Query 043965
Match_columns 342
No_of_seqs 449 out of 1852
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 10:05:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043965.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043965hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14369 zf-RING_3: zinc-finge 99.5 6.5E-15 1.4E-19 96.6 2.7 32 7-38 2-35 (35)
2 PF13639 zf-RING_2: Ring finge 99.4 5.3E-14 1.2E-18 97.0 1.7 44 214-257 1-44 (44)
3 KOG4628 Predicted E3 ubiquitin 99.4 3.2E-13 6.8E-18 130.4 6.8 71 193-263 203-280 (348)
4 COG5243 HRD1 HRD ubiquitin lig 99.2 2.2E-11 4.9E-16 116.7 6.6 69 198-266 268-350 (491)
5 PLN03208 E3 ubiquitin-protein 99.1 8.6E-11 1.9E-15 105.0 5.8 55 208-265 13-83 (193)
6 COG5540 RING-finger-containing 99.1 3.5E-11 7.5E-16 112.8 2.5 50 213-262 323-373 (374)
7 PF12678 zf-rbx1: RING-H2 zinc 99.1 5.5E-11 1.2E-15 91.0 2.8 45 213-257 19-73 (73)
8 PHA02929 N1R/p28-like protein; 99.1 1E-10 2.2E-15 108.4 4.0 64 198-261 151-227 (238)
9 KOG0823 Predicted E3 ubiquitin 99.0 6.1E-10 1.3E-14 101.4 4.8 53 212-267 46-101 (230)
10 PF13920 zf-C3HC4_3: Zinc fing 98.9 5.9E-10 1.3E-14 78.9 2.6 46 213-261 2-48 (50)
11 KOG0317 Predicted E3 ubiquitin 98.9 3.9E-10 8.3E-15 105.5 1.9 50 213-265 239-288 (293)
12 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.5E-09 3.2E-14 72.9 2.0 39 216-256 1-39 (39)
13 PF15227 zf-C3HC4_4: zinc fing 98.8 1.7E-09 3.7E-14 73.9 2.2 38 216-256 1-42 (42)
14 cd00162 RING RING-finger (Real 98.8 3.7E-09 8.1E-14 71.4 2.5 44 215-260 1-45 (45)
15 smart00504 Ubox Modified RING 98.7 6.1E-09 1.3E-13 76.6 2.7 48 214-264 2-49 (63)
16 KOG0320 Predicted E3 ubiquitin 98.7 3.8E-09 8.1E-14 92.6 1.6 51 213-264 131-181 (187)
17 PF12861 zf-Apc11: Anaphase-pr 98.7 1.2E-08 2.5E-13 79.7 2.5 51 212-262 20-83 (85)
18 KOG0802 E3 ubiquitin ligase [P 98.6 8.5E-09 1.8E-13 106.8 1.3 49 213-261 291-341 (543)
19 PF00097 zf-C3HC4: Zinc finger 98.6 1.6E-08 3.4E-13 68.3 2.0 38 216-256 1-41 (41)
20 PF14634 zf-RING_5: zinc-RING 98.6 2.4E-08 5.2E-13 68.8 2.2 44 215-258 1-44 (44)
21 TIGR00599 rad18 DNA repair pro 98.6 2.3E-08 5E-13 99.0 2.8 51 210-263 23-73 (397)
22 PHA02926 zinc finger-like prot 98.6 2.5E-08 5.4E-13 90.5 2.2 50 212-261 169-230 (242)
23 smart00184 RING Ring finger. E 98.6 3.7E-08 7.9E-13 64.1 2.2 38 216-256 1-39 (39)
24 COG5574 PEX10 RING-finger-cont 98.4 6.5E-08 1.4E-12 89.7 1.2 51 212-265 214-266 (271)
25 KOG2164 Predicted E3 ubiquitin 98.4 7.3E-08 1.6E-12 96.5 1.3 59 208-269 181-244 (513)
26 KOG0287 Postreplication repair 98.4 6.4E-08 1.4E-12 92.3 0.3 51 212-265 22-72 (442)
27 COG5194 APC11 Component of SCF 98.3 3.7E-07 8.1E-12 69.8 2.4 31 232-262 52-82 (88)
28 PF04564 U-box: U-box domain; 98.3 4.2E-07 9.2E-12 69.4 2.2 51 212-265 3-54 (73)
29 KOG1734 Predicted RING-contain 98.2 4.3E-07 9.4E-12 84.4 0.8 60 204-264 216-284 (328)
30 PF13445 zf-RING_UBOX: RING-ty 98.2 7.5E-07 1.6E-11 61.2 1.8 38 216-254 1-43 (43)
31 COG5432 RAD18 RING-finger-cont 98.1 6.9E-07 1.5E-11 83.8 1.4 48 212-262 24-71 (391)
32 KOG0828 Predicted E3 ubiquitin 98.1 6.7E-07 1.4E-11 89.1 1.3 50 213-262 571-635 (636)
33 KOG1493 Anaphase-promoting com 98.1 5.4E-07 1.2E-11 68.4 -0.1 49 213-261 20-81 (84)
34 COG5219 Uncharacterized conser 98.1 8E-07 1.7E-11 94.0 0.5 54 208-261 1464-1523(1525)
35 KOG2177 Predicted E3 ubiquitin 98.0 1.9E-06 4E-11 79.9 0.9 45 210-257 10-54 (386)
36 smart00744 RINGv The RING-vari 98.0 3.9E-06 8.4E-11 59.2 2.2 42 215-257 1-49 (49)
37 PF14835 zf-RING_6: zf-RING of 98.0 2.3E-06 4.9E-11 63.2 0.9 51 211-266 5-56 (65)
38 PF11793 FANCL_C: FANCL C-term 97.9 2.2E-06 4.8E-11 65.0 0.1 50 213-262 2-67 (70)
39 TIGR00570 cdk7 CDK-activating 97.8 8.4E-06 1.8E-10 78.1 2.6 54 213-266 3-59 (309)
40 KOG0311 Predicted E3 ubiquitin 97.8 2.6E-06 5.6E-11 82.0 -1.5 51 210-263 40-92 (381)
41 KOG0804 Cytoplasmic Zn-finger 97.8 8.3E-06 1.8E-10 80.7 1.7 54 206-261 168-222 (493)
42 KOG4265 Predicted E3 ubiquitin 97.7 1.3E-05 2.8E-10 77.6 2.1 47 213-262 290-337 (349)
43 KOG0824 Predicted E3 ubiquitin 97.7 1.1E-05 2.4E-10 76.2 1.3 49 213-264 7-56 (324)
44 KOG2930 SCF ubiquitin ligase, 97.7 1.4E-05 3E-10 64.3 1.5 30 232-261 79-108 (114)
45 KOG4172 Predicted E3 ubiquitin 97.5 1.5E-05 3.2E-10 56.9 -0.5 45 214-261 8-54 (62)
46 KOG4445 Uncharacterized conser 97.5 3.8E-05 8.2E-10 72.6 1.0 92 175-267 75-192 (368)
47 KOG1039 Predicted E3 ubiquitin 97.4 0.0001 2.2E-09 72.1 2.7 51 211-261 159-221 (344)
48 KOG0827 Predicted E3 ubiquitin 97.4 6.1E-05 1.3E-09 73.5 1.2 48 214-261 5-56 (465)
49 KOG0978 E3 ubiquitin ligase in 97.4 4.7E-05 1E-09 80.0 0.2 52 211-265 641-693 (698)
50 KOG0825 PHD Zn-finger protein 97.3 5.3E-05 1.1E-09 79.3 -0.7 53 213-265 123-175 (1134)
51 KOG2660 Locus-specific chromos 97.2 0.0001 2.2E-09 70.7 0.2 51 210-263 12-63 (331)
52 KOG4159 Predicted E3 ubiquitin 97.1 0.00017 3.8E-09 71.8 1.2 49 211-262 82-130 (398)
53 KOG0297 TNF receptor-associate 97.0 0.00026 5.6E-09 70.8 1.8 52 210-264 18-70 (391)
54 KOG1785 Tyrosine kinase negati 97.0 0.0002 4.4E-09 70.1 0.8 50 214-266 370-421 (563)
55 PF11789 zf-Nse: Zinc-finger o 96.8 0.00047 1E-08 50.2 0.9 41 213-255 11-53 (57)
56 KOG1645 RING-finger-containing 96.8 0.00062 1.3E-08 67.0 1.9 48 213-260 4-55 (463)
57 KOG1941 Acetylcholine receptor 96.5 0.00071 1.5E-08 66.3 0.3 48 213-260 365-415 (518)
58 COG5152 Uncharacterized conser 96.4 0.00093 2E-08 59.9 0.2 46 214-262 197-242 (259)
59 KOG4692 Predicted E3 ubiquitin 96.2 0.0035 7.5E-08 60.8 2.8 50 211-263 420-469 (489)
60 KOG1813 Predicted E3 ubiquitin 96.1 0.0017 3.8E-08 61.5 0.5 46 214-262 242-287 (313)
61 KOG1428 Inhibitor of type V ad 96.0 0.0032 7E-08 69.9 1.9 52 211-262 3484-3545(3738)
62 COG0375 HybF Zn finger protein 95.9 0.0041 8.8E-08 51.6 1.7 39 2-41 65-103 (115)
63 PF14570 zf-RING_4: RING/Ubox 95.9 0.0038 8.3E-08 43.8 1.2 44 216-260 1-47 (48)
64 KOG2879 Predicted E3 ubiquitin 95.9 0.0052 1.1E-07 57.8 2.4 48 212-261 238-287 (298)
65 KOG1571 Predicted E3 ubiquitin 95.7 0.0058 1.3E-07 59.5 2.3 43 213-261 305-347 (355)
66 KOG1002 Nucleotide excision re 95.7 0.003 6.4E-08 64.1 0.3 51 212-265 535-590 (791)
67 PF10367 Vps39_2: Vacuolar sor 95.7 0.0049 1.1E-07 49.6 1.4 37 207-244 72-108 (109)
68 KOG0801 Predicted E3 ubiquitin 95.5 0.0037 8E-08 54.5 -0.0 28 213-240 177-204 (205)
69 PF05883 Baculo_RING: Baculovi 95.4 0.0051 1.1E-07 52.2 0.7 35 213-247 26-66 (134)
70 KOG3970 Predicted E3 ubiquitin 95.4 0.0093 2E-07 54.6 2.1 49 214-263 51-107 (299)
71 PF12906 RINGv: RING-variant d 95.3 0.0093 2E-07 41.6 1.5 40 216-256 1-47 (47)
72 KOG1814 Predicted E3 ubiquitin 95.2 0.008 1.7E-07 59.5 1.2 46 213-258 184-237 (445)
73 KOG1952 Transcription factor N 95.2 0.0087 1.9E-07 63.8 1.5 50 211-260 189-246 (950)
74 KOG3039 Uncharacterized conser 95.0 0.017 3.8E-07 53.6 2.7 57 213-269 221-278 (303)
75 KOG0826 Predicted E3 ubiquitin 95.0 0.014 3.1E-07 56.2 2.2 47 212-261 299-346 (357)
76 KOG4275 Predicted E3 ubiquitin 94.9 0.0057 1.2E-07 58.0 -0.6 42 213-261 300-342 (350)
77 KOG4739 Uncharacterized protei 94.2 0.018 4E-07 53.3 1.0 47 215-264 5-51 (233)
78 KOG4185 Predicted E3 ubiquitin 94.1 0.027 5.8E-07 53.9 1.9 47 214-260 4-54 (296)
79 PHA03096 p28-like protein; Pro 93.9 0.022 4.8E-07 54.6 1.0 45 214-258 179-231 (284)
80 COG5236 Uncharacterized conser 93.8 0.034 7.5E-07 54.0 2.1 48 211-261 59-108 (493)
81 PF07800 DUF1644: Protein of u 93.8 0.045 9.7E-07 47.7 2.5 52 213-267 2-97 (162)
82 PHA02862 5L protein; Provision 93.6 0.036 7.8E-07 47.6 1.5 45 214-262 3-54 (156)
83 COG5222 Uncharacterized conser 93.5 0.029 6.4E-07 53.4 1.0 42 214-258 275-318 (427)
84 KOG0298 DEAD box-containing he 93.4 0.037 8E-07 61.6 1.6 84 171-258 1113-1196(1394)
85 KOG3268 Predicted E3 ubiquitin 93.3 0.039 8.4E-07 49.0 1.3 51 213-263 165-230 (234)
86 KOG0827 Predicted E3 ubiquitin 93.2 0.0063 1.4E-07 59.7 -4.0 50 214-263 197-247 (465)
87 PF14447 Prok-RING_4: Prokaryo 93.2 0.062 1.4E-06 38.7 2.0 45 214-263 8-52 (55)
88 PF08746 zf-RING-like: RING-li 93.0 0.034 7.3E-07 38.1 0.4 41 216-256 1-43 (43)
89 KOG2114 Vacuolar assembly/sort 92.7 0.048 1E-06 58.4 1.2 43 213-260 840-882 (933)
90 COG5175 MOT2 Transcriptional r 92.5 0.06 1.3E-06 52.2 1.5 57 212-268 13-71 (480)
91 PF04641 Rtf2: Rtf2 RING-finge 92.4 0.091 2E-06 49.7 2.6 53 213-266 113-166 (260)
92 PF07754 DUF1610: Domain of un 92.4 0.067 1.4E-06 32.0 1.0 22 10-31 1-23 (24)
93 KOG2932 E3 ubiquitin ligase in 92.3 0.056 1.2E-06 51.9 1.0 43 214-260 91-133 (389)
94 KOG1940 Zn-finger protein [Gen 92.2 0.061 1.3E-06 51.2 1.2 45 214-258 159-204 (276)
95 PF03854 zf-P11: P-11 zinc fin 92.2 0.047 1E-06 38.0 0.3 44 215-263 4-48 (50)
96 PHA02825 LAP/PHD finger-like p 92.2 0.089 1.9E-06 46.0 2.0 48 212-263 7-61 (162)
97 KOG1001 Helicase-like transcri 91.3 0.069 1.5E-06 57.0 0.5 49 214-266 455-505 (674)
98 COG1996 RPC10 DNA-directed RNA 91.0 0.13 2.9E-06 36.1 1.5 31 3-33 2-33 (49)
99 PF10272 Tmpp129: Putative tra 91.0 0.21 4.5E-06 49.4 3.4 31 234-264 311-354 (358)
100 KOG2817 Predicted E3 ubiquitin 90.0 0.18 4E-06 49.9 2.1 48 212-259 333-383 (394)
101 PF05290 Baculo_IE-1: Baculovi 89.9 0.11 2.4E-06 44.0 0.5 49 213-264 80-135 (140)
102 TIGR00100 hypA hydrogenase nic 89.4 0.23 5.1E-06 41.2 2.0 33 6-39 69-101 (115)
103 PRK00564 hypA hydrogenase nick 88.8 0.25 5.4E-06 41.2 1.8 34 6-39 70-103 (117)
104 PF14446 Prok-RING_1: Prokaryo 88.2 0.28 6.1E-06 35.2 1.5 39 213-255 5-44 (54)
105 KOG1100 Predicted E3 ubiquitin 88.2 0.27 5.8E-06 45.1 1.7 40 216-262 161-201 (207)
106 PRK03681 hypA hydrogenase nick 88.0 0.33 7.2E-06 40.2 2.1 34 6-39 69-102 (114)
107 COG2093 DNA-directed RNA polym 87.1 0.29 6.3E-06 36.1 1.0 29 10-41 7-36 (64)
108 KOG4367 Predicted Zn-finger pr 86.5 0.3 6.5E-06 49.0 1.1 36 211-249 2-37 (699)
109 KOG3800 Predicted E3 ubiquitin 86.4 0.44 9.5E-06 45.5 2.1 53 215-267 2-57 (300)
110 KOG2034 Vacuolar sorting prote 86.4 0.27 5.8E-06 53.2 0.7 37 210-247 814-850 (911)
111 PRK00398 rpoP DNA-directed RNA 85.6 0.73 1.6E-05 31.7 2.4 32 5-36 1-33 (46)
112 PRK12380 hydrogenase nickel in 85.4 0.66 1.4E-05 38.4 2.4 31 8-39 71-101 (113)
113 PF01155 HypA: Hydrogenase exp 85.4 0.41 8.8E-06 39.6 1.2 31 8-39 71-101 (113)
114 COG5270 PUA domain (predicted 85.0 0.57 1.2E-05 42.0 2.0 25 8-37 15-39 (202)
115 KOG3002 Zn finger protein [Gen 84.9 0.58 1.3E-05 45.3 2.2 44 211-261 46-91 (299)
116 smart00659 RPOLCX RNA polymera 84.5 0.74 1.6E-05 31.7 2.0 29 7-35 2-30 (44)
117 KOG1812 Predicted E3 ubiquitin 84.4 0.58 1.3E-05 46.8 2.0 38 213-250 146-184 (384)
118 PRK03824 hypA hydrogenase nick 84.0 0.8 1.7E-05 39.1 2.4 33 7-39 70-122 (135)
119 KOG4362 Transcriptional regula 84.0 0.28 6E-06 52.0 -0.5 49 212-263 20-71 (684)
120 KOG0309 Conserved WD40 repeat- 83.9 0.48 1E-05 50.5 1.2 39 216-255 1031-1069(1081)
121 PRK00762 hypA hydrogenase nick 80.9 0.99 2.2E-05 37.9 1.8 32 7-39 70-107 (124)
122 PF03604 DNA_RNApol_7kD: DNA d 80.6 1.5 3.2E-05 28.1 2.1 26 8-33 1-26 (32)
123 smart00834 CxxC_CXXC_SSSS Puta 80.3 1.5 3.2E-05 28.9 2.2 25 8-32 6-34 (41)
124 PF02891 zf-MIZ: MIZ/SP-RING z 79.0 1.6 3.4E-05 30.8 2.0 43 214-259 3-50 (50)
125 PF06906 DUF1272: Protein of u 78.3 0.59 1.3E-05 33.7 -0.3 27 8-36 27-53 (57)
126 COG5183 SSM4 Protein involved 76.8 1.2 2.6E-05 48.0 1.3 54 212-266 11-71 (1175)
127 PRK14890 putative Zn-ribbon RN 76.8 1.7 3.7E-05 31.8 1.7 32 1-32 1-33 (59)
128 KOG3053 Uncharacterized conser 76.5 0.82 1.8E-05 43.0 0.0 52 212-263 19-84 (293)
129 KOG3899 Uncharacterized conser 76.1 0.9 2E-05 43.5 0.2 32 234-265 325-369 (381)
130 COG5220 TFB3 Cdk activating ki 75.3 1.2 2.7E-05 41.4 0.8 48 213-260 10-63 (314)
131 KOG0269 WD40 repeat-containing 72.5 2.4 5.2E-05 45.4 2.2 41 214-255 780-820 (839)
132 KOG3993 Transcription factor ( 72.2 1.7 3.7E-05 43.7 1.0 25 11-39 286-310 (500)
133 PF13240 zinc_ribbon_2: zinc-r 71.9 1.9 4.2E-05 25.4 0.8 22 9-33 1-22 (23)
134 PF00628 PHD: PHD-finger; Int 71.2 0.87 1.9E-05 31.5 -0.9 44 215-258 1-50 (51)
135 KOG3579 Predicted E3 ubiquitin 71.0 2.5 5.4E-05 40.4 1.8 36 213-251 268-307 (352)
136 KOG1609 Protein involved in mR 69.8 1.8 4E-05 41.2 0.7 53 213-265 78-138 (323)
137 KOG0802 E3 ubiquitin ligase [P 69.4 2.5 5.4E-05 44.2 1.5 47 212-265 478-524 (543)
138 COG5109 Uncharacterized conser 68.8 2.9 6.3E-05 40.5 1.8 47 212-258 335-384 (396)
139 PF10571 UPF0547: Uncharacteri 68.3 2.9 6.3E-05 25.5 1.1 23 10-35 3-25 (26)
140 KOG1812 Predicted E3 ubiquitin 68.1 2.7 5.9E-05 42.1 1.5 43 214-256 307-351 (384)
141 KOG3161 Predicted E3 ubiquitin 68.0 1.6 3.5E-05 45.9 -0.1 44 212-258 10-54 (861)
142 KOG1829 Uncharacterized conser 67.5 1.8 3.8E-05 45.5 0.0 43 213-258 511-558 (580)
143 PRK06266 transcription initiat 67.1 3.9 8.5E-05 36.5 2.1 30 7-36 117-148 (178)
144 KOG0825 PHD Zn-finger protein 66.7 2.2 4.7E-05 46.0 0.5 54 213-266 96-159 (1134)
145 KOG2807 RNA polymerase II tran 65.7 5.1 0.00011 39.1 2.7 47 212-258 329-375 (378)
146 PF09723 Zn-ribbon_8: Zinc rib 65.1 6 0.00013 26.7 2.3 26 8-33 6-35 (42)
147 smart00249 PHD PHD zinc finger 63.6 3.3 7.1E-05 27.2 0.8 31 215-245 1-31 (47)
148 PF08792 A2L_zn_ribbon: A2L zi 62.2 3.9 8.4E-05 26.3 0.9 27 8-34 4-31 (33)
149 PF13901 DUF4206: Domain of un 61.5 5 0.00011 36.5 1.8 41 213-258 152-197 (202)
150 TIGR00373 conserved hypothetic 58.5 5.2 0.00011 35.0 1.3 32 8-40 110-143 (158)
151 PF03107 C1_2: C1 domain; Int 58.0 4.1 8.9E-05 25.4 0.4 22 8-31 1-22 (30)
152 PF03811 Zn_Tnp_IS1: InsA N-te 57.5 4.5 9.8E-05 26.6 0.6 11 23-33 4-14 (36)
153 KOG2066 Vacuolar assembly/sort 56.8 6.3 0.00014 42.6 1.8 48 208-256 779-830 (846)
154 KOG4317 Predicted Zn-finger pr 56.5 6.9 0.00015 38.0 1.8 21 8-33 8-28 (383)
155 smart00661 RPOL9 RNA polymeras 55.6 7 0.00015 27.0 1.3 29 9-39 2-33 (52)
156 PF13248 zf-ribbon_3: zinc-rib 55.4 5.7 0.00012 23.9 0.7 23 8-33 3-25 (26)
157 KOG4718 Non-SMC (structural ma 54.9 5.7 0.00012 36.4 1.0 45 214-260 182-226 (235)
158 PF08772 NOB1_Zn_bind: Nin one 54.5 7.8 0.00017 29.6 1.5 30 8-39 10-39 (73)
159 PF05605 zf-Di19: Drought indu 54.3 7 0.00015 27.6 1.2 12 24-35 2-13 (54)
160 KOG2068 MOT2 transcription fac 54.1 12 0.00026 36.5 3.1 48 214-261 250-298 (327)
161 PF04216 FdhE: Protein involve 53.3 3.2 7E-05 39.7 -0.9 46 213-258 172-219 (290)
162 PRK06393 rpoE DNA-directed RNA 52.9 7.1 0.00015 29.1 1.0 18 10-32 8-25 (64)
163 KOG1815 Predicted E3 ubiquitin 52.5 5.4 0.00012 40.6 0.5 36 212-249 69-104 (444)
164 PF07975 C1_4: TFIIH C1-like d 52.1 8.8 0.00019 27.3 1.4 42 216-257 2-50 (51)
165 PF06906 DUF1272: Protein of u 51.1 20 0.00042 26.0 3.0 46 215-262 7-53 (57)
166 PF01363 FYVE: FYVE zinc finge 51.0 12 0.00026 27.5 2.0 36 212-247 8-44 (69)
167 KOG0824 Predicted E3 ubiquitin 50.6 21 0.00046 34.5 4.1 50 212-263 104-153 (324)
168 KOG3039 Uncharacterized conser 49.8 8.9 0.00019 36.1 1.4 34 211-247 41-74 (303)
169 PRK08351 DNA-directed RNA poly 49.8 9.2 0.0002 28.2 1.2 18 10-32 6-23 (61)
170 TIGR02605 CxxC_CxxC_SSSS putat 48.7 17 0.00037 25.2 2.4 31 8-38 6-40 (52)
171 COG4391 Uncharacterized protei 48.6 7.3 0.00016 28.7 0.5 13 23-35 47-59 (62)
172 PF09538 FYDLN_acid: Protein o 48.4 13 0.00029 30.5 2.1 30 8-37 10-39 (108)
173 PF10122 Mu-like_Com: Mu-like 46.8 4.8 0.0001 28.6 -0.7 25 8-32 5-32 (51)
174 PF06844 DUF1244: Protein of u 46.0 8 0.00017 28.9 0.4 12 237-248 11-22 (68)
175 KOG3005 GIY-YIG type nuclease 45.8 9.3 0.0002 36.3 0.9 47 214-260 183-242 (276)
176 PF07860 CCD: WisP family C-Te 44.1 12 0.00027 30.4 1.2 32 303-334 51-82 (141)
177 KOG3113 Uncharacterized conser 44.0 14 0.00031 34.8 1.8 51 214-266 112-163 (293)
178 TIGR00155 pqiA_fam integral me 43.9 12 0.00027 37.6 1.5 25 8-34 216-240 (403)
179 PF15135 UPF0515: Uncharacteri 43.6 11 0.00023 35.6 0.9 26 10-35 135-166 (278)
180 TIGR00622 ssl1 transcription f 43.5 27 0.00058 29.0 3.1 44 214-257 56-110 (112)
181 PF13719 zinc_ribbon_5: zinc-r 43.3 10 0.00022 24.9 0.5 11 25-35 3-13 (37)
182 PRK12495 hypothetical protein; 43.2 13 0.00028 34.4 1.4 31 5-36 40-70 (226)
183 smart00132 LIM Zinc-binding do 42.9 22 0.00047 22.2 2.1 36 216-260 2-37 (39)
184 TIGR02300 FYDLN_acid conserved 42.7 18 0.00039 30.6 2.0 30 8-37 10-39 (129)
185 PF00412 LIM: LIM domain; Int 42.0 22 0.00048 24.7 2.2 40 216-264 1-40 (58)
186 PF14803 Nudix_N_2: Nudix N-te 41.5 9.6 0.00021 24.7 0.2 23 9-31 2-29 (34)
187 PF06677 Auto_anti-p27: Sjogre 41.0 18 0.00039 24.5 1.5 24 8-31 18-41 (41)
188 smart00647 IBR In Between Ring 40.5 17 0.00038 25.7 1.5 30 8-37 19-53 (64)
189 PF08271 TF_Zn_Ribbon: TFIIB z 40.4 15 0.00032 24.7 1.0 11 25-35 1-11 (43)
190 PHA00616 hypothetical protein 39.0 8.4 0.00018 26.5 -0.4 13 25-37 2-14 (44)
191 smart00154 ZnF_AN1 AN1-like Zi 38.8 17 0.00037 24.2 1.1 25 10-37 1-25 (39)
192 cd07973 Spt4 Transcription elo 37.6 18 0.00039 29.3 1.2 26 10-36 6-31 (98)
193 TIGR02098 MJ0042_CXXC MJ0042 f 37.1 21 0.00045 23.1 1.3 27 9-35 4-36 (38)
194 PF14353 CpXC: CpXC protein 36.5 19 0.0004 30.0 1.2 18 24-41 1-18 (128)
195 COG1066 Sms Predicted ATP-depe 36.5 27 0.00059 35.5 2.5 38 1-41 1-40 (456)
196 PF04710 Pellino: Pellino; In 36.3 12 0.00026 37.5 0.0 33 228-263 303-341 (416)
197 KOG2169 Zn-finger transcriptio 36.3 39 0.00085 36.2 3.9 47 214-265 307-360 (636)
198 COG4416 Com Mu-like prophage p 36.1 8.7 0.00019 27.6 -0.7 26 7-32 4-32 (60)
199 PF13913 zf-C2HC_2: zinc-finge 35.5 14 0.00031 22.0 0.3 13 25-37 3-15 (25)
200 PRK13794 hypothetical protein; 34.8 45 0.00098 34.4 4.0 22 8-34 11-32 (479)
201 COG5151 SSL1 RNA polymerase II 34.8 21 0.00044 34.8 1.3 22 7-31 308-329 (421)
202 KOG1729 FYVE finger containing 34.5 13 0.00028 35.9 -0.1 36 215-250 216-251 (288)
203 KOG2113 Predicted RNA binding 34.4 36 0.00077 33.2 2.9 44 212-260 342-386 (394)
204 PLN02189 cellulose synthase 32.6 46 0.001 37.5 3.7 49 213-261 34-87 (1040)
205 KOG2807 RNA polymerase II tran 32.5 27 0.00059 34.2 1.8 25 7-34 276-300 (378)
206 COG1867 TRM1 N2,N2-dimethylgua 32.0 29 0.00063 34.6 1.9 27 8-34 241-267 (380)
207 TIGR00686 phnA alkylphosphonat 32.0 22 0.00047 29.3 0.9 28 10-37 5-32 (109)
208 PRK10220 hypothetical protein; 31.5 26 0.00056 28.9 1.2 28 10-37 6-33 (111)
209 PF13465 zf-H2C2_2: Zinc-finge 31.4 11 0.00024 22.5 -0.7 12 24-35 14-25 (26)
210 TIGR01562 FdhE formate dehydro 30.9 18 0.00039 35.2 0.3 45 213-258 184-232 (305)
211 KOG4185 Predicted E3 ubiquitin 30.5 12 0.00025 35.7 -1.1 46 214-259 208-265 (296)
212 PF00096 zf-C2H2: Zinc finger, 30.0 12 0.00026 21.1 -0.7 11 25-35 1-11 (23)
213 PF12760 Zn_Tnp_IS1595: Transp 29.5 31 0.00068 23.5 1.2 12 22-33 16-27 (46)
214 PF03966 Trm112p: Trm112p-like 29.1 19 0.0004 26.7 0.1 15 20-34 49-63 (68)
215 PF14787 zf-CCHC_5: GAG-polypr 29.1 28 0.00062 22.9 0.9 11 25-35 3-13 (36)
216 KOG1815 Predicted E3 ubiquitin 28.4 22 0.00048 36.2 0.4 37 214-250 227-268 (444)
217 TIGR01384 TFS_arch transcripti 28.3 27 0.00059 27.9 0.9 23 9-32 2-24 (104)
218 PRK03564 formate dehydrogenase 28.1 30 0.00065 33.7 1.3 44 213-258 187-234 (309)
219 cd04718 BAH_plant_2 BAH, or Br 28.0 32 0.0007 29.9 1.3 28 238-265 2-33 (148)
220 TIGR01206 lysW lysine biosynth 27.9 33 0.0007 24.7 1.1 28 8-35 3-33 (54)
221 PRK06450 threonine synthase; V 27.9 38 0.00082 33.2 2.0 27 5-33 1-27 (338)
222 PLN02436 cellulose synthase A 27.4 64 0.0014 36.6 3.7 48 214-261 37-89 (1094)
223 PRK00464 nrdR transcriptional 27.3 32 0.00069 30.1 1.2 17 25-41 1-17 (154)
224 PF14569 zf-UDP: Zinc-binding 27.1 50 0.0011 25.6 2.1 49 213-261 9-62 (80)
225 PRK00432 30S ribosomal protein 27.0 30 0.00066 24.3 0.8 13 25-37 21-33 (50)
226 PRK00420 hypothetical protein; 26.9 36 0.00078 28.2 1.4 26 8-33 24-49 (112)
227 PRK13795 hypothetical protein; 26.8 87 0.0019 33.5 4.6 22 8-34 13-34 (636)
228 cd00065 FYVE FYVE domain; Zinc 26.7 31 0.00066 24.1 0.8 34 214-247 3-37 (57)
229 PF07282 OrfB_Zn_ribbon: Putat 26.7 30 0.00066 25.3 0.8 23 9-31 30-53 (69)
230 PF07191 zinc-ribbons_6: zinc- 26.6 23 0.00049 26.9 0.1 10 8-17 18-27 (70)
231 smart00064 FYVE Protein presen 26.4 26 0.00057 25.5 0.5 35 213-247 10-45 (68)
232 PRK04338 N(2),N(2)-dimethylgua 26.2 51 0.0011 33.0 2.6 28 8-35 245-272 (382)
233 cd00730 rubredoxin Rubredoxin; 26.1 57 0.0012 23.0 2.1 13 21-33 31-43 (50)
234 KOG3799 Rab3 effector RIM1 and 25.9 27 0.00057 30.0 0.4 52 208-259 60-116 (169)
235 PF13453 zf-TFIIB: Transcripti 25.8 26 0.00056 23.3 0.3 28 10-37 2-32 (41)
236 PRK11088 rrmA 23S rRNA methylt 25.8 40 0.00087 31.6 1.7 25 214-238 3-27 (272)
237 smart00109 C1 Protein kinase C 25.5 43 0.00093 22.1 1.4 23 8-31 12-34 (49)
238 PLN02638 cellulose synthase A 25.0 74 0.0016 36.1 3.7 48 214-261 18-70 (1079)
239 COG2888 Predicted Zn-ribbon RN 24.9 59 0.0013 23.9 2.0 9 22-30 48-56 (61)
240 PF13717 zinc_ribbon_4: zinc-r 24.8 42 0.00091 21.8 1.1 25 10-34 5-35 (36)
241 PRK15103 paraquat-inducible me 24.8 41 0.00089 34.2 1.6 24 8-34 222-245 (419)
242 TIGR00155 pqiA_fam integral me 24.8 38 0.00083 34.2 1.4 26 9-34 15-43 (403)
243 PF01485 IBR: IBR domain; Int 24.7 43 0.00093 23.6 1.3 28 8-35 19-51 (64)
244 PF14255 Cys_rich_CPXG: Cystei 24.3 36 0.00078 24.3 0.8 17 25-41 1-17 (52)
245 TIGR00416 sms DNA repair prote 24.0 46 0.00099 34.1 1.8 36 1-39 1-38 (454)
246 KOG2463 Predicted RNA-binding 23.9 37 0.0008 33.3 1.0 28 9-38 244-271 (376)
247 KOG2231 Predicted E3 ubiquitin 23.8 42 0.0009 36.1 1.5 46 215-263 2-54 (669)
248 TIGR02159 PA_CoA_Oxy4 phenylac 23.7 42 0.00092 29.0 1.3 17 24-40 105-121 (146)
249 PF12773 DZR: Double zinc ribb 23.4 42 0.00092 22.9 1.0 25 8-32 13-37 (50)
250 COG1645 Uncharacterized Zn-fin 23.4 39 0.00085 28.8 1.0 29 8-37 29-57 (131)
251 cd00350 rubredoxin_like Rubred 23.1 79 0.0017 20.0 2.1 25 8-33 2-26 (33)
252 PRK06260 threonine synthase; V 23.1 54 0.0012 32.7 2.1 27 5-32 1-27 (397)
253 PF02591 DUF164: Putative zinc 23.1 32 0.00069 24.4 0.3 24 8-31 23-53 (56)
254 COG3813 Uncharacterized protei 22.4 84 0.0018 24.1 2.5 47 216-264 8-55 (84)
255 COG3492 Uncharacterized protei 22.4 31 0.00068 27.5 0.2 12 237-248 42-53 (104)
256 PF08274 PhnA_Zn_Ribbon: PhnA 22.2 31 0.00067 21.7 0.1 22 10-31 5-26 (30)
257 PF00301 Rubredoxin: Rubredoxi 22.1 84 0.0018 21.8 2.3 12 22-33 32-43 (47)
258 PRK11823 DNA repair protein Ra 21.7 63 0.0014 33.0 2.3 35 1-38 1-37 (446)
259 PF13894 zf-C2H2_4: C2H2-type 21.7 30 0.00066 19.0 -0.0 10 26-35 2-11 (24)
260 KOG3842 Adaptor protein Pellin 21.6 60 0.0013 31.8 1.9 51 213-263 341-416 (429)
261 KOG1245 Chromatin remodeling c 21.3 30 0.00064 40.5 -0.2 48 213-260 1108-1159(1404)
262 cd01121 Sms Sms (bacterial rad 21.1 45 0.00097 33.3 1.1 29 8-39 1-31 (372)
263 PF04423 Rad50_zn_hook: Rad50 21.0 25 0.00055 24.7 -0.6 15 24-38 20-34 (54)
264 KOG0956 PHD finger protein AF1 20.6 33 0.00071 36.9 -0.0 58 201-260 107-181 (900)
265 COG4847 Uncharacterized protei 20.6 66 0.0014 25.9 1.6 34 213-247 6-39 (103)
266 TIGR01053 LSD1 zinc finger dom 20.5 76 0.0016 20.1 1.6 23 9-31 3-26 (31)
267 PLN02400 cellulose synthase 20.5 87 0.0019 35.6 3.1 48 214-261 37-89 (1085)
268 COG1198 PriA Primosomal protei 20.5 53 0.0011 35.8 1.5 28 8-39 463-490 (730)
269 PF02318 FYVE_2: FYVE-type zin 20.4 71 0.0015 26.3 1.9 46 212-258 53-102 (118)
No 1
>PF14369 zf-RING_3: zinc-finger
Probab=99.51 E-value=6.5e-15 Score=96.59 Aligned_cols=32 Identities=34% Similarity=0.995 Sum_probs=27.0
Q ss_pred ceeeeccCceeecCC--CCCccCCCCCCCceecc
Q 043965 7 GYWCYICSQMVNPRM--EAGIKCPFCESGIVEQM 38 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~--~~e~~CP~C~sGFvEE~ 38 (342)
+||||+|++.|++.. +.+++||+|++||||||
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei 35 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI 35 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence 499999999998653 34556999999999997
No 2
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.42 E-value=5.3e-14 Score=97.01 Aligned_cols=44 Identities=52% Similarity=1.217 Sum_probs=40.3
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (342)
++|+||++.|..++.++.++|+|+||..||.+|++.+.+||+||
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 36999999999888999999999999999999999999999997
No 3
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.40 E-value=3.2e-13 Score=130.41 Aligned_cols=71 Identities=42% Similarity=0.882 Sum_probs=61.3
Q ss_pred CCCcccHHHHHcCCcccccC---c---ccccccccccccCCceeEecccccccccchHHHhhcCC-CCCCcccccCCC
Q 043965 193 GCPAANKAVLKALPTVTIDK---N---LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSD 263 (342)
Q Consensus 193 g~~~~~~~~i~~~p~~~~~~---~---~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~ 263 (342)
......|..++++|..++.. . ..|+||+|+|+.|++++.|||+|.||..||.+||..+. .||+||..+...
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 45577889999999887753 1 38999999999999999999999999999999998776 599999977654
No 4
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=2.2e-11 Score=116.75 Aligned_cols=69 Identities=33% Similarity=0.753 Sum_probs=52.6
Q ss_pred cHHHHHcCCccccc----Ccccccccccc-cccC---------CceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 198 NKAVLKALPTVTID----KNLQCAVCLEE-FEIG---------NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 198 ~~~~i~~~p~~~~~----~~~~C~ICle~-~~~~---------~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
.|+.-+-++++..+ .+..|.||+++ |..+ .+++.|||||++|.+|++.|++++++||+||.++.-+
T Consensus 268 ~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd 347 (491)
T COG5243 268 TKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFD 347 (491)
T ss_pred hhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccc
Confidence 34444455555443 46789999999 4432 2579999999999999999999999999999997554
Q ss_pred Ccc
Q 043965 264 DFK 266 (342)
Q Consensus 264 ~~~ 266 (342)
..+
T Consensus 348 ~~~ 350 (491)
T COG5243 348 QSS 350 (491)
T ss_pred cCC
Confidence 433
No 5
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.11 E-value=8.6e-11 Score=105.00 Aligned_cols=55 Identities=27% Similarity=0.706 Sum_probs=45.3
Q ss_pred ccccCcccccccccccccCCceeEecccccccccchHHHhhc----------------CCCCCCcccccCCCCc
Q 043965 208 VTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV----------------RSSCPVCRFQVPSDDF 265 (342)
Q Consensus 208 ~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~~ 265 (342)
+...+..+|+||++.++ .++.++|+|.||..||.+|+.. ...||+||..+.....
T Consensus 13 ~~~~~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 13 VDSGGDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred ccCCCccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 34446789999999987 7788999999999999999852 2479999999976554
No 6
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.09 E-value=3.5e-11 Score=112.82 Aligned_cols=50 Identities=36% Similarity=1.030 Sum_probs=46.1
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPS 262 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~ 262 (342)
..+|+|||+.|..+++.+.|||+|.||..|+.+|+. .+..||+||.+++.
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 468999999999999999999999999999999997 66799999999874
No 7
>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=99.08 E-value=5.5e-11 Score=91.03 Aligned_cols=45 Identities=40% Similarity=0.877 Sum_probs=35.9
Q ss_pred ccccccccccccc----------CCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965 213 NLQCAVCLEEFEI----------GNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257 (342)
Q Consensus 213 ~~~C~ICle~~~~----------~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (342)
+..|+||++.|.. .-.+...+|+|.||..||.+||+.+.+||+||
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 4469999999932 12345567999999999999999999999997
No 8
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.06 E-value=1e-10 Score=108.40 Aligned_cols=64 Identities=34% Similarity=0.671 Sum_probs=49.9
Q ss_pred cHHHHHcCCcccc--------cCcccccccccccccCCc-----eeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965 198 NKAVLKALPTVTI--------DKNLQCAVCLEEFEIGNE-----AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 198 ~~~~i~~~p~~~~--------~~~~~C~ICle~~~~~~~-----~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
.+..++.+|.+.. ..+.+|+||++.+..... ++.++|+|.||..||.+|++.+.+||+||..+.
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 5667777776642 235789999999764321 244569999999999999999999999999875
No 9
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.95 E-value=6.1e-10 Score=101.36 Aligned_cols=53 Identities=30% Similarity=0.736 Sum_probs=45.0
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccccCCCCccc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQVPSDDFKI 267 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~~~~~~~ 267 (342)
..++|.|||+.-+ +++++.|||.||+.||.+||..+. .||+||..|..+.+..
T Consensus 46 ~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP 101 (230)
T KOG0823|consen 46 GFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP 101 (230)
T ss_pred CceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence 4679999999877 788888999999999999997554 6999999998776543
No 10
>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=98.92 E-value=5.9e-10 Score=78.88 Aligned_cols=46 Identities=30% Similarity=0.822 Sum_probs=40.6
Q ss_pred cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
+..|.||++... .+..+||+|. ||..|+..|++....||+||+++.
T Consensus 2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 568999999977 7899999999 999999999999999999999874
No 11
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=3.9e-10 Score=105.52 Aligned_cols=50 Identities=30% Similarity=0.830 Sum_probs=45.3
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (342)
...|.+||+... .+..+||||+||..||..|+..+..||+||..+...+.
T Consensus 239 ~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 239 TRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV 288 (293)
T ss_pred CCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence 478999999987 88999999999999999999999999999998876543
No 12
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.83 E-value=1.5e-09 Score=72.89 Aligned_cols=39 Identities=44% Similarity=1.031 Sum_probs=32.9
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCCCCCCc
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (342)
|+||++.+.. .++.++|||+||..||.+|++.+..||+|
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 8999999882 33788999999999999999998899998
No 13
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.82 E-value=1.7e-09 Score=73.94 Aligned_cols=38 Identities=37% Similarity=0.993 Sum_probs=30.8
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCC----CCCCc
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~C 256 (342)
|+||++.|. +++.|+|||+||..||..|++... .||+|
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 899999999 999999999999999999996542 69988
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=98.77 E-value=3.7e-09 Score=71.39 Aligned_cols=44 Identities=41% Similarity=1.104 Sum_probs=36.3
Q ss_pred cccccccccccCCceeEecccccccccchHHHhhc-CCCCCCccccc
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQV 260 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l 260 (342)
.|+||++.+. +....++|+|.||..|+..|++. ...||+||..+
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 4999999984 24445559999999999999987 67899998754
No 15
>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=98.73 E-value=6.1e-09 Score=76.58 Aligned_cols=48 Identities=21% Similarity=0.484 Sum_probs=42.8
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
+.|+||++.+. .++.++|||+|+..||.+|++.+.+||+|+..+..++
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 57999999998 6788999999999999999988889999999885544
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=3.8e-09 Score=92.60 Aligned_cols=51 Identities=25% Similarity=0.664 Sum_probs=43.2
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
...|+|||+.+... .++.+.|||+||..||...++....||+|++.|..+.
T Consensus 131 ~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 131 TYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 46899999999832 2355789999999999999999999999999887654
No 17
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.66 E-value=1.2e-08 Score=79.74 Aligned_cols=51 Identities=31% Similarity=0.767 Sum_probs=39.0
Q ss_pred Cccccccccccccc--------CC--ceeEecccccccccchHHHhhc---CCCCCCcccccCC
Q 043965 212 KNLQCAVCLEEFEI--------GN--EAKEMPCKHKFHGECIMPWLEV---RSSCPVCRFQVPS 262 (342)
Q Consensus 212 ~~~~C~ICle~~~~--------~~--~~~~lpC~H~Fh~~Ci~~Wl~~---~~~CP~CR~~l~~ 262 (342)
+++.|.||...|.. |+ .++.-.|+|.||..||.+||.. +..||+||++...
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 47789999988862 22 2333459999999999999975 3589999998753
No 18
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=8.5e-09 Score=106.80 Aligned_cols=49 Identities=39% Similarity=1.018 Sum_probs=43.8
Q ss_pred cccccccccccccCCc--eeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEIGNE--AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
+..|+||+|.+..+.. ++.|+|+|+||..|+..|+++.++||+||..+.
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY 341 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence 6789999999985543 899999999999999999999999999999543
No 19
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.62 E-value=1.6e-08 Score=68.29 Aligned_cols=38 Identities=45% Similarity=1.215 Sum_probs=33.1
Q ss_pred ccccccccccCCcee-EecccccccccchHHHhh--cCCCCCCc
Q 043965 216 CAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLE--VRSSCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~--~~~~CP~C 256 (342)
|+||++.+. .+. .++|+|.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999988 445 888999999999999998 44589998
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.59 E-value=2.4e-08 Score=68.79 Aligned_cols=44 Identities=25% Similarity=0.740 Sum_probs=38.3
Q ss_pred cccccccccccCCceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
.|.||++.|.....+..++|+|+||..|+..+......||+||+
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 49999999955567889999999999999999866679999984
No 21
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.58 E-value=2.3e-08 Score=99.03 Aligned_cols=51 Identities=29% Similarity=0.722 Sum_probs=45.0
Q ss_pred ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
+...+.|+||++.|. .++.++|+|.||..||..|+.....||+||..+...
T Consensus 23 Le~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 445689999999998 677899999999999999998888999999988654
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.57 E-value=2.5e-08 Score=90.53 Aligned_cols=50 Identities=30% Similarity=0.672 Sum_probs=37.9
Q ss_pred CcccccccccccccCC-----c-eeEecccccccccchHHHhhcC------CCCCCcccccC
Q 043965 212 KNLQCAVCLEEFEIGN-----E-AKEMPCKHKFHGECIMPWLEVR------SSCPVCRFQVP 261 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~-----~-~~~lpC~H~Fh~~Ci~~Wl~~~------~~CP~CR~~l~ 261 (342)
++.+|+||+|..-... . ....+|+|.||..||..|.+.+ .+||+||..+.
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 4688999999864221 1 2344699999999999999753 36999999764
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=98.55 E-value=3.7e-08 Score=64.14 Aligned_cols=38 Identities=42% Similarity=1.206 Sum_probs=33.5
Q ss_pred ccccccccccCCceeEecccccccccchHHHhh-cCCCCCCc
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~C 256 (342)
|+||++... .+..++|+|.||..|+..|++ ....||+|
T Consensus 1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789999854 788899999999999999998 56689987
No 24
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.43 E-value=6.5e-08 Score=89.69 Aligned_cols=51 Identities=33% Similarity=0.791 Sum_probs=43.9
Q ss_pred CcccccccccccccCCceeEecccccccccchHH-HhhcCCC-CCCcccccCCCCc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP-WLEVRSS-CPVCRFQVPSDDF 265 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~-Wl~~~~~-CP~CR~~l~~~~~ 265 (342)
.+..|+||++... .+..++|||+||..||.. |-..+.. ||+||+.+..+..
T Consensus 214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 4778999999988 889999999999999999 8777665 9999998765543
No 25
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.41 E-value=7.3e-08 Score=96.54 Aligned_cols=59 Identities=31% Similarity=0.638 Sum_probs=46.6
Q ss_pred ccccCcccccccccccccCCceeEecccccccccchHHHhhcC-----CCCCCcccccCCCCcccCC
Q 043965 208 VTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-----SSCPVCRFQVPSDDFKIQG 269 (342)
Q Consensus 208 ~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-----~~CP~CR~~l~~~~~~~~~ 269 (342)
+.+..+..|+|||+... .+..+.|||+||..||.++|... ..||+||..|..+++....
T Consensus 181 v~~~t~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 181 VYGSTDMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred hhcCcCCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence 33333778999999987 67777899999999999987544 3799999999887665443
No 26
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.39 E-value=6.4e-08 Score=92.31 Aligned_cols=51 Identities=33% Similarity=0.813 Sum_probs=46.1
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (342)
..+.|.||.++|. .+.++||+|.||..||..+|..+..||+|+.++....+
T Consensus 22 ~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 22 DLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence 4568999999999 88999999999999999999999999999998876553
No 27
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.29 E-value=3.7e-07 Score=69.83 Aligned_cols=31 Identities=35% Similarity=0.826 Sum_probs=27.9
Q ss_pred ecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 232 MPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 232 lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
-.|.|.||..||.+||..++.||++|+....
T Consensus 52 G~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred EecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 3499999999999999999999999987743
No 28
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.26 E-value=4.2e-07 Score=69.42 Aligned_cols=51 Identities=22% Similarity=0.470 Sum_probs=40.7
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhc-CCCCCCcccccCCCCc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-RSSCPVCRFQVPSDDF 265 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~~~ 265 (342)
+.+.|+||.+.+. +++.++|||+|.+.||..||+. +.+||+|+..+...+.
T Consensus 3 ~~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred cccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence 4578999999999 8999999999999999999988 7799999998876543
No 29
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=4.3e-07 Score=84.37 Aligned_cols=60 Identities=30% Similarity=0.739 Sum_probs=46.4
Q ss_pred cCCcccccCcccccccccccccCC-------ceeEecccccccccchHHHh--hcCCCCCCcccccCCCC
Q 043965 204 ALPTVTIDKNLQCAVCLEEFEIGN-------EAKEMPCKHKFHGECIMPWL--EVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 204 ~~p~~~~~~~~~C~ICle~~~~~~-------~~~~lpC~H~Fh~~Ci~~Wl--~~~~~CP~CR~~l~~~~ 264 (342)
.+|+..+ ++..|+||-..+.... +...|.|+|+||..||.-|. .++++||.|+..+..+.
T Consensus 216 glPtkhl-~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 216 GLPTKHL-SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CCCCCCC-CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence 3444444 3567999998886544 66789999999999999997 56679999999876543
No 30
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.18 E-value=7.5e-07 Score=61.16 Aligned_cols=38 Identities=32% Similarity=0.836 Sum_probs=22.7
Q ss_pred cccccccccc-CCceeEecccccccccchHHHhhcCC----CCC
Q 043965 216 CAVCLEEFEI-GNEAKEMPCKHKFHGECIMPWLEVRS----SCP 254 (342)
Q Consensus 216 C~ICle~~~~-~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP 254 (342)
|+||++ |.. ...++.|+|||+|+.+||.++++... .||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 753 34588999999999999999997542 576
No 31
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.15 E-value=6.9e-07 Score=83.81 Aligned_cols=48 Identities=31% Similarity=0.602 Sum_probs=43.2
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
..+.|-||-+.|. .+..++|||.||..||...|..+..||+||.+...
T Consensus 24 s~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 24 SMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred hHHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence 3568999999999 78889999999999999999999999999987643
No 32
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=6.7e-07 Score=89.06 Aligned_cols=50 Identities=30% Similarity=0.974 Sum_probs=39.9
Q ss_pred cccccccccccccCC--------------ceeEecccccccccchHHHhh-cCCCCCCcccccCC
Q 043965 213 NLQCAVCLEEFEIGN--------------EAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPS 262 (342)
Q Consensus 213 ~~~C~ICle~~~~~~--------------~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~ 262 (342)
...|+||+..+.... .-..+||.|+||..|+.+|+. .+..||+||.+|+.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 467999999885211 133568999999999999998 56699999999874
No 33
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=5.4e-07 Score=68.40 Aligned_cols=49 Identities=33% Similarity=0.836 Sum_probs=36.7
Q ss_pred ccccccccccccc--------C-CceeEec-ccccccccchHHHhhcC---CCCCCcccccC
Q 043965 213 NLQCAVCLEEFEI--------G-NEAKEMP-CKHKFHGECIMPWLEVR---SSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~--------~-~~~~~lp-C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~ 261 (342)
+..|.||.-.|.. + +.+.++- |.|.||..||.+|+... ..||+||+.+.
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 4589999888852 2 2333333 99999999999999643 47999998764
No 34
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.09 E-value=8e-07 Score=94.01 Aligned_cols=54 Identities=28% Similarity=0.820 Sum_probs=40.6
Q ss_pred ccccCcccccccccccccCC---cee-EecccccccccchHHHhhcCC--CCCCcccccC
Q 043965 208 VTIDKNLQCAVCLEEFEIGN---EAK-EMPCKHKFHGECIMPWLEVRS--SCPVCRFQVP 261 (342)
Q Consensus 208 ~~~~~~~~C~ICle~~~~~~---~~~-~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~ 261 (342)
.++.+..+|+||+..+..-+ .-+ .-.|+|.||..|+.+|++... +||+||.+++
T Consensus 1464 ~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1464 EKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 34556789999998886221 122 334999999999999997654 8999998775
No 35
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=1.9e-06 Score=79.90 Aligned_cols=45 Identities=42% Similarity=0.941 Sum_probs=39.4
Q ss_pred ccCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcc
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCR 257 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (342)
+.+...|+||++.|. .++.++|+|.||..||..++.....||.||
T Consensus 10 ~~~~~~C~iC~~~~~---~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFR---EPVLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhh---cCccccccchHhHHHHHHhcCCCcCCcccC
Confidence 345688999999999 558999999999999999888555899999
No 36
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=97.98 E-value=3.9e-06 Score=59.25 Aligned_cols=42 Identities=24% Similarity=0.790 Sum_probs=33.5
Q ss_pred cccccccccccCCceeEeccc-----ccccccchHHHhhcCC--CCCCcc
Q 043965 215 QCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVRS--SCPVCR 257 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~~--~CP~CR 257 (342)
.|-||++ ...++.+..+||. |.+|..|+.+|+..+. +||+|+
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 4445567788985 8999999999996554 899995
No 37
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.97 E-value=2.3e-06 Score=63.25 Aligned_cols=51 Identities=29% Similarity=0.733 Sum_probs=26.4
Q ss_pred cCcccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (342)
++...|++|.+.++ .++.| .|.|+||..||..-+. ..||+|+.+.-..+.+
T Consensus 5 e~lLrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 5 EELLRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp HHTTS-SSS-S--S---S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS--
T ss_pred HHhcCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHH
Confidence 44578999999998 66554 5999999999988654 3599999877666554
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.92 E-value=2.2e-06 Score=65.01 Aligned_cols=50 Identities=28% Similarity=0.657 Sum_probs=23.3
Q ss_pred cccccccccccc-cCCce-eEe---cccccccccchHHHhhc----C-------CCCCCcccccCC
Q 043965 213 NLQCAVCLEEFE-IGNEA-KEM---PCKHKFHGECIMPWLEV----R-------SSCPVCRFQVPS 262 (342)
Q Consensus 213 ~~~C~ICle~~~-~~~~~-~~l---pC~H~Fh~~Ci~~Wl~~----~-------~~CP~CR~~l~~ 262 (342)
+..|.||+..+. .+..+ +.- .|++.||..||.+||.. + ..||.|+.+|..
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 357999999876 33222 222 49999999999999952 1 159999998753
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=97.84 E-value=8.4e-06 Score=78.14 Aligned_cols=54 Identities=19% Similarity=0.428 Sum_probs=38.9
Q ss_pred cccccccccccccCCc--eeEecccccccccchHHHh-hcCCCCCCcccccCCCCcc
Q 043965 213 NLQCAVCLEEFEIGNE--AKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~--~~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~ 266 (342)
+..|+||+..-..... ....+|||.||..||...+ .....||.|+..+......
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr 59 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR 59 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence 3579999995332222 2233799999999999965 4455899999988766543
No 40
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.81 E-value=2.6e-06 Score=82.03 Aligned_cols=51 Identities=29% Similarity=0.699 Sum_probs=41.8
Q ss_pred ccCcccccccccccccCCceeEec-ccccccccchHHHhhc-CCCCCCcccccCCC
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEV-RSSCPVCRFQVPSD 263 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~l~~~ 263 (342)
+.....|+|||+.++ ..+.++ |.|.||..||..-++. .+.||.||+.+..+
T Consensus 40 ~~~~v~c~icl~llk---~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 40 FDIQVICPICLSLLK---KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred hhhhhccHHHHHHHH---hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 345678999999998 555555 9999999999988865 45899999988655
No 41
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.79 E-value=8.3e-06 Score=80.71 Aligned_cols=54 Identities=37% Similarity=0.896 Sum_probs=41.3
Q ss_pred CcccccCcccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965 206 PTVTIDKNLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 206 p~~~~~~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
+...+.+-.+|+||||.+.... .++.+.|.|.||..|+.+|. ..+||+||.-..
T Consensus 168 ~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 168 PPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred CCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 3344456678999999997543 23445599999999999994 568999998665
No 42
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.3e-05 Score=77.60 Aligned_cols=47 Identities=26% Similarity=0.728 Sum_probs=41.7
Q ss_pred cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
..+|.||+.+.. +..+|||.|. .|..|.+..--+++.||+||+++..
T Consensus 290 gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 290 GKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred CCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 568999999988 8999999999 8999998877788999999998854
No 43
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=1.1e-05 Score=76.24 Aligned_cols=49 Identities=29% Similarity=0.564 Sum_probs=41.1
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcC-CCCCCcccccCCCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR-SSCPVCRFQVPSDD 264 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~-~~CP~CR~~l~~~~ 264 (342)
..+|+||+.... .++.|+|+|.||..||.--.+.. .+|++||.+++...
T Consensus 7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 457999998876 77899999999999998766544 47999999998764
No 44
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=1.4e-05 Score=64.25 Aligned_cols=30 Identities=37% Similarity=0.778 Sum_probs=26.7
Q ss_pred ecccccccccchHHHhhcCCCCCCcccccC
Q 043965 232 MPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 232 lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
--|.|.||..||.+||+.++.||+|.++..
T Consensus 79 G~CNHaFH~hCisrWlktr~vCPLdn~eW~ 108 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRNVCPLDNKEWV 108 (114)
T ss_pred eecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence 349999999999999999999999987653
No 45
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=1.5e-05 Score=56.86 Aligned_cols=45 Identities=22% Similarity=0.606 Sum_probs=36.5
Q ss_pred ccccccccccccCCceeEeccccc-ccccchHHHhh-cCCCCCCcccccC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLE-VRSSCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~-~~~~CP~CR~~l~ 261 (342)
.+|.||+|.-. +.+...|||. .|..|-.+.++ .+..||+||.++.
T Consensus 8 dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 68999998765 4556669998 88999876554 8889999999875
No 46
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.47 E-value=3.8e-05 Score=72.61 Aligned_cols=92 Identities=22% Similarity=0.448 Sum_probs=61.1
Q ss_pred CchhHHHHHHHhcCCCCCCCCcccHHHHHcCCcc---cccCcccccccccccccCCceeEecccccccccchHHHhhc--
Q 043965 175 PGLDLLLQHLLENDPNRYGCPAANKAVLKALPTV---TIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-- 249 (342)
Q Consensus 175 ~~l~~l~~~L~~~~~~~~g~~~~~~~~i~~~p~~---~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-- 249 (342)
+.|..|.+++.+......|.| .--+.++..... .-.....|.|||.-|..++....++|-|.||..|+-++|..
T Consensus 75 ~~~~~i~~~~~~iikq~~g~p-ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 75 PEFREIQRQIQEIIKQNSGMP-IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred HHHHHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 456666666665444445543 333333332221 11235689999999998888899999999999999887631
Q ss_pred ---------------------CCCCCCcccccCCCCccc
Q 043965 250 ---------------------RSSCPVCRFQVPSDDFKI 267 (342)
Q Consensus 250 ---------------------~~~CP~CR~~l~~~~~~~ 267 (342)
...||+||..|..+.-.+
T Consensus 154 ~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~sl 192 (368)
T KOG4445|consen 154 TGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENSL 192 (368)
T ss_pred HHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccce
Confidence 125999999887665433
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.0001 Score=72.11 Aligned_cols=51 Identities=29% Similarity=0.768 Sum_probs=38.1
Q ss_pred cCcccccccccccccCC----ceeEec-ccccccccchHHHh--hc-----CCCCCCcccccC
Q 043965 211 DKNLQCAVCLEEFEIGN----EAKEMP-CKHKFHGECIMPWL--EV-----RSSCPVCRFQVP 261 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl--~~-----~~~CP~CR~~l~ 261 (342)
..+..|.||++...... .-.+|| |.|.||..||..|- .+ ...||.||....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 56778999999976322 012345 99999999999998 33 458999998653
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=6.1e-05 Score=73.46 Aligned_cols=48 Identities=27% Similarity=0.853 Sum_probs=36.2
Q ss_pred ccccccccccccCCceeEec-ccccccccchHHHhhcCC---CCCCcccccC
Q 043965 214 LQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRS---SCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~---~CP~CR~~l~ 261 (342)
..|.||.+-+.....+..+. |||+||..|+.+|++.-. .||+|+-.++
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~ 56 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ 56 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence 46999966555444555555 999999999999997644 7999994443
No 49
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=4.7e-05 Score=79.96 Aligned_cols=52 Identities=29% Similarity=0.673 Sum_probs=43.6
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHhh-cCCCCCCcccccCCCCc
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE-VRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l~~~~~ 265 (342)
.+.+.|++|-..++ .++++.|+|+||..|+.+-+. ++..||.|...|-..++
T Consensus 641 K~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 641 KELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HhceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 34678999998887 788888999999999999885 55699999998866554
No 50
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.25 E-value=5.3e-05 Score=79.31 Aligned_cols=53 Identities=28% Similarity=0.490 Sum_probs=45.0
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (342)
...|++|+..+..+......+|+|.||..||..|-+...+||+||..+....+
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V 175 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKV 175 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeee
Confidence 35799999999866666667799999999999999999999999998865443
No 51
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.16 E-value=0.0001 Score=70.72 Aligned_cols=51 Identities=25% Similarity=0.707 Sum_probs=42.8
Q ss_pred ccCcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
+....+|.+|..+|. ++..+. |-|.||..||...|....+||.|...+-..
T Consensus 12 ~n~~itC~LC~GYli---DATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLI---DATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred cccceehhhccceee---cchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 445678999999998 555555 999999999999999999999998776443
No 52
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.11 E-value=0.00017 Score=71.77 Aligned_cols=49 Identities=29% Similarity=0.697 Sum_probs=44.0
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
..++.|.||+..+. .++.+||||.||..||.+-+.....||+||..+..
T Consensus 82 ~sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCccccccccc
Confidence 34688999999998 88888999999999999988888899999999875
No 53
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.05 E-value=0.00026 Score=70.80 Aligned_cols=52 Identities=29% Similarity=0.835 Sum_probs=44.5
Q ss_pred ccCcccccccccccccCCceeE-ecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
+.+++.|+||...+. .+.. +.|+|.||..|+..|+..+..||.|+..+....
T Consensus 18 ~~~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 18 LDENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE 70 (391)
T ss_pred CcccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence 567789999999998 5555 579999999999999999999999988775443
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.03 E-value=0.0002 Score=70.09 Aligned_cols=50 Identities=26% Similarity=0.731 Sum_probs=42.0
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhc--CCCCCCcccccCCCCcc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~ 266 (342)
..|.||-|.-+ ++++-||||..|..|+..|-.. .++||.||.++...+..
T Consensus 370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v 421 (563)
T KOG1785|consen 370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV 421 (563)
T ss_pred HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence 35999988755 8889999999999999999843 46999999999876643
No 55
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.80 E-value=0.00047 Score=50.21 Aligned_cols=41 Identities=34% Similarity=0.834 Sum_probs=27.9
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcC--CCCCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--SSCPV 255 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--~~CP~ 255 (342)
...|+|.+..|+ +.++...|+|+|-+..|.+||..+ ..||+
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 578999999998 344455799999999999999443 37998
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.78 E-value=0.00062 Score=67.01 Aligned_cols=48 Identities=27% Similarity=0.827 Sum_probs=36.7
Q ss_pred cccccccccccccCC--ceeEecccccccccchHHHhhc--CCCCCCccccc
Q 043965 213 NLQCAVCLEEFEIGN--EAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQV 260 (342)
Q Consensus 213 ~~~C~ICle~~~~~~--~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l 260 (342)
..+|+||++.+.... ....+.|+|.|...||.+||.+ ...||.|..+-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 357999999997543 3445569999999999999952 23799997644
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.52 E-value=0.00071 Score=66.26 Aligned_cols=48 Identities=38% Similarity=0.796 Sum_probs=38.5
Q ss_pred cccccccccccccCC-ceeEecccccccccchHHHhhcCC--CCCCccccc
Q 043965 213 NLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRS--SCPVCRFQV 260 (342)
Q Consensus 213 ~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l 260 (342)
.+-|..|-+.+-..+ ....|||.|+||..|+...|.++. +||.||+-.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr 415 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR 415 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence 467999999885433 566789999999999999996655 899999533
No 58
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.37 E-value=0.00093 Score=59.95 Aligned_cols=46 Identities=22% Similarity=0.574 Sum_probs=40.7
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
+.|.||.++|+ .++.+.|||.||..|...-++....|-+|-+....
T Consensus 197 F~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 197 FLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred eeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 57999999999 78888999999999999998888999999765543
No 59
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.16 E-value=0.0035 Score=60.84 Aligned_cols=50 Identities=24% Similarity=0.428 Sum_probs=43.4
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
.++..|+||...-. .++..||+|.-|+.||.+.|...+.|=.|+..+...
T Consensus 420 sEd~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 420 SEDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV 469 (489)
T ss_pred cccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence 45678999987655 788899999999999999999999999999887643
No 60
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.10 E-value=0.0017 Score=61.51 Aligned_cols=46 Identities=24% Similarity=0.514 Sum_probs=41.2
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
+.|-||...|. .++...|+|.||..|...-++....|.+|-+....
T Consensus 242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 56999999999 88899999999999999999988999999876543
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.99 E-value=0.0032 Score=69.94 Aligned_cols=52 Identities=33% Similarity=0.680 Sum_probs=41.5
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHhhcCC----------CCCCcccccCC
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----------SCPVCRFQVPS 262 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----------~CP~CR~~l~~ 262 (342)
..++.|.||+.+--.....+.|.|+|+||..|....|+..- +||+|+.++..
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 34678999998766566788999999999999987765432 79999988753
No 62
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=95.89 E-value=0.0041 Score=51.58 Aligned_cols=39 Identities=23% Similarity=0.497 Sum_probs=30.5
Q ss_pred CCCCCceeeeccCceeecCCCCCccCCCCCCCceeccccC
Q 043965 2 GDAMVGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMSSS 41 (342)
Q Consensus 2 ~~~~~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~~~ 41 (342)
++..+..||..|.+++.+..- ++.||.|+|..+.-+...
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~-~~~CP~C~s~~~~i~~G~ 103 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEEL-DYRCPKCGSINLRIIGGD 103 (115)
T ss_pred EEeccEEEeccCCCeecchhh-eeECCCCCCCceEEecCC
Confidence 344556999999999976543 777999999998877644
No 63
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.85 E-value=0.0038 Score=43.75 Aligned_cols=44 Identities=30% Similarity=0.612 Sum_probs=22.1
Q ss_pred ccccccccccCCceeEec--ccccccccchHHHhh-cCCCCCCccccc
Q 043965 216 CAVCLEEFEIGNEAKEMP--CKHKFHGECIMPWLE-VRSSCPVCRFQV 260 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lp--C~H~Fh~~Ci~~Wl~-~~~~CP~CR~~l 260 (342)
|++|.+++... ....+| |++.+|..|...-++ ....||-||.+.
T Consensus 1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CC-CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccC-CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 78999999433 334455 899999999888876 467999999864
No 64
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.85 E-value=0.0052 Score=57.79 Aligned_cols=48 Identities=25% Similarity=0.394 Sum_probs=36.6
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhc--CCCCCCcccccC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--RSSCPVCRFQVP 261 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--~~~CP~CR~~l~ 261 (342)
.+.+|++|-+.-. ..-...+|+|+||+.||..-+.. ..+||.|-.++.
T Consensus 238 ~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCCC--CCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4578999998866 23344559999999999886643 359999987665
No 65
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.72 E-value=0.0058 Score=59.53 Aligned_cols=43 Identities=35% Similarity=0.681 Sum_probs=33.0
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
...|.||++..+ ..+.+||||.-| |..--. .-.+||+||..+.
T Consensus 305 p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 305 PDLCVVCLDEPK---SAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIR 347 (355)
T ss_pred CCceEEecCCcc---ceeeecCCcEEE--chHHHh-hCCCCchhHHHHH
Confidence 467999999988 789999999966 654432 2335999998764
No 66
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.72 E-value=0.003 Score=64.13 Aligned_cols=51 Identities=31% Similarity=0.720 Sum_probs=41.2
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhc-----CCCCCCcccccCCCCc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV-----RSSCPVCRFQVPSDDF 265 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~-----~~~CP~CR~~l~~~~~ 265 (342)
+...|.+|-+.-+ +.+...|.|.||+.||..++.. .-+||+|-..|..+..
T Consensus 535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDls 590 (791)
T KOG1002|consen 535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLS 590 (791)
T ss_pred CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccccc
Confidence 3467999999877 7888899999999999888742 3489999888876643
No 67
>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=95.69 E-value=0.0049 Score=49.60 Aligned_cols=37 Identities=30% Similarity=0.602 Sum_probs=30.5
Q ss_pred cccccCcccccccccccccCCceeEecccccccccchH
Q 043965 207 TVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIM 244 (342)
Q Consensus 207 ~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~ 244 (342)
.+.+.+...|+||...+.. ......||+|+||..|+.
T Consensus 72 ~v~i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 3455677889999999875 577788999999999974
No 68
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.49 E-value=0.0037 Score=54.48 Aligned_cols=28 Identities=32% Similarity=0.877 Sum_probs=26.2
Q ss_pred cccccccccccccCCceeEecccccccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHG 240 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~ 240 (342)
..+|.||||+++.++.+..|||-.+||+
T Consensus 177 kGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 177 KGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred CCcEEEEhhhccCCCceeccceEEEeec
Confidence 4689999999999999999999999996
No 69
>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=95.43 E-value=0.0051 Score=52.19 Aligned_cols=35 Identities=14% Similarity=0.537 Sum_probs=30.2
Q ss_pred cccccccccccccCCceeEeccc------ccccccchHHHh
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCK------HKFHGECIMPWL 247 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~------H~Fh~~Ci~~Wl 247 (342)
..+|.||++.+...+.++.++|+ |.||..|+.+|-
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 46899999999875677888886 899999999994
No 70
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.37 E-value=0.0093 Score=54.64 Aligned_cols=49 Identities=22% Similarity=0.584 Sum_probs=38.9
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhc--------CCCCCCcccccCCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV--------RSSCPVCRFQVPSD 263 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~--------~~~CP~CR~~l~~~ 263 (342)
.-|..|--.+..++.+ .|-|-|.||.+|+..|-.. ...||.|..+|...
T Consensus 51 pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 4599999999877655 5669999999999999743 22799999888544
No 71
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.29 E-value=0.0093 Score=41.62 Aligned_cols=40 Identities=30% Similarity=0.839 Sum_probs=26.7
Q ss_pred ccccccccccCCceeEeccc--c---cccccchHHHhhc--CCCCCCc
Q 043965 216 CAVCLEEFEIGNEAKEMPCK--H---KFHGECIMPWLEV--RSSCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~--~~~CP~C 256 (342)
|-||++.-.... ....||+ - ..|..|+.+|+.. ..+|++|
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 679998876443 5667754 3 6899999999964 4479887
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.20 E-value=0.008 Score=59.48 Aligned_cols=46 Identities=26% Similarity=0.636 Sum_probs=37.2
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcC--------CCCCCccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR--------SSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~--------~~CP~CR~ 258 (342)
...|.||++........+.+||+|+||..|+..++..+ -.||-|..
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 46899999998755788999999999999999988532 25877654
No 73
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.18 E-value=0.0087 Score=63.85 Aligned_cols=50 Identities=26% Similarity=0.679 Sum_probs=36.7
Q ss_pred cCcccccccccccccCCcee-EecccccccccchHHHhhcCC-------CCCCccccc
Q 043965 211 DKNLQCAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLEVRS-------SCPVCRFQV 260 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~-------~CP~CR~~l 260 (342)
....+|.||++.+.....+- .-.|-|+||..||..|-.... .||.|+...
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 35678999999997544332 234889999999999985422 599998433
No 74
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.99 E-value=0.017 Score=53.60 Aligned_cols=57 Identities=16% Similarity=0.219 Sum_probs=46.9
Q ss_pred cccccccccccccCCceeEe-cccccccccchHHHhhcCCCCCCcccccCCCCcccCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFKIQG 269 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~ 269 (342)
...|+||.+.+........| ||||+|+..|+.+.+.....||+|-.++...++....
T Consensus 221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence 46899999999865544444 5999999999999999999999999999877664433
No 75
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.014 Score=56.19 Aligned_cols=47 Identities=21% Similarity=0.499 Sum_probs=37.3
Q ss_pred CcccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCCcccccC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
....|+||+.... .+..+. -|.+||+.||.+.+..++.||+=-.+..
T Consensus 299 ~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 3567999998876 333443 6999999999999999999998765543
No 76
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.93 E-value=0.0057 Score=57.99 Aligned_cols=42 Identities=24% Similarity=0.626 Sum_probs=33.6
Q ss_pred cccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
...|.||++... +.+.|+|||. -|..|-... +.||+||+.+.
T Consensus 300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----NECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence 457999999877 8899999997 677776442 38999998764
No 77
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.23 E-value=0.018 Score=53.33 Aligned_cols=47 Identities=19% Similarity=0.482 Sum_probs=34.7
Q ss_pred cccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
.|-.|..--. ++...++.|.|+||..|...-. ...||+|+..+....
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~ 51 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQ 51 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeeeee
Confidence 5777766544 6677778899999999986522 228999999875543
No 78
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.11 E-value=0.027 Score=53.93 Aligned_cols=47 Identities=23% Similarity=0.627 Sum_probs=39.0
Q ss_pred ccccccccccccCC---ceeEecccccccccchHHHhhcCC-CCCCccccc
Q 043965 214 LQCAVCLEEFEIGN---EAKEMPCKHKFHGECIMPWLEVRS-SCPVCRFQV 260 (342)
Q Consensus 214 ~~C~ICle~~~~~~---~~~~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l 260 (342)
..|-||-++|...+ .++.|.|||.||..|+.+.+.... .||.||...
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 47999999998653 577888999999999988775444 799999985
No 79
>PHA03096 p28-like protein; Provisional
Probab=93.93 E-value=0.022 Score=54.56 Aligned_cols=45 Identities=27% Similarity=0.458 Sum_probs=31.6
Q ss_pred ccccccccccccCC----ceeEec-ccccccccchHHHhhcCC---CCCCccc
Q 043965 214 LQCAVCLEEFEIGN----EAKEMP-CKHKFHGECIMPWLEVRS---SCPVCRF 258 (342)
Q Consensus 214 ~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~Wl~~~~---~CP~CR~ 258 (342)
..|.||++...... .-..|+ |.|.||..||..|-.... +||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 57999999876432 233566 999999999999985432 4444443
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.84 E-value=0.034 Score=53.98 Aligned_cols=48 Identities=25% Similarity=0.721 Sum_probs=39.7
Q ss_pred cCcccccccccccccCCceeEecccccccccchHH--HhhcCCCCCCcccccC
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP--WLEVRSSCPVCRFQVP 261 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~--Wl~~~~~CP~CR~~l~ 261 (342)
++...|.||.+.+. -...+||+|..|-.|..+ -|.....||+||.+..
T Consensus 59 Een~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 59 EENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred cccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 34567999999887 678899999999999865 4677889999998653
No 81
>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=93.78 E-value=0.045 Score=47.72 Aligned_cols=52 Identities=23% Similarity=0.559 Sum_probs=36.7
Q ss_pred cccccccccccccCCceeEeccc-------------ccccccchHHHhhc------------------------------
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCK-------------HKFHGECIMPWLEV------------------------------ 249 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~-------------H~Fh~~Ci~~Wl~~------------------------------ 249 (342)
+..|+||||.-. .++.|-|. -.-|..|+.+.-+.
T Consensus 2 d~~CpICme~PH---NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (162)
T PF07800_consen 2 DVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ 78 (162)
T ss_pred CccCceeccCCC---ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence 567999999877 66666553 22477899887431
Q ss_pred -CCCCCCcccccCCCCccc
Q 043965 250 -RSSCPVCRFQVPSDDFKI 267 (342)
Q Consensus 250 -~~~CP~CR~~l~~~~~~~ 267 (342)
+..||+||.+|..+....
T Consensus 79 ~~L~CPLCRG~V~GWtvve 97 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVE 97 (162)
T ss_pred ccccCccccCceeceEEch
Confidence 125999999998876543
No 82
>PHA02862 5L protein; Provisional
Probab=93.58 E-value=0.036 Score=47.59 Aligned_cols=45 Identities=18% Similarity=0.551 Sum_probs=33.5
Q ss_pred ccccccccccccCCceeEeccc-----ccccccchHHHhhcC--CCCCCcccccCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCK-----HKFHGECIMPWLEVR--SSCPVCRFQVPS 262 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~Wl~~~--~~CP~CR~~l~~ 262 (342)
..|=||.+.-. +. .-||. ..-|..|+.+|+... ..|++|+.++.-
T Consensus 3 diCWIC~~~~~--e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 3 DICWICNDVCD--ER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CEEEEecCcCC--CC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 57999999843 22 35654 468999999999644 389999988753
No 83
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.50 E-value=0.029 Score=53.42 Aligned_cols=42 Identities=33% Similarity=0.757 Sum_probs=35.0
Q ss_pred ccccccccccccCCceeEec-ccccccccchHHHh-hcCCCCCCccc
Q 043965 214 LQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWL-EVRSSCPVCRF 258 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl-~~~~~CP~CR~ 258 (342)
+.|+.|...+. .+..++ |+|.||..||..-| .....||.|..
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 68999999887 666777 99999999998765 56669999954
No 84
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=93.36 E-value=0.037 Score=61.65 Aligned_cols=84 Identities=24% Similarity=0.472 Sum_probs=55.6
Q ss_pred ccccCchhHHHHHHHhcCCCCCCCCcccHHHHHcCCcccccCcccccccccccccCCceeEecccccccccchHHHhhcC
Q 043965 171 YLVGPGLDLLLQHLLENDPNRYGCPAANKAVLKALPTVTIDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR 250 (342)
Q Consensus 171 ~~~g~~l~~l~~~L~~~~~~~~g~~~~~~~~i~~~p~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (342)
+...+|+-.++..|.+.........+..++.+.- ...+.....|.||++.+.. ...+..|+|.+|..|+..|+..+
T Consensus 1113 ~ls~~G~~r~lk~l~e~~~~~~~~i~~~es~~~y--~~~~~~~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~ 1188 (1394)
T KOG0298|consen 1113 FLSIPGLLRYLKGLKESKADTPCKIAQTESDVRY--LMNLSGHFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYAS 1188 (1394)
T ss_pred hhccchHHHHHHHHHHHhccCccccCCccchHHH--HHHhhcccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHh
Confidence 3444677777777776554333222222222221 1222345589999999873 33455699999999999999999
Q ss_pred CCCCCccc
Q 043965 251 SSCPVCRF 258 (342)
Q Consensus 251 ~~CP~CR~ 258 (342)
..||.|+.
T Consensus 1189 s~~~~~ks 1196 (1394)
T KOG0298|consen 1189 SRCPICKS 1196 (1394)
T ss_pred ccCcchhh
Confidence 99999984
No 85
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.26 E-value=0.039 Score=48.97 Aligned_cols=51 Identities=24% Similarity=0.576 Sum_probs=36.5
Q ss_pred cccccccccccccCCce----eEecccccccccchHHHhhcC-----------CCCCCcccccCCC
Q 043965 213 NLQCAVCLEEFEIGNEA----KEMPCKHKFHGECIMPWLEVR-----------SSCPVCRFQVPSD 263 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~----~~lpC~H~Fh~~Ci~~Wl~~~-----------~~CP~CR~~l~~~ 263 (342)
...|.||+.+-..|..+ --..|+..||.-|+..||+.- ..||.|-.++..+
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 34699998776544422 234599999999999999632 1599998877543
No 86
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.25 E-value=0.0063 Score=59.74 Aligned_cols=50 Identities=22% Similarity=0.630 Sum_probs=42.6
Q ss_pred ccccccccccccC-CceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 214 LQCAVCLEEFEIG-NEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 214 ~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
..|+||.+.++.. +....+-|+|.+|..||.+||.....||.|+.+|+..
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN 247 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence 4699999988754 4566777999999999999999999999999988654
No 87
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.17 E-value=0.062 Score=38.66 Aligned_cols=45 Identities=24% Similarity=0.516 Sum_probs=33.1
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
..|..|...-. ....+||+|+.+..|..- ++-+-||+|-.++...
T Consensus 8 ~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 8 QPCVFCGFVGT---KGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFD 52 (55)
T ss_pred eeEEEcccccc---ccccccccceeeccccCh--hhccCCCCCCCcccCC
Confidence 34666655433 678899999999999643 4667899998888654
No 88
>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=92.99 E-value=0.034 Score=38.07 Aligned_cols=41 Identities=29% Similarity=0.821 Sum_probs=23.2
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCC--CCCCc
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--SCPVC 256 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~C 256 (342)
|.+|.+....|..-....|+-.+|..|+..++.... .||.|
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 678888877543333334888999999999997666 79987
No 89
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.68 E-value=0.048 Score=58.42 Aligned_cols=43 Identities=21% Similarity=0.683 Sum_probs=34.4
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (342)
...|.+|--.+.. ..+...|+|.||.+|+. .....||.|+.++
T Consensus 840 ~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 3579999888773 56777899999999997 4556899998844
No 90
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.51 E-value=0.06 Score=52.21 Aligned_cols=57 Identities=19% Similarity=0.513 Sum_probs=40.6
Q ss_pred CcccccccccccccCC-ceeEecccccccccchHHHh-hcCCCCCCcccccCCCCcccC
Q 043965 212 KNLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWL-EVRSSCPVCRFQVPSDDFKIQ 268 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl-~~~~~CP~CR~~l~~~~~~~~ 268 (342)
+++.|+.|+|++...+ ...-.+||...|.-|....- .....||.||.....+..++.
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~ 71 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV 71 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence 3456999999997655 34455699888888865433 245689999998877765543
No 91
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.39 E-value=0.091 Score=49.69 Aligned_cols=53 Identities=23% Similarity=0.422 Sum_probs=40.6
Q ss_pred cccccccccccccCCcee-EecccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965 213 NLQCAVCLEEFEIGNEAK-EMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (342)
...|||....|......+ ..+|||+|...+|...- ....||+|-.++...+..
T Consensus 113 ~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI 166 (260)
T PF04641_consen 113 RFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDII 166 (260)
T ss_pred eeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEE
Confidence 468999999995443444 44799999999998872 355899999999866654
No 92
>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=92.37 E-value=0.067 Score=32.05 Aligned_cols=22 Identities=32% Similarity=0.871 Sum_probs=18.8
Q ss_pred eeccCceeecCC-CCCccCCCCC
Q 043965 10 CYICSQMVNPRM-EAGIKCPFCE 31 (342)
Q Consensus 10 Ch~C~~~V~p~~-~~e~~CP~C~ 31 (342)
|..|.+.|.|.- ...++||.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 889999998775 5689999996
No 93
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=92.27 E-value=0.056 Score=51.85 Aligned_cols=43 Identities=30% Similarity=0.621 Sum_probs=30.2
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (342)
-.|.-|--.+. .--+.+||+|+||.+|... ..-+.||.|-..|
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 35777765554 1346779999999999754 3456899996655
No 94
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=92.23 E-value=0.061 Score=51.20 Aligned_cols=45 Identities=24% Similarity=0.658 Sum_probs=37.9
Q ss_pred ccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 214 LQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 214 ~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
..|+||.+.+.... .+..++|+|..|..|.......+-+||+|.+
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 34999999886544 5678899999999999888877789999988
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=92.22 E-value=0.047 Score=38.04 Aligned_cols=44 Identities=23% Similarity=0.605 Sum_probs=26.1
Q ss_pred cccccccccccCCceeEeccc-ccccccchHHHhhcCCCCCCcccccCCC
Q 043965 215 QCAVCLEEFEIGNEAKEMPCK-HKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
-|.-|+-..+ ..+.|. |..|..|+...|.....||+|..+||.+
T Consensus 4 nCKsCWf~~k-----~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFANK-----GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S--S-----SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred cChhhhhcCC-----CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 3666664433 455675 8899999999999999999999999865
No 96
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=92.21 E-value=0.089 Score=45.97 Aligned_cols=48 Identities=23% Similarity=0.628 Sum_probs=34.6
Q ss_pred CcccccccccccccCCceeEeccc--c---cccccchHHHhhcCC--CCCCcccccCCC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCK--H---KFHGECIMPWLEVRS--SCPVCRFQVPSD 263 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~ 263 (342)
.+..|=||.+.-. . ...||. . .-|..|+..|+..+. .|++|+.++...
T Consensus 7 ~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 4567999998843 2 234654 4 459999999996544 899999877544
No 97
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=91.29 E-value=0.069 Score=57.04 Aligned_cols=49 Identities=22% Similarity=0.590 Sum_probs=39.8
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCC--CCCCcccccCCCCcc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS--SCPVCRFQVPSDDFK 266 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~~~ 266 (342)
..|.||++ . +.+...+|+|.||..|+..-+.... .||+||..+..+...
T Consensus 455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~ 505 (674)
T KOG1001|consen 455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLL 505 (674)
T ss_pred cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHh
Confidence 78999999 3 3788889999999999998775433 699999988766443
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=91.00 E-value=0.13 Score=36.15 Aligned_cols=31 Identities=39% Similarity=0.909 Sum_probs=24.2
Q ss_pred CCCCceeeeccCceee-cCCCCCccCCCCCCC
Q 043965 3 DAMVGYWCYICSQMVN-PRMEAGIKCPFCESG 33 (342)
Q Consensus 3 ~~~~~ywCh~C~~~V~-p~~~~e~~CP~C~sG 33 (342)
+++..|=|-.|.+.|. .....++.||+|++-
T Consensus 2 ~~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 2 EAMMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred cceEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 4556699999999996 223467999999984
No 99
>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=90.99 E-value=0.21 Score=49.41 Aligned_cols=31 Identities=32% Similarity=0.795 Sum_probs=23.7
Q ss_pred ccccccccchHHHhhcCC-------------CCCCcccccCCCC
Q 043965 234 CKHKFHGECIMPWLEVRS-------------SCPVCRFQVPSDD 264 (342)
Q Consensus 234 C~H~Fh~~Ci~~Wl~~~~-------------~CP~CR~~l~~~~ 264 (342)
|...+|..|+-+|+..++ .||+||+.+..-|
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence 556678999999985332 6999999887554
No 100
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.00 E-value=0.18 Score=49.89 Aligned_cols=48 Identities=21% Similarity=0.376 Sum_probs=40.0
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCcccc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRFQ 259 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~~ 259 (342)
..+.|||=.+.-.....+..|.|||+....-|.+..+... .||+|-..
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 4578999888888888999999999999999988776544 79999543
No 101
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=89.90 E-value=0.11 Score=43.99 Aligned_cols=49 Identities=22% Similarity=0.558 Sum_probs=37.4
Q ss_pred cccccccccccccCCceeEec----ccccccccchHHHhh---cCCCCCCcccccCCCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMP----CKHKFHGECIMPWLE---VRSSCPVCRFQVPSDD 264 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lp----C~H~Fh~~Ci~~Wl~---~~~~CP~CR~~l~~~~ 264 (342)
-.+|-||.|... +.+.|+ ||-..|..|-...|+ .+..||+|+..+....
T Consensus 80 lYeCnIC~etS~---ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 80 LYECNICKETSA---EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred ceeccCcccccc---hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 468999999876 333343 999999999887654 4568999999886553
No 102
>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=89.38 E-value=0.23 Score=41.17 Aligned_cols=33 Identities=27% Similarity=0.512 Sum_probs=25.1
Q ss_pred CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
+..||+.|...+.+. ...+.||.|+|..++-+.
T Consensus 69 ~~~~C~~Cg~~~~~~-~~~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 69 VECECEDCSEEVSPE-IDLYRCPKCHGIMLQVRA 101 (115)
T ss_pred cEEEcccCCCEEecC-CcCccCcCCcCCCcEEec
Confidence 339999999988643 336789999998766554
No 103
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.81 E-value=0.25 Score=41.15 Aligned_cols=34 Identities=26% Similarity=0.310 Sum_probs=23.9
Q ss_pred CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
+.+||..|...+.+.......||.|+|-.++-+.
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNVIITQ 103 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCceEEec
Confidence 3499999998875432223459999998776544
No 104
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.22 E-value=0.28 Score=35.23 Aligned_cols=39 Identities=26% Similarity=0.676 Sum_probs=30.6
Q ss_pred cccccccccccccCCceeEec-ccccccccchHHHhhcCCCCCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMP-CKHKFHGECIMPWLEVRSSCPV 255 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~ 255 (342)
...|.+|-+.|+.++++++-| |+-.+|+.|... ...|-+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~ 44 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN 44 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence 346999999998778888888 999999999533 445544
No 105
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.19 E-value=0.27 Score=45.10 Aligned_cols=40 Identities=33% Similarity=0.688 Sum_probs=30.8
Q ss_pred ccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCcccccCC
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
|-+|.+.=. .+..+||.|. +|..|-.. -..||+|+.....
T Consensus 161 Cr~C~~~~~---~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGEREA---TVLLLPCRHLCLCGICDES----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcCCc---eEEeecccceEeccccccc----CccCCCCcChhhc
Confidence 889987755 7999999987 88888643 4469999876543
No 106
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=88.05 E-value=0.33 Score=40.20 Aligned_cols=34 Identities=24% Similarity=0.654 Sum_probs=23.8
Q ss_pred CceeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 6 VGYWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 6 ~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
+.+||..|...+......-..||.|+|.-++-+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDMLRIVA 102 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCCcEEcc
Confidence 3399999998885332212669999988766544
No 107
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=87.12 E-value=0.29 Score=36.06 Aligned_cols=29 Identities=28% Similarity=0.605 Sum_probs=21.9
Q ss_pred eeccCceeecCCCCCccCCCCCCC-ceeccccC
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESG-IVEQMSSS 41 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sG-FvEE~~~~ 41 (342)
|+.|.+.+. ++.-+||.|+|- |.||-...
T Consensus 7 C~~Ck~l~~---~d~e~CP~Cgs~~~te~W~G~ 36 (64)
T COG2093 7 CKNCKRLTP---EDTEICPVCGSTDLTEEWFGL 36 (64)
T ss_pred HhhccccCC---CCCccCCCCCCcccchhhccE
Confidence 899998874 224579999996 88886543
No 108
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=86.50 E-value=0.3 Score=48.95 Aligned_cols=36 Identities=28% Similarity=0.638 Sum_probs=31.0
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHhhc
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV 249 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~ 249 (342)
++.+.|+||..-|. ++++|||+|..|..|...-+..
T Consensus 2 eeelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFYR---EPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhcc---CceEeecccHHHHHHHHhhccc
Confidence 46788999999999 8999999999999998866543
No 109
>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=86.44 E-value=0.44 Score=45.46 Aligned_cols=53 Identities=19% Similarity=0.584 Sum_probs=37.1
Q ss_pred cccccccccccCCcee--EecccccccccchHHHhhcCC-CCCCcccccCCCCccc
Q 043965 215 QCAVCLEEFEIGNEAK--EMPCKHKFHGECIMPWLEVRS-SCPVCRFQVPSDDFKI 267 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~--~lpC~H~Fh~~Ci~~Wl~~~~-~CP~CR~~l~~~~~~~ 267 (342)
.|++|....-.....+ .-+|+|..|..|....+.... .||.|-..+.......
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~ 57 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRV 57 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccch
Confidence 4888876543332332 336999999999999886554 8999988776555443
No 110
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.41 E-value=0.27 Score=53.24 Aligned_cols=37 Identities=24% Similarity=0.610 Sum_probs=30.0
Q ss_pred ccCcccccccccccccCCceeEecccccccccchHHHh
Q 043965 210 IDKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247 (342)
Q Consensus 210 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl 247 (342)
++....|.+|...+... .-...||||.||..||.+..
T Consensus 814 ~ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred ecCccchHHhcchhhcC-cceeeeccchHHHHHHHHHH
Confidence 45678899999988643 66677899999999998764
No 111
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.62 E-value=0.73 Score=31.66 Aligned_cols=32 Identities=31% Similarity=0.730 Sum_probs=24.0
Q ss_pred CCceeeeccCceeecCCC-CCccCCCCCCCcee
Q 043965 5 MVGYWCYICSQMVNPRME-AGIKCPFCESGIVE 36 (342)
Q Consensus 5 ~~~ywCh~C~~~V~p~~~-~e~~CP~C~sGFvE 36 (342)
|..|=|-.|...+..... ..++||+|++-++-
T Consensus 1 ~~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 1 MAEYKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred CCEEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 345889999998854332 26899999988774
No 112
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=85.37 E-value=0.66 Score=38.37 Aligned_cols=31 Identities=29% Similarity=0.786 Sum_probs=23.6
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
+||..|.....+. ...+.||.|+|.-++-+.
T Consensus 71 ~~C~~Cg~~~~~~-~~~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 71 AWCWDCSQVVEIH-QHDAQCPHCHGERLRVDT 101 (113)
T ss_pred EEcccCCCEEecC-CcCccCcCCCCCCcEEcc
Confidence 9999999888643 346779999987665543
No 113
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=85.36 E-value=0.41 Score=39.56 Aligned_cols=31 Identities=32% Similarity=0.538 Sum_probs=22.3
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
+||..|.....+... .+.||.|++..++-+.
T Consensus 71 ~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEF-DFSCPRCGSPDVEIIS 101 (113)
T ss_dssp EEETTTS-EEECHHC-CHH-SSSSSS-EEEEE
T ss_pred EECCCCCCEEecCCC-CCCCcCCcCCCcEEcc
Confidence 999999999975543 5889999998775544
No 114
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=85.00 E-value=0.57 Score=41.96 Aligned_cols=25 Identities=36% Similarity=0.930 Sum_probs=20.1
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceec
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
|||-.|+-++. .-.|+-|+++|-|-
T Consensus 15 yWCe~cNlPl~-----~~~c~~cg~~~~~l 39 (202)
T COG5270 15 YWCEKCNLPLL-----GRRCSVCGSKVEEL 39 (202)
T ss_pred eehhhCCCccc-----cccccccCCcceEE
Confidence 99999998773 45899999776544
No 115
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=84.91 E-value=0.58 Score=45.27 Aligned_cols=44 Identities=27% Similarity=0.697 Sum_probs=34.0
Q ss_pred cCcccccccccccccCCceeEecc--cccccccchHHHhhcCCCCCCcccccC
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPC--KHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC--~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
.+-++|+||.+.+. .+ ++.| ||.-|..|-. +..+.||.||.++.
T Consensus 46 ~~lleCPvC~~~l~---~P-i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLS---PP-IFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhhccCchhhccCc---cc-ceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 35578999999988 33 3446 6888888865 46779999999886
No 116
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.54 E-value=0.74 Score=31.66 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=23.5
Q ss_pred ceeeeccCceeecCCCCCccCCCCCCCce
Q 043965 7 GYWCYICSQMVNPRMEAGIKCPFCESGIV 35 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~~~e~~CP~C~sGFv 35 (342)
.|=|-.|..+|.......+.||+|++--+
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEE
Confidence 48899999999866556799999997533
No 117
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.36 E-value=0.58 Score=46.84 Aligned_cols=38 Identities=26% Similarity=0.721 Sum_probs=28.1
Q ss_pred cccccccc-cccccCCceeEecccccccccchHHHhhcC
Q 043965 213 NLQCAVCL-EEFEIGNEAKEMPCKHKFHGECIMPWLEVR 250 (342)
Q Consensus 213 ~~~C~ICl-e~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (342)
..+|.||. +............|+|.||..|+.+.++.+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~ 184 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK 184 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence 56899999 444433344456699999999999988644
No 118
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.05 E-value=0.8 Score=39.08 Aligned_cols=33 Identities=27% Similarity=0.389 Sum_probs=23.6
Q ss_pred ceeeeccCceeecCC--------------------CCCccCCCCCCCceeccc
Q 043965 7 GYWCYICSQMVNPRM--------------------EAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~--------------------~~e~~CP~C~sGFvEE~~ 39 (342)
.|||..|...+.... ...+.||.|++.-++-+.
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 399999998876431 234779999987665443
No 119
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=83.95 E-value=0.28 Score=52.05 Aligned_cols=49 Identities=29% Similarity=0.734 Sum_probs=39.0
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcC---CCCCCcccccCCC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR---SSCPVCRFQVPSD 263 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~~CP~CR~~l~~~ 263 (342)
...+|+||+..+. .+..+.|.|.|+..|+..-|... ..||+|+..+...
T Consensus 20 k~lEc~ic~~~~~---~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 20 KILECPICLEHVK---EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hhccCCceeEEee---ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 3578999999998 55788899999999997766444 3799999766544
No 120
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=83.90 E-value=0.48 Score=50.52 Aligned_cols=39 Identities=31% Similarity=0.749 Sum_probs=28.5
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCCCCCC
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPV 255 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~ 255 (342)
|.||--.+. +.......|+|+.|..|...|++....||.
T Consensus 1031 C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 444433322 334456679999999999999999999985
No 121
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=80.86 E-value=0.99 Score=37.93 Aligned_cols=32 Identities=19% Similarity=0.369 Sum_probs=22.2
Q ss_pred ceeeeccCceeecCCCC------CccCCCCCCCceeccc
Q 043965 7 GYWCYICSQMVNPRMEA------GIKCPFCESGIVEQMS 39 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~~~------e~~CP~C~sGFvEE~~ 39 (342)
.+|| .|.....+.... -+.||.|+|..++-+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 3999 999886533110 1569999998876554
No 122
>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=80.61 E-value=1.5 Score=28.12 Aligned_cols=26 Identities=31% Similarity=0.660 Sum_probs=19.7
Q ss_pred eeeeccCceeecCCCCCccCCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
|-|-.|..+|.....+.+.||.|+.-
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCe
Confidence 77999999998555567999999853
No 123
>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=80.33 E-value=1.5 Score=28.89 Aligned_cols=25 Identities=24% Similarity=0.586 Sum_probs=19.2
Q ss_pred eeeeccCceeecCC----CCCccCCCCCC
Q 043965 8 YWCYICSQMVNPRM----EAGIKCPFCES 32 (342)
Q Consensus 8 ywCh~C~~~V~p~~----~~e~~CP~C~s 32 (342)
|-|..|...+.... +..+.||.|++
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 99999999764332 34588999998
No 124
>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=79.01 E-value=1.6 Score=30.80 Aligned_cols=43 Identities=23% Similarity=0.590 Sum_probs=20.5
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcC---C--CCCCcccc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR---S--SCPVCRFQ 259 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~---~--~CP~CR~~ 259 (342)
+.|+|....+. ..++...|.|.-|.+ +..||... . .||+|.++
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 46999988877 245555699986543 34565322 2 69999763
No 125
>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=78.30 E-value=0.59 Score=33.74 Aligned_cols=27 Identities=22% Similarity=0.658 Sum_probs=17.6
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCcee
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVE 36 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvE 36 (342)
|=|--|..=+.-.+ .-+||.|+|+||.
T Consensus 27 fECTFC~~C~e~~l--~~~CPNCgGelv~ 53 (57)
T PF06906_consen 27 FECTFCADCAETML--NGVCPNCGGELVR 53 (57)
T ss_pred EeCcccHHHHHHHh--cCcCcCCCCcccc
Confidence 55555554443222 5789999999984
No 126
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=76.85 E-value=1.2 Score=48.02 Aligned_cols=54 Identities=28% Similarity=0.706 Sum_probs=39.8
Q ss_pred CcccccccccccccCCceeEecccc-----cccccchHHHhhcCC--CCCCcccccCCCCcc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKH-----KFHGECIMPWLEVRS--SCPVCRFQVPSDDFK 266 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H-----~Fh~~Ci~~Wl~~~~--~CP~CR~~l~~~~~~ 266 (342)
++..|-||..+=.. +.+..-||+. ..|..|+..|+.-.. .|-+|+.++.-++.-
T Consensus 11 d~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY 71 (1175)
T COG5183 11 DKRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIY 71 (1175)
T ss_pred cchhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeec
Confidence 34689999877543 3555667763 479999999997444 799999988766543
No 127
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.77 E-value=1.7 Score=31.80 Aligned_cols=32 Identities=25% Similarity=0.551 Sum_probs=20.2
Q ss_pred CCCCCCceeeeccCceeecCC-CCCccCCCCCC
Q 043965 1 MGDAMVGYWCYICSQMVNPRM-EAGIKCPFCES 32 (342)
Q Consensus 1 m~~~~~~ywCh~C~~~V~p~~-~~e~~CP~C~s 32 (342)
|.+.+..+-|-.|.+.|.|.- .....||.|+.
T Consensus 1 ~~~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 1 ISEMMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred CcccccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 445555577777777776554 34567777754
No 128
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.54 E-value=0.82 Score=42.97 Aligned_cols=52 Identities=25% Similarity=0.567 Sum_probs=35.4
Q ss_pred CcccccccccccccCCce-eEeccc-----ccccccchHHHhhcCC--------CCCCcccccCCC
Q 043965 212 KNLQCAVCLEEFEIGNEA-KEMPCK-----HKFHGECIMPWLEVRS--------SCPVCRFQVPSD 263 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~-~~lpC~-----H~Fh~~Ci~~Wl~~~~--------~CP~CR~~l~~~ 263 (342)
.+..|-||+..=+..... -.-||. |.-|..|+..|+..+. +||-|+.+....
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv 84 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIV 84 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheee
Confidence 355799998875432222 234553 8899999999995433 699999876543
No 129
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.15 E-value=0.9 Score=43.45 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=25.0
Q ss_pred ccccccccchHHHhh-------------cCCCCCCcccccCCCCc
Q 043965 234 CKHKFHGECIMPWLE-------------VRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 234 C~H~Fh~~Ci~~Wl~-------------~~~~CP~CR~~l~~~~~ 265 (342)
|...+|..|+-+|+. .+-+||.||+.+...+.
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv 369 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDV 369 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeee
Confidence 677889999999874 23379999999876554
No 130
>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=75.28 E-value=1.2 Score=41.43 Aligned_cols=48 Identities=23% Similarity=0.574 Sum_probs=35.6
Q ss_pred cccccccccccccCCceeE--ec-ccccccccchHHHhhcCC-CCC--Cccccc
Q 043965 213 NLQCAVCLEEFEIGNEAKE--MP-CKHKFHGECIMPWLEVRS-SCP--VCRFQV 260 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~--lp-C~H~Fh~~Ci~~Wl~~~~-~CP--~CR~~l 260 (342)
+..|+||..+--....++. -| |-|..|..|+.+.+.... .|| -|-+-|
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 4579999876544334433 35 999999999999987665 899 786544
No 131
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=72.45 E-value=2.4 Score=45.43 Aligned_cols=41 Identities=24% Similarity=0.468 Sum_probs=30.8
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCC
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPV 255 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~ 255 (342)
..|.+|-..+. |..+-.--|+|.-|..|+.+|+..+.-||.
T Consensus 780 ~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred cCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 36888877765 222222239999999999999999998887
No 132
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=72.21 E-value=1.7 Score=43.66 Aligned_cols=25 Identities=20% Similarity=0.539 Sum_probs=20.1
Q ss_pred eccCceeecCCCCCccCCCCCCCceeccc
Q 043965 11 YICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 11 h~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
|.|.|.|. .||+||.|+.-|-.=-+
T Consensus 286 HrC~RIV~----vEYrCPEC~KVFsCPAN 310 (500)
T KOG3993|consen 286 HRCPRIVH----VEYRCPECDKVFSCPAN 310 (500)
T ss_pred ccCCeeEE----eeecCCcccccccCchh
Confidence 77888885 48999999999976543
No 133
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=71.93 E-value=1.9 Score=25.40 Aligned_cols=22 Identities=23% Similarity=0.720 Sum_probs=17.4
Q ss_pred eeeccCceeecCCCCCccCCCCCCC
Q 043965 9 WCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 9 wCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
||..|-.+|. +...+||.|+.-
T Consensus 1 ~Cp~CG~~~~---~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIE---DDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCC---CcCcchhhhCCc
Confidence 6899999995 236789999864
No 134
>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=71.19 E-value=0.87 Score=31.54 Aligned_cols=44 Identities=30% Similarity=0.565 Sum_probs=28.6
Q ss_pred cccccccccccCCceeEecccccccccchHHHhh------cCCCCCCccc
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLE------VRSSCPVCRF 258 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~------~~~~CP~CR~ 258 (342)
.|.||......+..+.--.|+..||..|+..-.. ..-.||.|+.
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 3889988444333343445999999999965432 1236888853
No 135
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.03 E-value=2.5 Score=40.36 Aligned_cols=36 Identities=28% Similarity=0.599 Sum_probs=28.3
Q ss_pred cccccccccccccCCceeEecc----cccccccchHHHhhcCC
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPC----KHKFHGECIMPWLEVRS 251 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC----~H~Fh~~Ci~~Wl~~~~ 251 (342)
.+.|.+|.|.++ +.-.+.| .|.||..|-..-++.+.
T Consensus 268 pLcCTLC~ERLE---DTHFVQCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 268 PLCCTLCHERLE---DTHFVQCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred ceeehhhhhhhc---cCceeecCCCcccceecccCHHHHHhhc
Confidence 478999999998 3344445 79999999999887654
No 136
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=69.83 E-value=1.8 Score=41.17 Aligned_cols=53 Identities=25% Similarity=0.517 Sum_probs=37.6
Q ss_pred cccccccccccccCCc-eeEeccc-----ccccccchHHHhh--cCCCCCCcccccCCCCc
Q 043965 213 NLQCAVCLEEFEIGNE-AKEMPCK-----HKFHGECIMPWLE--VRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~-~~~lpC~-----H~Fh~~Ci~~Wl~--~~~~CP~CR~~l~~~~~ 265 (342)
...|-||.++...... ....||. +..|..|+..|+. ....|-+|.........
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~ 138 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGT 138 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecce
Confidence 3579999997653221 4566764 5679999999997 44489999886655433
No 137
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.36 E-value=2.5 Score=44.23 Aligned_cols=47 Identities=40% Similarity=0.966 Sum_probs=38.4
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCCc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDF 265 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~ 265 (342)
....|.||+... ..+..+|. |..|+.+|+..+..||+|+..+..++.
T Consensus 478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~ 524 (543)
T KOG0802|consen 478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDF 524 (543)
T ss_pred ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhcccc
Confidence 356799999987 44666788 899999999999999999988766543
No 138
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=68.82 E-value=2.9 Score=40.51 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=36.1
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCC---CCCCccc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS---SCPVCRF 258 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~---~CP~CR~ 258 (342)
.-+.|||-.+.-.....++.|.|||+.-..-+...-+... .||.|-.
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 3478999888777777899999999998887776544332 6999943
No 139
>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=68.26 E-value=2.9 Score=25.46 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=18.1
Q ss_pred eeccCceeecCCCCCccCCCCCCCce
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESGIV 35 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sGFv 35 (342)
|-.|..+|. . ...+||+|+=-|.
T Consensus 3 CP~C~~~V~-~--~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVP-E--SAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCch-h--hcCcCCCCCCCCc
Confidence 778999994 2 3678999998774
No 140
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.06 E-value=2.7 Score=42.10 Aligned_cols=43 Identities=26% Similarity=0.532 Sum_probs=31.4
Q ss_pred ccccccccccccCCce--eEecccccccccchHHHhhcCCCCCCc
Q 043965 214 LQCAVCLEEFEIGNEA--KEMPCKHKFHGECIMPWLEVRSSCPVC 256 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~--~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (342)
..|++|.-.++..... ..-.|+|.||+.|...|......|..|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 5699888776644433 333499999999999998777766555
No 141
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.04 E-value=1.6 Score=45.93 Aligned_cols=44 Identities=30% Similarity=0.698 Sum_probs=32.9
Q ss_pred CcccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 212 KNLQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
+-+.|.||+..|-... .++.+-|||+.|..|+..- .+.+|| |++
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 3467999988886433 5677789999999998764 355788 544
No 142
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=67.45 E-value=1.8 Score=45.47 Aligned_cols=43 Identities=28% Similarity=0.699 Sum_probs=27.7
Q ss_pred ccccccccc-----ccccCCceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 213 NLQCAVCLE-----EFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle-----~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
...|.||.. .|+.....+...|+++||..|+.. ....||.|-.
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~R 558 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCER 558 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchHH
Confidence 467888832 232233345556999999999644 4445999943
No 143
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.10 E-value=3.9 Score=36.54 Aligned_cols=30 Identities=30% Similarity=0.638 Sum_probs=23.6
Q ss_pred ceeeeccCceeec--CCCCCccCCCCCCCcee
Q 043965 7 GYWCYICSQMVNP--RMEAGIKCPFCESGIVE 36 (342)
Q Consensus 7 ~ywCh~C~~~V~p--~~~~e~~CP~C~sGFvE 36 (342)
.|.|-.|...++- +++.+.+||.|++-.+|
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 3999999988842 24568999999987766
No 144
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=66.69 E-value=2.2 Score=45.96 Aligned_cols=54 Identities=15% Similarity=0.111 Sum_probs=37.3
Q ss_pred cccccccccccccCC-ceeEec---ccccccccchHHHhhc------CCCCCCcccccCCCCcc
Q 043965 213 NLQCAVCLEEFEIGN-EAKEMP---CKHKFHGECIMPWLEV------RSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 213 ~~~C~ICle~~~~~~-~~~~lp---C~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~~~~ 266 (342)
...|.||.-++...+ ..-.+| |.|.||..||..|+.+ +-.|++|..-|..+...
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~ 159 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC 159 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh
Confidence 356777777766411 233444 9999999999999842 33799998888766543
No 145
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=65.71 E-value=5.1 Score=39.06 Aligned_cols=47 Identities=23% Similarity=0.428 Sum_probs=33.8
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
....|-.|.+........+.-.|++.||.+|-.-.-+.-..||-|..
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 34569999888775555555569999999996543344457999963
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=65.08 E-value=6 Score=26.66 Aligned_cols=26 Identities=31% Similarity=0.644 Sum_probs=18.4
Q ss_pred eeeeccCceeecC---CC-CCccCCCCCCC
Q 043965 8 YWCYICSQMVNPR---ME-AGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~---~~-~e~~CP~C~sG 33 (342)
|-|-.|....... .+ ..+.||.|++.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 8999999654322 22 46899999983
No 147
>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 PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=62.20 E-value=3.9 Score=26.34 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=19.7
Q ss_pred eeeeccCceeec-CCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNP-RMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p-~~~~e~~CP~C~sGF 34 (342)
+=|..|...... .....++|++|+.-|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 448889888754 344569999998755
No 149
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=61.54 E-value=5 Score=36.49 Aligned_cols=41 Identities=32% Similarity=0.831 Sum_probs=27.8
Q ss_pred cccccccccc-----cccCCceeEecccccccccchHHHhhcCCCCCCccc
Q 043965 213 NLQCAVCLEE-----FEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle~-----~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
...|-||-.. |......+.-.|+-+||..|.. ...||.|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 5678899752 3332233444599999999975 267999954
No 150
>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=58.54 E-value=5.2 Score=34.99 Aligned_cols=32 Identities=19% Similarity=0.423 Sum_probs=23.3
Q ss_pred eeeeccCceeec--CCCCCccCCCCCCCceecccc
Q 043965 8 YWCYICSQMVNP--RMEAGIKCPFCESGIVEQMSS 40 (342)
Q Consensus 8 ywCh~C~~~V~p--~~~~e~~CP~C~sGFvEE~~~ 40 (342)
|.|-.|...++- ++..+.+||.|++- ++++++
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~-L~~~dn 143 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGAM-LDYLDN 143 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCCE-eeeccC
Confidence 999999988742 23468999999976 444443
No 151
>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=58.02 E-value=4.1 Score=25.39 Aligned_cols=22 Identities=23% Similarity=0.818 Sum_probs=17.5
Q ss_pred eeeeccCceeecCCCCCccCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCE 31 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~ 31 (342)
|||..|.+++.... -+.|-.|.
T Consensus 1 ~~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE--eEEeCCCC
Confidence 79999999997442 67888887
No 152
>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=57.46 E-value=4.5 Score=26.58 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.1
Q ss_pred CCccCCCCCCC
Q 043965 23 AGIKCPFCESG 33 (342)
Q Consensus 23 ~e~~CP~C~sG 33 (342)
.+++||+|++-
T Consensus 4 i~v~CP~C~s~ 14 (36)
T PF03811_consen 4 IDVHCPRCQST 14 (36)
T ss_pred EeeeCCCCCCC
Confidence 47899999983
No 153
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.81 E-value=6.3 Score=42.56 Aligned_cols=48 Identities=23% Similarity=0.479 Sum_probs=33.7
Q ss_pred ccccCcccccccccccccC----CceeEecccccccccchHHHhhcCCCCCCc
Q 043965 208 VTIDKNLQCAVCLEEFEIG----NEAKEMPCKHKFHGECIMPWLEVRSSCPVC 256 (342)
Q Consensus 208 ~~~~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~C 256 (342)
+.+..+..|.-|.+..... +.++.+.|+|.||..|+.--..+.. |-.|
T Consensus 779 v~v~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 779 VLVSVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred eeEeehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 3344456799999887533 3677888999999999976554443 5555
No 154
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=56.51 E-value=6.9 Score=37.95 Aligned_cols=21 Identities=29% Similarity=0.577 Sum_probs=16.6
Q ss_pred eeeeccCceeecCCCCCccCCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
-+||.|...-+ +|+||+|+=-
T Consensus 8 ~~C~ic~vq~~-----~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKR-----EYTCPRCNLL 28 (383)
T ss_pred eeccccccccc-----cccCCCCCcc
Confidence 78999986553 6999999743
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=55.57 E-value=7 Score=27.03 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=20.8
Q ss_pred eeeccCceeecCCC---CCccCCCCCCCceeccc
Q 043965 9 WCYICSQMVNPRME---AGIKCPFCESGIVEQMS 39 (342)
Q Consensus 9 wCh~C~~~V~p~~~---~e~~CP~C~sGFvEE~~ 39 (342)
||-.|..++.+... ..++||.|+ |++.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg--~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG--YEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC--CeEECC
Confidence 79999998866533 148899998 555554
No 156
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.45 E-value=5.7 Score=23.91 Aligned_cols=23 Identities=22% Similarity=0.652 Sum_probs=16.7
Q ss_pred eeeeccCceeecCCCCCccCCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
..|..|...|. ..+-.||+|+.-
T Consensus 3 ~~Cp~Cg~~~~---~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID---PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC---cccccChhhCCC
Confidence 36889998663 347889999853
No 157
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=54.94 E-value=5.7 Score=36.45 Aligned_cols=45 Identities=24% Similarity=0.530 Sum_probs=36.1
Q ss_pred ccccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (342)
..|.+|...... ..+.-.|+-.+|..|+...+.....||.|..-.
T Consensus 182 k~Cn~Ch~LvIq--g~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w 226 (235)
T KOG4718|consen 182 KNCNLCHCLVIQ--GIRCGSCNIQYHRGCIQTYLQRRDICPHCGDLW 226 (235)
T ss_pred HHHhHhHHHhhe--eeccCcccchhhhHHHHHHhcccCcCCchhccc
Confidence 579999988762 334455888999999999999999999995443
No 158
>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=54.49 E-value=7.8 Score=29.64 Aligned_cols=30 Identities=23% Similarity=0.604 Sum_probs=14.4
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
++||.|-.... .+ .-..||.|+..=+.-+.
T Consensus 10 lrC~aCf~~t~-~~-~k~FCp~CGn~TL~rvs 39 (73)
T PF08772_consen 10 LRCHACFKITK-DM-TKQFCPKCGNATLKRVS 39 (73)
T ss_dssp EE-SSS--EES--S-S--S-SSS--S--EEEE
T ss_pred EEccccccCcC-CC-CceeCcccCCCcceEEE
Confidence 79999999885 33 36899999987666554
No 159
>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=54.29 E-value=7 Score=27.61 Aligned_cols=12 Identities=33% Similarity=1.196 Sum_probs=8.6
Q ss_pred CccCCCCCCCce
Q 043965 24 GIKCPFCESGIV 35 (342)
Q Consensus 24 e~~CP~C~sGFv 35 (342)
.++||+|+.+|-
T Consensus 2 ~f~CP~C~~~~~ 13 (54)
T PF05605_consen 2 SFTCPYCGKGFS 13 (54)
T ss_pred CcCCCCCCCccC
Confidence 477888887653
No 160
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=54.09 E-value=12 Score=36.52 Aligned_cols=48 Identities=21% Similarity=0.539 Sum_probs=35.5
Q ss_pred ccccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCcccccC
Q 043965 214 LQCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~ 261 (342)
..|+||.+.....+ ...-.||++..|..|+..-...+..||.||.+..
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 57999999874332 3333448888888888887788889999995544
No 161
>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=53.34 E-value=3.2 Score=39.71 Aligned_cols=46 Identities=22% Similarity=0.293 Sum_probs=21.2
Q ss_pred cccccccccccccCCceeEe--cccccccccchHHHhhcCCCCCCccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEM--PCKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~l--pC~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
...|+||-..-..+.-...- --.|.+|..|-..|-.....||.|-.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 46899998775421100000 02567888999999888889999954
No 162
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=52.89 E-value=7.1 Score=29.08 Aligned_cols=18 Identities=22% Similarity=0.687 Sum_probs=14.8
Q ss_pred eeccCceeecCCCCCccCCCCCC
Q 043965 10 CYICSQMVNPRMEAGIKCPFCES 32 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~s 32 (342)
|..|++.+. +-+||.|++
T Consensus 8 C~~C~~i~~-----~~~Cp~Cgs 25 (64)
T PRK06393 8 CKKCKRLTP-----EKTCPVHGD 25 (64)
T ss_pred HhhCCcccC-----CCcCCCCCC
Confidence 888988873 449999999
No 163
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.48 E-value=5.4 Score=40.62 Aligned_cols=36 Identities=28% Similarity=0.707 Sum_probs=29.6
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEV 249 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~ 249 (342)
....|.||.+.+.. ....+.|+|.||..|+...+..
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 45689999999873 4667789999999999888854
No 164
>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=52.14 E-value=8.8 Score=27.28 Aligned_cols=42 Identities=31% Similarity=0.647 Sum_probs=20.8
Q ss_pred ccccccccccCC------ceeEec-ccccccccchHHHhhcCCCCCCcc
Q 043965 216 CAVCLEEFEIGN------EAKEMP-CKHKFHGECIMPWLEVRSSCPVCR 257 (342)
Q Consensus 216 C~ICle~~~~~~------~~~~lp-C~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (342)
|.-|+..|.... ....-+ |++.||.+|=.=--+.-..||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 666777776432 233444 999999999543223334799883
No 165
>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=51.14 E-value=20 Score=26.04 Aligned_cols=46 Identities=22% Similarity=0.490 Sum_probs=32.5
Q ss_pred cccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCcccccCC
Q 043965 215 QCAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPS 262 (342)
Q Consensus 215 ~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~ 262 (342)
.|-.|-.++.... .+.+-.=...||..|....| +..||.|-..|..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCcccc
Confidence 4777777777554 34443334579999998876 7899999877654
No 166
>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=50.96 E-value=12 Score=27.52 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=18.4
Q ss_pred CcccccccccccccCCceeEe-cccccccccchHHHh
Q 043965 212 KNLQCAVCLEEFEIGNEAKEM-PCKHKFHGECIMPWL 247 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~Wl 247 (342)
+...|.+|...|..-.....- .||++||..|.....
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 456799999999743333333 399999999987654
No 167
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.62 E-value=21 Score=34.52 Aligned_cols=50 Identities=20% Similarity=0.499 Sum_probs=38.5
Q ss_pred CcccccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCC
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSD 263 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~ 263 (342)
....|-||...+.... +.--|.|.|+..|...|......||.|+......
T Consensus 104 ~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~pv 153 (324)
T KOG0824|consen 104 DHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKISPV 153 (324)
T ss_pred CccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCcCce
Confidence 3467999998887322 2222999999999999999999999998765433
No 168
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.83 E-value=8.9 Score=36.06 Aligned_cols=34 Identities=18% Similarity=0.294 Sum_probs=29.9
Q ss_pred cCcccccccccccccCCceeEecccccccccchHHHh
Q 043965 211 DKNLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247 (342)
Q Consensus 211 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl 247 (342)
..-..|..||..+. .+++.|=||+|++.||.+.+
T Consensus 41 K~FdcCsLtLqPc~---dPvit~~GylfdrEaILe~i 74 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCR---DPVITPDGYLFDREAILEYI 74 (303)
T ss_pred CCcceeeeeccccc---CCccCCCCeeeeHHHHHHHH
Confidence 34467999999998 88999999999999999876
No 169
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=49.78 E-value=9.2 Score=28.23 Aligned_cols=18 Identities=33% Similarity=0.931 Sum_probs=14.5
Q ss_pred eeccCceeecCCCCCccCCCCCC
Q 043965 10 CYICSQMVNPRMEAGIKCPFCES 32 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~s 32 (342)
|..|+..+. +-+||.|++
T Consensus 6 C~~C~~i~~-----~~~CP~Cgs 23 (61)
T PRK08351 6 CRHCHYITT-----EDRCPVCGS 23 (61)
T ss_pred hhhCCcccC-----CCcCCCCcC
Confidence 888988773 337999998
No 170
>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=48.69 E-value=17 Score=25.19 Aligned_cols=31 Identities=19% Similarity=0.514 Sum_probs=21.3
Q ss_pred eeeeccCceeecCC--C--CCccCCCCCCCceecc
Q 043965 8 YWCYICSQMVNPRM--E--AGIKCPFCESGIVEQM 38 (342)
Q Consensus 8 ywCh~C~~~V~p~~--~--~e~~CP~C~sGFvEE~ 38 (342)
|-|-.|......+. . ..+.||.|++.=++.+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 99999999654332 1 3478999999544444
No 171
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.61 E-value=7.3 Score=28.70 Aligned_cols=13 Identities=23% Similarity=0.892 Sum_probs=10.7
Q ss_pred CCccCCCCCCCce
Q 043965 23 AGIKCPFCESGIV 35 (342)
Q Consensus 23 ~e~~CP~C~sGFv 35 (342)
.|++||+|+.-|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 5799999997664
No 172
>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=48.42 E-value=13 Score=30.51 Aligned_cols=30 Identities=20% Similarity=0.383 Sum_probs=23.9
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceec
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
.-|..|.....=+.-.-|+||+|+.-|.-+
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 789999887754444468899999999877
No 173
>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=46.80 E-value=4.8 Score=28.58 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=18.0
Q ss_pred eeeeccCceeecC---CCCCccCCCCCC
Q 043965 8 YWCYICSQMVNPR---MEAGIKCPFCES 32 (342)
Q Consensus 8 ywCh~C~~~V~p~---~~~e~~CP~C~s 32 (342)
+=|-.|++-+--. ..-+||||+|..
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 6688898876321 124799999986
No 174
>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=45.96 E-value=8 Score=28.94 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=8.7
Q ss_pred cccccchHHHhh
Q 043965 237 KFHGECIMPWLE 248 (342)
Q Consensus 237 ~Fh~~Ci~~Wl~ 248 (342)
-||+.|+.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999985
No 175
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=45.84 E-value=9.3 Score=36.28 Aligned_cols=47 Identities=26% Similarity=0.576 Sum_probs=31.6
Q ss_pred ccccccccccc-cCCceeEec---ccccccccchHHHh-h--------cCCCCCCccccc
Q 043965 214 LQCAVCLEEFE-IGNEAKEMP---CKHKFHGECIMPWL-E--------VRSSCPVCRFQV 260 (342)
Q Consensus 214 ~~C~ICle~~~-~~~~~~~lp---C~H~Fh~~Ci~~Wl-~--------~~~~CP~CR~~l 260 (342)
..|-+|.+.+. .+.....-+ |.-++|..|+-.-+ . ....||.|++.+
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 57999999984 222222222 88889999998843 2 223799998854
No 176
>PF07860 CCD: WisP family C-Terminal Region; InterPro: IPR012421 This entry represents the C-terminal domain found in the Tropheryma whipplei WisP family of proteins [].
Probab=44.13 E-value=12 Score=30.44 Aligned_cols=32 Identities=31% Similarity=0.718 Sum_probs=23.3
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 043965 303 YWIPIPWPFDSLFSMSGSQEGGTSNSESSSVG 334 (342)
Q Consensus 303 ~~~s~p~Pf~~~f~~~~~~s~~~s~~~s~s~~ 334 (342)
.|--+-|||+-+|++.+...++..+..+.+.|
T Consensus 51 iwhgitwpfrklfgsrseapssttnatgntng 82 (141)
T PF07860_consen 51 IWHGITWPFRKLFGSRSEAPSSTTNATGNTNG 82 (141)
T ss_pred hhhcccchHHHHhCCcccCCcccccCccCcCC
Confidence 35668999999999887776666555555544
No 177
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.95 E-value=14 Score=34.81 Aligned_cols=51 Identities=22% Similarity=0.263 Sum_probs=35.5
Q ss_pred ccccccccccccCCc-eeEecccccccccchHHHhhcCCCCCCcccccCCCCcc
Q 043965 214 LQCAVCLEEFEIGNE-AKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDDFK 266 (342)
Q Consensus 214 ~~C~ICle~~~~~~~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~~~ 266 (342)
+.|+|---+|...-. ....+|||+|-..-+.+. ...+|++|...+..++..
T Consensus 112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvI 163 (293)
T KOG3113|consen 112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVI 163 (293)
T ss_pred eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeE
Confidence 579987666652222 334569999988776653 366899999988877654
No 178
>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=43.94 E-value=12 Score=37.63 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=19.2
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
.=||.|...+.+ ++...||+|+.--
T Consensus 216 ~~C~~Cd~~~~~--~~~a~CpRC~~~L 240 (403)
T TIGR00155 216 RSCSACHTTILP--AQEPVCPRCSTPL 240 (403)
T ss_pred CcCCCCCCccCC--CCCcCCcCCCCcc
Confidence 449999997743 4578899999754
No 179
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=43.58 E-value=11 Score=35.56 Aligned_cols=26 Identities=27% Similarity=0.642 Sum_probs=20.7
Q ss_pred eeccCceeecCCC------CCccCCCCCCCce
Q 043965 10 CYICSQMVNPRME------AGIKCPFCESGIV 35 (342)
Q Consensus 10 Ch~C~~~V~p~~~------~e~~CP~C~sGFv 35 (342)
|+.|.+...|+.. .|+.||.|.--|-
T Consensus 135 Cr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 135 CRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccccccCCCccccccceeeeecccccccch
Confidence 8889888877642 5899999998664
No 180
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.51 E-value=27 Score=28.98 Aligned_cols=44 Identities=25% Similarity=0.366 Sum_probs=31.8
Q ss_pred ccccccccccccCC----------c-eeEecccccccccchHHHhhcCCCCCCcc
Q 043965 214 LQCAVCLEEFEIGN----------E-AKEMPCKHKFHGECIMPWLEVRSSCPVCR 257 (342)
Q Consensus 214 ~~C~ICle~~~~~~----------~-~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR 257 (342)
..|--|+..|.... . .....|++.||.+|-.-+-+.-..||-|.
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 45999988876321 1 12334999999999887777777899995
No 181
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=43.26 E-value=10 Score=24.86 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=7.7
Q ss_pred ccCCCCCCCce
Q 043965 25 IKCPFCESGIV 35 (342)
Q Consensus 25 ~~CP~C~sGFv 35 (342)
++||.|+..|-
T Consensus 3 i~CP~C~~~f~ 13 (37)
T PF13719_consen 3 ITCPNCQTRFR 13 (37)
T ss_pred EECCCCCceEE
Confidence 56777777663
No 182
>PRK12495 hypothetical protein; Provisional
Probab=43.22 E-value=13 Score=34.37 Aligned_cols=31 Identities=26% Similarity=0.571 Sum_probs=24.3
Q ss_pred CCceeeeccCceeecCCCCCccCCCCCCCcee
Q 043965 5 MVGYWCYICSQMVNPRMEAGIKCPFCESGIVE 36 (342)
Q Consensus 5 ~~~ywCh~C~~~V~p~~~~e~~CP~C~sGFvE 36 (342)
|..|+|-.|-.+|- .++..++||.|+.-+-+
T Consensus 40 msa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF-RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc-CCCCeeECCCCCCcccc
Confidence 33499999999995 55668999999965553
No 183
>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=42.88 E-value=22 Score=22.23 Aligned_cols=36 Identities=25% Similarity=0.512 Sum_probs=23.1
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCCCCCCccccc
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQV 260 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (342)
|..|.+.+...+ .....=+..||..|. .|..|...|
T Consensus 2 C~~C~~~i~~~~-~~~~~~~~~~H~~Cf--------~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGE-LVLRALGKVWHPECF--------KCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCc-EEEEeCCccccccCC--------CCcccCCcC
Confidence 778888776432 222224677888775 677887665
No 184
>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=42.67 E-value=18 Score=30.62 Aligned_cols=30 Identities=7% Similarity=0.015 Sum_probs=24.2
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceec
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
.-|..|.....=+.-..++||+|+.-|-.+
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 889999988764544579999999988766
No 185
>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=41.99 E-value=22 Score=24.74 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=27.1
Q ss_pred ccccccccccCCceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 216 CAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 216 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
|..|...+... ......-+..||..|. .|-.|+..|....
T Consensus 1 C~~C~~~I~~~-~~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT-EIVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS-SEEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc-EEEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 67787877733 2222346788998875 6888888886554
No 186
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.49 E-value=9.6 Score=24.71 Aligned_cols=23 Identities=26% Similarity=0.804 Sum_probs=11.8
Q ss_pred eeeccCceeecCCC--CC---ccCCCCC
Q 043965 9 WCYICSQMVNPRME--AG---IKCPFCE 31 (342)
Q Consensus 9 wCh~C~~~V~p~~~--~e---~~CP~C~ 31 (342)
||-+|-..+..... ++ .+||.|+
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 78889888754432 22 7899885
No 187
>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=41.03 E-value=18 Score=24.46 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=16.9
Q ss_pred eeeeccCceeecCCCCCccCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCE 31 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~ 31 (342)
-.|..|..+.-...+.++.||.|+
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCCC
Confidence 679999766543234479999995
No 188
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=40.48 E-value=17 Score=25.73 Aligned_cols=30 Identities=23% Similarity=0.511 Sum_probs=22.4
Q ss_pred eeee--ccCceeecC---CCCCccCCCCCCCceec
Q 043965 8 YWCY--ICSQMVNPR---MEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 8 ywCh--~C~~~V~p~---~~~e~~CP~C~sGFvEE 37 (342)
=||. .|...|... ....++||.|+--|.-.
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 6999 999888654 23458899999888643
No 189
>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=40.44 E-value=15 Score=24.68 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=8.9
Q ss_pred ccCCCCCCCce
Q 043965 25 IKCPFCESGIV 35 (342)
Q Consensus 25 ~~CP~C~sGFv 35 (342)
++||.|++..|
T Consensus 1 m~Cp~Cg~~~~ 11 (43)
T PF08271_consen 1 MKCPNCGSKEI 11 (43)
T ss_dssp ESBTTTSSSEE
T ss_pred CCCcCCcCCce
Confidence 47999999874
No 190
>PHA00616 hypothetical protein
Probab=38.97 E-value=8.4 Score=26.53 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=10.5
Q ss_pred ccCCCCCCCceec
Q 043965 25 IKCPFCESGIVEQ 37 (342)
Q Consensus 25 ~~CP~C~sGFvEE 37 (342)
+.||+|+..|+.-
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 5799999999753
No 191
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=38.77 E-value=17 Score=24.16 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=19.5
Q ss_pred eeccCceeecCCCCCccCCCCCCCceec
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
|+.|.+.+. ++ -++|.+|+.-|-.+
T Consensus 1 C~~C~~~~~-l~--~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVG-LT--GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccc-cc--CeECCccCCccccc
Confidence 888999875 22 58899999998754
No 192
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=37.62 E-value=18 Score=29.25 Aligned_cols=26 Identities=31% Similarity=0.738 Sum_probs=17.8
Q ss_pred eeccCceeecCCCCCccCCCCCCCcee
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESGIVE 36 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sGFvE 36 (342)
|..|+..+...--.+-.||.|+ +|++
T Consensus 6 C~~C~~I~~~~qf~~~gCpnC~-~~l~ 31 (98)
T cd07973 6 CLLCSLIKTEDQFERDGCPNCE-GYLD 31 (98)
T ss_pred hccCCcccccccccCCCCCCCc-chhc
Confidence 8889888753222346899998 6654
No 193
>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=37.13 E-value=21 Score=23.09 Aligned_cols=27 Identities=15% Similarity=0.345 Sum_probs=17.2
Q ss_pred eeeccCceeecC---C---CCCccCCCCCCCce
Q 043965 9 WCYICSQMVNPR---M---EAGIKCPFCESGIV 35 (342)
Q Consensus 9 wCh~C~~~V~p~---~---~~e~~CP~C~sGFv 35 (342)
=|-.|...+... + +..+.||.|+.-|.
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 377788765422 1 22488999988664
No 194
>PF14353 CpXC: CpXC protein
Probab=36.52 E-value=19 Score=29.97 Aligned_cols=18 Identities=28% Similarity=0.573 Sum_probs=15.4
Q ss_pred CccCCCCCCCceeccccC
Q 043965 24 GIKCPFCESGIVEQMSSS 41 (342)
Q Consensus 24 e~~CP~C~sGFvEE~~~~ 41 (342)
+++||.|+.-|--++...
T Consensus 1 ~itCP~C~~~~~~~v~~~ 18 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTS 18 (128)
T ss_pred CcCCCCCCCeeEEEEEeE
Confidence 589999999998888755
No 195
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=36.46 E-value=27 Score=35.49 Aligned_cols=38 Identities=24% Similarity=0.590 Sum_probs=30.2
Q ss_pred CCCCCCceeeeccCceeecCCCCCccCCCCCC--CceeccccC
Q 043965 1 MGDAMVGYWCYICSQMVNPRMEAGIKCPFCES--GIVEQMSSS 41 (342)
Q Consensus 1 m~~~~~~ywCh~C~~~V~p~~~~e~~CP~C~s--GFvEE~~~~ 41 (342)
|+-....|-|-.|--.-.-+++ +||.|+. -|+||....
T Consensus 1 MaK~~t~f~C~~CG~~s~KW~G---kCp~Cg~Wns~vE~~~~~ 40 (456)
T COG1066 1 MAKKKTAFVCQECGYVSPKWLG---KCPACGAWNTLVEEVLAA 40 (456)
T ss_pred CCCcccEEEcccCCCCCccccc---cCCCCCCccceEEeeccc
Confidence 5555534999999887766777 9999996 999999654
No 196
>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=36.34 E-value=12 Score=37.54 Aligned_cols=33 Identities=24% Similarity=0.431 Sum_probs=0.0
Q ss_pred ceeEecccccccccchHHHhhc------CCCCCCcccccCCC
Q 043965 228 EAKEMPCKHKFHGECIMPWLEV------RSSCPVCRFQVPSD 263 (342)
Q Consensus 228 ~~~~lpC~H~Fh~~Ci~~Wl~~------~~~CP~CR~~l~~~ 263 (342)
..+.|.|||++.. ..|-.. ...||+||..-+..
T Consensus 303 P~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g~~V 341 (416)
T PF04710_consen 303 PWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVGPYV 341 (416)
T ss_dssp ------------------------------------------
T ss_pred ceeeccccceeee---cccccccccccccccCCCccccCCce
Confidence 4556789998764 356532 34799999865543
No 197
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=36.31 E-value=39 Score=36.20 Aligned_cols=47 Identities=26% Similarity=0.631 Sum_probs=27.2
Q ss_pred ccccccccccccCCceeEecccccccccchHH-Hhhc----CC--CCCCcccccCCCCc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKFHGECIMP-WLEV----RS--SCPVCRFQVPSDDF 265 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~-Wl~~----~~--~CP~CR~~l~~~~~ 265 (342)
+.|+|+.-.+.. .++...|+|+ .|... |+.. +. .||+|.+....+.+
T Consensus 307 L~CPl~~~Rm~~--P~r~~~CkHl---QcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l 360 (636)
T KOG2169|consen 307 LNCPLSKMRMSL--PARGHTCKHL---QCFDALSYLQMNEQKPTWRCPVCQKAAPFEGL 360 (636)
T ss_pred ecCCcccceeec--CCcccccccc---eecchhhhHHhccCCCeeeCccCCccccccch
Confidence 568887766552 3444456664 45543 4321 11 69999887765553
No 198
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=36.11 E-value=8.7 Score=27.61 Aligned_cols=26 Identities=23% Similarity=0.590 Sum_probs=16.7
Q ss_pred ceeeeccCceeecCCC---CCccCCCCCC
Q 043965 7 GYWCYICSQMVNPRME---AGIKCPFCES 32 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~~---~e~~CP~C~s 32 (342)
+--|-.|..-.-..-+ -|++||+|--
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccce
Confidence 3457778776532222 4799999964
No 199
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.53 E-value=14 Score=21.99 Aligned_cols=13 Identities=23% Similarity=0.800 Sum_probs=10.5
Q ss_pred ccCCCCCCCceec
Q 043965 25 IKCPFCESGIVEQ 37 (342)
Q Consensus 25 ~~CP~C~sGFvEE 37 (342)
+.||.|+-.|..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 5799999999654
No 200
>PRK13794 hypothetical protein; Provisional
Probab=34.84 E-value=45 Score=34.42 Aligned_cols=22 Identities=41% Similarity=0.892 Sum_probs=18.1
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
|||-.|+.+|- .-+|..|+..+
T Consensus 11 ~wc~~cn~p~~-----~~~c~~cg~~~ 32 (479)
T PRK13794 11 KWCDNCNVPVL-----GKKCAICGSET 32 (479)
T ss_pred EEcCCCCCeec-----CCchhHhCCCe
Confidence 99999999883 34699999963
No 201
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=34.77 E-value=21 Score=34.79 Aligned_cols=22 Identities=41% Similarity=1.081 Sum_probs=16.9
Q ss_pred ceeeeccCceeecCCCCCccCCCCC
Q 043965 7 GYWCYICSQMVNPRMEAGIKCPFCE 31 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~~~e~~CP~C~ 31 (342)
+|+|-.|+.+|- .++ +.||.|+
T Consensus 308 Gy~CP~CktkVC-sLP--i~CP~Cs 329 (421)
T COG5151 308 GYECPVCKTKVC-SLP--ISCPICS 329 (421)
T ss_pred ceeCCcccceee-cCC--ccCcchh
Confidence 399999998884 443 7899885
No 202
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=34.45 E-value=13 Score=35.88 Aligned_cols=36 Identities=33% Similarity=0.768 Sum_probs=23.4
Q ss_pred cccccccccccCCceeEecccccccccchHHHhhcC
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVR 250 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~ 250 (342)
.|.+|+++|..+......-|.-+||..|+..|+...
T Consensus 216 vC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 216 VCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred ecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 677888777654444444455577777777776543
No 203
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=34.37 E-value=36 Score=33.24 Aligned_cols=44 Identities=7% Similarity=-0.044 Sum_probs=34.4
Q ss_pred CcccccccccccccCCceeEeccccc-ccccchHHHhhcCCCCCCccccc
Q 043965 212 KNLQCAVCLEEFEIGNEAKEMPCKHK-FHGECIMPWLEVRSSCPVCRFQV 260 (342)
Q Consensus 212 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~Wl~~~~~CP~CR~~l 260 (342)
...+|.+|-+.+. .....+|+|. ||..|.. +....+||+|...+
T Consensus 342 s~~~~~~~~~~~~---st~~~~~~~n~~~~~~a~--~s~~~~~~~c~~~~ 386 (394)
T KOG2113|consen 342 SSLKGTSAGFGLL---STIWSGGNMNLSPGSLAS--ASASPTSSTCDHND 386 (394)
T ss_pred hhcccccccCcee---eeEeecCCcccChhhhhh--cccCCccccccccc
Confidence 3568999988776 6677889987 8888876 56677999997643
No 204
>PLN02189 cellulose synthase
Probab=32.61 E-value=46 Score=37.52 Aligned_cols=49 Identities=20% Similarity=0.463 Sum_probs=33.6
Q ss_pred ccccccccccccc---CCceeEec-ccccccccchHH-HhhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEI---GNEAKEMP-CKHKFHGECIMP-WLEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~---~~~~~~lp-C~H~Fh~~Ci~~-Wl~~~~~CP~CR~~l~ 261 (342)
...|.||.+++.. |+.-+... |+--.|+.|..- .-+.++.||-|+....
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3479999999753 22333333 777899999842 2245568999998776
No 205
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.51 E-value=27 Score=34.17 Aligned_cols=25 Identities=36% Similarity=0.996 Sum_probs=18.2
Q ss_pred ceeeeccCceeecCCCCCccCCCCCCCc
Q 043965 7 GYWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 7 ~ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
+|+|-+|...|= .++ +.||-|+=-.
T Consensus 276 Gy~CP~CkakvC-sLP--~eCpiC~ltL 300 (378)
T KOG2807|consen 276 GYFCPQCKAKVC-SLP--IECPICSLTL 300 (378)
T ss_pred ceeCCcccCeee-cCC--ccCCccceeE
Confidence 399999999884 443 6799887433
No 206
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=32.01 E-value=29 Score=34.63 Aligned_cols=27 Identities=33% Similarity=0.815 Sum_probs=19.1
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
|+|-.|-..+.-..+.+-+||+|++-|
T Consensus 241 ~~c~~cg~~~~~~~~~~~~c~~Cg~~~ 267 (380)
T COG1867 241 YHCSRCGEIVGSFREVDEKCPHCGGKV 267 (380)
T ss_pred EEcccccceecccccccccCCcccccc
Confidence 999999833332334578899999844
No 207
>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=31.96 E-value=22 Score=29.26 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=19.3
Q ss_pred eeccCceeecCCCCCccCCCCCCCceec
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
|-+|.-+..=..+..++||.|.--+-++
T Consensus 5 CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEecCCeeECcccccccccc
Confidence 7778777654555568888888766544
No 208
>PRK10220 hypothetical protein; Provisional
Probab=31.46 E-value=26 Score=28.86 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=21.2
Q ss_pred eeccCceeecCCCCCccCCCCCCCceec
Q 043965 10 CYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
|-+|.-+..=..+..++||.|.--+-.+
T Consensus 6 CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 6 CPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred CCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 7888887755556668899998877655
No 209
>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=31.38 E-value=11 Score=22.47 Aligned_cols=12 Identities=33% Similarity=1.007 Sum_probs=9.8
Q ss_pred CccCCCCCCCce
Q 043965 24 GIKCPFCESGIV 35 (342)
Q Consensus 24 e~~CP~C~sGFv 35 (342)
-++||.|+..|.
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 488999998874
No 210
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=30.94 E-value=18 Score=35.21 Aligned_cols=45 Identities=18% Similarity=0.320 Sum_probs=29.5
Q ss_pred cccccccccccccCCceeEe--c--ccccccccchHHHhhcCCCCCCccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEM--P--CKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~l--p--C~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
...|+||-..-..+. ++.- . =.|.+|..|-..|-.....||.|-.
T Consensus 184 ~~~CPvCGs~P~~s~-~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACGSPPVASM-VRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCcCCCCCChhhhhh-hcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 458999987643110 0000 1 2355777899999888889999965
No 211
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.49 E-value=12 Score=35.72 Aligned_cols=46 Identities=22% Similarity=0.484 Sum_probs=36.4
Q ss_pred ccccccccccccC---CceeEec--------ccccccccchHHHhhcCC-CCCCcccc
Q 043965 214 LQCAVCLEEFEIG---NEAKEMP--------CKHKFHGECIMPWLEVRS-SCPVCRFQ 259 (342)
Q Consensus 214 ~~C~ICle~~~~~---~~~~~lp--------C~H~Fh~~Ci~~Wl~~~~-~CP~CR~~ 259 (342)
..|.||...+... ..+..+. |+|..|..|+..-+.... .||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 4699999998732 2455666 999999999999876555 89999874
No 212
>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=30.05 E-value=12 Score=21.13 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=7.5
Q ss_pred ccCCCCCCCce
Q 043965 25 IKCPFCESGIV 35 (342)
Q Consensus 25 ~~CP~C~sGFv 35 (342)
++||.|+..|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 36778877664
No 213
>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=29.48 E-value=31 Score=23.46 Aligned_cols=12 Identities=42% Similarity=0.996 Sum_probs=9.5
Q ss_pred CCCccCCCCCCC
Q 043965 22 EAGIKCPFCESG 33 (342)
Q Consensus 22 ~~e~~CP~C~sG 33 (342)
+..++||+|++-
T Consensus 16 ~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCCe
Confidence 346899999985
No 214
>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=29.14 E-value=19 Score=26.72 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=10.8
Q ss_pred CCCCCccCCCCCCCc
Q 043965 20 RMEAGIKCPFCESGI 34 (342)
Q Consensus 20 ~~~~e~~CP~C~sGF 34 (342)
.++..++||.|+--|
T Consensus 49 i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 49 IVEGELICPECGREY 63 (68)
T ss_dssp TTTTEEEETTTTEEE
T ss_pred ccCCEEEcCCCCCEE
Confidence 344579999998654
No 215
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.13 E-value=28 Score=22.90 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=7.6
Q ss_pred ccCCCCCCCce
Q 043965 25 IKCPFCESGIV 35 (342)
Q Consensus 25 ~~CP~C~sGFv 35 (342)
-.||+|..||-
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 36999999985
No 216
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.38 E-value=22 Score=36.21 Aligned_cols=37 Identities=24% Similarity=0.497 Sum_probs=26.5
Q ss_pred ccccccccccccCCce-----eEecccccccccchHHHhhcC
Q 043965 214 LQCAVCLEEFEIGNEA-----KEMPCKHKFHGECIMPWLEVR 250 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~-----~~lpC~H~Fh~~Ci~~Wl~~~ 250 (342)
..|+.|...++..... ...+|+|.||..|+..|....
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 3499999988755422 222499999999988886543
No 217
>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=28.34 E-value=27 Score=27.87 Aligned_cols=23 Identities=26% Similarity=0.795 Sum_probs=18.8
Q ss_pred eeeccCceeecCCCCCccCCCCCC
Q 043965 9 WCYICSQMVNPRMEAGIKCPFCES 32 (342)
Q Consensus 9 wCh~C~~~V~p~~~~e~~CP~C~s 32 (342)
||-.|...+.+.- ..++||.|+-
T Consensus 2 fC~~Cg~~l~~~~-~~~~C~~C~~ 24 (104)
T TIGR01384 2 FCPKCGSLMTPKN-GVYVCPSCGY 24 (104)
T ss_pred CCcccCcccccCC-CeEECcCCCC
Confidence 7999999987653 4799999984
No 218
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=28.10 E-value=30 Score=33.70 Aligned_cols=44 Identities=20% Similarity=0.371 Sum_probs=30.1
Q ss_pred cccccccccccccCCceeEe--c--ccccccccchHHHhhcCCCCCCccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEM--P--CKHKFHGECIMPWLEVRSSCPVCRF 258 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~l--p--C~H~Fh~~Ci~~Wl~~~~~CP~CR~ 258 (342)
...|+||-..-... ++.+ . =.|.+|..|-..|-.....||.|-.
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 56899998774311 1111 1 2456778899999888889999965
No 219
>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=27.97 E-value=32 Score=29.91 Aligned_cols=28 Identities=29% Similarity=0.617 Sum_probs=20.6
Q ss_pred ccccchHHHhhcCC----CCCCcccccCCCCc
Q 043965 238 FHGECIMPWLEVRS----SCPVCRFQVPSDDF 265 (342)
Q Consensus 238 Fh~~Ci~~Wl~~~~----~CP~CR~~l~~~~~ 265 (342)
||..||.+=|..-. .||.|+..-..+..
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~ 33 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQSA 33 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCCCCcc
Confidence 89999998886544 79999876544433
No 220
>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=27.93 E-value=33 Score=24.67 Aligned_cols=28 Identities=14% Similarity=0.413 Sum_probs=19.9
Q ss_pred eeeeccCceeecC---CCCCccCCCCCCCce
Q 043965 8 YWCYICSQMVNPR---MEAGIKCPFCESGIV 35 (342)
Q Consensus 8 ywCh~C~~~V~p~---~~~e~~CP~C~sGFv 35 (342)
|=|-.|-..|... .+..+.||.|+.-|-
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 4588899988532 245588999987663
No 221
>PRK06450 threonine synthase; Validated
Probab=27.93 E-value=38 Score=33.22 Aligned_cols=27 Identities=26% Similarity=0.486 Sum_probs=20.7
Q ss_pred CCceeeeccCceeecCCCCCccCCCCCCC
Q 043965 5 MVGYWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 5 ~~~ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
|++|-|..|-++..+ ...++||.|++=
T Consensus 1 ~~~~~C~~Cg~~~~~--~~~~~C~~cg~~ 27 (338)
T PRK06450 1 MVKEVCMKCGKERES--IYEIRCKKCGGP 27 (338)
T ss_pred CceeEECCcCCcCCC--cccccCCcCCCE
Confidence 456899999999753 335899999753
No 222
>PLN02436 cellulose synthase A
Probab=27.39 E-value=64 Score=36.55 Aligned_cols=48 Identities=23% Similarity=0.526 Sum_probs=32.9
Q ss_pred cccccccccccc---CCceeEec-ccccccccchHH-HhhcCCCCCCcccccC
Q 043965 214 LQCAVCLEEFEI---GNEAKEMP-CKHKFHGECIMP-WLEVRSSCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~---~~~~~~lp-C~H~Fh~~Ci~~-Wl~~~~~CP~CR~~l~ 261 (342)
..|.||-+++.. |+.-+... |+--.|+.|..- .-+.++.||-|+....
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 479999999742 33333333 777799999843 2244558999998776
No 223
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=27.25 E-value=32 Score=30.10 Aligned_cols=17 Identities=29% Similarity=0.790 Sum_probs=12.9
Q ss_pred ccCCCCCCCceeccccC
Q 043965 25 IKCPFCESGIVEQMSSS 41 (342)
Q Consensus 25 ~~CP~C~sGFvEE~~~~ 41 (342)
++||+|++-+++.+++.
T Consensus 1 m~cp~c~~~~~~~~~s~ 17 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSR 17 (154)
T ss_pred CcCCCCCCCCCEeEecc
Confidence 47999999887766544
No 224
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.06 E-value=50 Score=25.59 Aligned_cols=49 Identities=18% Similarity=0.412 Sum_probs=18.5
Q ss_pred cccccccccccccCC--c--eeEecccccccccchHHH-hhcCCCCCCcccccC
Q 043965 213 NLQCAVCLEEFEIGN--E--AKEMPCKHKFHGECIMPW-LEVRSSCPVCRFQVP 261 (342)
Q Consensus 213 ~~~C~ICle~~~~~~--~--~~~lpC~H~Fh~~Ci~~W-l~~~~~CP~CR~~l~ 261 (342)
...|.||-+.+-... . +...-|+--.|+.|..-= -...+.||-|+....
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 457999999875332 1 222337777888887533 345668999997664
No 225
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.99 E-value=30 Score=24.32 Aligned_cols=13 Identities=38% Similarity=0.879 Sum_probs=9.9
Q ss_pred ccCCCCCCCceec
Q 043965 25 IKCPFCESGIVEQ 37 (342)
Q Consensus 25 ~~CP~C~sGFvEE 37 (342)
..||.|+++|+..
T Consensus 21 ~fCP~Cg~~~m~~ 33 (50)
T PRK00432 21 KFCPRCGSGFMAE 33 (50)
T ss_pred CcCcCCCcchhec
Confidence 3799999985544
No 226
>PRK00420 hypothetical protein; Validated
Probab=26.90 E-value=36 Score=28.20 Aligned_cols=26 Identities=15% Similarity=0.370 Sum_probs=20.2
Q ss_pred eeeeccCceeecCCCCCccCCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
.-|-.|.-+.--....++.||.|+.-
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 67999998775434558999999983
No 227
>PRK13795 hypothetical protein; Provisional
Probab=26.77 E-value=87 Score=33.53 Aligned_cols=22 Identities=36% Similarity=0.910 Sum_probs=18.2
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
|||..|+.+|- .-+|..|+.+.
T Consensus 13 ~wc~~cn~p~~-----~~~c~~c~~~~ 34 (636)
T PRK13795 13 YWCEKCNVPLL-----GKKCGICGKEG 34 (636)
T ss_pred EEcccCCCeec-----cccccccCCCc
Confidence 99999999883 34699999964
No 228
>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=26.74 E-value=31 Score=24.11 Aligned_cols=34 Identities=18% Similarity=0.445 Sum_probs=23.0
Q ss_pred ccccccccccccCCceeE-ecccccccccchHHHh
Q 043965 214 LQCAVCLEEFEIGNEAKE-MPCKHKFHGECIMPWL 247 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~Wl 247 (342)
..|.+|...|..-..... ..||++||..|.....
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRI 37 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCee
Confidence 468899888874332222 3499999999976544
No 229
>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=26.68 E-value=30 Score=25.30 Aligned_cols=23 Identities=26% Similarity=0.556 Sum_probs=12.8
Q ss_pred eeeccCceeec-CCCCCccCCCCC
Q 043965 9 WCYICSQMVNP-RMEAGIKCPFCE 31 (342)
Q Consensus 9 wCh~C~~~V~p-~~~~e~~CP~C~ 31 (342)
-|+.|-..+.. .....++||.|+
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCG 53 (69)
T ss_pred CccCcccccccccccceEEcCCCC
Confidence 36666666543 223456677763
No 230
>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=26.63 E-value=23 Score=26.91 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=4.1
Q ss_pred eeeeccCcee
Q 043965 8 YWCYICSQMV 17 (342)
Q Consensus 8 ywCh~C~~~V 17 (342)
|.|-.|.+.+
T Consensus 18 ~~C~~C~~~~ 27 (70)
T PF07191_consen 18 YHCEACQKDY 27 (70)
T ss_dssp EEETTT--EE
T ss_pred EECccccccc
Confidence 5555555544
No 231
>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 PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=26.17 E-value=51 Score=32.98 Aligned_cols=28 Identities=21% Similarity=0.472 Sum_probs=19.3
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCce
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIV 35 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFv 35 (342)
|+|+.|...........-+||.|++-|+
T Consensus 245 ~~C~~c~~~~~~~~~~~~~C~~c~~~~~ 272 (382)
T PRK04338 245 YYCPKCLYREEVEGLPPEECPVCGGKFG 272 (382)
T ss_pred EECCCCCcEEEecCCCCCCCCCCCCcce
Confidence 9999999865322133468999987554
No 233
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=26.13 E-value=57 Score=22.99 Aligned_cols=13 Identities=31% Similarity=0.928 Sum_probs=9.1
Q ss_pred CCCCccCCCCCCC
Q 043965 21 MEAGIKCPFCESG 33 (342)
Q Consensus 21 ~~~e~~CP~C~sG 33 (342)
++.+.+||.|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (50)
T cd00730 31 LPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCc
Confidence 3456789998753
No 234
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.91 E-value=27 Score=29.95 Aligned_cols=52 Identities=21% Similarity=0.462 Sum_probs=27.8
Q ss_pred ccccCcccccccccc-cccCCceeEecccccccccchHHHhhcCC----CCCCcccc
Q 043965 208 VTIDKNLQCAVCLEE-FEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQ 259 (342)
Q Consensus 208 ~~~~~~~~C~ICle~-~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~ 259 (342)
+-+..+.+|.||+.. |..|-.-...-|.-.||..|--+.-.+.+ .|-+|+..
T Consensus 60 aGv~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 60 AGVGDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred cccCcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 345567899999864 22222222222444555566544322222 58899764
No 235
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=25.80 E-value=26 Score=23.25 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=16.8
Q ss_pred eeccCceeecCCCCC---ccCCCCCCCceec
Q 043965 10 CYICSQMVNPRMEAG---IKCPFCESGIVEQ 37 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e---~~CP~C~sGFvEE 37 (342)
|-.|.....+..-.+ ..||.|+|-|+..
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W~d~ 32 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIWFDA 32 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEEccH
Confidence 666776543322112 4599999888753
No 236
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=25.77 E-value=40 Score=31.59 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=19.1
Q ss_pred ccccccccccccCCceeEecccccc
Q 043965 214 LQCAVCLEEFEIGNEAKEMPCKHKF 238 (342)
Q Consensus 214 ~~C~ICle~~~~~~~~~~lpC~H~F 238 (342)
+.||||...+...+.....+.+|.|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 5799999999765555555568888
No 237
>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=25.49 E-value=43 Score=22.13 Aligned_cols=23 Identities=22% Similarity=0.862 Sum_probs=17.6
Q ss_pred eeeeccCceeecCCCCCccCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCE 31 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~ 31 (342)
-||..|.+.|.-.. ..++|+.|+
T Consensus 12 ~~C~~C~~~i~~~~-~~~~C~~C~ 34 (49)
T smart00109 12 TKCCVCRKSIWGSF-QGLRCSWCK 34 (49)
T ss_pred CCccccccccCcCC-CCcCCCCCC
Confidence 68999999985322 478999984
No 238
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=24.96 E-value=74 Score=36.10 Aligned_cols=48 Identities=17% Similarity=0.331 Sum_probs=32.9
Q ss_pred ccccccccccccCC---cee-EecccccccccchH-HHhhcCCCCCCcccccC
Q 043965 214 LQCAVCLEEFEIGN---EAK-EMPCKHKFHGECIM-PWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~~~---~~~-~lpC~H~Fh~~Ci~-~Wl~~~~~CP~CR~~l~ 261 (342)
..|.||-+++.... .-+ .--|+--.|+.|.. ..-+.++.||-|+....
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 47999999975332 222 22377779999983 23345668999998775
No 239
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.91 E-value=59 Score=23.92 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=4.9
Q ss_pred CCCccCCCC
Q 043965 22 EAGIKCPFC 30 (342)
Q Consensus 22 ~~e~~CP~C 30 (342)
+..|+||.|
T Consensus 48 g~~Y~Cp~C 56 (61)
T COG2888 48 GNPYRCPKC 56 (61)
T ss_pred CCceECCCc
Confidence 344566655
No 240
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.84 E-value=42 Score=21.80 Aligned_cols=25 Identities=16% Similarity=0.418 Sum_probs=14.3
Q ss_pred eeccCceeecC------CCCCccCCCCCCCc
Q 043965 10 CYICSQMVNPR------MEAGIKCPFCESGI 34 (342)
Q Consensus 10 Ch~C~~~V~p~------~~~e~~CP~C~sGF 34 (342)
|..|....... .+..++||.|+--|
T Consensus 5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 66777655321 12347788887544
No 241
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.76 E-value=41 Score=34.15 Aligned_cols=24 Identities=21% Similarity=0.503 Sum_probs=17.6
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGI 34 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGF 34 (342)
--||.|..-+ .+....||+|+.--
T Consensus 222 ~~C~~Cd~l~---~~~~a~CpRC~~~L 245 (419)
T PRK15103 222 RSCSCCTAIL---PADQPVCPRCHTKG 245 (419)
T ss_pred CcCCCCCCCC---CCCCCCCCCCCCcC
Confidence 4599999965 23456899999764
No 242
>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=24.76 E-value=38 Score=34.17 Aligned_cols=26 Identities=23% Similarity=0.588 Sum_probs=18.5
Q ss_pred eeeccCceeecC---CCCCccCCCCCCCc
Q 043965 9 WCYICSQMVNPR---MEAGIKCPFCESGI 34 (342)
Q Consensus 9 wCh~C~~~V~p~---~~~e~~CP~C~sGF 34 (342)
=||.|..-++.. .++...||+|+.--
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 399999877422 23457899999854
No 243
>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=24.70 E-value=43 Score=23.56 Aligned_cols=28 Identities=21% Similarity=0.736 Sum_probs=15.2
Q ss_pred eeeec--cCceeecCCC-CC--ccCCCCCCCce
Q 043965 8 YWCYI--CSQMVNPRME-AG--IKCPFCESGIV 35 (342)
Q Consensus 8 ywCh~--C~~~V~p~~~-~e--~~CP~C~sGFv 35 (342)
-||-. |...|....+ .. ++||.|+.-|-
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC 51 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFC 51 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEEC
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCc
Confidence 49977 9999865543 23 78999987663
No 244
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.30 E-value=36 Score=24.25 Aligned_cols=17 Identities=35% Similarity=0.831 Sum_probs=13.0
Q ss_pred ccCCCCCCCceeccccC
Q 043965 25 IKCPFCESGIVEQMSSS 41 (342)
Q Consensus 25 ~~CP~C~sGFvEE~~~~ 41 (342)
|.||+|+..|-=.++..
T Consensus 1 i~CPyCge~~~~~iD~s 17 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPS 17 (52)
T ss_pred CCCCCCCCeeEEEEecC
Confidence 57999998877666655
No 245
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.96 E-value=46 Score=34.11 Aligned_cols=36 Identities=28% Similarity=0.505 Sum_probs=27.0
Q ss_pred CCCCCCceeeeccCceeecCCCCCccCCCCCC--Cceeccc
Q 043965 1 MGDAMVGYWCYICSQMVNPRMEAGIKCPFCES--GIVEQMS 39 (342)
Q Consensus 1 m~~~~~~ywCh~C~~~V~p~~~~e~~CP~C~s--GFvEE~~ 39 (342)
|+..-..|-|..|--.-.-+.+ +||.|+. -|+||+.
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g---~Cp~C~~w~t~~~~~~ 38 (454)
T TIGR00416 1 MAKAKSKFVCQHCGADSPKWQG---KCPACHAWNTITEERL 38 (454)
T ss_pred CCCCCCeEECCcCCCCCccccE---ECcCCCCccccchhhc
Confidence 6644334999999887765655 8999997 8888753
No 246
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=23.93 E-value=37 Score=33.34 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=21.2
Q ss_pred eeeccCceeecCCCCCccCCCCCCCceecc
Q 043965 9 WCYICSQMVNPRMEAGIKCPFCESGIVEQM 38 (342)
Q Consensus 9 wCh~C~~~V~p~~~~e~~CP~C~sGFvEE~ 38 (342)
-||.|=..+. .++ -.+||.|+.+=+--+
T Consensus 244 RCh~Cfsit~-~m~-k~FCp~CG~~TL~K~ 271 (376)
T KOG2463|consen 244 RCHGCFSITS-EMP-KDFCPSCGHKTLTKC 271 (376)
T ss_pred EeeeeeEecC-ccc-hhcccccCCCeeeEE
Confidence 5999988774 454 689999999855443
No 247
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.76 E-value=42 Score=36.08 Aligned_cols=46 Identities=26% Similarity=0.589 Sum_probs=34.3
Q ss_pred cccccccccccCCceeEecccc-cccccchHHHhh--c----CCCCCCcccccCCC
Q 043965 215 QCAVCLEEFEIGNEAKEMPCKH-KFHGECIMPWLE--V----RSSCPVCRFQVPSD 263 (342)
Q Consensus 215 ~C~ICle~~~~~~~~~~lpC~H-~Fh~~Ci~~Wl~--~----~~~CP~CR~~l~~~ 263 (342)
.|+||-..+. -+..-.|+| ..|..|..+... . ...||+||..+...
T Consensus 2 ~c~ic~~s~~---~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~~ 54 (669)
T KOG2231|consen 2 SCAICAFSPD---FVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVETK 54 (669)
T ss_pred CcceeecCcc---ccccccccccccchhhhhhhhhhcccccccccCcccccceeee
Confidence 5999988776 555666999 899999987652 2 34689999877544
No 248
>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=23.74 E-value=42 Score=28.99 Aligned_cols=17 Identities=29% Similarity=0.556 Sum_probs=14.7
Q ss_pred CccCCCCCCCceecccc
Q 043965 24 GIKCPFCESGIVEQMSS 40 (342)
Q Consensus 24 e~~CP~C~sGFvEE~~~ 40 (342)
.+.||+|+|...++++.
T Consensus 105 ~~~cp~c~s~~t~~~s~ 121 (146)
T TIGR02159 105 SVQCPRCGSADTTITSI 121 (146)
T ss_pred CCcCCCCCCCCcEeecC
Confidence 58999999999988864
No 249
>PF12773 DZR: Double zinc ribbon
Probab=23.38 E-value=42 Score=22.88 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=12.6
Q ss_pred eeeeccCceeecCCCCCccCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCES 32 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~s 32 (342)
=||..|-..+.......++||.|+.
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcC
Confidence 4566666655411222355666655
No 250
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.36 E-value=39 Score=28.78 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=22.3
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceec
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQ 37 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE 37 (342)
|-|-.|--+.--. +.+++||.|+--++-+
T Consensus 29 ~hCp~Cg~PLF~K-dG~v~CPvC~~~~~~v 57 (131)
T COG1645 29 KHCPKCGTPLFRK-DGEVFCPVCGYREVVV 57 (131)
T ss_pred hhCcccCCcceee-CCeEECCCCCceEEEe
Confidence 8899999987644 4499999999655433
No 251
>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=23.11 E-value=79 Score=19.96 Aligned_cols=25 Identities=28% Similarity=0.720 Sum_probs=17.0
Q ss_pred eeeeccCceeecCCCCCccCCCCCCC
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESG 33 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sG 33 (342)
|=|-.|--.+.+.. .+-+||.|+.+
T Consensus 2 ~~C~~CGy~y~~~~-~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-CCCcCcCCCCc
Confidence 44667776666443 47899999863
No 252
>PRK06260 threonine synthase; Validated
Probab=23.11 E-value=54 Score=32.71 Aligned_cols=27 Identities=30% Similarity=0.588 Sum_probs=20.3
Q ss_pred CCceeeeccCceeecCCCCCccCCCCCC
Q 043965 5 MVGYWCYICSQMVNPRMEAGIKCPFCES 32 (342)
Q Consensus 5 ~~~ywCh~C~~~V~p~~~~e~~CP~C~s 32 (342)
|..|-|..|-++..+. +..+.||.|++
T Consensus 1 ~~~~~C~~cg~~~~~~-~~~~~Cp~cg~ 27 (397)
T PRK06260 1 MYWLKCIECGKEYDPD-EIIYTCPECGG 27 (397)
T ss_pred CCEEEECCCCCCCCCC-CccccCCCCCC
Confidence 4458999999998533 23588999974
No 253
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=23.09 E-value=32 Score=24.41 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=17.4
Q ss_pred eeeeccCceeecCC------C-CCccCCCCC
Q 043965 8 YWCYICSQMVNPRM------E-AGIKCPFCE 31 (342)
Q Consensus 8 ywCh~C~~~V~p~~------~-~e~~CP~C~ 31 (342)
-=|-.|...|.|.. . .-+.||+|+
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCG 53 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence 46888998887642 2 237899997
No 254
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.43 E-value=84 Score=24.05 Aligned_cols=47 Identities=17% Similarity=0.464 Sum_probs=30.9
Q ss_pred ccccccccccCC-ceeEecccccccccchHHHhhcCCCCCCcccccCCCC
Q 043965 216 CAVCLEEFEIGN-EAKEMPCKHKFHGECIMPWLEVRSSCPVCRFQVPSDD 264 (342)
Q Consensus 216 C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~Wl~~~~~CP~CR~~l~~~~ 264 (342)
|--|-.++..+. ++.+..=.|.||.+|...- .+..||.|-..|....
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~--l~g~CPnCGGelv~RP 55 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENR--LHGLCPNCGGELVARP 55 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHh--hcCcCCCCCchhhcCc
Confidence 555656655433 3333334689999998764 5789999987775543
No 255
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.36 E-value=31 Score=27.50 Aligned_cols=12 Identities=25% Similarity=0.864 Sum_probs=10.6
Q ss_pred cccccchHHHhh
Q 043965 237 KFHGECIMPWLE 248 (342)
Q Consensus 237 ~Fh~~Ci~~Wl~ 248 (342)
-||+.|+..|+.
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999985
No 256
>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=22.18 E-value=31 Score=21.74 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=7.6
Q ss_pred eeccCceeecCCCCCccCCCCC
Q 043965 10 CYICSQMVNPRMEAGIKCPFCE 31 (342)
Q Consensus 10 Ch~C~~~V~p~~~~e~~CP~C~ 31 (342)
|-.|.-+..-..+.-++||.|.
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECG 26 (30)
T ss_dssp -TTT-----EE-SSSEEETTTT
T ss_pred CCCCCCcceeccCCEEeCCccc
Confidence 4445544432223346666665
No 257
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.07 E-value=84 Score=21.83 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=6.4
Q ss_pred CCCccCCCCCCC
Q 043965 22 EAGIKCPFCESG 33 (342)
Q Consensus 22 ~~e~~CP~C~sG 33 (342)
+.+.+||.|+.+
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 356788888753
No 258
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.67 E-value=63 Score=32.95 Aligned_cols=35 Identities=26% Similarity=0.625 Sum_probs=26.3
Q ss_pred CCCCCCceeeeccCceeecCCCCCccCCCCCC--Cceecc
Q 043965 1 MGDAMVGYWCYICSQMVNPRMEAGIKCPFCES--GIVEQM 38 (342)
Q Consensus 1 m~~~~~~ywCh~C~~~V~p~~~~e~~CP~C~s--GFvEE~ 38 (342)
|+-.-..|-|..|--.-.-+.+ +||.|+. .|+||+
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g---~Cp~C~~w~t~~e~~ 37 (446)
T PRK11823 1 MAKKKTAYVCQECGAESPKWLG---RCPECGAWNTLVEEV 37 (446)
T ss_pred CCCCCCeEECCcCCCCCcccCe---eCcCCCCccceeeec
Confidence 5444334999999887765655 8999997 888876
No 259
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.67 E-value=30 Score=18.98 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=5.1
Q ss_pred cCCCCCCCce
Q 043965 26 KCPFCESGIV 35 (342)
Q Consensus 26 ~CP~C~sGFv 35 (342)
+|+.|+..|-
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 5777776553
No 260
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=21.62 E-value=60 Score=31.79 Aligned_cols=51 Identities=22% Similarity=0.583 Sum_probs=32.5
Q ss_pred cccccccccccc-----cCC-----------ceeEecccccccccchHHHhhc---------CCCCCCcccccCCC
Q 043965 213 NLQCAVCLEEFE-----IGN-----------EAKEMPCKHKFHGECIMPWLEV---------RSSCPVCRFQVPSD 263 (342)
Q Consensus 213 ~~~C~ICle~~~-----~~~-----------~~~~lpC~H~Fh~~Ci~~Wl~~---------~~~CP~CR~~l~~~ 263 (342)
..+|++|+..-. .|- .-...||||+--.+-..-|-+. +..||.|-..|..+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 358999987532 111 1234579998766666667642 33699998877544
No 261
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=21.29 E-value=30 Score=40.45 Aligned_cols=48 Identities=29% Similarity=0.483 Sum_probs=36.4
Q ss_pred cccccccccccccCCceeEecccccccccchHHHhhcCC----CCCCccccc
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWLEVRS----SCPVCRFQV 260 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl~~~~----~CP~CR~~l 260 (342)
...|.||.......+.....-|.-.||..|+.+-+.... .||-||..-
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 357999998877443444445888999999999886544 799998766
No 262
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=21.14 E-value=45 Score=33.26 Aligned_cols=29 Identities=31% Similarity=0.738 Sum_probs=23.3
Q ss_pred eeeeccCceeecCCCCCccCCCCCC--Cceeccc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCES--GIVEQMS 39 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~s--GFvEE~~ 39 (342)
|-|..|--.-.-+.+ +||.|+. .|+||..
T Consensus 1 ~~c~~cg~~~~~~~g---~cp~c~~w~~~~e~~~ 31 (372)
T cd01121 1 YVCSECGYVSPKWLG---KCPECGEWNTLVEEIE 31 (372)
T ss_pred CCCCCCCCCCCCccE---ECcCCCCceeeeehhc
Confidence 789999887765665 8999997 7888753
No 263
>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=20.95 E-value=25 Score=24.73 Aligned_cols=15 Identities=27% Similarity=0.567 Sum_probs=8.1
Q ss_pred CccCCCCCCCceecc
Q 043965 24 GIKCPFCESGIVEQM 38 (342)
Q Consensus 24 e~~CP~C~sGFvEE~ 38 (342)
+-+||-|+..|=+|=
T Consensus 20 ~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 20 KGCCPLCGRPLDEEH 34 (54)
T ss_dssp SEE-TTT--EE-HHH
T ss_pred CCcCCCCCCCCCHHH
Confidence 448999999987653
No 264
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=20.62 E-value=33 Score=36.85 Aligned_cols=58 Identities=24% Similarity=0.554 Sum_probs=0.0
Q ss_pred HHHcCCcccccCcccccccccccccCC-------ceeEecccccccccchHHH----------hhcCCCCCCccccc
Q 043965 201 VLKALPTVTIDKNLQCAVCLEEFEIGN-------EAKEMPCKHKFHGECIMPW----------LEVRSSCPVCRFQV 260 (342)
Q Consensus 201 ~i~~~p~~~~~~~~~C~ICle~~~~~~-------~~~~lpC~H~Fh~~Ci~~W----------l~~~~~CP~CR~~l 260 (342)
++..+|..++.+ +|.||-|.=...+ ..-+-.|+..||..|.... +..-+.|-+|+..+
T Consensus 107 iLq~VP~dRfnK--tCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hf 181 (900)
T KOG0956|consen 107 ILQDVPHDRFNK--TCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHF 181 (900)
T ss_pred eeccCchhhhcc--eeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHH
No 265
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.57 E-value=66 Score=25.91 Aligned_cols=34 Identities=24% Similarity=0.322 Sum_probs=28.0
Q ss_pred cccccccccccccCCceeEecccccccccchHHHh
Q 043965 213 NLQCAVCLEEFEIGNEAKEMPCKHKFHGECIMPWL 247 (342)
Q Consensus 213 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~Wl 247 (342)
...|.||-..+..|+....++ +-..|+.|+..-.
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~ 39 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESK 39 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHH
Confidence 357999999999998888887 6678999987654
No 266
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=20.52 E-value=76 Score=20.09 Aligned_cols=23 Identities=17% Similarity=0.608 Sum_probs=16.6
Q ss_pred eeeccCceeecCCC-CCccCCCCC
Q 043965 9 WCYICSQMVNPRME-AGIKCPFCE 31 (342)
Q Consensus 9 wCh~C~~~V~p~~~-~e~~CP~C~ 31 (342)
+|+.|.....--.+ .-+.|..|+
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQ 26 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCC
Confidence 69999988743333 358899996
No 267
>PLN02400 cellulose synthase
Probab=20.52 E-value=87 Score=35.58 Aligned_cols=48 Identities=15% Similarity=0.408 Sum_probs=32.5
Q ss_pred ccccccccccccCC---c-eeEecccccccccchH-HHhhcCCCCCCcccccC
Q 043965 214 LQCAVCLEEFEIGN---E-AKEMPCKHKFHGECIM-PWLEVRSSCPVCRFQVP 261 (342)
Q Consensus 214 ~~C~ICle~~~~~~---~-~~~lpC~H~Fh~~Ci~-~Wl~~~~~CP~CR~~l~ 261 (342)
..|.||-+++.... . +..--|+---|+.|.. ..-+.++.||-|+....
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 47999999975332 2 2233377779999983 22244558999998776
No 268
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.50 E-value=53 Score=35.81 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=20.1
Q ss_pred eeeeccCceeecCCCCCccCCCCCCCceeccc
Q 043965 8 YWCYICSQMVNPRMEAGIKCPFCESGIVEQMS 39 (342)
Q Consensus 8 ywCh~C~~~V~p~~~~e~~CP~C~sGFvEE~~ 39 (342)
..||.|...- +. -..||.|+|-=+..+.
T Consensus 463 L~CH~Cg~~~-~~---p~~Cp~Cgs~~L~~~G 490 (730)
T COG1198 463 LRCHYCGYQE-PI---PQSCPECGSEHLRAVG 490 (730)
T ss_pred eEeCCCCCCC-CC---CCCCCCCCCCeeEEec
Confidence 7899999883 22 4689999997554443
No 269
>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=20.39 E-value=71 Score=26.30 Aligned_cols=46 Identities=24% Similarity=0.501 Sum_probs=28.8
Q ss_pred Cccccccccccccc--CCceeEecccccccccchHHHhhcCC--CCCCccc
Q 043965 212 KNLQCAVCLEEFEI--GNEAKEMPCKHKFHGECIMPWLEVRS--SCPVCRF 258 (342)
Q Consensus 212 ~~~~C~ICle~~~~--~~~~~~lpC~H~Fh~~Ci~~Wl~~~~--~CP~CR~ 258 (342)
....|.+|...|.. +.......|+|.+|..|-.. ..... .|-+|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 34589999988742 23455556999999999765 11122 5888865
Done!