
||-+|-..+.... .-.+||.|+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 5667766665432 114777664
No 211
>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=31.88 E-value=16 Score=22.52 Aligned_cols=23 Identities=26% Similarity=0.501 Sum_probs=9.6
Q ss_pred cccCCCceeecC-CCccCCCCCCC
Q 021640 10 CYRCRRPVRLQG-EDAVCLYCSGG 32 (309)
Q Consensus 10 Ch~C~r~v~~~~-~~~~CP~C~~g 32 (309)
|-.|.-+..... .-++||.|++.
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp -TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCcceeccCCEEeCCccccc
Confidence 556666554433 34578877653
No 212
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.99 E-value=25 Score=22.79 Aligned_cols=26 Identities=31% Similarity=0.682 Sum_probs=16.0
Q ss_pred cccCCCceeecC-CC---ccCCCCCCCceE
Q 021640 10 CYRCRRPVRLQG-ED---AVCLYCSGGFVQ 35 (309)
Q Consensus 10 Ch~C~r~v~~~~-~~---~~CP~C~~gFvE 35 (309)
|-.|+....... .+ -.||.|+|-|+.
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 666776544332 33 268888887764
No 213
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.96 E-value=14 Score=21.49 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=10.0
Q ss_pred ccCCCCCCCceEE
Q 021640 24 AVCLYCSGGFVQE 36 (309)
Q Consensus 24 ~~CP~C~~gFvEE 36 (309)
+.||.|+-.|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 5799999988543
No 214
>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=30.50 E-value=29 Score=23.92 Aligned_cols=28 Identities=21% Similarity=0.698 Sum_probs=16.0
Q ss_pred ceeccc--CCCceeecC--CC--ccCCCCCCCce
Q 021640 7 THWCYR--CRRPVRLQG--ED--AVCLYCSGGFV 34 (309)
Q Consensus 7 ~ywCh~--C~r~v~~~~--~~--~~CP~C~~gFv 34 (309)
.-||-. |...+.... .. ++|+.|+..|-
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC 51 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFC 51 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTTSCCSEEC
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECCCCCCcCc
Confidence 349987 999998776 23 78999987764
No 215
>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=30.41 E-value=42 Score=22.12 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=14.0
Q ss_pred ecccCCCceee-cCCCccCCCCC
Q 021640 9 WCYRCRRPVRL-QGEDAVCLYCS 30 (309)
Q Consensus 9 wCh~C~r~v~~-~~~~~~CP~C~ 30 (309)
.|..|.-..-. ....++||.|+
T Consensus 19 ~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEecCCCEECCCCC
Confidence 57778655443 33567888885
No 216
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.58 E-value=26 Score=34.92 Aligned_cols=37 Identities=19% Similarity=0.501 Sum_probs=26.8
Q ss_pred ccccccccccccCC-----ceEEccccceeccccchhhhccC
Q 021640 183 SHCPVCQDKFELGS-----EARQMPCNHIYHSDCIVPWLVQH 219 (309)
Q Consensus 183 ~~C~IC~~~~~~~~-----~~~~lpC~H~fh~~Ci~~Wl~~~ 219 (309)
..|+.|....+... .....+|+|.||.-|+..|....
T Consensus 227 k~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 227 KECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred ccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 34999988776544 12233599999999999997764
No 217
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=29.41 E-value=35 Score=37.29 Aligned_cols=37 Identities=19% Similarity=0.381 Sum_probs=32.1
Q ss_pred CCCceecccCCCceeecCCCccCCCCCCCceEEecCC
Q 021640 4 GRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDM 40 (309)
Q Consensus 4 ~~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~~ 40 (309)
+++.|-|-.|+...+...-..+||.|++..|=-+...
T Consensus 1009 srQ~fRC~kC~~kYRR~PL~G~C~kCGg~lilTV~~G 1045 (1095)
T TIGR00354 1009 SRQEVRCTKCNTKYRRIPLVGKCLKCGNNLTLTVSKG 1045 (1095)
T ss_pred hccceeecccCCccccCCCCCcccccCCeEEEEEecc
Confidence 3588999999999998888889999999998888553
No 218
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=29.31 E-value=30 Score=27.05 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=19.7
Q ss_pred ecccCCCceeecCCCccCCCCCCC
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGG 32 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~g 32 (309)
||-.|...+......++||.|+.-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 799999888765567899999854
No 219
>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=29.30 E-value=25 Score=22.51 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=8.6
Q ss_pred CccCCCCCCC
Q 021640 23 DAVCLYCSGG 32 (309)
Q Consensus 23 ~~~CP~C~~g 32 (309)
++.||+|++.
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 6789999986
No 220
>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 COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=28.78 E-value=33 Score=24.61 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=17.3
Q ss_pred ecccCCCceeecC--CCccCCCCCCC
Q 021640 9 WCYRCRRPVRLQG--EDAVCLYCSGG 32 (309)
Q Consensus 9 wCh~C~r~v~~~~--~~~~CP~C~~g 32 (309)
.|-.|.+.|.+.. ..+.||.|+..
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCce
Confidence 5888888885543 45789988854
No 222
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=28.75 E-value=34 Score=32.64 Aligned_cols=15 Identities=40% Similarity=1.083 Sum_probs=11.7
Q ss_pred ceecccCCCceeecC
Q 021640 7 THWCYRCRRPVRLQG 21 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~ 21 (309)
-+||-+|.-.|.++.
T Consensus 90 VHfCd~Cd~PI~IYG 104 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYG 104 (389)
T ss_pred eEeecccCCcceeee
Confidence 478888888888765
No 223
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=28.41 E-value=36 Score=38.55 Aligned_cols=36 Identities=17% Similarity=0.402 Sum_probs=31.0
Q ss_pred CCCceecccCCCceeecCCCccCCCCCCCceEEecCC
Q 021640 4 GRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDM 40 (309)
Q Consensus 4 ~~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~~ 40 (309)
+++.|-| .|+...+...-..+||.|+|..|=-+...
T Consensus 1539 srQ~~RC-kC~~kyRR~PL~G~C~kCGg~~ilTV~kG 1574 (1627)
T PRK14715 1539 SRQEFRC-KCGAKYRRVPLKGKCPKCGSKLILTVSKG 1574 (1627)
T ss_pred hccceee-cCCCccccCCCCCcCcccCCeEEEEEecc
Confidence 3588999 99999999888889999999998887543
No 224
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.28 E-value=27 Score=25.19 Aligned_cols=13 Identities=38% Similarity=0.951 Sum_probs=10.4
Q ss_pred CCccCCCCCCCce
Q 021640 22 EDAVCLYCSGGFV 34 (309)
Q Consensus 22 ~~~~CP~C~~gFv 34 (309)
.+++||+|+--|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 5789999987654
No 225
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.24 E-value=53 Score=26.59 Aligned_cols=44 Identities=25% Similarity=0.469 Sum_probs=30.7
Q ss_pred ccccccccccccCC-----------ceEEccccceeccccchhhhccCCCcCccc
Q 021640 183 SHCPVCQDKFELGS-----------EARQMPCNHIYHSDCIVPWLVQHNSCPVCR 226 (309)
Q Consensus 183 ~~C~IC~~~~~~~~-----------~~~~lpC~H~fh~~Ci~~Wl~~~~sCP~CR 226 (309)
..|--|+..|.... .-....|++.|+.+|=.-+-+.-..||-|-
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 45888888775321 111334999999999777777667799985
No 226
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.15 E-value=34 Score=25.94 Aligned_cols=25 Identities=20% Similarity=0.559 Sum_probs=16.9
Q ss_pred cccCCCceeecC-C--Cc-cCCCCCCCce
Q 021640 10 CYRCRRPVRLQG-E--DA-VCLYCSGGFV 34 (309)
Q Consensus 10 Ch~C~r~v~~~~-~--~~-~CP~C~~gFv 34 (309)
|-.|+....... + ++ -||.|.|-.+
T Consensus 4 CP~C~v~l~~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 4 CPICGVELVMSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred cCcCCceeeeeeecCceeeeCCccccEee
Confidence 778888765543 2 33 6999988654
No 227
>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=27.93 E-value=24 Score=21.18 Aligned_cols=21 Identities=29% Similarity=0.687 Sum_probs=8.8
Q ss_pred cccCCCceeecC----CCccCCCCC
Q 021640 10 CYRCRRPVRLQG----EDAVCLYCS 30 (309)
Q Consensus 10 Ch~C~r~v~~~~----~~~~CP~C~ 30 (309)
|..|-..+.... ...+||+|.
T Consensus 4 C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 4 CPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp -TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CccCCCcceEeEecCCCCeECcCCc
Confidence 555665554433 235666665
No 228
>PRK06260 threonine synthase; Validated
Probab=27.80 E-value=51 Score=32.22 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=23.6
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
..|-|..|.++.....-...||.|++-|--.+
T Consensus 2 ~~~~C~~cg~~~~~~~~~~~Cp~cg~~l~~~y 33 (397)
T PRK06260 2 YWLKCIECGKEYDPDEIIYTCPECGGLLEVIY 33 (397)
T ss_pred CEEEECCCCCCCCCCCccccCCCCCCeEEEEe
Confidence 46889999999866555578999986544443
No 229
>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=27.59 E-value=35 Score=20.46 Aligned_cols=15 Identities=27% Similarity=0.663 Sum_probs=8.4
Q ss_pred cCCCCCCCceEEecC
Q 021640 25 VCLYCSGGFVQELDD 39 (309)
Q Consensus 25 ~CP~C~~gFvEE~~~ 39 (309)
.||.|++-.+.+-++
T Consensus 1 ~CP~C~s~l~~~~~e 15 (28)
T PF03119_consen 1 TCPVCGSKLVREEGE 15 (28)
T ss_dssp B-TTT--BEEE-CCT
T ss_pred CcCCCCCEeEcCCCC
Confidence 599999999866654
No 230
>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=27.34 E-value=42 Score=20.49 Aligned_cols=24 Identities=25% Similarity=0.647 Sum_probs=13.6
Q ss_pred eecccCCCceeecCC--CccCCCCCC
Q 021640 8 HWCYRCRRPVRLQGE--DAVCLYCSG 31 (309)
Q Consensus 8 ywCh~C~r~v~~~~~--~~~CP~C~~ 31 (309)
=||-.|-........ ...||.|+.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 378888888777653 468999875
No 231
>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=26.67 E-value=38 Score=21.89 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=11.3
Q ss_pred CccCCCCCCCceEEec
Q 021640 23 DAVCLYCSGGFVQELD 38 (309)
Q Consensus 23 ~~~CP~C~~gFvEE~~ 38 (309)
+..||.|++-.|+-..
T Consensus 1 ~~~CP~Cg~~lv~r~~ 16 (39)
T PF01396_consen 1 VEKCPKCGGPLVLRRG 16 (39)
T ss_pred CcCCCCCCceeEEEEC
Confidence 3579999966666553
No 232
>PF12773 DZR: Double zinc ribbon
Probab=26.42 E-value=47 Score=22.14 Aligned_cols=26 Identities=19% Similarity=0.680 Sum_probs=15.7
Q ss_pred ceecccCCCceeecC-CCccCCCCCCC
Q 021640 7 THWCYRCRRPVRLQG-EDAVCLYCSGG 32 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~-~~~~CP~C~~g 32 (309)
.=||..|-..+.... ..++||.|+.-
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 346777777766222 34677777763
No 233
>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=26.08 E-value=31 Score=23.56 Aligned_cols=35 Identities=26% Similarity=0.507 Sum_probs=23.8
Q ss_pred ccccccccccccCCc-eEEccccceeccccchhhhc
Q 021640 183 SHCPVCQDKFELGSE-ARQMPCNHIYHSDCIVPWLV 217 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~-~~~lpC~H~fh~~Ci~~Wl~ 217 (309)
..|.+|...|..-.. ..--.|+++|+..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 469999888865321 22233999999999876544
No 234
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.92 E-value=44 Score=36.77 Aligned_cols=37 Identities=19% Similarity=0.454 Sum_probs=32.0
Q ss_pred CCCceecccCCCceeecCCCccCCCCCCCceEEecCC
Q 021640 4 GRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDM 40 (309)
Q Consensus 4 ~~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~~ 40 (309)
+++.|-|-.|+...+...-..+||.|++..|=-+...
T Consensus 1034 srQ~fRC~kC~~kYRR~PL~G~C~kCGg~lilTVh~G 1070 (1121)
T PRK04023 1034 SRQEFRCTKCGAKYRRPPLSGKCPKCGGNLILTVHKG 1070 (1121)
T ss_pred cccceeecccCcccccCCCCCcCccCCCeEEEEEecc
Confidence 3588999999999999888889999999999888543
No 235
>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=25.89 E-value=43 Score=23.47 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=20.8
Q ss_pred eecccCCCceeecC----CCccCCCCCCCce
Q 021640 8 HWCYRCRRPVRLQG----EDAVCLYCSGGFV 34 (309)
Q Consensus 8 ywCh~C~r~v~~~~----~~~~CP~C~~gFv 34 (309)
|-|-.|...|.+.. .-+.||.|+-.|-
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 56999999998764 3368999988753
No 236
>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=25.46 E-value=17 Score=26.65 Aligned_cols=12 Identities=17% Similarity=0.728 Sum_probs=8.8
Q ss_pred eeccccchhhhc
Q 021640 206 IYHSDCIVPWLV 217 (309)
Q Consensus 206 ~fh~~Ci~~Wl~ 217 (309)
-||..||.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999986
No 237
>PRK07591 threonine synthase; Validated
Probab=25.41 E-value=56 Score=32.34 Aligned_cols=31 Identities=23% Similarity=0.325 Sum_probs=22.5
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
..+.|..|.++.-+... ..||.|++-+--++
T Consensus 17 ~~l~C~~Cg~~~~~~~~-~~C~~cg~~l~~~y 47 (421)
T PRK07591 17 VALKCRECGAEYPLGPI-HVCEECFGPLEVAY 47 (421)
T ss_pred eEEEeCCCCCcCCCCCC-ccCCCCCCeEEEEe
Confidence 45779999999876544 89999986544444
No 238
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.29 E-value=37 Score=24.29 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=11.9
Q ss_pred cccCCCceee--cCCCccCCCCC
Q 021640 10 CYRCRRPVRL--QGEDAVCLYCS 30 (309)
Q Consensus 10 Ch~C~r~v~~--~~~~~~CP~C~ 30 (309)
|+.|-..+.. ....++||.|+
T Consensus 31 C~~CG~~~~~~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 31 CPRCGHRNKKRRSGRVFTCPNCG 53 (69)
T ss_pred ccCcccccccccccceEEcCCCC
Confidence 6666666554 22445676664
No 239
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=24.92 E-value=57 Score=31.92 Aligned_cols=29 Identities=24% Similarity=0.608 Sum_probs=20.7
Q ss_pred CceecccCCCceeecC-CCccCCCCCCCce
Q 021640 6 NTHWCYRCRRPVRLQG-EDAVCLYCSGGFV 34 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~-~~~~CP~C~~gFv 34 (309)
--|+|+.|........ ..-.||+|++.++
T Consensus 243 ~~~~C~~c~~~~~~~~~~~~~C~~c~~~~~ 272 (382)
T PRK04338 243 YVYYCPKCLYREEVEGLPPEECPVCGGKFG 272 (382)
T ss_pred eEEECCCCCcEEEecCCCCCCCCCCCCcce
Confidence 3578999998765433 3458999988554
No 240
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=24.91 E-value=50 Score=33.54 Aligned_cols=44 Identities=25% Similarity=0.618 Sum_probs=29.0
Q ss_pred cccccccccccccCCceEEccccceeccccchhhhccC-----C---CcCcc
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQH-----N---SCPVC 225 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~-----~---sCP~C 225 (309)
...|.||...-..---+..=.|.-.||..||.+=|.+- + .|--|
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccc
Confidence 57899998763321111122388889999999988741 2 38888
No 241
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.85 E-value=41 Score=33.39 Aligned_cols=25 Identities=28% Similarity=0.620 Sum_probs=19.7
Q ss_pred cccCCCceeecC----CCccCCCCCCCce
Q 021640 10 CYRCRRPVRLQG----EDAVCLYCSGGFV 34 (309)
Q Consensus 10 Ch~C~r~v~~~~----~~~~CP~C~~gFv 34 (309)
||.|..-+.... +...||+|+.-.-
T Consensus 13 C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 13 CPQCDMLVALPRLEHGQKAACPRCGTTLT 41 (419)
T ss_pred CCCCCceeecCCCCCCCeeECCCCCCCCc
Confidence 999998876553 3468999999873
No 242
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.70 E-value=62 Score=22.21 Aligned_cols=20 Identities=25% Similarity=0.713 Sum_probs=9.7
Q ss_pred cccCCCceeecC-----CCccCCCC
Q 021640 10 CYRCRRPVRLQG-----EDAVCLYC 29 (309)
Q Consensus 10 Ch~C~r~v~~~~-----~~~~CP~C 29 (309)
|..|.-+..... ....||+|
T Consensus 31 C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 31 CPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CCCCCCeeEccHhhhccCCCCCCCC
Confidence 666644433321 23456666
No 243
>PRK08197 threonine synthase; Validated
Probab=24.11 E-value=64 Score=31.51 Aligned_cols=36 Identities=14% Similarity=0.254 Sum_probs=26.6
Q ss_pred CCCCCCceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 1 MSSGRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 1 mss~~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
|++....|-|..|.++.........| .|++-|.-.+
T Consensus 1 ~~~~~~~~~C~~Cg~~~~~~~~~~~C-~cg~~l~~~~ 36 (394)
T PRK08197 1 PFSYVSHLECSKCGETYDADQVHNLC-KCGKPLLVRY 36 (394)
T ss_pred CCceeeEEEECCCCCCCCCCCcceec-CCCCeeEEEe
Confidence 67776778999999998665556789 8986654443
No 244
>PHA00616 hypothetical protein
Probab=24.09 E-value=20 Score=24.11 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=9.4
Q ss_pred ccCCCCCCCceE
Q 021640 24 AVCLYCSGGFVQ 35 (309)
Q Consensus 24 ~~CP~C~~gFvE 35 (309)
..||.|+..|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 469999988864
No 245
>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=23.93 E-value=25 Score=21.14 Aligned_cols=29 Identities=24% Similarity=0.555 Sum_probs=9.2
Q ss_pred cccccccccccCCceEEccccceeccccc
Q 021640 184 HCPVCQDKFELGSEARQMPCNHIYHSDCI 212 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci 212 (309)
.|.+|.+.......-.-..|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 47778776544233445557777777764
No 246
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=23.89 E-value=31 Score=25.92 Aligned_cols=33 Identities=18% Similarity=0.456 Sum_probs=20.8
Q ss_pred cccccccccccccCCceEEccccceeccccchh
Q 021640 182 DSHCPVCQDKFELGSEARQMPCNHIYHSDCIVP 214 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~ 214 (309)
...|.+|.......-....-.|...||..|...
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 468999986532211222233899999999644
No 247
>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=23.68 E-value=20 Score=19.61 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=6.5
Q ss_pred cCCCCCCCce
Q 021640 25 VCLYCSGGFV 34 (309)
Q Consensus 25 ~CP~C~~gFv 34 (309)
.|+.|+..|.
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 5777776653
No 248
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=23.64 E-value=23 Score=27.80 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=21.5
Q ss_pred cccccccccccccCCceEEcc--ccceeccccchh
Q 021640 182 DSHCPVCQDKFELGSEARQMP--CNHIYHSDCIVP 214 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~lp--C~H~fh~~Ci~~ 214 (309)
...|.||... .|..+.-.. |...||..|...
T Consensus 55 ~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKS--GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHH
Confidence 4689999976 333333333 888999999754
No 249
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.61 E-value=45 Score=28.48 Aligned_cols=16 Identities=19% Similarity=0.492 Sum_probs=12.7
Q ss_pred ccCCCCCCCceEEecC
Q 021640 24 AVCLYCSGGFVQELDD 39 (309)
Q Consensus 24 ~~CP~C~~gFvEE~~~ 39 (309)
+.||+|++-+.+-++.
T Consensus 1 m~cp~c~~~~~~~~~s 16 (154)
T PRK00464 1 MRCPFCGHPDTRVIDS 16 (154)
T ss_pred CcCCCCCCCCCEeEec
Confidence 4799999998777744
No 250
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=23.52 E-value=43 Score=32.03 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=22.3
Q ss_pred ceecccCCCceeecC---------C------------CccCCCCCCCceEEec
Q 021640 7 THWCYRCRRPVRLQG---------E------------DAVCLYCSGGFVQELD 38 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~---------~------------~~~CP~C~~gFvEE~~ 38 (309)
.-||..|...|--.. . -+.||.|.+-|+=.-+
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTD 92 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTD 92 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecC
Confidence 369999999875321 1 2589999998765543
No 251
>PRK00420 hypothetical protein; Validated
Probab=23.46 E-value=62 Score=26.21 Aligned_cols=28 Identities=18% Similarity=0.411 Sum_probs=20.6
Q ss_pred eecccCCCceee-cCCCccCCCCCCCceE
Q 021640 8 HWCYRCRRPVRL-QGEDAVCLYCSGGFVQ 35 (309)
Q Consensus 8 ywCh~C~r~v~~-~~~~~~CP~C~~gFvE 35 (309)
--|-.|.-..-. .....+||.|+.-.+.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeee
Confidence 458889877654 5578999999985443
No 252
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=23.38 E-value=15 Score=23.37 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=12.4
Q ss_pred cccCCCceeecC------CCccCCCCCCC
Q 021640 10 CYRCRRPVRLQG------EDAVCLYCSGG 32 (309)
Q Consensus 10 Ch~C~r~v~~~~------~~~~CP~C~~g 32 (309)
|..|.+++.... +.+.|+.|+=.
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr 30 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPR 30 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-S
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCC
Confidence 666777764332 56789999854
No 253
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.33 E-value=51 Score=37.16 Aligned_cols=37 Identities=19% Similarity=0.460 Sum_probs=32.1
Q ss_pred CCCceecccCCCceeecCCCccCCCCCCCceEEecCC
Q 021640 4 GRNTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELDDM 40 (309)
Q Consensus 4 ~~~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~~~ 40 (309)
+++.|-|-.|+...+...-..+||.|+|..|=-+...
T Consensus 1250 srQ~~RC~kC~~kyRR~PL~G~C~kCGg~iilTv~~G 1286 (1337)
T PRK14714 1250 SRQEFRCLKCGTKYRRMPLAGKCRKCGGRIILTVHEG 1286 (1337)
T ss_pred hccceeecccCcccccCCCCCcccccCCeEEEEEecc
Confidence 3588999999999999888889999999998888543
No 254
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=23.32 E-value=38 Score=35.35 Aligned_cols=45 Identities=29% Similarity=0.747 Sum_probs=27.7
Q ss_pred cccccccccccccCCc---eEEccccceeccccchhhhccC-----CCcCcccc
Q 021640 182 DSHCPVCQDKFELGSE---ARQMPCNHIYHSDCIVPWLVQH-----NSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~---~~~lpC~H~fh~~Ci~~Wl~~~-----~sCP~CR~ 227 (309)
...|.||-.. ..+.. +..-.|+-.||..|+..|+..- -.||-||.
T Consensus 18 ~~mc~l~~s~-G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 18 CLMCPLCGSS-GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhhhhhhccc-cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 4567777533 22211 1222389999999999998732 24887765
No 255
>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=23.19 E-value=32 Score=31.69 Aligned_cols=26 Identities=19% Similarity=0.511 Sum_probs=9.9
Q ss_pred eecccCCCc-eeec-----CCCccCCCCCCCc
Q 021640 8 HWCYRCRRP-VRLQ-----GEDAVCLYCSGGF 33 (309)
Q Consensus 8 ywCh~C~r~-v~~~-----~~~~~CP~C~~gF 33 (309)
+||-.|... +... ..|+.||.|...|
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 578888877 3322 1578888888664
No 256
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=23.19 E-value=29 Score=32.48 Aligned_cols=81 Identities=23% Similarity=0.409 Sum_probs=46.6
Q ss_pred HHhcCCCCCCCcchhhhhcCCceeeecccccccccccccccccccCCceEEccccceeccccchhhhcc----CCCcCcc
Q 021640 150 LSANGRRGPPPAARSAIDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWLVQ----HNSCPVC 225 (309)
Q Consensus 150 l~~~~~~~~ppa~~~~i~~lp~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl~~----~~sCP~C 225 (309)
..+-++.|.|.--+-...-+..|+.-...-.+...|.||-..-..++-+..--|.--||.-||.+=+.. .-+|.+|
T Consensus 249 csdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KO 328 (336)
T KOG1244|consen 249 CSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLC 328 (336)
T ss_pred hhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHH
Confidence 445556666543333322222233333333456789999866333322233348899999999987753 3369999
Q ss_pred ccccc
Q 021640 226 RQELP 230 (309)
Q Consensus 226 R~~l~ 230 (309)
-..|.
T Consensus 329 G~~~~ 333 (336)
T KOG1244|consen 329 LEELK 333 (336)
T ss_pred HHHHh
Confidence 76654
No 257
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=23.19 E-value=53 Score=31.89 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=21.4
Q ss_pred CceecccCCCceeecCCCccCCCCCCCc
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGF 33 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gF 33 (309)
.-|-|..|.+. .....+.+||.|+..-
T Consensus 56 ~i~kC~~c~~~-~~y~~~~~C~~cg~~~ 82 (415)
T COG5257 56 KIYKCPECYRP-ECYTTEPKCPNCGAET 82 (415)
T ss_pred ceEeCCCCCCC-cccccCCCCCCCCCCc
Confidence 45789999988 5555789999998753
No 258
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.17 E-value=39 Score=33.52 Aligned_cols=38 Identities=16% Similarity=0.389 Sum_probs=29.1
Q ss_pred CCCCCceecccCCCceeec---------CCCccCCCCCCCceEEecC
Q 021640 2 SSGRNTHWCYRCRRPVRLQ---------GEDAVCLYCSGGFVQELDD 39 (309)
Q Consensus 2 ss~~~~ywCh~C~r~v~~~---------~~~~~CP~C~~gFvEE~~~ 39 (309)
...++.|-|-.|++....- ...+.|-.|++..||+-..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~ 169 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENK 169 (436)
T ss_pred ccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchhccccc
Confidence 3446899999999995421 1468999999999988744
No 259
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.82 E-value=56 Score=27.21 Aligned_cols=28 Identities=21% Similarity=0.524 Sum_probs=22.1
Q ss_pred ceecccCCCceeecCCCccCCCCCCCce
Q 021640 7 THWCYRCRRPVRLQGEDAVCLYCSGGFV 34 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~~~~~CP~C~~gFv 34 (309)
-+-|-.|-...-....+++||.|+.-++
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCceEE
Confidence 3569999988766668899999996544
No 260
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.61 E-value=34 Score=26.85 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=27.6
Q ss_pred ccccccccccccCCceEEccccceeccccchhhh
Q 021640 183 SHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL 216 (309)
Q Consensus 183 ~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl 216 (309)
-.|.||-..+..|++-...+ +-..|.+|+..=.
T Consensus 7 wkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~ 39 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESK 39 (103)
T ss_pred eeEeeeCCEeeeccEEEEee-CCcchHHHHHHHH
Confidence 46999999999998877777 7789999987643
No 261
>KOG4517 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.60 E-value=40 Score=27.15 Aligned_cols=33 Identities=18% Similarity=0.372 Sum_probs=25.0
Q ss_pred CCceecccCCCceeecCCC----ccCCCCCCCceEEe
Q 021640 5 RNTHWCYRCRRPVRLQGED----AVCLYCSGGFVQEL 37 (309)
Q Consensus 5 ~~~ywCh~C~r~v~~~~~~----~~CP~C~~gFvEE~ 37 (309)
+..|+|+.|+..|.-.... .-||-|+.|.+|.-
T Consensus 45 q~~p~~tp~~~~v~~R~t~~~v~~~~P~~g~g~lEdt 81 (117)
T KOG4517|consen 45 QGTPYATPCQCDVVKRTTTIAVLGGCPGCGYGVLEDT 81 (117)
T ss_pred cCCcccccceeeccccccceEEEcCCCccccchhhhH
Confidence 4689999999988665432 36999999966654
No 262
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.48 E-value=53 Score=32.66 Aligned_cols=23 Identities=22% Similarity=0.478 Sum_probs=17.8
Q ss_pred ecccCCCceeecCCCccCCCCCCCc
Q 021640 9 WCYRCRRPVRLQGEDAVCLYCSGGF 33 (309)
Q Consensus 9 wCh~C~r~v~~~~~~~~CP~C~~gF 33 (309)
-||.|..-+ ..+...||+|+.-.
T Consensus 223 ~C~~Cd~l~--~~~~a~CpRC~~~L 245 (419)
T PRK15103 223 SCSCCTAIL--PADQPVCPRCHTKG 245 (419)
T ss_pred cCCCCCCCC--CCCCCCCCCCCCcC
Confidence 499999864 33556899999886
No 263
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.26 E-value=35 Score=28.58 Aligned_cols=49 Identities=22% Similarity=0.563 Sum_probs=29.1
Q ss_pred cccccccccccc-cccCCceEEccccceeccccchhhhccCC----CcCccccc
Q 021640 180 RSDSHCPVCQDK-FELGSEARQMPCNHIYHSDCIVPWLVQHN----SCPVCRQE 228 (309)
Q Consensus 180 ~~~~~C~IC~~~-~~~~~~~~~lpC~H~fh~~Ci~~Wl~~~~----sCP~CR~~ 228 (309)
..+.+|-||+.. |.+|-.-...=|.-.||..|--.--.+++ .|-+|++.
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 456799999865 44442222223556677777655444433 38888864
No 264
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=17 Score=33.88 Aligned_cols=47 Identities=21% Similarity=0.552 Sum_probs=36.8
Q ss_pred cccccccccccccC---CceEEcc--------ccceeccccchhhhccCC-CcCccccc
Q 021640 182 DSHCPVCQDKFELG---SEARQMP--------CNHIYHSDCIVPWLVQHN-SCPVCRQE 228 (309)
Q Consensus 182 ~~~C~IC~~~~~~~---~~~~~lp--------C~H~fh~~Ci~~Wl~~~~-sCP~CR~~ 228 (309)
...|.||...|... ...+.+. |+|..+..|+..-+.+.. .||.|+..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 36799999998732 2455666 999999999999877654 79999874
No 265
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=21.72 E-value=50 Score=32.33 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=18.6
Q ss_pred CceecccCCCceeecC--CCccCCCCCCC
Q 021640 6 NTHWCYRCRRPVRLQG--EDAVCLYCSGG 32 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~--~~~~CP~C~~g 32 (309)
-.|+|-.|. ++.... -+-.||+|++-
T Consensus 239 ~~~~c~~cg-~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 239 YIYHCSRCG-EIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred cEEEccccc-ceecccccccccCCccccc
Confidence 469999998 443333 45689999983
No 266
>PHA00626 hypothetical protein
Probab=21.67 E-value=70 Score=22.70 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=16.6
Q ss_pred cccCCCc-eee------cCCCccCCCCCCCceEE
Q 021640 10 CYRCRRP-VRL------QGEDAVCLYCSGGFVQE 36 (309)
Q Consensus 10 Ch~C~r~-v~~------~~~~~~CP~C~~gFvEE 36 (309)
|-.|... |.. ..+.++||.|+--|-..
T Consensus 3 CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 3 CPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 6666652 322 23678888888776554
No 267
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.52 E-value=48 Score=21.32 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=7.3
Q ss_pred ccCCCCCCCce
Q 021640 24 AVCLYCSGGFV 34 (309)
Q Consensus 24 ~~CP~C~~gFv 34 (309)
-.||.|+.||-
T Consensus 3 ~~CprC~kg~H 13 (36)
T PF14787_consen 3 GLCPRCGKGFH 13 (36)
T ss_dssp -C-TTTSSSCS
T ss_pred ccCcccCCCcc
Confidence 36999999873
No 268
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.50 E-value=48 Score=34.92 Aligned_cols=49 Identities=27% Similarity=0.624 Sum_probs=35.2
Q ss_pred cccccccccccCCceEEccccc-eeccccchhhhc--c----CCCcCcccccccCCCCC
Q 021640 184 HCPVCQDKFELGSEARQMPCNH-IYHSDCIVPWLV--Q----HNSCPVCRQELPLQGSS 235 (309)
Q Consensus 184 ~C~IC~~~~~~~~~~~~lpC~H-~fh~~Ci~~Wl~--~----~~sCP~CR~~l~~~~~~ 235 (309)
.|+||-... +-+..-.|+| ..+..|...... . ++.||+||.++......
T Consensus 2 ~c~ic~~s~---~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~~s~~ 57 (669)
T KOG2231|consen 2 SCAICAFSP---DFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVETKSNG 57 (669)
T ss_pred CcceeecCc---cccccccccccccchhhhhhhhhhcccccccccCcccccceeeeccc
Confidence 599998665 3345556999 899999877654 2 44689999987655543
No 269
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=21.46 E-value=37 Score=36.47 Aligned_cols=50 Identities=16% Similarity=0.200 Sum_probs=31.5
Q ss_pred hhcCCceeeecccccccccccccccccccCCceEEccccceeccccchhhh
Q 021640 166 IDAMPTVRITQRHLRSDSHCPVCQDKFELGSEARQMPCNHIYHSDCIVPWL 216 (309)
Q Consensus 166 i~~lp~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~lpC~H~fh~~Ci~~Wl 216 (309)
++...++..+...-.....|-.|....-. -.-+.--|++.||.+|+..|.
T Consensus 213 ~~~~~~~a~k~a~~g~~~mC~~C~~tlfn-~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 213 QRPDQKVAWKRAVKGIREMCDRCETTLFN-IHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred cCcccccchhhcccCcchhhhhhcccccc-eeEEccccCCeeeecchhhcc
Confidence 33444444444443445789999865421 123444499999999999995
No 270
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.41 E-value=37 Score=32.19 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=19.9
Q ss_pred ecccCCCceeecC---CCccCCCCCCCce
Q 021640 9 WCYRCRRPVRLQG---EDAVCLYCSGGFV 34 (309)
Q Consensus 9 wCh~C~r~v~~~~---~~~~CP~C~~gFv 34 (309)
-|-.|...+.... ...+||.|+.-|-
T Consensus 40 kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 40 QCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred ECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 3999999886654 3469999998653
No 271
>PRK13795 hypothetical protein; Provisional
Probab=21.38 E-value=58 Score=34.15 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=19.3
Q ss_pred CceecccCCCceeecCCCccCCCCCCCc
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGF 33 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gF 33 (309)
.-|||..||..|.- ..|..|+.+.
T Consensus 11 ~~~wc~~cn~p~~~----~~c~~c~~~~ 34 (636)
T PRK13795 11 HIYWCEKCNVPLLG----KKCGICGKEG 34 (636)
T ss_pred eEEEcccCCCeecc----ccccccCCCc
Confidence 46999999998854 3599999864
No 272
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=21.31 E-value=68 Score=33.14 Aligned_cols=35 Identities=34% Similarity=0.812 Sum_probs=23.6
Q ss_pred cccccccccccccc------CC----ceEEccccceeccccchhh
Q 021640 181 SDSHCPVCQDKFEL------GS----EARQMPCNHIYHSDCIVPW 215 (309)
Q Consensus 181 ~~~~C~IC~~~~~~------~~----~~~~lpC~H~fh~~Ci~~W 215 (309)
....|+||.|.|+. +. ..+.+.=|-+||..|+..-
T Consensus 512 ~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~ 556 (579)
T KOG2071|consen 512 RQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEK 556 (579)
T ss_pred cccCCcccccccceeecchhhheeecceeeeccCceeeccccchH
Confidence 44679999999842 00 2333335889999998653
No 273
>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=21.28 E-value=34 Score=23.50 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=5.3
Q ss_pred CcCcccccccC
Q 021640 221 SCPVCRQELPL 231 (309)
Q Consensus 221 sCP~CR~~l~~ 231 (309)
.||+|..+|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 69999887753
No 274
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.16 E-value=39 Score=24.43 Aligned_cols=12 Identities=17% Similarity=0.708 Sum_probs=9.6
Q ss_pred CCccCCCCCCCc
Q 021640 22 EDAVCLYCSGGF 33 (309)
Q Consensus 22 ~~~~CP~C~~gF 33 (309)
...+||.|+.-|
T Consensus 52 g~L~Cp~c~r~Y 63 (68)
T PF03966_consen 52 GELICPECGREY 63 (68)
T ss_dssp TEEEETTTTEEE
T ss_pred CEEEcCCCCCEE
Confidence 668999998665
No 275
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.15 E-value=60 Score=25.96 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=14.3
Q ss_pred eeecCCCccCCCCCCCceEEe
Q 021640 17 VRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 17 v~~~~~~~~CP~C~~gFvEE~ 37 (309)
|.+......||.|+..|=--+
T Consensus 43 V~ie~G~t~CP~Cg~~~e~~f 63 (115)
T COG1885 43 VEIEVGSTSCPKCGEPFESAF 63 (115)
T ss_pred EEEecccccCCCCCCccceeE
Confidence 444446679999998874443
No 276
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.97 E-value=41 Score=30.12 Aligned_cols=52 Identities=21% Similarity=0.465 Sum_probs=30.7
Q ss_pred ccccccccccccccCC----ceEEcc-----ccceeccccchhhhccCCCcCcccccccCCCCC
Q 021640 181 SDSHCPVCQDKFELGS----EARQMP-----CNHIYHSDCIVPWLVQHNSCPVCRQELPLQGSS 235 (309)
Q Consensus 181 ~~~~C~IC~~~~~~~~----~~~~lp-----C~H~fh~~Ci~~Wl~~~~sCP~CR~~l~~~~~~ 235 (309)
....|+||..+|.... ..+... |.|.=. +.|-+-.-.+||.|-......+..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~---vnP~~Y~V~vCP~CgyA~~~~~F~ 64 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKG---VNPLFYEVWVCPHCGYAAFEEDFE 64 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCC---CCCeeeeEEECCCCCCcccccccc
Confidence 3468999999996532 111111 443211 566555666899998766555433
No 277
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.96 E-value=38 Score=32.02 Aligned_cols=25 Identities=20% Similarity=0.417 Sum_probs=19.7
Q ss_pred ecccCCCceeecC---CCccCCCCCCCc
Q 021640 9 WCYRCRRPVRLQG---EDAVCLYCSGGF 33 (309)
Q Consensus 9 wCh~C~r~v~~~~---~~~~CP~C~~gF 33 (309)
-|-.|...+.... ...+||.|+.-|
T Consensus 29 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 29 KCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred ECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3999999886543 346999999987
No 278
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.78 E-value=27 Score=20.27 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=8.7
Q ss_pred CccCCCCCCCce
Q 021640 23 DAVCLYCSGGFV 34 (309)
Q Consensus 23 ~~~CP~C~~gFv 34 (309)
-+.|+.|+..|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 367888887764
No 279
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.57 E-value=41 Score=31.45 Aligned_cols=49 Identities=24% Similarity=0.614 Sum_probs=31.6
Q ss_pred cccccccccccccCC------ceEEccccceeccccc-hhhhccC----------CCcCccccccc
Q 021640 182 DSHCPVCQDKFELGS------EARQMPCNHIYHSDCI-VPWLVQH----------NSCPVCRQELP 230 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~------~~~~lpC~H~fh~~Ci-~~Wl~~~----------~sCP~CR~~l~ 230 (309)
...|.+|-..|..-- ....|+|...+|..-+ .+||.+. .+||.|.+.+-
T Consensus 161 a~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFA 226 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFA 226 (279)
T ss_pred cccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhc
Confidence 457999988773210 1235677666665544 5999753 25999988663
No 280
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=20.45 E-value=48 Score=31.35 Aligned_cols=29 Identities=28% Similarity=0.541 Sum_probs=20.2
Q ss_pred ecccCCCcee-ec----CCCccCCCCCCCceEEe
Q 021640 9 WCYRCRRPVR-LQ----GEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 9 wCh~C~r~v~-~~----~~~~~CP~C~~gFvEE~ 37 (309)
||+.|.+.-. ++ ..+.+|+.|+--+=+.+
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~ 35 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRI 35 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeecccc
Confidence 7888888644 22 27899999987654443
No 281
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.44 E-value=91 Score=31.18 Aligned_cols=38 Identities=18% Similarity=0.321 Sum_probs=28.6
Q ss_pred CCCCCCceecccCCCceeecCCCccCCCCC--CCceEEecCC
Q 021640 1 MSSGRNTHWCYRCRRPVRLQGEDAVCLYCS--GGFVQELDDM 40 (309)
Q Consensus 1 mss~~~~ywCh~C~r~v~~~~~~~~CP~C~--~gFvEE~~~~ 40 (309)
|.-....|-|..|--.-.-| -..||.|+ ..|+||....
T Consensus 1 MaK~~t~f~C~~CG~~s~KW--~GkCp~Cg~Wns~vE~~~~~ 40 (456)
T COG1066 1 MAKKKTAFVCQECGYVSPKW--LGKCPACGAWNTLVEEVLAA 40 (456)
T ss_pred CCCcccEEEcccCCCCCccc--cccCCCCCCccceEEeeccc
Confidence 55544678899998776555 46899999 7899998543
No 282
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.41 E-value=35 Score=31.34 Aligned_cols=27 Identities=22% Similarity=0.704 Sum_probs=18.8
Q ss_pred ceecccCCCceeecC--------CCccCCCCCCCc
Q 021640 7 THWCYRCRRPVRLQG--------EDAVCLYCSGGF 33 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~--------~~~~CP~C~~gF 33 (309)
.=||+-|||++.... ..++|-.|..-+
T Consensus 10 kpwcwycnrefddekiliqhqkakhfkchichkkl 44 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAKHFKCHICHKKL 44 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhccceeeeehhhh
Confidence 359999999876432 347888887543
No 283
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.29 E-value=65 Score=34.04 Aligned_cols=27 Identities=26% Similarity=0.542 Sum_probs=17.2
Q ss_pred ceecccCCCceeecCCCccCCCCCCCceEEe
Q 021640 7 THWCYRCRRPVRLQGEDAVCLYCSGGFVQEL 37 (309)
Q Consensus 7 ~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~ 37 (309)
..-||.|.... ....||.|++.-+..+
T Consensus 410 ~l~Ch~CG~~~----~p~~Cp~Cgs~~l~~~ 436 (665)
T PRK14873 410 TPRCRWCGRAA----PDWRCPRCGSDRLRAV 436 (665)
T ss_pred eeECCCCcCCC----cCccCCCCcCCcceee
Confidence 45577777642 2457888887766655
No 284
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.21 E-value=75 Score=30.34 Aligned_cols=44 Identities=25% Similarity=0.493 Sum_probs=29.4
Q ss_pred cccccccccccccCCceEEc--c--ccceeccccchhhhccCCCcCcccc
Q 021640 182 DSHCPVCQDKFELGSEARQM--P--CNHIYHSDCIVPWLVQHNSCPVCRQ 227 (309)
Q Consensus 182 ~~~C~IC~~~~~~~~~~~~l--p--C~H~fh~~Ci~~Wl~~~~sCP~CR~ 227 (309)
...|+||-..-... ++.+ . =.+.+|.-|-..|--....||.|-.
T Consensus 187 ~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 46899998653211 1111 1 2456778899999888888999964
No 285
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.12 E-value=95 Score=33.22 Aligned_cols=30 Identities=13% Similarity=0.319 Sum_probs=22.0
Q ss_pred CceecccCCCceeecCCCccCCCCCCCceEEec
Q 021640 6 NTHWCYRCRRPVRLQGEDAVCLYCSGGFVQELD 38 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~~~~~CP~C~~gFvEE~~ 38 (309)
....||.|..+.. .-..||.|++--+....
T Consensus 461 ~~L~CH~Cg~~~~---~p~~Cp~Cgs~~L~~~G 490 (730)
T COG1198 461 GQLRCHYCGYQEP---IPQSCPECGSEHLRAVG 490 (730)
T ss_pred CeeEeCCCCCCCC---CCCCCCCCCCCeeEEec
Confidence 4567999988733 34689999998666663
No 286
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=20.11 E-value=40 Score=23.42 Aligned_cols=24 Identities=29% Similarity=0.660 Sum_probs=18.7
Q ss_pred CceecccCCCceeecC-----CCccCCCC
Q 021640 6 NTHWCYRCRRPVRLQG-----EDAVCLYC 29 (309)
Q Consensus 6 ~~ywCh~C~r~v~~~~-----~~~~CP~C 29 (309)
.+-|||-|.-+-.+|. .+.+|--|
T Consensus 2 ~Rq~CyLCdlPr~PWami~df~EpVCRgC 30 (54)
T PF11261_consen 2 RRQQCYLCDLPRMPWAMIWDFSEPVCRGC 30 (54)
T ss_pred CceeEEeccCCCCchHHHhhccchhhhhh
Confidence 3679999999988876 56777666
Done!